website/2dbase-ecoli.html0000644000244100017570000000746611606605735015457 0ustar jisonindustry Bioinformatics Data Resource Catalogue

2DBase-Ecoli

2D-PAGE database of Escherichia coli

This Database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on varios functional categories enabling quick and subsequent analysis.

ID2DBase-Ecoli
IDaltEC-2D-GEL
AccDB-0122
Homehttp://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonEscherichia coli

Available data

Data Format Query Link
Experiment annotation (2D PAGE) {ECO2DBASE entry} HTML UniProt accession http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) {ECO2DBASE entry} HTML UniProt accession P02930
Experiment annotation (2D PAGE) {ECO2DBASE entry} HTML UniProt accession P52697
website/2dpage.html0000644000244100017570000000303711606605726014356 0ustar jisonindustry Bioinformatics Data Resource Catalogue

2dpage

2D-PAGE proteome database system for microbial research

Two-dimensional gel electrophoresis (2-DE) and mass spectrometry data of diverse microorganisms and other organisms.

ID2dpage
Homehttp://www.mpiib-berlin.mpg.de/2D-PAGE
EDAM topicTwo-dimensional gel electrophoresis
EDAM topicMass spectrometry
Taxonall
website/3dgenomics.html0000644000244100017570000000274611606605726015255 0ustar jisonindustry Bioinformatics Data Resource Catalogue

3Dgenomics

3D-Genomics database of structural annotations for proteomes

Structural annotations for the proteomes of just under 100 organisms. Using data derived from public databases of translated genomic sequences, representatives from the major branches of Life are included: Prokaryota, Eukaryota and Archaea.

ID3Dgenomics
Homehttp://www.sbg.bio.ic.ac.uk/3dgenomics
EDAM topicProteome
Taxonall
website/3did.html0000644000244100017570000002235611606605726014044 0ustar jisonindustry Bioinformatics Data Resource Catalogue

3did

3DID database of 3D interacting domains

A collection of domain-domain interactions in proteins for which high-resolution three-dimensional structures are known.

ID3did
Homehttp://3did.irbbarcelona.org/
EDAM topicProtein-protein interactions
Taxonall

Available data

Data Format Query Link
Protein structure report (domain) HTML Pfam domain name http://3did.irbbarcelona.org/cgi-bin/query_domain_cgi.pl?draw=graph&domain=%s
Protein structure report (domain) HTML Pfam accession number http://3did.irbbarcelona.org/cgi-bin/query_pfamID_cgi.pl?draw=graph&id=%s
Domain-domain interaction HTML Pfam domain name; Pfam domain name http://3did.irbbarcelona.org/cgi-bin/query_interaction_cgi.pl?domain1=%s1&db=Pfam&domain2=%s2
Domain-domain interaction HTML Pfam domain name; Pfam domain name http://3did.irbbarcelona.org/cgi-bin/query_path_cgi.pl?domain1=%s1&domain2=%s2
Protein structure report (domain) HTML ELM ID http://3did.irbbarcelona.org/cgi-bin/query_peptide_cgi.pl?draw=graph&peptide=%s
Protein-motif interaction HTML Pfam domain name; ELM ID http://3did.irbbarcelona.org//cgi-bin/query_dmi_cgi.pl?domain=%s1&ddb=%&peptide=%s2&mdb=ELM

Example queries

Data Format Query Example
Protein structure report (domain) HTML Pfam domain name SH3_1
Protein structure report (domain) HTML Pfam accession number PF00018
Protein structure report (domain) HTML Pfam domain name Ank
Protein structure report (domain) HTML Pfam domain name SH3_1
Protein structure report (domain) HTML Pfam domain name SH2
Protein structure report (domain) HTML Pfam domain name efhand
Protein structure report (domain) HTML ELM ID LIG_SH3_1
Protein structure report (domain) HTML ELM ID LIG_SH3_1
website/3dmet.html0000644000244100017570000000260211606605726014225 0ustar jisonindustry Bioinformatics Data Resource Catalogue

3DMET

3DMET

Three-dimensional structures of natural metabolites.

ID3DMET
Homehttp://www.3dmet.dna.affrc.go.jp/
EDAM topicSmall molecules
EDAM topicMetabolites
Taxonall
website/4dxpress.html0000644000244100017570000000561711606605726014776 0ustar jisonindustry Bioinformatics Data Resource Catalogue

4dxpress

4DXpress cross species gene expression pattern database

A platform to query and compare gene expression data during the development of the major model animals (zebrafish, drosophila, medaka, mouse). The high resolution expression data was acquired through whole mount in situ hybridsation-, antibody- or transgenic experiments.

ID4dxpress
Homehttp://4dx.embl.de/4DXpress
EDAM topicGene expression and regulation
Taxonall

Available data

Data Format Query Link
Gene annotation HTML Gene ID (Ensembl) http://4dx.embl.de/4DXpress/reg/all/search/bquery.do?id=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID (Ensembl) ENSMUSG00000036026
website/5srrna.html0000644000244100017570000000265111606605726014427 0ustar jisonindustry Bioinformatics Data Resource Catalogue

5srrna

5S rRNA database

Information on nucleotide sequences of 5S rRNAs and their genes.

ID5srrna
Homehttp://biobases.ibch.poznan.pl/5SData/
EDAM topicrRNA
EDAM topicGene family or system
Taxonall
website/a1atvar.html0000644000244100017570000000245411606605726014555 0ustar jisonindustry Bioinformatics Data Resource Catalogue

a1atvar

A1ATVar A1-antitrypsin database

Database of human SERPINA1 gene variants leading to alpha1-antitrypsin deficiency

IDa1atvar
Homehttp://www.goldenhelix.org/a1atvar/
EDAM topicHuman disease
TaxonHomo sapiens
website/aarhus_ghent-2dpage.html0000644000244100017570000000307111606605726017022 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Aarhus_Ghent-2DPAGE

Human keratinocyte 2D gel protein database from Aarhus and Ghent universities

Human keratinocyte 2D gel protein database from Aarhus and Ghent universities

IDAarhus_Ghent-2DPAGE
AccDB-0114
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonHomo sapiens

Example queries

Data Format Query Example
website/abcdb.html0000644000244100017570000000253211606605726014246 0ustar jisonindustry Bioinformatics Data Resource Catalogue

abcdb

Archaeal and bacterial ABC transporter database (ABCdb)

Archaeal and bacterial ABC transporter database.

IDabcdb
Homehttp://www-abcdb.biotoul.fr
EDAM topicMembrane protein
TaxonBacteria, Archaea
website/abs.html0000644000244100017570000000552311606605726013763 0ustar jisonindustry Bioinformatics Data Resource Catalogue

abs

ABS database of binding sites from orthologous promoters

Annotated regulatory binding sites from orthologous promoters.

IDabs
Homehttp://genome.imim.es/datasets/abs2005/
EDAM topicNucleic acid functional sites
EDAM topicTranscription
Taxonall

Available data

Data Format Query Link
Gene features (promoter) HTML ABS ID http://genome.crg.es/datasets/abs2005/entries/%s.html

Example queries

Data Format Query Example
Gene features (promoter) HTML ABS ID A0001
website/aceview.html0000644000244100017570000002020611606605726014634 0ustar jisonindustry Bioinformatics Data Resource Catalogue

aceview

AceView genes database

A curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace).

IDaceview
Homehttp://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/
EDAM topicmRNA, EST or cDNA
EDAM topicGene family or system
CategoryNot available
TaxonArabidopsis thaliana, Caenorhabditis elegans, Homo sapiens, Mus, Rattus
Linkinghttp://www.ncbi.nlm.nih.gov/ieb/research/acembly/AboutAceView.v69.html#quote

Available data

Data Format Query Link
Gene annotation HTML Species name; Gene name (AceView) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Gene annotation (expression) HTML Species name; Gene name (AceView) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fexp
Gene annotation (functional) HTML Species name; Gene name (AceView) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=ffunc
Nucleic acid features (gene structure) HTML {AceView alternative} Species name; Gene name (AceView) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fmol
Nucleic acid features (gene structure) HTML {AceView single} Species name; Gene name (AceView) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fiche
Gene annotation HTML Species name; Gene ID (NCBI) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Gene annotation HTML Species name; Clone ID (RefSeq) http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Gene annotation HTML Species name; Clone ID (IMAGE) {GenBank cDNA ID} http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2&a=fgene
Gene annotation (clone or EST) {Genbank to human AceView} HTML Species name; GenBank accession http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?db=%s1&q=%s2

Example queries

Data Format Query Example
website/aclame.html0000644000244100017570000000252711606605726014441 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ACLAME

ACLAME classification of mobile genetic elements

Collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons.

IDACLAME
Homehttp://aclame.ulb.ac.be
EDAM topicMobile genetic elements
Taxonall
website/affindb.html0000644000244100017570000000243111606605726014602 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AffinDB

Affinity database (AffinDB) for protein–ligand complexes

Affinity database for protein–ligand complexes

IDAffinDB
Homehttp://www.agklebe.de/affinity
EDAM topicProtein-ligand interactions
Taxonall
website/aftol.html0000644000244100017570000000554411606605726014326 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AFTOL

Assembling the Fungal Tree of Life (AFTOL) database

Fungal structural and biochemical database.

IDAFTOL
Homehttp://www.aftol.org/index.php
EDAM topicFungal
CategoryNot available
TaxonFungi

Available data

Data Format Query Link
Fungi annotation HTML Genus name; Species name http://aftol.umn.edu/species/%s1_%s2
Fungi annotation (anamorph) HTML Genus name; Species name http://aftol.umn.edu/species/%s1_%s2__(anamorph)

Example queries

Data Format Query Example
website/agd.html0000644000244100017570000002615511606605726013755 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AGD

Ashbya genome database (AGD)

A genome/transcriptome database containing gene annotation and high-density oligonucleotide microarray expression data for protein-coding genes from Ashbya gossypii and the model organism Saccharomyces cerevisiae. It also provides access to comparative genomics data from those two fungi as well as Schizosaccharomyces pombe and Neurospora crassa.

IDAGD
AccDB-0001
Homehttp://agd.vital-it.ch/
EDAM topicFungal
EDAM topicGenomes
EDAM topicComparative genomics
EDAM topicGene expression and regulation
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonEremothecium gossypii

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://agd.vital-it.ch/Ashbya_gossypii/geneview?db=core;gene=%s
Gene annotation (transcript) HTML Gene symbol http://agd.vital-it.ch/Ashbya_gossypii/transview?db=core;transcript=%s
Gene features (exon) HTML Gene symbol http://agd.vital-it.ch/Ashbya_gossypii/exonview?db=core;transcript=%s
Protein report HTML Gene symbol http://agd.vital-it.ch/Ashbya_gossypii/protview?db=core;peptide=%s
Gene annotation HTML Species name; Gene symbol http://agd.vital-it.ch/%s1/geneview?gene=%s2

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol AAL011C
Gene annotation (transcript) HTML Gene symbol AAL011C
Gene features (exon) HTML Gene symbol AAL011C
Protein report HTML Gene symbol AAL011C
Gene annotation HTML Gene symbol ACL127W
Gene annotation (transcript) HTML Gene symbol ACL127W
Gene features (exon) HTML Gene symbol ACL127W
Protein report HTML Gene symbol ACL127W
Gene annotation HTML Gene symbol RLP7
Gene annotation (transcript) HTML Gene symbol RLP7
Gene features (exon) HTML Gene symbol RLP7
Protein report HTML Gene symbol RLP7
website/allergome.html0000644000244100017570000000545711606605727015174 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Allergome

Allergome; a platform for allergen knowledge

Allergome; a platform for allergen knowledge

IDAllergome
AccDB-0160
Homehttp://www.allergome.org/
EDAM topicDisease
CategoryProtein family/group databases
TaxonHomo sapiens

Available data

Data Format Query Link
Metadata and annotation HTML Identifier {Allergome} http://www.allergome.org/script/dettaglio.php?id_molecule=%s

Example queries

Data Format Query Example
Metadata and annotation HTML Identifier {Allergome} 2681
website/amypdb.html0000644000244100017570000000242511606605727014471 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AMYPDB

Amyloid precursor proteins database (AMYPDB)

Amyloid precursor families and their amino acid sequence signatures.

IDAMYPDB
Homehttp://amyPDB.univ-rennes1.fr/
EDAM topicDisease
TaxonHomo sapiens
website/anpr.html0000644000244100017570000000327511606605727014161 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ANPR

Arabidopsis nucleolar protein database (ANPR)

Comparative analysis of human and Arabidopsis nucleolar proteomes

IDANPR
Homehttp://bioinf.scri.sari.ac.uk/cgi-bin/atnoPDB/proteome_comparison
EDAM topicProteome
EDAM topicPlant
EDAM topicComparative genomics
TaxonArabidopsis
website/antibodypedia.html0000644000244100017570000000253211606605727016030 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Antibodypedia

Antibodypedia database of antibodies to human proteins

Application-specific validation of publicly available antibodies to human protein targets.

IDAntibodypedia
Homehttp://www.antibodypedia.org
EDAM topicImmune-related proteins and peptides
TaxonHomo sapiens
website/antijen.html0000644000244100017570000000356211606605727014650 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AntiJen

AntiJen database for peptides binding to immunity related proteins

Quantitative binding data for peptides binding to MHC Ligand, TCR-MHC Complexes, T Cell Epitope, TAP, B Cell Epitope molecules and immunological protein-protein interactions. AntiJen includes Peptide Library, Copy Numbers and Diffusion Coefficient data.

IDAntiJen
Homehttp://www.darrenflower.info/AntiJen
EDAM topicImmune-related proteins and peptides
EDAM topicProtein-protein interactions
EDAM topicPeptides and amino acids
TaxonChordata
website/anu-2dpage.html0000644000244100017570000000641711606605727015145 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ANU-2DPAGE

Australian National University 2-DE database (ANU-2DPAGE)

2-DE PAGE database.

IDANU-2DPAGE
AccDB-0002
Homehttp://semele.anu.edu.au
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML UniProt accession http://semele.anu.edu.au/cgi-bin/get-2d-entry?%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML UniProt accession P02930
Experiment annotation (2D PAGE) HTML UniProt accession Q9SIB9
website/aphidbase.html0000644000244100017570000000262011606605727015132 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AphidBase

Aphid genome database (AphidBase)

Aphid genome database

IDAphidBase
Homehttp://www.aphidbase.com/aphidbase/
EDAM topicInvertebrate
EDAM topicGenomes
TaxonAphididae
website/apidb_cryptodb.html0000644000244100017570000000627211606605727016206 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ApiDB_CryptoDB

Cryptosporidium genome resources (CryptoDB)

Genomic-scale dataset associated with the eukaryotic pathogens Cryptosporidium.

IDApiDB_CryptoDB
IDaltCryptoDB
Homehttp://cryptodb.org/cryptodb/
EDAM topicUnicellular eukaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonCryptosporidium
RESThttp://eupathdb.org/eupathdb/serviceList.jsp

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://cryptodb.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID cgd7_20
website/apidb_giardiadb.html0000644000244100017570000000626011606605727016263 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ApiDB_GiardiaDB

Giardia genome resources (GiardiaDB)

Genomic-scale datasets for the eukaryotic pathogen Giardia.

IDApiDB_GiardiaDB
IDaltGiardiaDB
Homehttp://giardiadb.org/giardiadb/
EDAM topicUnicellular eukaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonGiardia
RESThttp://eupathdb.org/eupathdb/serviceList.jsp

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://giardiadb.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID GL50803_102438
website/apidb_plasmodb.html0000644000244100017570000000625111606605727016156 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ApiDB_PlasmoDB

Plasmodium genome resources (PlasmoDB)

Genomic-scale dataset associated with the eukaryotic pathogens Plasmodium.

IDApiDB_PlasmoDB
IDaltPlasmoDB
Homehttp://plasmodb.org/plasmo/
EDAM topicUnicellular eukaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonPlasmodium
RESThttp://eupathdb.org/eupathdb/serviceList.jsp

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://plasmodb.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID PF11_0344
website/apidb_toxodb.html0000644000244100017570000000622211606605727015652 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ApiDB_ToxoDB

Toxoplasma genome resources (ToxoDB)

Genomic-scale datasets associated with the eukaryotic pathogens Toxoplasma.

IDApiDB_ToxoDB
IDaltToxoDB
Homehttp://toxodb.org/toxo/
EDAM topicUnicellular eukaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonToxoplasma
RESThttp://eupathdb.org/eupathdb/serviceList.jsp

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://toxodb.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID 49.m00014
website/apidb_trichdb.html0000644000244100017570000000624111606605727015773 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ApiDB_TrichDB

Trichomonas genome resources (TrichDB)

Genomic-scale datasets associated with the eukaryotic Trichomonas.

IDApiDB_TrichDB
IDaltTrichDB
Homehttp://trichdb.org/trichdb/
EDAM topicUnicellular eukaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonTrichomonas
RESThttp://eupathdb.org/eupathdb/serviceList.jsp

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://trichdb.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID TVAG_386080
website/apidb_tritrypdb.html0000644000244100017570000000623311606605727016400 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ApiDB_TriTryPDB

Kinetoplastid genome resources (TritryPDB)

Kinetoplastid genome resources.

IDApiDB_TriTryPDB
IDaltTritryPDB
Homehttp://tritryPDB.org/tritryPDB/
EDAM topicUnicellular eukaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonKinetoplastida
RESThttp://eupathdb.org/eupathdb/serviceList.jsp

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://tritryPDB.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID Tb927.8.620
website/apid.html0000644000244100017570000000266011606605727014133 0ustar jisonindustry Bioinformatics Data Resource Catalogue

APID

Agile protein interaction data analyzer (APID)

Integrated database of protein-protein interactions providing access to all known experimentally validated protein-protein interactions (BIND, BioGRID, DIP, HPRD, IntAct and MINT).

IDAPID
Homehttp://bioinfow.dep.usal.es/apid/index.htm
EDAM topicProtein-protein interactions
Taxonall
website/appadb.html0000644000244100017570000000351511606605727014445 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AppaDB

Pristionchus.org P. pacificus database (AppaDB)

Genomic data of P.pacificus, including the physical map, genetic linkage map, EST and BAC end sequence and hybridization data.

IDAppaDB
Homehttp://www.pristionchus.org
EDAM topicVertebrate
EDAM topicGenomes
EDAM topicGenetic mapping and linkage
EDAM topicmRNA, EST or cDNA
TaxonPristionchus pacificus
website/arachnoserver.html0000644000244100017570000000560511606605727016062 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ArachnoServer

ArachnoServer

Spider toxin database

IDArachnoServer
AccDB-0145
Homehttp://www.arachnoserver.org
EDAM topicOrganism
EDAM topicToxins and targets
CategoryOrganism-specific databases
TaxonArachnida

Available data

Data Format Query Link
Toxin annotation HTML ArachnoServer ID http://www.arachnoserver.org/toxincard.html?id=%s

Example queries

Data Format Query Example
Toxin annotation HTML ArachnoServer ID AS000014
website/arac-xyls.html0000644000244100017570000000640411606605727015121 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AraC-XylS

AraC-XylS database of a family of Helix-Turn-Helix transcription factors from bacteria

A database on a family of Helix-Turn-Helix transcription factors from bacteria.

IDAraC-XylS
AccDB-0003
Homehttp://www.eez.csic.es/arac-xyls/
EDAM topicSpecific protein
EDAM topicTranscription factor and binding site
EDAM topicProtein families
CategoryProtein family/group databases
Taxonall

Available data

Data Format Query Link
Protein report (transcription factor) {AraC-XylS entry} HTML AraC-XylS ID http://www.eez.csic.es/arac-xyls/wfichas/%s.HTM

Example queries

Data Format Query Example
Protein report (transcription factor) {AraC-XylS entry} HTML AraC-XylS ID HpaA
website/aramemnon.html0000644000244100017570000000552011606605727015171 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ARAMEMNON

ARAMEMNON database of plant membrane proteins

Plant membrane proteins.

IDARAMEMNON
Homehttp://aramemnon.botanik.uni-koeln.de/
EDAM topicMembrane protein
EDAM topicPlant
TaxonArabidopsis thaliana

Available data

Data Format Query Link
Protein report (membrane protein) HTML Locus ID (AGI) http://aramemnon.uni-koeln.de/seq_view.ep?search=%s

Example queries

Data Format Query Example
Protein report (membrane protein) HTML Locus ID (AGI) At1g10970
website/archdb.html0000644000244100017570000000532011606605727014435 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ArchDB

ArchDB database of loop structures

ArchDB database of loop structures.

IDArchDB
Homehttp://sbi.imim.es/cgi-bin/archdb/loops.pl
EDAM topicProtein structural motifs
Taxonall

Available data

Data Format Query Link
Protein structure report (3D motif) {Loop structure annotation} HTML PDB ID http://sbi.imim.es/cgi-bin/archdb//loops.pl?PDB=%s

Example queries

Data Format Query Example
Protein structure report (3D motif) {Loop structure annotation} HTML PDB ID 1iiu
website/argonaute.html0000644000244100017570000000407011606605727015200 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Argonaute

Argonaute database of mammalian microRNAs regulatory function

A database on mammalian miRNAs and their known or predicted regulatory targets. It provides information on origin of miRNAs, tissue specificity of their expressions and their known or proposed functions, their potential target genes as well as data on miRNA families based on their coexpression and proteins known to be involved in miRNA processing.

IDArgonaute
Homehttp://argonaute.uni-hd.de
EDAM topicmiRNA
EDAM topicNucleic acid functional sites
EDAM topicTranscription
EDAM topicGene regulatory networks
TaxonMammalia
website/arrayexpress.html0000644000244100017570000001071711606605727015750 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ArrayExpress

ArrayExpress repository for microarray data

A public archive for functional genomics data compliant with MIAME- and MINSEQE requirements in accordance with compliant data in accordance with MGED recommendations. Includes gene-indexed expression profiles.

IDArrayExpress
AccDB-0004
Homehttp://www.ebi.ac.uk/arrayexpress/
EDAM topicGene expression and regulation
EDAM topicGene expression profiling
EDAM topicMicroarrays
CategoryGene expression databases
Taxonall

Available data

Data Format Query Link
Gene annotation (expression) {ArrayExpress gene expression summary} HTML Protein identifier http://www.ebi.ac.uk/arrayexpress/genes/uniprot/%s
Experiment annotation (microarray) {ArrayExpress entry} HTML ArrayExpress accession number http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=%s

Example queries

Data Format Query Example
Gene annotation (expression) {ArrayExpress gene expression summary} HTML Protein identifier P15455
Experiment annotation (microarray) {ArrayExpress entry} HTML ArrayExpress accession number E-MEXP-700
website/asap.html0000644000244100017570000000345011606605730014132 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ASAP

Systematic annotation package for community analysis of genomes (ASAP)

Genome sequences, associated annotations and functional characterization data for E. coli K-12.

IDASAP
Homehttp://www.genome.wisc.edu/tools/asap.htm
EDAM topicProkaryote
EDAM topicGenomes
CategoryNot available
TaxonEscherichia coli

Example queries

Data Format Query Example
website/asc.html0000644000244100017570000000306411606605730013755 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ASC

Active sequence collection (ASC)

A collection of active protein sequences, or protein fragments or subsequences, collected in the form of function-oriented databases. The sequences have known biological activity.

IDASC
Homehttp://bioinformatica.isa.cnr.it/ASC/
EDAM topicProtein sequences
EDAM topicPeptides and amino acids
Taxonall
website/aspicdb.html0000644000244100017570000000765211606605730014623 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ASPICdb

Alternative splicing prediction database (ASPICdb)

A database designed to provide access to reliable annotations of the alternative splicing pattern of human genes, obtained by ASPic algorithm (Castrignano' et al. 2006), and to the functional annotation of predicted isoforms.

IDASPICdb
Homehttp://t.caspur.it/ASPicDB/
EDAM topicGene structure
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation (transcript) HTML Gene symbol http://www.caspur.it/ASPicDB/resultsj.php?table=Transcript&organism=human&accession=Hugo&gene_name=%s
Protein report HTML Gene symbol http://www.caspur.it/ASPicDB/resultsj.php?table=Protein&organism=human&accession=Hugo&gene_name=%s

Example queries

Data Format Query Example
Gene annotation (transcript) HTML Gene symbol tp53
Protein report HTML Gene symbol tp53
website/astd.html0000644000244100017570000003753411606605730014153 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ASTD

Alternative splicing and transcript diversity (ASTD) database

Alternative splicing and transcript diversity.

IDASTD
Homehttp://www.ebi.ac.uk/astd/
EDAM topicGene structure
Taxonall

Available data

Data Format Query Link
Gene annotation HTML Gene ID (Ensembl) http://www.ebi.ac.uk/astd/geneview.html?acc=%s
Gene annotation EMBL format Gene ID (Ensembl) http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=embl
Gene annotation FASTA format Gene ID (Ensembl) http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=fasta
Gene annotation GFF Gene ID (Ensembl) http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=gff
Gene annotation GTF Gene ID (Ensembl) http://www.ebi.ac.uk/astd/geneview.html?acc=%s&export=gtf
Gene annotation (transcript) HTML ASTD ID http://www.ebi.ac.uk/astd/transview.html?acc=%s
Gene annotation (transcript) EMBL format ASTD ID http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=embl
Gene annotation (transcript) GFF ASTD ID http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gff
Gene annotation (transcript) GTF ASTD ID http://www.ebi.ac.uk/astd/transview.html?acc=%s&export=gtf
Protein report HTML Protein ID (Ensembl) http://www.ebi.ac.uk/astd/peptideview.html?acc=%s
Protein report FASTA format Protein ID (Ensembl) http://www.ebi.ac.uk/astd/peptideview.html?acc=%s&export=fasta
Gene features (exon) HTML ASTD ID (exon); ASTD ID http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2
Gene features (intron) HTML ASTD ID (intron); ASTD ID http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2
Gene features (promoter) {TSS} HTML ASTD ID (tss); ASTD ID http://www.ebi.ac.uk/astd/featureview.html?acc=%s1&trans=%s2
Nucleic acid features (PolyA signal) HTML ASTD ID (polya) http://www.ebi.ac.uk/astd/featureview.html?acc=%s

Example queries

Data Format Query Example
Gene features (exon) HTML ASTD ID (exon); ASTD ID EXON00000830017;TRAN00000134394
Gene features (intron) HTML ASTD ID (intron); ASTD ID INTR00000830053;TRAN00000134394
Gene annotation (transcript) HTML ASTD ID TRAN00000134394
Gene annotation (transcript) EMBL format ASTD ID TRAN00000134394
Gene annotation (transcript) GFF ASTD ID TRAN00000134394
Gene annotation (transcript) GTF ASTD ID TRAN00000134394
Gene annotation HTML Gene ID (Ensembl) ENSG00000148680
Gene annotation EMBL format Gene ID (Ensembl) ENSG00000148680
Gene annotation FASTA format Gene ID (Ensembl) ENSG00000148680
Gene annotation GFF Gene ID (Ensembl) ENSG00000148680
Gene annotation GTF Gene ID (Ensembl) ENSG00000148680
Protein report HTML Protein ID (Ensembl) PEPT00000029170
Protein report FASTA format Protein ID (Ensembl) PEPT00000029170
website/atcc_dna.html0000644000244100017570000000250311606605730014740 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ATCC_dna

American type culture collection database (ATCC)

ATCC cultures and bioproducts.

IDATCC_dna
Homehttp://www.lgcstandards-atcc.org/
EDAM topicCell lines and culture
CategoryNot available
Taxonall
website/atcc.html0000644000244100017570000000433711606605730014125 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ATCC

American type culture collection database (ATCC)

ATCC cultures and bioproducts.

IDATCC
Homehttp://www.lgcstandards-atcc.org/
EDAM topicCell lines and culture
CategoryNot available
Taxonall

Available data

Data Format Query Link
Cell line annotation HTML Identifier {Strain ID} http://www.lgcstandards-atcc.org/SearchCatalogs/LinkIn?id=BAA-2146

Example queries

Data Format Query Example
website/atcc_in_host.html0000644000244100017570000000251211606605730015641 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ATCC_in_host

American type culture collection database (ATCC)

ATCC cultures and bioproducts

IDATCC_in_host
Homehttp://www.lgcstandards-atcc.org/
EDAM topicCell lines and culture
CategoryNot available
Taxonall
website/athamap.html0000644000244100017570000000347411606605730014627 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AthaMap

AthaMap database of Arabidopsis TFBS predictions

Genome-wide map of potential transcription factor and small RNA binding sites in Arabidopsis thaliana.

IDAthaMap
Homehttp://www.athamap.de/
EDAM topicNucleic acid functional sites
EDAM topicTranscription
EDAM topicTranscription factor and binding site
EDAM topicPlant
TaxonArabidopsis thaliana
website/atsd.html0000644000244100017570000000241511606605730014141 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ATSD

Aminoacyl-tRNA synthetases database (ATSD)

Aminoacyl-tRNA synthetases database.

IDATSD
Homehttp://rose.man.poznan.pl/aars/index.html
EDAM topicSpecific protein
Taxonall
website/autopsi.html0000644000244100017570000000244511606605730014675 0ustar jisonindustry Bioinformatics Data Resource Catalogue

AutoPSI

AutoPSI database of predicted SCOP classifications

Predicted SCOP classifications.

IDAutoPSI
Homehttp://services.bio.ifi.lmu.de:1046/AutoPSIDB/
EDAM topicProtein families
Taxonall
website/axeldb.html0000644000244100017570000000251211606605730014443 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Axeldb

Axeldb database of gene expression in Xenopus laevis

Gene expression in Xenopus laevis.

IDAxeldb
Homehttp://www.dkfz.de/en/mol_embryology/axeldb.html
EDAM topicGene expression and regulation
TaxonXenopus laevis
website/balibase.html0000644000244100017570000000263711606605730014756 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BAliBASE

BAliBASE benchmark alignment database

A benchmark alignment database, including enhancements for repeats, transmembrane sequences and circular permutations.

IDBAliBASE
Homehttp://www-igbmc.u-strasbg.fr/BioInfo/BAliBASE2/index.html
EDAM topicProtein sequence alignment
Taxonall
website/bcsdb.html0000644000244100017570000000242511606605730014264 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BCSDB

BCSDB database of bacterial carbohydrate structures

Bacterial carbohydrate structures.

IDBCSDB
Homehttp://www.glyco.ac.ru/bcsdb/start.shtml
EDAM topicCarbohydrates
TaxonBacteria
website/bdgp_est.html0000644000244100017570000000251111606605730014772 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BDGP_EST

Berkeley Drosophila genome project EST database (BDGP_EST)

Berkeley Drosophila genome project EST database.

IDBDGP_EST
Homehttp://www.fruitfly.org/
EDAM topicmRNA, EST or cDNA
CategoryNot available
TaxonDrosophila
website/bdgp_ins.html0000644000244100017570000000275611606605730015003 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BDGP_INS

Berkeley Drosophila genome project database: insertion (BDGP_INS)

Berkeley Drosophila genome project database: insertion

IDBDGP_INS
Homehttp://www.fruitfly.org/
EDAM topicInvertebrate
EDAM topicGenomes
CategoryNot available
TaxonDrosophila
website/bgee.html0000644000244100017570000003551711606605730014121 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Bgee

Bgee database for gene expression evolution

Bgee is a database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently EST, Affymetrix, and in situ hybridization data) on anatomical and developmental ontologies. Then, in order to perform automated cross species comparisons, homology relationships across anatomical ontologies, and comparison criteria between developmental ontologies, are designed.

IDBgee
AccDB-0133
Homehttp://bgee.unil.ch
EDAM topicGene family or system
EDAM topicGene expression and regulation
EDAM topicGene expression profiling
CategoryGene expression databases
Taxonall

Available data

Data Format Query Link
Gene annotation HTML UniProt accession http://bgee.unil.ch/bgee/bgee?uniprot_id=%s
Gene annotation HTML Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Gene expression profile HTML Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=gene&action=expression&gene_id=%s
Gene annotation (expression) HTML Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=expression&action=data&gene_id=%s
Gene annotation (expressed gene list) {Bgee ID file} Text Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv
Gene annotation (expressed gene list) {Bgee ID file with expression data} Text Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv&gene_information=2
Gene annotation (expressed gene list) {Bgee ID file with expression data count} Text Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&display_type=tsv&gene_information=1
Gene annotation (expressed gene list) {Bgee ID file} HTML Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s
Gene annotation (expressed gene list) {Bgee ID file with expression data} HTML Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=2
Gene annotation (expressed gene list) {Bgee ID file with expression data count} HTML Gene ID (Ensembl) http://bgee.unil.ch/bgee/bgee?page=expression&action=genes&search_by=1&organ_children=on&gene_organ_stage_information=on&attribut_list=species_name&attribut_list=gene_name&attribut_list=gene_id&gene_id=%s&gene_information=1

Example queries

Data Format Query Example
Gene annotation HTML Gene ID (Ensembl) ENSG00000091831
Gene expression profile HTML Gene ID (Ensembl) ENSG00000091831
Gene annotation (expression) HTML Gene ID (Ensembl) ENSG00000091831
Gene annotation (expressed gene list) {Bgee ID file} Text Gene ID (Ensembl) ENSG00000091831
Gene annotation (expressed gene list) {Bgee ID file with expression data} Text Gene ID (Ensembl) ENSG00000091831
Gene annotation (expressed gene list) {Bgee ID file with expression data count} Text Gene ID (Ensembl) ENSG00000091831
Gene annotation (expressed gene list) {Bgee ID file} HTML Gene ID (Ensembl) ENSG00000091831
Gene annotation (expressed gene list) {Bgee ID file with expression data} HTML Gene ID (Ensembl) ENSG00000091831
Gene annotation (expressed gene list) {Bgee ID file with expression data count} HTML Gene ID (Ensembl) ENSG00000091831
Gene annotation HTML UniProt accession P32234
website/bindingdb.html0000644000244100017570000002330211606605730015124 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BindingDB

BindingDB database of measured binding affinities

Database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules.

IDBindingDB
AccDB-0127
Homehttp://www.bindingdb.org/
EDAM topicProtein-ligand interactions
EDAM topicDrugs and targets
CategoryOther
Taxonall
Linkinghttp://www.bindingdb.org/bind/SearchTemplates.jsp

Available data

Data Format Query Link
Protein-drug interaction HTML UniProt accession http://www.bindingdb.org/uniprot/%s
Inhibitor annotation HTML Protein name {BindingDB target name} http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_ki.jsp?tag=tg&kiunit=nM&icunit=nM&column=ki&submit=Search&energyterm=kJ%2Fmole&target=%s
Small molecule report {ITC data} HTML Protein name {BindingDB target name} http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_itc.jsp?tag=tg&column=delta_G0&energyterm=kJ%2Fmole&startPg=0&Increment=50&submit=Search&target=%s
Database hits (sequence) {BindingDB entries} HTML Identifier {Protein sequence} http://www.bindingdb.org/bind/blastResult.jsp?DATASOURCE=protein&Search=B2&blastSeq=%s
Small molecule report HTML BindingDB Monomer ID http://www.bindingdb.org/bind/chemsearch/marvin/MolStructure.jsp?monomerid=%s
Small molecule report HTML Identifier {SMILES string} http://www.bindingdb.org/bind/searchby_smiles.jsp?SearchType=4&submit=Search&smilesStr=%s
Protein-drug interaction HTML PDB ID http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_PDBids.jsp?PDBids_submit=Search&PDBids=%s
Protein-drug interaction HTML PubMed ID http://www.bindingdb.org/jsp/dbsearch/PrimarySearch_pubmed.jsp?pubmed_submit=Search&pubmed=%s

Example queries

Data Format Query Example
Protein-drug interaction HTML UniProt accession Q29005
Database hits (sequence) {BindingDB entries} HTML Identifier {Protein sequence} VKCGSRRERCGYRLVRRQRSADEQLHCAGKAKRSGGHAPRVRELLLD
Small molecule report HTML BindingDB Monomer ID 100
Small molecule report HTML Identifier {SMILES string} CC%28C%29C1%28C%29SC%28Nc2ccccc2C%28F%29%28F%29F%29%3DNC1%3DO+%7Cc%3A18%7C
Protein-drug interaction HTML PDB ID 1OKZ
Protein-drug interaction HTML PubMed ID 17408953
website/biocyc.html0000644000244100017570000002334411606605730014462 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BioCyc

BioCyc collection of Pathway/Genome Databases

BioCyc collection of Pathway/Genome Databases. Each BioCyc database describes the genome and metabolic pathways of a single organism. This includes Escherichia coli K-12 MG1655 model-organism database (EcoCyc) and Multiorganism metabolic pathway and enzyme database (MetaCyc)

IDBioCyc
AccDB-0005
Homehttp://www.biocyc.org/
EDAM topicGenomes
EDAM topicEnzymes
EDAM topicMetabolic pathways
CategoryEnzyme and pathway databases
CategoryMetabolic pathways database
Taxonall
Linkinghttp://biocyc.org/linking.shtml

Available data

Data Format Query Link
Metadata and report HTML Identifier {BioCyc} http://biocyc.org/getid?id=%s
Pathway or network report HTML Pathway ID (BioCyc) http://biocyc.org/ECOLI/NEW-IMAGE?type=PATHWAY&object=%s
Small molecule report HTML Compound ID (BioCyc) http://biocyc.org/ECOLI/NEW-IMAGE?type=COMPOUND&object=%s
Reaction annotation HTML Reaction ID (BioCyc) http://biocyc.org/ECOLI/NEW-IMAGE?type=REACTION&object=%s
Protein report (enzyme) HTML Enzyme ID (BioCyc) http://biocyc.org/ECOLI/new-image?type=ENZYME&object=%s
Cytogenetic map HTML Chromosome name http://biocyc.org/ECOLI/substring-search?type=%s
Genome map HTML Gene ID (EcoGene) http://biocyc.org/ECOLI/new-image?type=LOCUS-POSITION&object=%s
Genome map HTML Identifier {Map position} http://biocyc.org/ECOLI/substring-search?type=MAPTICK&object=%s

Example queries

Data Format Query Example
Pathway or network report HTML Pathway ID (BioCyc) GLYCOLYSIS
Small molecule report HTML Compound ID (BioCyc) FRUCTOSE-6P
Reaction annotation HTML Reaction ID (BioCyc) PGLUCISOM-RXN
Protein report (enzyme) HTML Enzyme ID (BioCyc) PGLUCISOM
Cytogenetic map HTML Chromosome name COLI-K12
Genome map HTML Gene ID (EcoGene) EG11024
Genome map HTML Identifier {Map position} None
website/biogrid.html0000644000244100017570000000373711606605730014635 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BioGRID

BioGRID

Physical and genetic interactions in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, and Schizosaccharomyces pombe

IDBioGRID
Homehttp://thebiogrid.org/
EDAM topicProtein interactions
EDAM topicGene expression and regulation
TaxonSaccharomyces cerevisiae, Homo sapiens, Caenorhabditis elegans, Drosophila, Homo sapiens, Schizosaccharomyces pombe
website/biomodels.html0000644000244100017570000000746111606605730015171 0ustar jisonindustry Bioinformatics Data Resource Catalogue

biomodels

BioModels database of annotated published models

A that allows biologists to store, search and retrieve published mathematical models of biological interests. Models present in BioModels Database are annotated and linked to relevants, such as publications, databases of compounds and pathways, controlled vocabularies, etc.

IDbiomodels
Homehttp://www.ebi.ac.uk/biomodels-main/
EDAM topicBiological models
Taxonall

Available data

Data Format Query Link
Biological model HTML BioModel ID http://www.ebi.ac.uk/biomodels-main/%s
Biological model SBML BioModel ID http://www.ebi.ac.uk/biomodels/models-main/publ/%s.xml

Example queries

Data Format Query Example
Biological model HTML BioModel ID BIOMD0000000001
Biological model SBML BioModel ID BIOMD0000000001
website/bionumbers.html0000644000244100017570000000301311606605730015346 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BioNumbers

BioNumbers

A database of key numbers in molecular biology, along with relevant references to the original literature, useful comments, and related numbers.

IDBioNumbers
Homehttp://www.bionumbers.hms.harvard.edu/
EDAM topicData handling
EDAM topicLiterature and documentation
Taxonall
website/biosystems.html0000644000244100017570000000342611606605731015413 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BioSystems

BioSystems

BioSystems is a composite biological pathway and disease database and aims to: (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biological systems data.

IDBioSystems
Homehttp://www.ncbi.nlm.nih.gov/Structure/biosystems/docs/biosystems_about.html
EDAM topicPathways, networks and models
EDAM topicDisease
Taxonall
website/bipa.html0000644000244100017570000000722611606605731014127 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BIPA

BIPA database for interaction between protein and nucleic acid

Protein-nucleic acid interactions, with various features of protein-nuleic acid interfaces.

IDBIPA
Homehttp://www-cryst.bioc.cam.ac.uk/bipa
EDAM topicProtein-nucleic acid interactions
Taxonall

Available data

Data Format Query Link
Protein-nucleic acid interaction HTML PDB ID http://mordred.bioc.cam.ac.uk/bipa/structures/%s
Domain-nucleic acid interaction HTML SCOP sunid http://mordred.bioc.cam.ac.uk/bipa/scops/%s

Example queries

Data Format Query Example
Protein-nucleic acid interaction HTML PDB ID 10MH
Domain-nucleic acid interaction HTML SCOP sunid 120412
website/bloodexpress.html0000644000244100017570000000324211606605731015717 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BloodExpress

BloodExpress database of gene expression in mouse heamatopoesis

BloodExpress integrates 271 individual microarray experiments derived from 15 distinct studies done on most characterised mouse blood cell types. Gene expression information has been discretised to absent/present/unknown calls.

IDBloodExpress
Homehttp://hscl.cimr.cam.ac.uk/bloodexpress/
EDAM topicGene expression and regulation
EDAM topicMicroarrays
TaxonMus
website/blotbase.html0000644000244100017570000000756711606605731015017 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BlotBase

BlotBase Northern blots database

Northern blots database.

IDBlotBase
Homehttp://www.medicalgenomics.org/Databases/BlotBase
EDAM topicGene expression and regulation
Taxonall

Available data

Data Format Query Link
Northern blot image {BlotBase Blot Entry} HTML BlotBase blot ID http://www.medicalgenomics.org/databases/blotbase/search?action=show_details&blot_id=%s
Northern blot image {BlotBase Blot Listing by Gene} HTML Gene symbol http://www.medicalgenomics.org/databases/blotbase/search?action=query&filter=genes&exact_match=yes&query=%s

Example queries

Data Format Query Example
Northern blot image {BlotBase Blot Listing by Gene} HTML Gene symbol ace
Northern blot image {BlotBase Blot Entry} HTML BlotBase blot ID 524
website/bndb.html0000644000244100017570000000251411606605731014114 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BNDB

Biochemical network database (BNDB)

Biochemical network database for analyzing and visualizing complex biochemical networks and processes.

IDBNDB
Homehttp://www.bndb.org/index.php?idx=main
EDAM topicPathways, networks and models
Taxonall
website/bold.html0000644000244100017570000000333511606605731014131 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BOLD

Barcode of Life database (BOLD)

An online workbench that aids collection, management, analysis, and use of DNA barcodes. It consists of 3 components (MAS, IDS, and ECS) that each address the needs of various groups in the barcoding community.

IDBOLD
Homehttp://www.barcodinglife.org/views/login.php
EDAM topicGenotype and phenotype
CategoryNot available
Taxonall

Example queries

Data Format Query Example
website/brenda.html0000644000244100017570000001211511606605731014440 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BRENDA

BRENDA comprehensive enzyme information system

Comprehensive enzyme information.

IDBRENDA
AccDB-0131
Homehttp://www.brenda-enzymes.org
EDAM topicEnzymes
CategoryEnzyme and pathway databases
Taxonall
SOAPhttp://www.brenda-enzymes.org/soap2

Available data

Data Format Query Link
Protein report (enzyme) {BRENDA entry} HTML EC number http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s
Protein report (enzyme) {BRENDA entry} HTML EC number; BRENDA organism ID http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s1&&OrganismID=&s3&ShowAll=True
Protein report (enzyme) {BRENDA entry} HTML EC number; UniProt accession; BRENDA organism ID http://www.brenda-enzymes.org/php/result_flat.php4?ecno=%s1&UniProtAcc=%s2&OrganismID=&s3&ShowAll=True

Example queries

Data Format Query Example
Protein report (enzyme) {BRENDA entry} HTML EC number 1.1.5.82
Protein report (enzyme) {BRENDA entry} HTML EC number; UniProt accession; BRENDA organism ID 1.1.5.82;P15719;4577
website/brix.html0000644000244100017570000000255111606605731014154 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BriX

BriX classification of protein fragments

BriX is a structural classification of protein fragments. The library comprises fragments ranging from 4 to 14 amino acids that are clustered against 6 different distance thresholds.

IDBriX
Homehttp://brix.vub.ac.be/
EDAM topicStructural clustering
Taxonall
website/buchnerabase.html0000644000244100017570000000277311606605731015640 0ustar jisonindustry Bioinformatics Data Resource Catalogue

BuchneraBase

BuchneraBase database of Buchnera species

A database designed to encapsulate and reference information obtained from the complete genome sequence of the gamma-proteobacterium Buchnera species.

IDBuchneraBase
Homehttp://www.buchnera.org/
EDAM topicProkaryote
EDAM topicGenomes
TaxonBuchnera
website/butterflybase.html0000644000244100017570000000313511606605731016062 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ButterflyBase

ButterflyBase database of comparative Genomics of Lepidoptera

Gene database for butterflies and moths.

IDButterflyBase
Homehttp://www.butterflybase.org
EDAM topicInvertebrate
EDAM topicGenomes
EDAM topicComparative genomics
TaxonLepidoptera
website/cabri.html0000644000244100017570000000432611606605731014272 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CABRI

Common Access to Biotechnological Resources and Information (CABRI)

A collection of European Biological Resource Centre catalogues.

IDCABRI
Homehttp://www.cabri.org/
EDAM topicLaboratory resources
Taxon

Available data

Data Format Query Link
Cell line annotation Text CABRI catalogue name; CABRI accession http://www.cabri.org/CABRI/srs-bin/wgetz?-newId+-ascii+-e+[%s1:%s1 %s2]

Example queries

Data Format Query Example
website/cadre.html0000644000244100017570000000250111606605731014261 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CADRE

Central aspergillus data repository (CADRE)

Central aspergillus data repository (CADRE).

IDCADRE
Homehttp://www.cadre-genomes.org.uk/Aspergillus_fumigatus/
EDAM topicOrganism
TaxonEurotiales
website/cangem.html0000644000244100017570000000334611606605731014445 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CanGEM

CanGEM database of clinical tumor samples and microarray data

A public database for storing clinical information about tumor samples and microarray data, with emphasis on array comparative genomic hybridization (aCGH) and data mining of gene copy number changes.

IDCanGEM
Homehttp://www.cangem.org/
EDAM topicGene expression and regulation
EDAM topicMicroarrays
EDAM topicCancer
TaxonHomo sapiens
website/catdb.html0000644000244100017570000001420211606605731014261 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CATdb

Complete Arabidopsis transcriptome database (CATdb)

CATdb contains data on 105 Arabidopsis transcriptome projects (3262 hybridized samples) in public access out of a total of 172 projects (~6440 hybridized samples). The data are released one year after their production.

IDCATdb
Homehttp://urgv.evry.inra.fr/CATdb
EDAM topicGene expression and regulation
EDAM topicPlant
TaxonArabidopsis thaliana

Available data

Data Format Query Link
Gene annotation (expression) HTML TAIR accession (At gene) http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_diff_id.pl?idnum=%s
Gene annotation {CATdb Gene and Probe info} HTML TAIR accession (At gene) http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/seq_info.pl?ident=%s
Data reference {CATdb Search by keyword} HTML Identifier {Keyword} http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_proj_kw.pl?kwrd=%s
Gene annotation (expression) HTML TAIR accession (At gene) http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_diff_id.pl?idnum=AT1G69880
Gene annotation {CATdb Gene and Probe info} HTML TAIR accession (At gene) http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/seq_info.pl?ident=AT1G69880
Data reference {CATdb Search by keyword} HTML Identifier {Keyword} http://urgv.evry.inra.fr/cgi-bin/projects/CATdb/cons_proj_kw.pl?kwrd=%s

Example queries

Data Format Query Example
Data reference {CATdb Search by keyword} HTML Identifier {Keyword} nitrogen
Data reference {CATdb Search by keyword} HTML Identifier {Keyword} nitrogen
website/cath.html0000644000244100017570000001751411606605731014134 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CATH

CATH protein structure classification database

CATH is a hierarchical classification of protein domain structures, which clusters proteins at four major levels: Class (C), Architecture (A), Topology (T) and Homologous superfamily (H). The boundaries and assignments for each protein domain are determined using a combination of automated and manual procedures which include computational techniques, empirical and statistical evidence, literature review and expert analysis.

IDCATH
Homehttp://www.cathdb.info/
EDAM topicProtein domains
EDAM topicSequence clustering
Taxonall
SOAPhttp://api.cathdb.info/api/soap/dataservices/wsdl

Available data

Data Format Query Link
CATH domain report HTML CATH domain ID http://www.cathdb.info/domain/%s
CATH domain report XML CATH domain ID http://www.cathdb.info/domain/%s?view=xml
Protein features (domains) {CATH chain} HTML Polypeptide chain ID http://www.cathdb.info/chain/%s
Protein features (domains) {PDB} HTML PDB ID http://www.cathdb.info/PDB/%s
Protein features (domains) {PDB} XML PDB ID http://www.cathdb.info/PDB/%s?view=xml
CATH node HTML CATH node ID http://www.cathdb.info/cathnode/%s

Example queries

Data Format Query Example
CATH domain report HTML CATH domain ID 1cukA01
CATH domain report XML CATH domain ID 1cukA01
Protein features (domains) {CATH chain} HTML Polypeptide chain ID 1cukA
Protein features (domains) {PDB} HTML PDB ID 1cuk
Protein features (domains) {PDB} XML PDB ID 1cuk
CATH node HTML CATH node ID 1.10.10.10
website/catma.html0000644000244100017570000000351411606605731014275 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CATMA

Arabidopsis transcriptome microarray database (CATMA)

The aim of the Complete Arabidopsis Transcriptome MicroArray (CATMA) project was the design and production of high quality Gene-specific Sequence Tags (GSTs) covering most Arabidopsis genes. The GST repertoire is used by numerous groups for the production of DNA arrays for transcript profiling experiments.

IDCATMA
Homehttp://www.catma.org/
EDAM topicGene expression and regulation
EDAM topicMicroarrays
EDAM topicPlant
TaxonArabidopsis thaliana
website/cazy.html0000644000244100017570000000602511606605731014156 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CAZy

Carbohydrate-active enzymes database (CAZy)

The CAZy database describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

IDCAZy
AccDB-0136
Homehttp://www.cazy.org/
EDAM topicEnzymes
EDAM topicProtein families
CategoryProtein family/group databases
Taxonall

Available data

Data Format Query Link
Protein report (enzyme) {CAZy entry} HTML Enzyme ID (CAZy) http://www.cazy.org/fam/%s.html

Example queries

Data Format Query Example
Protein report (enzyme) {CAZy entry} HTML Enzyme ID (CAZy) GT2
website/cbs.html0000644000244100017570000000243711606605731013762 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CBS

Genome atlas database (CBS)

Summary of genomic information currently available for various organisms.

IDCBS
Homehttp://www.cbs.dtu.dk/services/GenomeAtlas/
EDAM topicGenomics
Taxonall
website/ccap.html0000644000244100017570000000525411606605731014121 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CCAP

Culture collection of algae and protozoa (CCAP)

Culture collection of algae and protozoa

IDCCAP
Homehttp://www.ccap.ac.uk/index.htm
EDAM topicCell lines and culture
Taxonall

Available data

Data Format Query Link
Cell line annotation {Strain information} HTML CCAP strain number http://www.ccap.ac.uk/strain_info.php?Strain_No=%s

Example queries

Data Format Query Example
Cell line annotation {Strain information} HTML CCAP strain number 211/11B
website/cc+.html0000644000244100017570000000243111606605731013645 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CC+

CC+ database of coiled-coil structures

A relational database of coiled-coil structures.

IDCC+
Homehttp://coiledcoils.chm.bris.ac.uk/ccplus
EDAM topicProtein structural motifs
Taxonall
website/cdd.html0000644000244100017570000002720411606605732013745 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CDD

Conserved domain database (CDD)

A collection of multiple sequence alignments for ancient domains and full-length proteins.

IDCDD
Homehttp://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml
EDAM topicProtein sequence alignment
EDAM topicSequence clustering
EDAM topicProtein domains
CategoryNot available
Taxonall

Available data

Data Format Query Link
Sequence alignment (protein) {Conserved Domain Summary} HTML CDD ID http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s
Sequence alignment (protein) {Conserved Domain Summary} HTML CDD PSSM-ID http://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=%s
Protein family annotation {Conserved Domain Document Summary} HTML CDD ID http://www.ncbi.nlm.nih.gov/sites/cdd?term=%s[Accn]
Protein family annotation {Conserved Domain Document Summary} HTML CDD PSSM-ID http://www.ncbi.nlm.nih.gov/cdd/%s
Protein family annotation {Conserved Domain description} XML CDD PSSM-ID http://www.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=cdd&id=%s&retmode=xml
Protein features (domains) {Conserved Protein structure report (domain)} HTML Sequence accession (protein) http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s
Protein features (domains) {Conserved Protein structure report (domain)} HTML GI number (protein) http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s
Protein features (domains) {Conserved Protein structure report (domain)} XML Sequence accession (protein) http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s&output=xml
Protein features (domains) {Conserved Protein structure report (domain)} XML GI number (protein) http://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?seqinput=%s&output=xml

Example queries

Data Format Query Example
Sequence alignment (protein) {Conserved Domain Summary} HTML CDD PSSM-ID 153083
Protein family annotation {Conserved Domain Document Summary} HTML CDD PSSM-ID 153083
Protein family annotation {Conserved Domain description} XML CDD PSSM-ID 153083
Sequence alignment (protein) {Conserved Domain Summary} HTML CDD ID cd00576
Protein family annotation {Conserved Domain Document Summary} HTML CDD ID cd00576
Protein features (domains) {Conserved Protein structure report (domain)} HTML Sequence accession (protein) P26675
Protein features (domains) {Conserved Protein structure report (domain)} XML Sequence accession (protein) P26675
Protein features (domains) {Conserved Protein structure report (domain)} HTML GI number (protein) 76800652
Protein features (domains) {Conserved Protein structure report (domain)} XML GI number (protein) 76800652
website/cellcycledb.html0000644000244100017570000001012511606605731015451 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CellCycleDB

Cell cycle database (CellCycleDB)

A collection of genes and proteins involved in human and yeast cell cycle.

IDCellCycleDB
Homehttp://www.itb.cnr.it/cellcycle/index.html
EDAM topicSpecific protein
EDAM topicCell cycle and development
EDAM topicFungal
TaxonSaccharomyces cerevisiae, Homo sapiens

Available data

Data Format Query Link
Gene annotation HTML Gene name (NCBI) http://www.itb.cnr.it/cellcycle/gene_rep.php?gene_name=%s
Protein report HTML Protein name (UniProt) http://www.itb.cnr.it/cellcycle/protein_rep.php?protein_name=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene name (NCBI) CCND1
Protein report HTML Protein name (UniProt) P53
website/celllinedb.html0000644000244100017570000000315611606605732015310 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CellLineDB

Cell line database (CellLineDB)

Information on 4.850 human and animal cell lines that are available in many Italian laboratories and in some of the most important European cell banks and cell culture collections.

IDCellLineDB
Homehttp://bioinformatics.istge.it/interlab/cldb.html
EDAM topicLaboratory resources
EDAM topicCell lines and culture
TaxonMetazoa
website/cellmint.html0000644000244100017570000000304511606605732015017 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CellMINT

CellMINT database of protein localization and interactions

A database tool to integrate protein localization and interaction information.

IDCellMINT
Homehttp://mint.bio.uniroma2.it/CellMINT/welcome.do
EDAM topicProtein-protein interactions
EDAM topicProtein targeting and localization
Taxonall
website/centrosome:db.html0000644000244100017570000000261411606605732015767 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Centrosome:db

Centrosomal proteins database (Centrosome:db)

Centrosome:db contains a set of human genes encoding proteins that are localized in the centrosome, either as centrosome constituents or as centrosome visitors.

IDCentrosome:db
Homehttp://centrosome.dacya.ucm.es/
EDAM topicSpecific protein
TaxonHomo sapiens
website/cephdb.html0000644000244100017570000000277711606605732014450 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CEPHdb

CEPH genotype database (CEPHdb)

A database of genotypes for genetic markers that have been typed on the CEPH reference family resource for linkage mapping.

IDCEPHdb
Homehttp://www.cephb.fr/fr/cephdb/
EDAM topicGenetic mapping and linkage
EDAM topicGenotype and phenotype
TaxonHomo sapiens
website/cgd.html0000644000244100017570000001004111606605732013737 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CGD

Candida genome database (CGD)

A resource for genomic sequence data and gene and protein information for Candida albicans.

IDCGD
AccDB-0126
Homehttp://www.candidagenome.org/
EDAM topicYeast
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonCandida albicans

Available data

Data Format Query Link
Gene annotation HTML ORF ID http://www.candidagenome.org/cgi-bin/locus.pl?locus=%s
Gene annotation HTML Locus ID (CGD) http://www.candidagenome.org/cgi-bin/locus.pl?locus=%s

Example queries

Data Format Query Example
Gene annotation HTML ORF ID orf19.3127
Gene annotation HTML Locus ID (CGD) CAL0002268
website/cg.html0000644000244100017570000001071011606605732013576 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CG

Comparative genometrics (CG) database

Devoted to the characterization of complete chromosome sequences by standardized genometric methods, the Comparative Genometrics website displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase. Although primarly focused on prokaryotic chromosomes, the CG website posts genometric information on paradigm plasmids, phages, viruses, and organelles.

IDCG
Homehttp://www2.unil.ch/comparativegenometrics/
EDAM topicComparative genomics
EDAM topicChromosomes
EDAM topicNucleic acid structure
Taxonall

Available data

Data Format Query Link
Nucleic acid structure report {Nucleotide skews page} HTML NCBI genome accession http://www2.unil.ch/comparativegenometrics/%s.htm
Nucleic acid structure report {Nucleotide skews data} Text NCBI genome accession http://www2.unil.ch/comparativegenometrics/docs/%s.txt

Example queries

Data Format Query Example
Nucleic acid structure report {Nucleotide skews page} HTML NCBI genome accession NC_000913
Nucleic acid structure report {Nucleotide skews data} Text NCBI genome accession NC_000913
website/chebi.html0000644000244100017570000000564011606605732014265 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ChEBI

Database of chemical entities of biological interest (ChEBI)

Dictionary of molecular entities focused on small chemical compounds. "Molecular entity" includes any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

IDChEBI
Homehttp://www.ebi.ac.uk/chebi/
EDAM topicSmall molecules
Taxon

Available data

Data Format Query Link
Small molecule report HTML ChEBI ID http://www.ebi.ac.uk/chebi/searchId.do;?chebiId=CHEBI:%s

Example queries

Data Format Query Example
Small molecule report HTML ChEBI ID 15356
website/chembl.html0000644000244100017570000000307411606605732014444 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ChEMBL

ChEMBL

A database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data).

IDChEMBL
Homehttps://www.ebi.ac.uk/chembl/
EDAM topicDrugs and targets
EDAM topicSmall molecules
Taxonall
website/chemidplus.html0000644000244100017570000000334711606605732015352 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ChemIDplus

ChemIDplus

Structure and nomenclature authority files used for the identification of chemical substances cited in National Library of Medicine (NLM) databases, including the TOXNET® system. ChemIDplus also provides structure searching and direct links to many biomedical resources at NLM and on the Internet for chemicals of interest.

IDChemIDplus
Homehttp://www.nlm.nih.gov/pubs/factsheets/chemidplusfs.html
EDAM topicSmall molecules
EDAM topicNomenclature
Taxonall
website/citexplore.html0000644000244100017570000000723611606605732015374 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CiteXplore

CiteXplore literature database

CiteXplore combines literature search with text mining tools for biology.

IDCiteXplore
Homehttp://www.ebi.ac.uk/citexplore
EDAM topicLiterature and documentation
Taxon

Available data

Data Format Query Link
Bibliographic reference {PubMedView} HTML PubMed ID http://www.ebi.ac.uk/citexplore/citationDetails.do?externalId=%s&dataSource=MED
Bibliographic reference {PubMedXML} XML PubMed ID http://www.ebi.ac.uk/citexplore/viewXML.do?externalId=%s&dataSource=MED

Example queries

Data Format Query Example
Bibliographic reference {PubMedView} HTML PubMed ID 7729218
Bibliographic reference {PubMedXML} XML PubMed ID 7729218
website/cleanex.html0000644000244100017570000001046311606605732014631 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CleanEx

CleanEx database of gene expression profiles

Public gene expression data via unique approved gene symbols and which represents heterogeneous expression data produced by different technologies in a way that facilitates joint analysis and cross-dataset comparisons.

IDCleanEx
AccDB-0008
Homehttp://www.cleanex.isb-sib.ch/
EDAM topicGene expression and regulation
EDAM topicGene expression profiling
CategoryGene expression databases
Taxonall

Available data

Data Format Query Link
Gene expression profile {CleanEx entry} HTML CleanEx entry name http://www.cleanex.isb-sib.ch/cgi-bin/get_doc?db=cleanex&format=nice&entry=%s
Experiment annotation (microarray) {CleanEx dataset} HTML CleanEx dataset code http://www.cleanex.isb-sib.ch/cgi-bin/get_doc?db=cleanex_ref&format=nice&entry=%s

Example queries

Data Format Query Example
Gene expression profile {CleanEx entry} HTML CleanEx entry name HS_BMP5
Experiment annotation (microarray) {CleanEx dataset} HTML CleanEx dataset code GSE2109_DOC
website/clima.html0000644000244100017570000001051711606605732014277 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CLIMA

Database for cell line integrated molecular authentication (CLIMA)

Cell line integrated molecular authentication.

IDCLIMA
Homehttp://bioinformatics.istge.it/clima/
EDAM topicCell lines and culture
Taxonall

Available data

Data Format Query Link
Cell line annotation {CLIMA entrys} HTML Cell line name (exact) http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=exact
Cell line annotation {CLIMA entry} HTML Cell line name (truncated) http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=truncated
Cell line annotation {CLIMA entry} HTML Cell line name (no punctuation) http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=nopunct
Cell line annotation {CLIMA entry} HTML Cell line name (assonant) http://bioinformatics.istge.it/clima/clima_search.php?cl_name=%s&cl_name_crit=soundex

Example queries

Data Format Query Example
Cell line annotation {CLIMA entrys} HTML Cell line name (exact) SaOS2
website/clustr.html0000644000244100017570000000305111606605732014521 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CluSTr

CluSTr protein classification database

Automatic classification of UniProt Knowledgebase and IPI proteins into groups of related proteins. The clustering is based on analysis of all pairwise comparisons between protein sequences.

IDCluSTr
Homehttp://www.ebi.ac.uk/clustr/
EDAM topicProtein families
EDAM topicSequence clustering
Taxonall
website/cmd.html0000644000244100017570000000731111606605732013753 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CMD

Collagen Mutation Database (CMD)

Database of osteogenesis imperfecta and type III collagen variants.

IDCMD
Homehttps://eds.gene.le.ac.uk
EDAM topicHuman disease
TaxonHomo sapiens

Available data

Data Format Query Link
Sequence variation annotation {Sequence variants} HTML Database name (CMD) https://eds.gene.le.ac.uk/home.php?select_db=%s

Example queries

Data Format Query Example
Sequence variation annotation {Sequence variants} HTML Database name (CMD) COL3A1
Sequence variation annotation {Sequence variants} HTML Database name (CMD) COL5A1
Sequence variation annotation {Sequence variants} HTML Database name (CMD) COL5A2
website/cmr.html0000644000244100017570000001627611606605732014003 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CMR

Comprehensive microbial genome resource (CMR)

Information on all of the publicly available, complete prokaryotic genomes. Common data types across all genomes in the CMR make searches more meaningful, and cross genome analysis highlight differences and similarities between the genomes.

IDCMR
AccDB-0009
Homehttp://cmr.tigr.org/
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicGenomics
CategoryGenome annotation databases
TaxonBacteria

Available data

Data Format Query Link
Gene annotation HTML Gene ID (JCVI) http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?locus=%s
Gene annotation HTML GenBank identifier http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=SP&acc=%s
Gene annotation HTML UniProt accession http://cmr.jcvi.org/cgi-bin/CMR/shared/GenePage.cgi?type=protein_id&acc=%s
Genome metadata {CMR genome page} HTML NCBI taxonomy ID http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?taxon_id=%s
Genome metadata {CMR genome page} HTML NCBI Genome Project ID http://cmr.jcvi.org/cgi-bin/CMR/GenomePage.cgi?ncbi_project_id=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID (JCVI) BA_0001
Gene annotation HTML GenBank identifier AAP24059.1
Gene annotation HTML UniProt accession Q81W35
Genome metadata {CMR genome page} HTML NCBI taxonomy ID 198094
Genome metadata {CMR genome page} HTML NCBI Genome Project ID 309
website/cogeme.html0000644000244100017570000000756611606605732014463 0ustar jisonindustry Bioinformatics Data Resource Catalogue

COGEME

Phytopathogenic fungi and oomycete EST database (COGEME)

Phytopathogenic fungi and oomycete EST database.

IDCOGEME
Homehttp://cogeme.ex.ac.uk/
EDAM topicmRNA, EST or cDNA
EDAM topicPathogen
EDAM topicFungal
TaxonFungi

Available data

Data Format Query Link
Sequence record {Unisequence} HTML COGEME unisequence ID http://cogeme.ex.ac.uk/cgi-bin/uni.pl?uni=x
Sequence record {EST} HTML COGEME EST ID http://cogeme.ex.ac.uk/cgi-bin/est.pl?est=x

Example queries

Data Format Query Example
Sequence record {EST} HTML COGEME EST ID Bg13901527
Sequence record {Unisequence} HTML COGEME unisequence ID BgCon[0123]
website/colibase.html0000644000244100017570000000321611606605732014771 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ColiBase

ColiBase Enterobactericaiae genome database

A database for comparative genome analysis of Enterobactericaiae, e.g. Escherichia, Shigella etc..

IDColiBase
Homehttp://xbase.bham.ac.uk/colibase/
EDAM topicComparative genomics
EDAM topicProkaryote
EDAM topicGenomes
TaxonEnterobactericaiae
website/columba.html0000644000244100017570000000310311606605732014625 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Columba

Columba protein structure annotation database

Annotations for protein structures from the Protein Data Bank (PDB) from several protein structure related sources, including KEGG and ENZYME. The calculated secondary structure from DSSP is included as well as the protein-fold classification databases SCOP and CATH. Further functional and taxonomic annotation is available from Swiss-Prot, the Gene Ontology (GO) and the NCBI Taxonomy.

IDColumba
Homehttp://www.columba-db.de
EDAM topicProtein structure
Taxonall
website/compluyeast-2dpage.html0000644000244100017570000000763311606605732016724 0ustar jisonindustry Bioinformatics Data Resource Catalogue

COMPLUYEAST-2DPAGE

COMPLUYEAST-2DPAGE database

A two-dimensional polyacrilamide gel electrophoresis federated database.

IDCOMPLUYEAST-2DPAGE
AccDB-0010
Homehttp://compluyeast2dpage.dacya.ucm.es/
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonSaccharomyces cerevisiae

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML UniProt accession http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s
Experiment annotation (2D PAGE) HTML Protein identifier http://compluyeast2dpage.dacya.ucm.es/cgi-bin/2d//2d.cgi?ac=%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML UniProt accession P83784
Experiment annotation (2D PAGE) HTML Protein identifier CAP6_CANAL
website/conoserver.html0000644000244100017570000000566411606605732015406 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ConoServer

Cone snail toxin database (ConoServer)

Conotoxin peptide sequences and structures.

IDConoServer
AccDB-0156
Homehttp://www.conoserver.org/
EDAM topicOrganism
EDAM topicToxins and targets
CategoryOrganism-specific databases
TaxonConus

Available data

Data Format Query Link
Protein report HTML Protein ID (ConoServer) http://www.conoserver.org/?page=card&table=protein&id=%s

Example queries

Data Format Query Example
Protein report HTML Protein ID (ConoServer) 3271
website/consensuspathdb.html0000644000244100017570000001751411606605733016422 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ConsensusPathDB

ConsensusPathDB database of human functional interaction networks

Information on physical molecular interactions, biochemical pathways, and gene regulatory networks in human.

IDConsensusPathDB
Homehttp://cPDB.molgen.mpg.de/
EDAM topicGene regulatory networks
EDAM topicProtein-protein interactions
EDAM topicPathways, networks and models
EDAM topicGene expression and regulation
TaxonHomo sapiens

Available data

Data Format Query Link
Pathway or network report HTML Pathway or network name http://cPDB.molgen.mpg.de/CPDB/search?nameacc=name&keywords=%s&searchspace=Pathway
Identifier metadata {Physical entities} HTML ConsensusPathDB entity name http://cPDB.molgen.mpg.de/CPDB/search?nameacc=name&keywords=%s&searchspace=PhysicalEntity
Identifier metadata {Physical entities} HTML Accession {Physical entity external accession number} http://cPDB.molgen.mpg.de/CPDB/search?nameacc=acc&keywords=PFKL&searchspace=PhysicalEntity
Protein interaction report {Interactions of pathway} HTML Pathway ID (ConsensusPathDB) http://cPDB.molgen.mpg.de/CPDB/getInteractionsOfObjs?objs:list=%s&objtype=p
Protein interaction report {Interactions of physical entity} HTML ConsensusPathDB entity ID http://cPDB.molgen.mpg.de/CPDB/getInteractionsOfObjs?objs:list=%s&objtype=e
Protein interaction report {Shortest interaction path between two physical entities} HTML ConsensusPathDB entity ID; ConsensusPathDB entity ID http://cPDB.molgen.mpg.de/CPDB/shortestPath?objs1:list=%s1&objs2:list=%s2

Example queries

Data Format Query Example
Identifier metadata {Physical entities} HTML ConsensusPathDB entity name puma
Protein interaction report {Interactions of pathway} HTML Pathway ID (ConsensusPathDB) 9494
Protein interaction report {Interactions of physical entity} HTML ConsensusPathDB entity ID 9304
Protein interaction report {Interactions of physical entity} HTML ConsensusPathDB entity ID 31812
website/corg.html0000644000244100017570000000310711606605733014142 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CORG

Comparative regulatory genomics database (CORG)

Conserved non-coding blocks from a collection of vertebrate species. Non-coding DNA segments that are conserved across multiple homologous genomic sequences are good indicators of putative regulatory elements.

IDCORG
Homehttp://corg.molgen.mpg.de
EDAM topicNucleic acid functional sites
EDAM topicTranscription
TaxonChordata
website/cornea-2dpage.html0000644000244100017570000000755111606605733015626 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Cornea-2DPAGE

Human cornea 2-DE database (Cornea-2DPAGE)

Two-dimensional polyacrylamide gel electrophoresis federated database.

IDCornea-2DPAGE
AccDB-0011
Homehttp://www.cornea-proteomics.com/
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonHomo sapiens

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML UniProt accession http://www.daimi.au.dk/cgi-jje/2d/2d.cgi#%s
Experiment annotation (2D PAGE) Text UniProt accession http://www.daimi.au.dk/cgi-jje/2d/2d.cgi?ac=%s&format=text&database=cornea

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML UniProt accession P02647
Experiment annotation (2D PAGE) Text UniProt accession P02647
website/corum.html0000644000244100017570000000637111606605733014343 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CORUM

CORUM comprehensive resource of mammalian protein complexes

The CORUM database provides a resource of manually annotated protein complexes from mammalian organisms. Annotation includes protein complex function, localization, subunit composition, literature references and more. All information is obtained from individual experiments published in scientific articles, data from high-throughput experiments is excluded.

IDCORUM
Homehttp://mips.gsf.de/genre/proj/corum
EDAM topicProtein-protein interactions
EDAM topicProtein targeting and localization
TaxonMammalia

Available data

Data Format Query Link
Protein structure report (protein complex) HTML Protein ID (CORUM) http://mips.helmholtz-muenchen.de/genre/proj/corum/complexdetails.html?id=%s

Example queries

Data Format Query Example
Protein structure report (protein complex) HTML Protein ID (CORUM) 178
website/coryneregnet4.html0000644000244100017570000000330011606605733015773 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CoryneRegNet4

CoryneRegNet 4.0 cornyebacterial gene regulation database

Reference database for cornyebacterial transcription factors and gene regulatory networks.

IDCoryneRegNet4
Homehttp://www.coryneregnet.de/
EDAM topicGene regulatory networks
EDAM topicGene expression and regulation
EDAM topicTranscription factor and binding site
TaxonCorynebacterium
website/cosmic.html0000644000244100017570000000253211606605733014466 0ustar jisonindustry Bioinformatics Data Resource Catalogue

COSMIC

Catalogue of somatic mutations in cancer (COSMIC)

Somatic mutation information and related details and information relating to human cancers.

IDCOSMIC
Homehttp://www.sanger.ac.uk/genetics/CGP/cosmic/
EDAM topicCancer
TaxonHomo sapiens
website/cpath.html0000644000244100017570000000267011606605752014314 0ustar jisonindustry Bioinformatics Data Resource Catalogue

cPath

Pathway Commons database

A collection of publicly available pathways from multiple organisms. It provides researchers with convenient access to a comprehensive collection of pathways from multiple sources represented in a common language.

IDcPath
Homehttp://www.pathwaycommons.org/pc/home.do
EDAM topicPathways, networks and models
Taxonall
website/crest.html0000644000244100017570000000321111606605733014324 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CREST

Crop ESTs database (CREST)

Sequence, classification, clustering, and annotation data of crop EST projects.

IDCREST
Homehttp://pgrc.ipk-gatersleben.de/cr-est/
EDAM topicmRNA, EST or cDNA
EDAM topicSequence clustering
EDAM topicNucleic acid classification
TaxonStreptophyta
website/crisprdb.html0000644000244100017570000000316711606605733015026 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CRISPRdb

Database of clustered regularly interspaced short palindromic repeats (CRISPRdb)

Clustered regularly interspaced short palindromic repeats.

IDCRISPRdb
Homehttp://crispr.u-psud.fr/
EDAM topicRepeat sequence
EDAM topicSequence clustering
EDAM topicNucleic acid classification
Taxonall
website/csa.html0000644000244100017570000000265511606605733013765 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CSA

Catalytic site atlas (CSA)

Catalytic sites in proteins.

IDCSA
Homehttp://www.ebi.ac.uk/thornton-srv/databases/CSA/
EDAM topicProtein functional sites
EDAM topicEnzymes
Taxonall
website/csdbase.html0000644000244100017570000000257411606605733014623 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CSDBase

Database of cold shock domain (CSD)-containing proteins (CSDBase)

An interactive database for cold shock domain (CSD) containing proteins and the bacterial cold shock response.

IDCSDBase
Homehttp://www.chemie.uni-marburg.de/~csdbase/
EDAM topicSpecific protein
TaxonBacteria
website/ctd.html0000644000244100017570000000603611606605733013766 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CTD

Comparative Toxicogenomics Database (CTD)

CTD includes manually curated data describing cross-species chemical–gene/protein interactions and chemical– and gene–disease relationships to illuminate molecular mechanisms underlying variable susceptibility and environmentally influenced diseases.

IDCTD
AccDB-0140
Homehttp://ctd.mdibl.org/
EDAM topicToxins and targets
EDAM topicGenotype and phenotype
Taxonall

Available data

Data Format Query Link
Gene annotation HTML Identifier {CTD} http://ctd.mdibl.org/detail.go?type=gene&db=GENE&acc=%s

Example queries

Data Format Query Example
Gene annotation HTML Identifier {CTD} 36288
website/cuticledb.html0000644000244100017570000000617211606605733015153 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CuticleDB

Structural proteins of the arthropod cuticle (CuticleDB)

A relational database containing all structural proteins of Arthropod cuticle identified to date. Many come from direct sequencing of proteins isolated from cuticle and from sequences from cDNAs that share common features with these authentic cuticular proteins. It also includes proteins from the Drosophila melanogaster and the Anopheles gambiae genomes, that have been predicted to be cuticular proteins, based on a Pfam motif responsible for chitin binding in Arthropod cuticle.

IDCuticleDB
Homehttp://biophysics.biol.uoa.gr/cuticleDB/
EDAM topicSpecific protein
TaxonArthropoda

Available data

Data Format Query Link
Protein report HTML Protein ID (CuticleDB) http://bioinformatics.biol.uoa.gr/cuticleDB/protview.jsp?id=%s

Example queries

Data Format Query Example
Protein report HTML Protein ID (CuticleDB) 639
website/cyclebase.html0000644000244100017570000000241011606605733015136 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CycleBase

CycleBase cell cycle database

A standardized resource for researchers to inspect and download cell-cycle datasets.

IDCycleBase
Homehttp://cyclebase.org/
EDAM topicCell cycle and development
Taxonall
website/cygd.html0000644000244100017570000000654611606605733014150 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CYGD

Comprehensive yeast genome database (CYGD)

Information on the molecular structure and functional network of the entirely sequenced, well-studied model eukaryote, the budding yeast Saccharomyces cerevisiae. In addition the data of various projects on related yeasts are used for comparative analysis.

IDCYGD
AccDB-0012
Homehttp://mips.gsf.de/genre/proj/yeast
EDAM topicPathways, networks and models
EDAM topicFungal
EDAM topicComparative genomics
CategoryOrganism-specific databases
TaxonSaccharomyces cerevisiae

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://mips.gsf.de/genre/proj/yeast/singleGeneReport.html?entry=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol YAL001c
website/cymobase.html0000644000244100017570000000266011606605733015015 0ustar jisonindustry Bioinformatics Data Resource Catalogue

CyMoBase

Database for cytoskeletal and motor proteins (CyMoBase)

Structure, function and phylogeny of cytoskeletal and motor proteins.

IDCyMoBase
Homehttp://www.cymobase.org
EDAM topicSpecific protein
EDAM topicPhylogenetics
Taxonall
website/cytokine.html0000644000244100017570000000266611606605733015046 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Cytokine

Cytokine gene polymorphism database

Cytokine gene polymorphism in human disease.

IDCytokine
Homehttp://www.nanea.dk/cytokinesnps/
EDAM topicMutation and polymorphism
EDAM topicHuman disease
TaxonHomo sapiens
website/dali.html0000644000244100017570000000277511606605733014133 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Dali

Dali database of 3D structure alignments

The Dali Database is based on all-against-all 3D structure comparison of protein structures in the Protein Data Bank (PDB). The structural neighbourhoods and alignments are automatically maintained and regularly updated using the Dali search engine.

IDDali
Homehttp://ekhidna.biocenter.helsinki.fi/dali/start
EDAM topicProtein structure alignment
Taxonall
website/dbali.html0000644000244100017570000000234711606605733014270 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DBAli

DBAli structure alignment database

Database of protein structure alignments.

IDDBAli
Homehttp://salilab.org/DBAli/
EDAM topicProtein structure alignment
Taxonall
website/dbd.html0000644000244100017570000000545011606605733013744 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DBD

Transcription factor prediction database (DBD)

Predicted transcription factors in completely sequenced genomes.

IDDBD
Homehttp://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Home
EDAM topicTranscription factor and binding site
Taxonall

Available data

Data Format Query Link
Protein report (transcription factor) {DBD entry} HTML DBD ID http://dbd.mrc-lmb.cam.ac.uk/DBD/index.cgi?Search/Domain+domain:%s+cat:DBD

Example queries

Data Format Query Example
Protein report (transcription factor) {DBD entry} HTML DBD ID PF02928
website/dbest.html0000644000244100017570000002642711606605733014323 0ustar jisonindustry Bioinformatics Data Resource Catalogue

dbEST

dbEST database of EST sequences

dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms.

IDdbEST
Homehttp://www.ncbi.nlm.nih.gov/dbEST/
EDAM topicmRNA, EST or cDNA
CategoryNot available
Taxonall

Available data

Data Format Query Link
Sequence record GenBank-HTML dbEST accession http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Sequence record HTML {est} dbEST accession http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Sequence record HTML {docsum} dbEST accession http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Sequence record FASTA-HTML dbEST accession http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Sequence record GenBank-HTML dbEST accession http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Sequence record GenBank-HTML GI number http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank
Sequence record HTML {est} GI number http://www.ncbi.nlm.nih.gov/nucest/%s?report=est
Sequence record HTML {docsum} GI number http://www.ncbi.nlm.nih.gov/nucest/%s?report=docsum
Sequence record FASTA-HTML GI number http://www.ncbi.nlm.nih.gov/nucest/%s?report=fasta
Sequence record GenBank-HTML GI number http://www.ncbi.nlm.nih.gov/nucest/%s?report=genbank

Example queries

Data Format Query Example
Sequence record GenBank-HTML dbEST accession f12345
Sequence record HTML {est} dbEST accession f12345
Sequence record HTML {docsum} dbEST accession f12345
Sequence record FASTA-HTML dbEST accession f12345
Sequence record GenBank-HTML dbEST accession f12345
Sequence record GenBank-HTML GI number 706694
Sequence record HTML {est} GI number 706694
Sequence record HTML {docsum} GI number 706694
Sequence record FASTA-HTML GI number 706694
Sequence record GenBank-HTML GI number 706694
website/dbprobe.html0000644000244100017570000000627511606605733014636 0ustar jisonindustry Bioinformatics Data Resource Catalogue

dbProbe

NCBI Probe database of nucleic acid reagents (dbProbe)

Public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

IDdbProbe
IDaltProbe
Homehttp://www.ncbi.nlm.nih.gov/probe
EDAM topicLaboratory resources
EDAM topicMolecular probes or primers
CategoryNot available
Taxonall

Available data

Data Format Query Link
Oligonucleotide probe annotation {dbProbe report} HTML dbProbe ID http://www.ncbi.nlm.nih.gov/genome/probe/reports/probereport.cgi?uid=%s

Example queries

Data Format Query Example
Oligonucleotide probe annotation {dbProbe report} HTML dbProbe ID 12019
website/dbsnp.html0000644000244100017570000000545011606605734014322 0ustar jisonindustry Bioinformatics Data Resource Catalogue

dbSNP

Database of single nucleotide polymorphism (dbSNP)

Single nucleotide polymorphisms.

IDdbSNP
AccDB-0013
Homehttp://www.ncbi.nlm.nih.gov/SNP/
EDAM topicMutation and polymorphism
CategoryPolymorphism databases
Taxonall

Available data

Data Format Query Link
SNP annotation {dbSNP entry} HTML dbSNP ID http://www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s

Example queries

Data Format Query Example
SNP annotation {dbSNP entry} HTML dbSNP ID rs11542705
website/ddbj.html0000644000244100017570000000755211606605734014124 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DDBJ

DNA databank of Japan (DDBJ)

A nucleotide sequence database.

IDDDBJ
AccDB-0014
Homehttp://www.ddbj.nig.ac.jp/
EDAM topicNucleic acid sequences
CategorySequence databases
Taxonall

Available data

Data Format Query Link
Sequence record full GenBank-HTML Sequence accession (nucleic acid) http://getentry.ddbj.nig.ac.jp/search/get_entry?accnumber=%s
Sequence record full GenBank format Sequence accession (nucleic acid) http://xml.nig.ac.jp/rest/Invoke?service=GetEntry&method=getDDBJEntry&accession=%s

Example queries

Data Format Query Example
Sequence record full GenBank-HTML Sequence accession (nucleic acid) AB000100
Sequence record full GenBank format Sequence accession (nucleic acid) AB000100
website/degradome.html0000644000244100017570000000236611606605734015146 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Degradome

Degradome database of mammalian proteases and diseases

Mammalian proteases and diseases.

IDDegradome
Homehttp://degradome.uniovi.es/
EDAM topicDisease
TaxonMammalia
website/diamond.html0000644000244100017570000001456211606605734014633 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Diamond

Blackfan Anemia mutation database (Diamond)

Blackfan Anemia mutation database.

IDDiamond
Homehttp://www.dbagenes.unito.it
EDAM topicHuman disease
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://www.dbagenes.unito.it/home.php?select_db=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol RPS19
Gene annotation HTML Gene symbol RPS24
Gene annotation HTML Gene symbol RPS17
Gene annotation HTML Gene symbol RPS7
Gene annotation HTML Gene symbol RPL5
Gene annotation HTML Gene symbol RPL11
Gene annotation HTML Gene symbol RPS10
Gene annotation HTML Gene symbol RPS26
Gene annotation HTML Gene symbol RPL35A
website/diark.html0000644000244100017570000000261311606605734014304 0ustar jisonindustry Bioinformatics Data Resource Catalogue

diArk

diArk eukaryotic genome research database

Database for eukaryotic sequencing projects.

IDdiArk
Homehttp://www.diark.org/diark/
EDAM topicEukaryote
EDAM topicGenomes
TaxonEukaryota
website/diatom.html0000644000244100017570000000274611606605734014476 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Diatom

Diatom EST database

A searchable databases of diatom ESTs (expressed sequence tags) that can be used to explore diatom biology. Diatoms are photosynthetic unicellular eukaryotes that play an essential role in marine ecosystems. On a global scale, they generate around one fifth of the oxygen we breathe.

IDDiatom
Homehttp://avesthagen.sznbowler.com/
EDAM topicmRNA, EST or cDNA
TaxonBacillariophyta
website/dictybase.html0000644000244100017570000000630411606605734015162 0ustar jisonindustry Bioinformatics Data Resource Catalogue

dictyBase

Dictyostelium discoideum online informatics resource (dictyBase)

Database for the biology and genomics of the social amoeba Dictyostelium discoideum.

IDdictyBase
IDaltDICB
AccDB-0015
Homehttp://dictybase.org/
EDAM topicOrganism
EDAM topicUnicellular eukaryote
EDAM topicGenomes
CategoryOrganism-specific databases
TaxonDictyostelium discoideum

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://dictybase.org/db/cgi-bin/gene_page.pl?primary_id=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID DDB_G0269138
website/dima.html0000644000244100017570000000541511606605734014127 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DIMA

DIMA domain interaction map

Functional and physical interactions among conserved protein-domains, including experimental data and computational predictions.

IDDIMA
Homehttp://mips.gsf.de/genre/proj/dtest/index.html
EDAM topicProtein-protein interactions
Taxonall

Available data

Data Format Query Link
Domain-domain interaction HTML Pfam accession number http://webclu.bio.wzw.tum.de/dima/DomQuery?domain=%s

Example queries

Data Format Query Example
Domain-domain interaction HTML Pfam accession number PF00419
website/dip.html0000644000244100017570000000632311606605734013770 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DIP

Database of interacting proteins (DIP)

The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data.

IDDIP
AccDB-0016
Homehttp://dip.doe-mbi.ucla.edu/
EDAM topicProtein-protein interactions
CategoryProtein-protein interaction databases
Taxonall

Available data

Data Format Query Link
Protein-protein interaction {DIP entry} HTML DIP ID dip.doe-mbi.ucla.edu/dip/Browse.cgi?ID=%s

Example queries

Data Format Query Example
Protein-protein interaction {DIP entry} HTML DIP ID DIP-27044N
website/diprodb.html0000644000244100017570000000673011606605734014641 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DiProDB

Dinucleotide property database (DiProDB)

The Dinucleotide Property Database is designed to collect and analyse thermodynamic, structural and other dinucleotide properties. The table presenting all the dinucleotide properties can be pruned and rearranged by different criteria. The database contains different export and analysis functions.

IDDiProDB
Homehttp://diprodb.fli-leibniz.de/
EDAM topicNucleic acid physicochemistry
EDAM topicNucleic acid structure
Taxon

Available data

Data Format Query Link
Nucleic acid structure report {DiProDB Table} HTML None http://diprodb.fli-leibniz.de/GetEntries.php
Dinucleotide property {Dinucleotide Property} HTML DiProDB ID http://diprodb.fli-leibniz.de/GetEntries.php?ID=%s

Example queries

Data Format Query Example
Dinucleotide property {Dinucleotide Property} HTML DiProDB ID 5
website/disprot.html0000644000244100017570000000567011606605734014704 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DisProt

Database of protein disorder (DisProt)

A curated database that provides information about proteins that lack fixed 3D structure in their putatively native states, either in their entirety or in part.

IDDisProt
AccDB-0017
Homehttp://www.disprot.org/
EDAM topicProtein tertiary structure
Category3D structure databases
Taxonall

Available data

Data Format Query Link
Protein structure report (disordered protein) {DisProt entry} HTML Protein ID (DisProt) http://www.disprot.org/protein.php?id=%s

Example queries

Data Format Query Example
Protein structure report (disordered protein) {DisProt entry} HTML Protein ID (DisProt) DP00001
website/dnareplication.html0000644000244100017570000000234711606605734016212 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DNAReplication

DNA replication database

A Resource for eukaryotic DNA replication.

IDDNAReplication
Homehttp://www.dnareplication.net/
EDAM topicDNA
Taxonall
website/dockground.html0000644000244100017570000000253711606605734015356 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Dockground

Dockground database for molecular modelling of protein interactions

Benchmarks, decoys, templates and other knowledge resources for docking.

IDDockground
Homehttp://dockground.bioinformatics.ku.edu/
EDAM topicProtein-protein interactions
Taxonall
website/domino.html0000644000244100017570000000261711606605734014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DOMINO

DOMINO domain peptide interactions database

Database of annotated experiments describing interactions mediated by protein-interaction domains.

IDDOMINO
Homehttp://mint.bio.uniroma2.it/domino/search/searchWelcome.do
EDAM topicProtein-protein interactions
Taxonall
website/doop.html0000644000244100017570000000275011606605734014155 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DoOP

Database of orthologous promoters (DoOP)

A database of eukaryotic promoter sequences (upstream regions), aiming to facilitate the recognition of regulatory sites conserved between species.

IDDoOP
Homehttp://doop.abc.hu/
EDAM topicNucleic acid functional sites
EDAM topicTranscription
Taxonall
website/dosac-cobs-2dpage.html0000644000244100017570000000551611606605734016374 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DOSAC-COBS-2DPAGE

DOSAC-COBS 2D-PAGE database

Two-dimensional polyacrylamide gel electrophoresis federated database.

IDDOSAC-COBS-2DPAGE
AccDB-0018
Homehttp://www.dosac.unipa.it/2d/
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML UniProt accession http://www.dosac.unipa.it/cgi-bin/2d/2d.cgi?ac=O43818

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML UniProt accession O43818
website/dpdb.html0000644000244100017570000000264711606605734014132 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DPDB

Drosophila polymorphism database (DPDB)

A collection of all the existing polymorphic sequences in the Drosophila genus. It allows the search for any polymorphic set according to different parameter values of nucleotide diversity.

IDDPDB
Homehttp://bioinf3.uab.cat/dPDB/dPDB.asp
EDAM topicMutation and polymorphism
TaxonDrosophila
website/dpvweb.html0000644000244100017570000001136311606605734014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DPVweb

DPVweb database of plant viruses

Information about viruses, viroids and satellites of plants, fungi and protozoa, with some additional data on related animal viruses.

IDDPVweb
Homehttp://www.dpvweb.net/
EDAM topicVirus
EDAM topicPlant
TaxonViruses

Available data

Data Format Query Link
Virus annotation HTML DPVweb ID http://www.dpvweb.net/dpv/showdpv.php?dpvno=%s
Virus annotation (taxonomy) HTML Family name (virus) http://www.dpvweb.net/notes/showfamily.php?family=%s
Virus annotation (taxonomy) HTML Genus name (virus) http://www.dpvweb.net/notes/showgenus.php?genus=%s

Example queries

Data Format Query Example
Virus annotation HTML DPVweb ID 1
Virus annotation (taxonomy) HTML Family name (virus) Alphaflexiviridae
Virus annotation (taxonomy) HTML Genus name (virus) Alfamovirus
website/dqcs.html0000644000244100017570000000252211606605734014143 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DQCS

The Database of Quantitative Cellular Signaling

A repository of models of signaling pathways. It includes reaction schemes, concentrations, rate constants, as well as annotations on the models.

IDDQCS
Homehttp://doqcs.ncbs.res.in/
EDAM topicSignalling pathways
Taxonall
website/DRCAT.id~0000644000244100017570000002537711605573173013711 0ustar jisonindustryID 2dpage ID 3Dgenomics ID 3did ID 3DMET ID 4dxpress ID 5srrna ID a1atvar ID Aarhus/Ghent-2DPAGE ID abcdb ID abs ID aceview ID ACLAME ID AffinDB ID AFTOL ID AGD ID Allergome ID AMYPDB ID ANPR ID Antibodypedia ID AntiJen ID ANU-2DPAGE ID AphidBase ID APID ID EuPathDB ID ApiDB_CryptoDB ID ApiDB_PlasmoDB ID ApiDB_ToxoDB ID ApiDB_TrichDB ID ApiDB_TriTryPDB ID ApiDB_GiardiaDB ID AppaDB ID ArachnoServer ID AraC-XylS ID ARAMEMNON ID ArchDB ID Argonaute ID ArrayExpress ID ASAP ID ASC ID ASPICdb ID ASTD ID ATCC ID ATCC(in host) ID ATCC(dna) ID ATSD ID AthaMap ID AutoPSI ID Axeldb ID BAliBASE ID BCSDB ID BDGP_EST ID BDGP_INS ID Bgee ID BindingDB ID BioCyc ID BioGRID ID biomodels ID BioNumbers ID BioSystems ID BIPA ID BloodExpress ID BlotBase ID BNDB ID BOLD ID BRENDA ID BriX ID BuchneraBase ID ButterflyBase ID CABRI ID CADRE ID CanGEM ID CATdb ID CATH ID CATMA ID CAZy ID CBS ID CC+ ID CCAP ID CellCycleDB ID CellLineDB ID CellMINT ID Centrosome:db ID CEPHdb ID CG ID CDD ID CGD ID ChEBI ID ChEMBL ID ChemIDplus ID CiteXplore ID CleanEx ID CLIMA ID CluSTr ID CMR ID COGEME ID ColiBase ID CMD ID Columba ID COMPLUYEAST-2DPAGE ID ConoServer ID ConsensusPathDB ID CORG ID CORUM ID CoryneRegNet4 ID COSMIC ID Cornea-2DPAGE ID CREST ID CRISPRdb ID CSA ID CSDBase ID CTD ID CuticleDB ID CycleBase ID CYGD ID CyMoBase ID Cytokine ID Dali ID DBAli ID DBD ID dbEST ID dbProbe ID dbSNP ID DDBJ ID Degradome ID Diamond ID diArk ID Diatom ID dictyBase ID DIMA ID DIP ID DiProDB ID DisProt ID DNAReplication ID Dockground ID DOMINO ID DoOP ID DOSAC-COBS-2DPAGE ID DPDB ID DPVweb ID DQCS ID DRC ID DrugBank ID DSD ID DSMM ID DSSP ID DynaProt ID EASED ID EcID ID ECO2DBASE ID 2DBase-Ecoli ID EcoGene ID EchoBASE ID emap ID EDS ID EGA ID eggNOG ID ELM ID EMBL ID EMDB ID EMGlib ID ENA ID EndoNet ID Ensembl ID Ensembl-Genome ID EnsemblBacteria ID EnsemblFungi ID EnsemblMetazoa ID EnsemblPlants ID EnsemblProtists ID ENZYME ID EPD ID ERIC ID eSLDB ID ESP-SOLDB ID ESTHER ID euHCVdb ID EuroPhenome ID EVEREST ID ExplorEnz ID EXProt ID ExTopoDB ID EyeSite ID FaCD ID FANTOM_DB ID FASTDB ID FCP ID FGDB ID FINDBase ID FireDB ID FLAGdb++ ID FLIGHT ID FlyBase ID FlyMine ID FLYSNP ID FlyTF ID FlyView ID FPSPD ID FunCoup ID FungalGenomeSize ID FUNPEP ID FunShift ID FunSimMat ID FUNYBASE ID FusionDB ID G2Cdb ID GabiPD ID GABI-Kat ID GBIFFI ID GDB ID GenAtlas ID GenBank ID GenBank - dbSTS ID Gene3D ID GeneAnnot ID GeneCards ID GeneDB ID GeneDB_Spombe ID GeneExpressionTooth ID GeneFarm ID GeneID ID GeneLoc ID GeneNest ID GeneNote ID GeneSapiens ID GeneSNPs ID GeneTide ID GeneTree ID Genevestigator ID Genolevures ID GenoList ID GenomeReviews ID GenomicThreadingDatabase ID GenomeRNAi ID Germlinep53Mutations ID GermOnline ID GlycateBase ID GlycomeDB ID GlycoSuiteDB ID GO ID GOA ID GOLD ID GOLDDB ID GoPubMed ID GPCRDB ID GPCR_NaVa ID GlycosciencesDB ID gPDB ID Gramene ID GreenPhylDB ID GRIN ID GyDB ID H-InvDB ID HaemB ID HAMAP ID HAMASTERS ID HCAD ID HepSeq ID HERVd ID HGDP-CEPH ID HGMD ID HGNC ID HGT-DB ID HGVbaseG2P ID HIC-Up ID HmtDB ID HOGENOM ID HOINVGEN ID HOVERGEN ID HomeoboxPage ID HomoMINT ID HOMSTRAD ID Hoppsigen ID HORDE ID HotSprint ID HPA ID HS3D ID HSSP ID HTPSELEX ID HUGE ID HumanPAX6 ID HMDB ID HumanMtDB ID HuSiDa ID HvrBase++ ID HyperCAT ID HyperCLDB ID IARCTP53 ID IDbases ID IDbases-BTKbase ID IMGT ID IMGT/HLA ID IMGT/3Dstructure-DB ID IMGT/GENE-DB ID IMGT/LIGM ID IMGT/PRIMER-DB ID INFEVERS ID InParanoid ID IntAct ID Integr8 ID INTEGRALL ID IntEnz ID InterPro ID ICD ID ICDS ID IPD ID IPD-ESTDAB ID IPD-HPA ID IPD-KIR ID IPD-MHC ID IPI ID iRefIndex ID IRESdb ID IRESite ID ISfinder ID ISOLA ID ITS2 ID ITTACA ID IUPAC ID IUPHAR-DB ID IXDB ID JAIL ID JASPAR ID JCM ID JenaLib ID JPGV ID JWS ID KaryotypeDB ID KEGG ID KDD ID KinMutBase ID Kinomer ID KNOTTIN ID L1Base ID LEGER ID LegioList ID Leproma ID LGICdb ID LigAsite ID LipidBank ID LMSD ID LipaseEngineering ID LumbriBASE ID MaizeGDB PMID 18628892 ID MAMEP ID MamPol ID MAPU ID MAtDB ID MatrixDB ID MACiE ID MedOBIS ID MeGX ID MMMP ID MEPD ID MEROPS ID MetaCrop ID MetaGrowth ID Metal-MACiE ID MethDB ID MfunGD ID MGI ID Micado ID ModelDB ID MMDB ID MTRDB ID MIM ID MINT ID MIPSPlantsDB ID miRBase ID miriam ID miROrtho ID MonosaccharideDB ID MMRUV ID MitoDrome ID MITOP2 ID MitoRes ID MLVAbank ID MMsINC ID MNCDB ID ModBase ID MODOMICS ID MoKA ID MolliGen ID MOSAIC ID MOsDB ID MouseSAGE ID MouseBook ID Mpact ID Mugen ID MUMDB ID MyHits ID NAPROC-13 ID Narcisse ID NBRC ID NCL ID ncRNAs ID NEMBASE ID NESbase ID NeuroMorpho ID NeuronDB ID NextBio ID NextDB ID neXtProt ID niaEST ID NMPDR ID NMRShift ID NOPDB ID NORINE ID NPC-db ID NPD ID NRESTdb ID NRSub ID NUREBASE ID OGLYCBASE ID OGP ID OMA ID OPTIC ID ORENZA ID Orphanet ID OrthoDB ID OryGenesDB ID Oryza ID Osteogenesis ID p53FamTaG ID PairsDB ID PANDIT ID PANDORA ID PANTHER ID ParameciumDB ID Pathema ID PathoPlant ID cPath ID Pathway_Interaction_DB ID PDB ID PDBe ID PDBFINDER ID PDBfun ID PDB-redo ID PDBREPORT ID PDBselect ID PDBsum ID PDBTM ID PED ID PEDANT ID PepSeeker ID Peptaibol ID PeptideAtlas ID PeptideDB ID PeroxiBase ID PeroxisomeDB ID PespotDB ID Pfam ID PGN ID PharmGKB ID PhenomicDB ID PHCI-2DPAGE ID PHI-base ID PhosPhAt ID PhosphoELM ID PHOSPHO3D ID PhosphoPep ID PhosphoSite ID PhosSite ID PhylomeDB ID PhyloPat ID PhytoProt ID PIPs ID PIR ID PIRSF ID PlantDNAC-values ID PlantsnoRNA ID PlantCARE ID PlantMarkers ID PLANT-Pis ID PlantProm ID PlasmoDraft ID PLMItRNA ID Plprot ID PMAP-CutDB ID PMDB ID Polymorphix ID PoMaMo ID PPD ID PPNEMA ID PptaseDB ID preDiCT ID PRIDE ID PRINTS ID Prism ID probeBase ID ProCMD ID PROCOGNATE ID ProDom ID PRODORIC ID PromEC ID ProMEX ID PROPHECY ID ProRule ID ProSAS ID PROSAT2 ID PROSITE ID ProtClustDB ID ProteinModelPortal ID ProtoNet ID Protepedia ID ProTeus ID PseudoBase ID PseudoCAP ID pSTIING ID PTCH ID PubChem ID PubMeth ID PMMA-2DPAGE ID Rat-heart-2DPAGE ID RATMAP ID RDG ID RB1GeneMutation ID Reactome ID REBASE ID REDIdb ID RefSeq ID REPAIRtoire ID REPRODUCTION-2DPAGE ID RESID ID RetrOryza ID RFAM ID RGD ID Rhea ID Rouge ID RISSC ID RNA-FRABASE ID RNAVirusDB ID RNRdb ID RsiteDB ID RTKdb ID RTPrimerDB ID S/MARtDB ID S4 ID SABIO-RK ID Saffron Genes ID SCOP ID SCOPPI ID SCOWL ID SeattleSNPs ID Sebida ID SEED ID Selectome ID SGD ID Siena-2DPAGE ID SignalingGateway ID SILVA-LSU ID SILVA-SSU ID SIMAP ID siRNAdb ID SISYPHUS ID SitesBase ID SMPDB ID SMART ID SMR ID SNAP ID SNAPPI ID Sno/scaRNAbase ID snoRNABase ID SNPeffect ID SNPnexus ID SNPSTR ID SOURCE ID SoyBase ID SpliceAid ID SpliceNest ID SpodoBase ID STCDB ID STITCH ID StrainInfo.net ID Strepto-DB ID STRING ID StructurallyConservedInterfaces ID Sulfolobus ID SuperDrug ID SUPFAM ID SuperHapten ID SuperNatural ID Superscent ID SuperSite ID SuperTarget-Matador ID Supertoxic ID SURFACE ID WORLD-2DPAGE(CGL14067-2DPAGE) ID WORLD-2DPAGE(NIBR 2D-PAGE) ID WORLD-2DPAGE(0003) ID WORLD-2DPAGE(0004) ID WORLD-2DPAGE(0005) ID WORLD-2DPAGE(0006) ID SWISS-2DPAGE ID SwissRegulon ID SYSTERS ID Systomonas ID SysZNFC2H2 ID T1Dbase ID TAED ID TAIR ID TarBase ID TassDB ID taxon ID TBMap ID TCACycle ID TCDB ID TDR ID 1000Genomes ID TTD ID TIGR ID TIGRFAMs ID TmaDB ID Tomatestdb ID ToPDB ID TOPDOM ID T3DB ID Transdab ID TRANSPATH ID TranspoGene ID TRBase ID TreeFam ID tRNASequences ID TropGENE-DB ID TrSDB ID TubercuList ID U12DB ID UCD-2DPAGE ID UCSC ID UMD-DMD ID UniGene ID UniHI ID UNILIB ID Unipathway ID UniSave ID UniSTS ID UNITE ID UniTrap ID UMD ID UniParc ID UniProt ID UniProtKB/Swiss-Prot ID UniProtKB/TrEMBL ID UniRef ID UTILLdb ID UTRdb ID UTRsite ID VBASE2 ID VectorBase ID VEGA ID VIDA ID VirusMINT ID VSGdb ID WorfDB ID World-2DPAGE ID WormBase ID Xenbase ID Yeast complexes ID Yeast-GFP ID YEASTRACT ID YGOB ID yMGV ID ZFIN website/drcatindex.html0000644000244100017570000017156511607011764015347 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DRCAT Resource Catalogue

Bioinformatics Web-based Data Resources

0, A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X, Y, Z


























website/drc.html0000644000244100017570000000256211606605734013765 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DRC

Database of ribosomal crosslinks (DRC)

Biochemical data about structure of the ribosome from ribosomal cross-linking.

IDDRC
Homehttp://www.mpimg-berlin-dahlem.mpg.de/~ag_ribo/ag_brimacombe/drc/
EDAM topicRibosomes
Taxonall
website/drugbank.html0000644000244100017570000000544011606605734015010 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DrugBank

DrugBank drug and drug target database

Detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.

IDDrugBank
AccDB-0019
Homehttp://www.drugbank.ca/
EDAM topicDrugs and targets
CategoryOther
TaxonHomo sapiens

Available data

Data Format Query Link
Drug annotation HTML DrugBank ID http://www.drugbank.ca/drugs/%s

Example queries

Data Format Query Example
Drug annotation HTML DrugBank ID None
website/dsd.html0000644000244100017570000000262111606605735013764 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DSD

Database of dehydrogenase stereospecificities (DSD)

Database on dehydrogenases, a class of enzymes that catalyze reversible oxidation-reduction reactions and are largely dependent on nicotinamide adenine dinucleotide coenzymes: NAD(H) or NADP(H).

IDDSD
Homehttp://www.darrenflower.info/DSD/
EDAM topicEnzymes
Taxonall
website/dsmm.html0000644000244100017570000000264611606605735014161 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DSMM

Database of simulated molecular motions (DSMM)

Movies showing biomolecular motions that have been generated by computer simulation. Molecules simulated include proteins, DNA, RNA, sugars and lipids. Simulation techniques include Molecular Dynamics, Brownian Dynamics and automated docking procedures.

IDDSMM
Homehttp://atlas.villa-bosch.de/dbase/dsmm/
EDAM topicMolecular flexibility and motion
Taxon
website/dssp.html0000644000244100017570000000561011606605735014164 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DSSP

DSSP secondary structure database

Secondary structure assignments (and much more) for all protein entries in the Protein Data Bank (PDB).

IDDSSP
Homehttp://swift.cmbi.ru.nl/gv/dssp/
EDAM topicProtein structure
EDAM topicProtein secondary structure
Taxonall

Available data

Data Format Query Link
Protein features (secondary structure) {DSSP report} HTML PDB ID http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=dssp&id=%s

Example queries

Data Format Query Example
Protein features (secondary structure) {DSSP report} HTML PDB ID 2hva
website/dynaprot.html0000644000244100017570000000254511606605735015057 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DynaProt

DynaProt 2D proteome database of Lactococcus lactis

2D reference maps and summarized protein information for Lactococcus lactis.

IDDynaProt
Homehttp://www.wzw.tum.de/proteomik/lactis/
EDAM topicTwo-dimensional gel electrophoresis
TaxonLactococcus lactis
website/eased.html0000644000244100017570000000234611606605735014277 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EASED

EASED database

Extended Alternatively Spliced EST Database

IDEASED
Homehttp://eased.bioinf.mdc-berlin.de/
EDAM topicmRNA, EST or cDNA
Taxonall
website/echobase.html0000644000244100017570000000637211606605735014772 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EchoBASE

EchoBASE: an integrated post-genomic database for E. coli

A database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

IDEchoBASE
AccDB-0020
Homehttp://www.york.ac.uk/res/thomas/
EDAM topicOrganism
EDAM topicProkaryote
EDAM topicGenomes
CategoryOrganism-specific databases
TaxonEscherichia coli

Available data

Data Format Query Link
Gene annotation {EchoBASE entry} HTML Gene symbol http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=%s

Example queries

Data Format Query Example
Gene annotation {EchoBASE entry} HTML Gene symbol EB1017
website/ecid.html0000644000244100017570000001636011606605735014123 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EcID

E Coli predicted protein interactions database (EcID)

Results of running an "in silico 2 hybrid system" for all the possible pairs among E. coli proteins.

IDEcID
Homehttp://www.pdg.cnb.uam.es/i2h/info.html
EDAM topicProtein-protein interactions
TaxonEscherichia coli

Available data

Data Format Query Link
Data reference {Protein sequence ID table} HTML Protein identifier http://ecid.bioinfo.cnio.es/Php/PreQuery.php?busca=%s
Protein-protein interaction {Predictions Mode} HTML Protein identifier; Protein ID (EcID); Gene symbol http://ecid.bioinfo.cnio.es/Php/Summary.php?view=pred&ID=%s1&seq=%s2&gn=%s3
Protein-protein interaction {Experimental Mode} HTML Protein identifier; Protein ID (EcID); Gene symbol http://ecid.bioinfo.cnio.es/Php/Summary.php?ID=%s1&seq=%s2&gn=%s3&view=exp
Protein report HTML Protein identifier; Protein ID (EcID); Gene symbol http://ecid.bioinfo.cnio.es/Php/ProtInfo.php?busca=%s1seq=%s2&gn=%s3

Example queries

Data Format Query Example
Data reference {Protein sequence ID table} HTML Protein identifier NRDD_ECOLI
Protein-protein interaction {Predictions Mode} HTML Protein identifier; Protein ID (EcID); Gene symbol NRDD_ECOLI;1639;nrdD
Protein-protein interaction {Experimental Mode} HTML Protein identifier; Protein ID (EcID); Gene symbol NRDD_ECOLI;1639;nrdD
Protein report HTML Protein identifier; Protein ID (EcID); Gene symbol NRDD_ECOLI;1639;nrdD
website/eco2dbase.html0000644000244100017570000000303511606605735015041 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ECO2DBASE

2D-PAGE database of Escherichia coli

2D-PAGE database of Escherichia coli

IDECO2DBASE
IDalt2DBase-Ecoli, EC-2D-GEL
AccDB-0115
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonEscherichia coli

Example queries

Data Format Query Example
website/ecogene.html0000644000244100017570000000723511606605735014625 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EcoGene

EcoGene database of Escherichia coli sequence and function

Information about the E. coli K-12 genome and proteome sequences, including extensive gene bibliographies. A major EcoGene focus has been the re-evaluation of translation start sites.

IDEcoGene
AccDB-0021
Homehttp://ecogene.org/
EDAM topicTranscription
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicProteome
EDAM topicProkaryote
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonEscherichia coli

Available data

Data Format Query Link
Gene annotation HTML Gene ID (EcoGene) http://www.ecogene.org/geneInfo.php?eg_id=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID (EcoGene) EG11277
website/eds.html0000644000244100017570000000575211606605735013775 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EDS

Electron density server at Uppsala university (EDS)

A service for evaluating the electron density (and, indirectly, some aspects of the model quality) of crystal structures deposited in the Protein Data Bank. In addition to electron density maps and tools to view these maps, statistics and plots are provided for assessing the goodness-of-fit between the deposited models (structures) and the experimental data represented by the electron density calculated using the models and their associated structure factor amplitudes.

IDEDS
Homehttp://eds.bmc.uu.se/eds/
EDAM topicStructure
Taxonall

Available data

Data Format Query Link
Protein report HTML PDB ID http://eds.bmc.uu.se/cgi-bin/eds/uusfs?PDBCode=%s

Example queries

Data Format Query Example
Protein report HTML PDB ID 2hha
website/ega.html0000644000244100017570000000562211606605735013752 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EGA

European genome-phenome Archive (EGA)

A repository for all types of genotype experiments, including case control, population, and family studies, including SNP and CNV genotypes from array based methods and genotyping done with re-sequencing methods.

IDEGA
Homehttp://www.ebi.ac.uk/ega/
EDAM topicGenotype and phenotype
TaxonHomo sapiens

Available data

Data Format Query Link
Experiment annotation (genotype) HTML EGA accession http://www.ebi.ac.uk/ega/page.php?page=study&study=%s&cat=www.ovcare.studies.xml&subcat=OVCARE

Example queries

Data Format Query Example
Experiment annotation (genotype) HTML EGA accession EGAS00000000040
website/eggnog.html0000644000244100017570000000336411606605735014465 0ustar jisonindustry Bioinformatics Data Resource Catalogue

eggNOG

Database of evolutionary genealogy of genes: non-supervised Orthologous Groups (eggNOG)

Orthologous groups of genes. The orthologous groups are annotated with functional descriptions, which are derived by identifying a common denominator for the genes based on their individual textual descriptions, annotated functional categories, and predicted protein domains.

IDeggNOG
AccDB-0152
Homehttp://eggnog.embl.de/
EDAM topicNucleic acid classification
EDAM topicGene family or system
Taxonall
website/elm.html0000644000244100017570000001544111606605735013773 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ELM

Eukaryotic linear motif resource (ELM)

A resource for predicting functional sites in eukaryotic proteins. Putative functional sites are identified by patterns (regular expressions). To improve the predictive power, context-based rules and logical filters are applied to reduce the amount of false positives.

IDELM
Homehttp://elm.eu.org/
EDAM topicSequence motifs
EDAM topicProtein functional sites
EDAM topicSequence motifs
Taxonall

Available data

Data Format Query Link
Sequence features (motifs) {ELM report} HTML UniProt ID http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s
Sequence features (motifs) {ELM report} HTML UniProt ID; Taxon; GO term ID (cellular compartment) http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&swissprotId=%s1&userSpecies=%s2&userCC=%s3
Sequence features (motifs) {ELM report} HTML Identifier {Protein sequence} http://elm.eu.org/basicELM/cgimodel.py?fun=Submit&sequence=%s

Example queries

Data Format Query Example
Sequence features (motifs) {ELM report} HTML UniProt ID; Taxon; GO term ID (cellular compartment) src_human;10116;GO:0005634
Sequence features (motifs) {ELM report} HTML UniProt ID src_human
Sequence features (motifs) {ELM report} HTML Identifier {Protein sequence} MGSNKSKPKDASQRRRSLEPAENVHGAGGGAFPASQTPSKPASADGHRGPSAAFAPAAAEPKLFGGFNSSDTVTSPQRAGPLAGGVTTFVALYDYESRTETDLSFKKGERLQIVNNTEGDWWLAHSLSTGQTGYIPSNYVAPSDSIQAEEWYFGKITRRESERLLLNAENPRGTFLVRESETTKGAYCLSVSDFDNAKGLNVKHYKIRKLDSGGFYITSRTQFNSLQQLVAYYSKHADGLCHRLTTVCPTSKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTRVAIKTLKPGTMSPEAFLQEAQVMKKLRHEKLVQLYAVVSEEPIYIVTEYMSKGSLLDFLKGETGKYLRLPQLVDMAAQIASGMAYVERMNYVHRDLRAANILVGENLVCKVADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILLTELTTKGRVPYPGMVNREVLDQVERGYRMPCPPECPESLHDLMCQCWRKEPEERPTFEYLQAFLEDYFTSTEPQYQPGENL
website/emap.html0000644000244100017570000000603511606605735014137 0ustar jisonindustry Bioinformatics Data Resource Catalogue

emap

Edinburgh Mouse Atlas project database (emap)

The emap Atlas is a digital Atlas of mouse embryonic development. It is based on the definitive books of mouse embryonic development by Theiler (1989) and Kaufman (1992) yet extends these studies by creating a series of interactive three-dimensional computer models of mouse embryos at successive stages of development with defined anatomical domains linked to a stage-by-stage ontology of anatomical names.

IDemap
Homehttp://genex.hgu.mrc.ac.uk/
EDAM topicCell cycle and development
TaxonMus

Available data

Data Format Query Link
Embryo annotation {Emage entry} HTML EMAGE ID http://www.emouseatlas.org/emagewebapp/pages/emage_entry_page.jsf?id=EMAGE:%s

Example queries

Data Format Query Example
Embryo annotation {Emage entry} HTML EMAGE ID 1000
website/embl.html0000644000244100017570000001005411606605735014130 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EMBL

The EMBL Nucleotide Sequence Database (EMBL)

Europe's primary nucleotide sequence resource. Main sources for DNA and RNA sequences are direct submissions from individual researchers, genome sequencing projects and patent applications.

IDEMBL
IDaltEMBL-Bank
AccDB-0022
Homehttp://www.ebi.ac.uk/embl/
EDAM topicNucleic acid sequences
CategorySequence databases
Taxonall

Available data

Data Format Query Link
Sequence record full EMBL-HTML Sequence accession (nucleic acid) http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&id=%s&Submit=Go
Sequence record full EMBL format Sequence accession (nucleic acid) http://www.ebi.ac.uk/cgi-bin/emblfetch?style=raw&id=%s&Submit=Go

Example queries

Data Format Query Example
Sequence record full EMBL-HTML Sequence accession (nucleic acid) AE014292
Sequence record full EMBL format Sequence accession (nucleic acid) AE014292
website/emdb.html0000644000244100017570000000264011606605735014122 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EMDB

Electron microscopy databank (EMDB)

Deposition and retrieval network for cryoEM map, model and associated metadata, as well as a portal for software tools for standardized map format conversion, map, segmentation and model assessment, visualization, and data integration.

IDEMDB
Homehttp://www.emdatabank.org
EDAM topicElectron microscopy
Taxonall
website/emglib.html0000644000244100017570000000362511606605735014456 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EMGlib

Enhanced microbial genomes library (EMGlib)

A database devoted to the completely sequenced bacterial genomes and the yeast genome. Starting from the sequences available in the "genome" division of GenBank, EMGlib improves and corrects the annotations.

IDEMGlib
Homehttp://pbil.univ-lyon1.fr/emglib/emglib.html
EDAM topicYeast
EDAM topicGenomes
EDAM topicProkaryote
EDAM topicGenomes
Taxonall
website/ena.html0000644000244100017570000000237511606605735013763 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ENA

European nucleotide short read and trace archive (ENA)

European nucleotide short read and trace archive (ENA).

IDENA
Homehttp://www.ebi.ac.uk/ena
EDAM topicNucleic acid sequences
Taxonall
website/endonet.html0000644000244100017570000000316511606605735014652 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EndoNet

Endocrine networks database (EndoNet)

Information about endocrine networks. Using information about hormones' donor and acceptor cells a network is built that represents hormonal signaling pathways as a bipartite graph comprising hormones and tissues as node classes. The involved components, the intercellular information flow and the inhibition or activation effects are displayed

IDEndoNet
Homehttp://endonet.bioinf.med.uni-goettingen.de/index.jsp
EDAM topicSignalling pathways
TaxonHomo sapiens
website/ensemblbacteria.html0000644000244100017570000000563511606605736016343 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EnsemblBacteria

Ensembl bacterial genome annotation project

Genome databases for bacterial species.

IDEnsemblBacteria
AccDB-0147
Homehttp://bacteria.ensembl.org/
EDAM topicGenomes
EDAM topicGenomes
CategoryGenome annotation databases
TaxonBacteria

Available data

Data Format Query Link
Gene annotation HTML Transcript ID (Ensembl) www.ensemblgenomes.org/id/%s

Example queries

Data Format Query Example
Gene annotation HTML Transcript ID (Ensembl) EBMYCT00000015323
website/ensemblfungi.html0000644000244100017570000000557711606605736015706 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EnsemblFungi

Ensembl gungial genome annotation project

Genome databases for fungal species.

IDEnsemblFungi
AccDB-0148
Homehttp://fungi.ensembl.org/
EDAM topicGenomes
EDAM topicGenomes
CategoryGenome annotation databases
TaxonFungi

Available data

Data Format Query Link
Gene annotation HTML Transcript ID (Ensembl) www.ensemblgenomes.org/id/%s

Example queries

Data Format Query Example
Gene annotation HTML Transcript ID (Ensembl) SPAC922.03-1
website/ensembl-genome.html0000644000244100017570000000250211606605735016105 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Ensembl-Genome

Ensembl-Genome

A system for the annotation, analysis and display of vertebrate genomes and for bacteria, protists, fungi, plants and invertebrate metazoa.

IDEnsembl-Genome
Homehttp://www.ensemblgenomes.org/
EDAM topicGenomes
Taxonall
website/ensembl.html0000644000244100017570000001027311606605735014641 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Ensembl

Ensembl eukaryotic genome annotation project

Genome databases for vertebrates and other eukaryotic species.

IDEnsembl
AccDB-0023
Homehttp://www.ensembl.org/
EDAM topicGenomes
EDAM topicEukaryote
EDAM topicGenomes
CategoryGenome annotation databases
TaxonMetazoa

Available data

Data Format Query Link
Gene annotation HTML Gene ID (Ensembl) http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s
Sequence record FASTA format Gene ID (Ensembl); Transcript ID (Ensembl) http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=%s1;output=fasta;r=13:31787617-31871809;strand=feature;t=%s2;time=1244110856.85314;st=cdna;st=coding;st=peptide;st=utr5;st=utr3;st=exons;st=introns;genomic=unmasked;_format=Text

Example queries

Data Format Query Example
Sequence record FASTA format Gene ID (Ensembl); Transcript ID (Ensembl) ENSG00000139618;ENST00000380152
website/ensemblmetazoa.html0000644000244100017570000000564711606605736016234 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EnsemblMetazoa

Ensembl invertebrate metazoan genome annotation project

Genome databases for invertebrate metazoan species.

IDEnsemblMetazoa
AccDB-0149
Homehttp://metazoa.ensembl.org/
EDAM topicGenomes
EDAM topicGenomes
CategoryGenome annotation databases
TaxonMetazoa

Available data

Data Format Query Link
Gene annotation HTML Transcript ID (Ensembl) www.ensemblgenomes.org/id/%s

Example queries

Data Format Query Example
Gene annotation HTML Transcript ID (Ensembl) FBtr0087976
website/ensemblplants.html0000644000244100017570000000561011606605736016063 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EnsemblPlants

Ensembl plant genome annotation project

Genome databases for plant species.

IDEnsemblPlants
AccDB-0150
Homehttp://plants.ensembl.org/
EDAM topicGenomes
EDAM topicGenomes
CategoryGenome annotation databases
TaxonSpermatophyta

Available data

Data Format Query Link
Gene annotation HTML Transcript ID (Ensembl) www.ensemblgenomes.org/id/%s

Example queries

Data Format Query Example
Gene annotation HTML Transcript ID (Ensembl) AT1G22300.1
website/ensemblprotists.html0000644000244100017570000000562111606605736016453 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EnsemblProtists

Ensembl protist genome annotation project

Genome databases for protist species.

IDEnsemblProtists
AccDB-0151
Homehttp://protists.ensembl.org/
EDAM topicGenomes
EDAM topicGenomes
CategoryGenome annotation databases
TaxonEukaryota

Available data

Data Format Query Link
Gene annotation HTML Transcript ID (Ensembl) www.ensemblgenomes.org/id/%s

Example queries

Data Format Query Example
Gene annotation HTML Transcript ID (Ensembl) AT1G22300.1
website/enzyme.html0000644000244100017570000001015611606605736014524 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ENZYME

Enzyme nomenclature database (ENZYME)

A repository of information relative to the nomenclature of enzymes. It is primarily based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (IUBMB) and it describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.

IDENZYME
IDaltEC_number
AccDB-0024
Homehttp://www.expasy.org/enzyme/
EDAM topicEnzymes
EDAM topicNomenclature
CategoryEnzyme and pathway databases
Taxonall

Available data

Data Format Query Link
Protein report (enzyme) Text EC number http://www.expasy.ch/enzyme/%s.txt
Protein report (enzyme) HTML EC number http://www.expasy.ch/enzyme/%s

Example queries

Data Format Query Example
Protein report (enzyme) Text EC number 1.5.99.11
Protein report (enzyme) HTML EC number 1.5.99.11
website/epd.html0000644000244100017570000001204311606605736013762 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EPD

Eukaryotic promoter database (EPD)

An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally.

IDEPD
Homehttp://www.epd.isb-sib.ch/
EDAM topicNucleic acid functional sites
EDAM topicTranscription
TaxonEukaryota

Available data

Data Format Query Link
Gene features (promoter) {EPD entry} Text EPD ID http://www.epd.isb-sib.ch/cgi-bin/query_result.pl?out_format=text&from=-499&to=100&Entry_0=%s
Gene features (promoter) {EPD entry} HTML EPD ID http://www.epd.isb-sib.ch/cgi-bin/query_result.pl?out_format=HTML&from=-499&to=100&Entry_0=%s
Gene features (promoter) {EPD entry} HTML {nice view} EPD ID http://www.epd.isb-sib.ch/cgi-bin/get_doc?db=epd&format=nice&entry=%s

Example queries

Data Format Query Example
Gene features (promoter) {EPD entry} Text EPD ID MSV_105_1
Gene features (promoter) {EPD entry} HTML EPD ID MSV_105_1
Gene features (promoter) {EPD entry} HTML {nice view} EPD ID MSV_105_1
website/eric.html0000644000244100017570000000324011606605736014133 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ERIC

Enteropathogen resource integration center (ERIC)

Annotated enterobacterial genome and associated information.

IDERIC
Homehttp://www.ericbrc.org/portal/eric/
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonEnterobacteriaceae
website/esldb.html0000644000244100017570000000317611606605736014312 0ustar jisonindustry Bioinformatics Data Resource Catalogue

eSLDB

Eukaryotic subcellular localization database (eSLDB)

A database of protein subcellular localization annotation for eukaryotic organisms. It contains experimental annotations derived from primary protein databases, homology based annotations and computational predictions.

IDeSLDB
Homehttp://gpcr.biocomp.unibo.it/esldb/
EDAM topicMembrane protein
EDAM topicProtein targeting and localization
TaxonEukaryota
website/esp-soldb.html0000644000244100017570000000273211606605736015106 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ESP-SOLDB

Genomic generic database applied to tomato fruit quality (ESP-SOLDB)

Genomic generic database applied to tomato fruit quality (ESP-SOLDB).

IDESP-SOLDB
Homehttp://www.bitlab-es.com/espsol
EDAM topicPlant
EDAM topicGenomes
TaxonSolanum lycopersicum
website/esther.html0000644000244100017570000000264311606605736014511 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ESTHER

ESTHER database on alpha/beta hydrolases

Database for the analysis of protein and nucleic acid sequences belonging to the superfamily of alpha/beta hydrolases homologous to cholinesterases.

IDESTHER
Homehttp://bioweb.ensam.inra.fr/ESTHER/general?what=index
EDAM topicSpecific protein
Taxonall
website/euhcvdb.html0000644000244100017570000000600711606605736014635 0ustar jisonindustry Bioinformatics Data Resource Catalogue

euHCVdb

European Hepatitis C virus database (euHCVdb)

European Hepatitis C virus database.

IDeuHCVdb
AccDB-0025
Homehttp://euhcvdb.ibcp.fr/euHCVdb/
EDAM topicVirus
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonHepatitis C virus

Available data

Data Format Query Link
Sequence record {euHCVdb entry} HTML Sequence accession (nucleic acid) http://euhcvdb.ibcp.fr/euHCVdb/jsp/HCVResultTextForm.jsp?AC=%s

Example queries

Data Format Query Example
Sequence record {euHCVdb entry} HTML Sequence accession (nucleic acid) AF009606
website/eupathdb.html0000644000244100017570000000654511606605727015020 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EuPathDB

Apicomplexan database resources (ApiDB)

A portal for accessing genomic-scale datasets associated with the eukaryotic pathogens (Cryptosporidium, Giardia, Leishmania, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma).

IDEuPathDB
IDaltApiDB
AccDB-0153
Homehttp://eupathdb.org/eupathdb/
EDAM topicUnicellular eukaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
TaxonApicomplexa
RESThttp://eupathdb.org/eupathdb/serviceList.jsp

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://www.eupathdb.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol cgd1_1090
website/europhenome.html0000644000244100017570000000246711606605736015551 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EuroPhenome

EuroPhenome mouse phenotype resource

Software system for capturing, storing and analysing raw phenotyping data from SOPs contained in EMPReSS.

IDEuroPhenome
Homehttp://www.europhenome.org
EDAM topicGenotype and phenotype
TaxonMus
website/everest.html0000644000244100017570000000244111606605736014670 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EVEREST

Evolutionary ensembles of recurrent segments (EVEREST)

An automatic identification and classification of protein domains.

IDEVEREST
Homehttp://www.everest.cs.huji.ac.il
EDAM topicProtein domains
Taxonall
website/explorenz.html0000644000244100017570000000275311606605736015247 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ExplorEnz

ExplorEnz enzyme database

The Enzyme Database with data from the IUBMB Enzyme Nomenclature List. Formatting of chemical names according to IUPAC standards is preserved.

IDExplorEnz
Homehttp://www.enzyme-database.org/
EDAM topicEnzymes
EDAM topicNomenclature
Taxonall
website/exprot.html0000644000244100017570000000345711606605736014544 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EXProt

Database for proteins with an experimentally verified function (EXProt)

A non-redundant database of protein sequences for which the function has been experimentally verified, from Pseudomonas Community Annotation Project, from E. coli genome and proteome database and from division Prokaryotes of the EMBL Nucleotide Sequence Database.

IDEXProt
Homehttp://www.cmbi.kun.nl/EXProt/
EDAM topicProteome
EDAM topicProkaryote
EDAM topicProtein sequences
Taxonall
website/extopodb.html0000644000244100017570000000253411606605736015042 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ExTopoDB

Experimentally derived topological models of transmembrane proteins (ExTopoDB)

Experimentally derived topological models of transmembrane proteins.

IDExTopoDB
Homehttp://bioinformatics.biol.uoa.gr/ExTopoDB
EDAM topicMembrane protein
Taxonall
website/eyesite.html0000644000244100017570000000334711606605736014670 0ustar jisonindustry Bioinformatics Data Resource Catalogue

EyeSite

EyeSite eye protein database

An information and modelling resource for families of proteins that function in the eye. Homologues are collected from all species and clustered according to tissue type, function and sequence similarity.

IDEyeSite
Homehttp://eyesite.cryst.bbk.ac.uk/
EDAM topicSpecific protein
EDAM topicProtein families
EDAM topicSequence clustering
TaxonEukaryota
website/facd.html0000644000244100017570000000264011606605736014111 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FaCD

Familial cancer database (FaCD)

Database to assist clinicians and genetic counselors in making a genetic differential diagnosis in cancer patients, as well as in becoming aware of the tumor spectrum associated with hereditary disorders that have already been diagnosed in their patients.

IDFaCD
Homehttp://www.facd.info
EDAM topicCancer
TaxonHomo sapiens
website/fantom_db.html0000644000244100017570000000305611606605736015147 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FANTOM_DB

Database of functional annotation of mammalian Genome (FANTOM_DB)

Functional annotation of mammalian genome.

IDFANTOM_DB
Homehttp://fantom.gsc.riken.jp/4/
EDAM topicGenomes
CategoryNot available
TaxonMammalia

Example queries

Data Format Query Example
website/fastdb.html0000644000244100017570000000236511606605736014463 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FASTDB

Friendly alternative splicing and transcripts database (FASTDB)

Alternative splicing and transcripts database.

IDFASTDB
Homehttp://www.fast-db.com
EDAM topicGene structure
Taxonall
website/fcp.html0000644000244100017570000000231411606605737013763 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FCP

Functional coverage of the proteome (FCP)

Functional coverage of the proteome.

IDFCP
Homehttp://cgl.imim.es/fcp/
EDAM topicProteome
Taxonall
website/fgdb.html0000644000244100017570000000330711606605737014120 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FGDB

Fusarium graminearum genome database (FGDB)

Information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Fusarium graminearum (Anamorph of Gibberella zeae).

IDFGDB
Homehttp://mips.gsf.de/genre/proj/FGDB/
EDAM topicPathways, networks and models
EDAM topicFungal
EDAM topicGenomes
TaxonGibberella
website/findbase.html0000644000244100017570000000244311606605737014771 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FINDBase

FINDBase

Information about the frequency of different mutations leading to inherited disorders in various populations around the globe.

IDFINDBase
Homehttp://www.findbase.org/
EDAM topicHuman disease
TaxonHomo sapiens
website/firedb.html0000644000244100017570000000303511606605737014447 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FireDB

Database of functionally important residues from protein structures (FireDB)

A database of Protein Data Bank structures, ligands and annotated functional site residues.

IDFireDB
Homehttp://firedb.bioinfo.cnio.es/index.php
EDAM topicProtein functional sites
EDAM topicProtein-ligand interactions
Taxonall
website/flagdb++.html0000644000244100017570000000302611606605737014561 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FLAGdb++

FLAGdb++ a database for the functional analysis of the Arabidopsis genome

Integrative database around plant genomes.

IDFLAGdb++
Homehttp://urgv.evry.inra.fr/projects/FLAGdb++/HTML/index.shtml
EDAM topicGenomes
EDAM topicPlant
TaxonArabidopsis thaliana
website/flight.html0000644000244100017570000000366611606605737014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FLIGHT

FLIGHT database integrating genomic and high-throughput data

Database for the integration of data from high-throughput experiments carried out in Drosophila cell culture. It includes phenotypic information from published cell-based RNAi screens, gene expression data from Drosophila cell lines, protein interaction data, together with novel tools to cross-correlate these diverse datasets, such as the phenotype clustering tool Shuffle.

IDFLIGHT
Homehttp://flight.licr.org/
EDAM topicProtein-protein interactions
EDAM topicGene expression and regulation
EDAM topicGenotype and phenotype
TaxonDrosophila
website/flybase.html0000644000244100017570000001414711606605737014647 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FlyBase

FlyBase database of genetic and molecular data of Drosophila

A Database of Drosophila genes and genomes.

IDFlyBase
AccDB-0026
Homehttp://flybase.bio.indiana.edu/
EDAM topicInvertebrate
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonDrosophila

Available data

Data Format Query Link
Gene annotation {FlyBase entry} HTML Gene ID (FlyBase) http://flybase.org/cgi-bin/gbrowse/dmel/?dontadjust=1&name=%s
Gene annotation {FlyBase entry} XML Gene ID (FlyBase) http://flybase.org/chadoxml/id/%s

Example queries

Data Format Query Example
Gene annotation {FlyBase entry} HTML Gene ID (FlyBase) FBgn0000165
Gene annotation {FlyBase entry} XML Gene ID (FlyBase) FBgn0000165
Gene annotation {FlyBase entry} HTML Gene ID (FlyBase) FBgn0000024
Gene annotation {FlyBase entry} XML Gene ID (FlyBase) FBgn0000024
Gene annotation {FlyBase entry} HTML Gene ID (FlyBase) FBgn0000490
Gene annotation {FlyBase entry} XML Gene ID (FlyBase) FBgn0000490
website/flymine.html0000644000244100017570000000261611606605737014663 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FlyMine

FlyMine Drosophila genome database

An integrated database for Drosophila and Anopheles genomics.

IDFlyMine
Homehttp://www.flymine.org
EDAM topicInvertebrate
EDAM topicGenomes
TaxonDrosophila
website/flysnp.html0000644000244100017570000000275011606605737014532 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FLYSNP

SNPs database for Drosophila (FLYSNP)

Database of a high-density genome-wide map of single nucleotide polymorphisms (SNPs) and high-throughput assays for SNP genotyping.

IDFLYSNP
Homehttp://flysnp.imp.ac.at/
EDAM topicMutation and polymorphism
EDAM topicGenomes
TaxonDrosophila
website/flytf.html0000644000244100017570000000264211606605737014343 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FlyTF

FlyTF Drosophila Site-Specific Transcription Factor Database

Information on the manual curation of FlyBase identifiers, which are putative site-specific transcription factors, based on FlyBase/Gene Ontology annotation or the DBD Transcription Factor Database

IDFlyTF
Homehttp://www.flytf.org
EDAM topicTranscription factor and binding site
TaxonDrosophila
website/flyview.html0000644000244100017570000000337511606605737014710 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FlyView

FlyView database

An image database on Drosophila development and genetics, especially on expression patterns of genes (enhancer trap lines, cloned genes).The concept of FlyView includes compatibility to FlyBase, the main Drosophila database.

IDFlyView
Homehttp://flyview.uni-muenster.de/
EDAM topicOrganism
EDAM topicCell cycle and development
EDAM topicGene expression and regulation
TaxonDrosophila
website/fpspd.html0000644000244100017570000000262011606605737014327 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FPSPD

Functional protein sequence pattern database (FPSPD)

Accumulates functional protein sequence patterns derived from the structurally-aligned homologous families in the HOMSTRAD database.

IDFPSPD
Homehttp://torsa.bioc.cam.ac.uk/~fpspd/home_d.html
EDAM topicProtein functional sites
Taxonall
website/funcoup.html0000644000244100017570000000406511606605737014677 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FunCoup

FunCoup database

FunCoup is a statistical framework of data integration for finding functional coupling (FC) between proteins. It transfers information from model organisms (M. musculus, D. melanogaster, C. elegans, S. cerevisiae etc.) via orthologs found by InParanoid program. Data of different sources and various natures, such as contacts of whole proteins and individual domains, mRNA and protein expression, localization in tissues and cellular compartments, miRNA and TF targeting, similar phylogenetic profiles etc. are collected and evaluated.

IDFunCoup
Homehttp://funcoup.sbc.su.se/
EDAM topicPathways, networks and models
EDAM topicGene expression and regulation
EDAM topicProtein targeting and localization
Taxonall
website/fungalgenomesize.html0000644000244100017570000000262711606605737016564 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FungalGenomeSize

Fungal genome size database

Fungal genome size database

IDFungalGenomeSize
Homehttp://www.zbi.ee/fungal-genomesize/
EDAM topicGenomics
EDAM topicFungal
TaxonFungi
website/funpep.html0000644000244100017570000000251011606605737014506 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FUNPEP

FUNPEP information system for "low complexity sequence regions"

Information system for "low complexity sequence regions".

IDFUNPEP
Homehttp://swift.cmbi.kun.nl/swift/FUNPEP/info/
EDAM topicLow complexity sequence
Taxonall
website/funshift.html0000644000244100017570000000240311606605737015040 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FunShift

FunShift database

A compilation of function shift analysis performed between subfamilies in protein families.

IDFunShift
Homehttp://FunShift.cgb.ki.se
EDAM topicProtein families
Taxonall
website/funsimmat.html0000644000244100017570000000311511606605737015216 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FunSimMat

FunSimMat database of semantic and functional similarity

A resource of semantic and functional similarity values. It allows searching for functional similarity values for proteins (extracted from UniProt), and protein families (Pfam, SMART). FunSimMat provides several different semantic and functional similarity measures for each protein pair using the Gene Ontology annotation from UniProtKB.

IDFunSimMat
Homehttp://funsimmat.bioinf.mpi-inf.mpg.de/
EDAM topicProtein families
Taxonall
website/funybase.html0000644000244100017570000000406511606605737015034 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FUNYBASE

FUNYBASE fungal phylogenomic database

Database dedicated to the analysis of fungal proteins extracted from complete public fungal genomes, and their classification in clusters of orthologs.

IDFUNYBASE
Homehttp://genome.jouy.inra.fr/funybase/funybase_start.cgi
EDAM topicProteome
EDAM topicProtein families
EDAM topicSequence clustering
EDAM topicFungal
EDAM topicPhylogenomics
TaxonFungi
website/fusiondb.html0000644000244100017570000000261011606605737015023 0ustar jisonindustry Bioinformatics Data Resource Catalogue

FusionDB

FusionDB database of bacterial and archaeal gene fusion events

A database of bacterial and archaeal gene fusion events.

IDFusionDB
Homehttp://www.igs.cnrs-mrs.fr/FusionDB/
EDAM topicGene structure
TaxonBacteria, Archaea
website/g2cdb.html0000644000244100017570000000272611606605737014203 0ustar jisonindustry Bioinformatics Data Resource Catalogue

G2Cdb

Genes to cognition database (G2Cdb)

Genes to Cognition (G2C) is a neuroscience research programme that studies genes, the brain and behaviour in an integrated manner, established to elucidate the molecular mechanisms of learning and memory, and shed light on the pathogenesis of disorders of cognition.

IDG2Cdb
Homehttp://www.genes2cognition.org
EDAM topicHuman disease
TaxonHomo sapiens
website/gabi-kat.html0000644000244100017570000000245311606605740014670 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GABI-Kat

GABI-Kat tags mutagenised A. thaliana

Generation of flanking sequence tags (FSTs) from T-DNA mutagenised A. thaliana plants.

IDGABI-Kat
Homehttp://www.gabi-kat.de/
EDAM topicGenetic mapping and linkage
TaxonArabidopsis thaliana
website/gabipd.html0000644000244100017570000000271611606605737014447 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GabiPD

GabiPD: primary database of plant integrative biology

Primary database of plant integrative biology.

IDGabiPD
Homehttp://www.gabipd.org/
EDAM topicPlant
TaxonSpermatophyta

Example queries

Data Format Query Example
website/gbiffi.html0000644000244100017570000000231711606605740014436 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GBIFFI

Global biodiversity information facility, Finland (GBIFFI)

Global biodiversity data.

IDGBIFFI
Homehttp://www.gbif.fi
EDAM topicEcoinformatics
Taxonall
website/gdb.html0000644000244100017570000000271611606605740013747 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GDB

Human Genome Database (GDB)

Community curated collection of human genomic data - now obsolete.

IDGDB
EDAM topicHuman
EDAM topicGenomes
TaxonHomo sapiens

Example queries

Data Format Query Example
website/genatlas.html0000644000244100017570000000620511606605740015006 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GenAtlas

GenAtlas human gene database

Information on gene apping and genetic diseases.

IDGenAtlas
AccDB-0027
Homehttp://www.dsi.univ-paris5.fr/genatlas/
EDAM topicHuman disease
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation {GenAtlas entry} HTML Gene symbol http://www.dsi.univ-paris5.fr/genatlas/fiche.php?symbol=%s

Example queries

Data Format Query Example
Gene annotation {GenAtlas entry} HTML Gene symbol RPL35A
website/genbank-dbsts.html0000644000244100017570000000575511606605740015743 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GenBank-dbSTS

STS database maintained at the NCBI (dbSTS)

An NCBI resource that contains sequence and mapping data on short genomic landmark sequences or Sequence Tagged Sites. All STS sequences are incorporated into the STS Division of GenBank.

IDGenBank-dbSTS
IDaltdbSTS
Homehttp://www.ncbi.nlm.nih.gov/dbSTS/
EDAM topicGenetic mapping and linkage
CategoryNot available
Taxonall

Available data

Data Format Query Link
Sequence record full GenBank-HTML Sequence accession (nucleic acid) http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=%s

Example queries

Data Format Query Example
Sequence record full GenBank-HTML Sequence accession (nucleic acid) G06709
website/genbank.html0000644000244100017570000000550211606605740014614 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GenBank

GenBank nucleotide sequence database

Nucleotide sequence database.

IDGenBank
AccDB-0028
Homehttp://www.ncbi.nlm.nih.gov/
EDAM topicNucleic acid sequences
CategorySequence databases
Taxonall

Available data

Data Format Query Link
Sequence record full GenBank-HTML Sequence accession (nucleic acid) http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=%s

Example queries

Data Format Query Example
Sequence record full GenBank-HTML Sequence accession (nucleic acid) AE014292
website/gene3d.html0000644000244100017570000001446011606605740014357 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Gene3D

Gene3D structural and functional annotation of protein families

Gene3D structural and functional annotation of protein families incorporates several different sources including CATH, DRUGBANK, PFAM etc.

IDGene3D
AccDB-0029
Homehttp://cathwww.biochem.ucl.ac.uk:8080/Gene3D/
EDAM topicProtein families
CategoryFamily and domain databases
Taxonall
Linkinghttp://gene3d.biochem.ucl.ac.uk/Gene3D/linking
SOAPhttp://funcnet.eu/

Available data

Data Format Query Link
Protein family annotation {Gene3D entry} HTML CATH node ID (family) http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?family=%s
Protein family annotation {Gene3D entry} HTML CATH domain ID http://gene3d.biochem.ucl.ac.uk/Gene3D/cathLink?domain_id=%s
Protein family annotation {Gene3D entry} HTML CATH node ID (family) http://www.cathdb.info/cgi-bin/GotoCath.pl?cath=%s

Example queries

Data Format Query Example
Protein family annotation {Gene3D entry} HTML CATH node ID (family) 2.10.10.10
Protein family annotation {Gene3D entry} HTML CATH node ID (family) 2.10.10.10
Protein family annotation {Gene3D entry} HTML CATH domain ID 1cukA00
Protein family annotation {Gene3D entry} HTML CATH node ID (family) G3DSA:3.40.30.10
Protein family annotation {Gene3D entry} HTML CATH node ID (family) G3DSA:3.40.30.10
website/geneannot.html0000644000244100017570000000260111606605740015162 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneAnnot

Affymetrix probe-sets database (GeneAnnot)

GeneAnnot provides a revised and improved annotation of Affymetrix probe-sets from HG-U95, HG-U133 and HG-U133 Plus2.0.

IDGeneAnnot
Homehttp://bioinfo2.weizmann.ac.il/geneannot/
EDAM topicMolecular probes or primers
TaxonHomo sapiens
website/genecards.html0000644000244100017570000002242611606605740015146 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneCards

GeneCards database of human genes, protein and diseases

GeneCards is a searchable, integrated database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. Information featured in GeneCards includes orthologies, disease relationships, mutations and SNPs, gene expression, gene function, pathways, protein-protein interactions, related drugs & compounds and direct links to cutting edge research reagents and tools such as antibodies, recombinant proteins, clones, expression assays and RNAi reagents.

IDGeneCards
AccDB-0030
Homehttp://www.genecards.org/
EDAM topicHuman disease
EDAM topicProteins
EDAM topicProtein-protein interactions
EDAM topicPathways, networks and models
EDAM topicMutation and polymorphism
EDAM topicGenomes
CategoryHuman genes and diseases database
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s
Gene annotation HTML UniProt accession http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Gene annotation HTML Locus ID (EntrezGene) http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Gene annotation HTML Ensembl ID http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Gene annotation HTML Gene ID (HGNC) http://www.genecards.org/cgi-bin/carddisp.pl?id=%s
Gene annotation XML Gene symbol http://www.genecards.org/cgi-bin/carddisp.pl?gene=%s&format=xmlByFunction
Gene annotation HTML Gene identifier {GeneCards} http://www.genecards.org/cgi-bin/carddisp.pl?gc_id=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol CASP3
Gene annotation XML Gene symbol CASP3
Gene annotation HTML Locus ID (EntrezGene) 1956
Gene annotation HTML Ensembl ID ENSG00000146648
Gene annotation HTML Gene ID (HGNC) 2041
Gene annotation HTML Gene identifier {GeneCards} GC20P040256
website/genedb.html0000644000244100017570000000545111606605740014436 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneDB

GeneDB database from Sanger Institute Pathogen Sequencing Units

Sequence data and annotation/curation for the whole range of organisms sequenced by the PSU (Sanger Institute Pathogen Sequencing Units).

IDGeneDB
Homehttp://www.genedb.org/
EDAM topicGenomes
EDAM topicPathogen
Taxonall

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://www.genedb.org/gene/%s

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol ECA4014
website/genedb_spombe.html0000644000244100017570000000732111606605740016001 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneDB_Spombe

Schizosaccharomyces pombe genome database (GeneDB_Spombe)

Sequence data and annotation/curation for Schizosaccharomyces pombe (fission yeast), including known and predicted protein coding genes, pseudogenes, transposons, tRNAs, rRNAs, snRNAs, snoRNAs and other known and predicted non-coding RNAs.

IDGeneDB_Spombe
AccDB-0031
Homehttp://www.genedb.org/genedb/pombe/
EDAM topicGenomes
EDAM topicYeast
EDAM topicFunctional RNA
EDAM topicOrganism
EDAM topicMobile genetic elements
CategoryOrganism-specific databases
TaxonSchizosaccharomyces pombe

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://www.genedb.org/genedb/Search?submit=Search+for&name=%s&organism=pombe&desc=yes

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol SPAC922.03
website/geneexpressiontooth.html0000644000244100017570000000241311606605740017321 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneExpressionTooth

Gene expression in tooth database

Gene expression in tooth database

IDGeneExpressionTooth
Homehttp://bite-it.helsinki.fi/
EDAM topicGene expression and regulation
TaxonEutheria
website/genefarm.html0000644000244100017570000001041311606605740014770 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneFarm

GeneFarm annotation of Arabidopsis thaliana gene and protein families

Structural and functionnal annotation of plant gene and protein families by a network of experts.

IDGeneFarm
AccDB-0032
Homehttp://urgi.versailles.inra.fr/Genefarm/index.htpl
EDAM topicProtein families
EDAM topicPlant
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonArabidopsis thaliana

Available data

Data Format Query Link
Gene annotation HTML Gene ID http://urgi.versailles.inra.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s
Protein family annotation HTML Protein family ID (GeneFarm) http://urgi.versailles.inra.fr/Genefarm/Family/display_family.htpl?FAM_ID=%s

Example queries

Data Format Query Example
Protein family annotation HTML Protein family ID (GeneFarm) 59
Gene annotation HTML Gene ID 907
website/geneid.html0000644000244100017570000002440711606605740014447 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneID

GeneID database of genes from NCBI RefSeq genomes

Database of genes from NCBI RefSeq genomes

IDGeneID
AccDB-0118
Homehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=gene
EDAM topicGene family or system
EDAM topicGenomes
CategoryGenome annotation databases
Taxonall

Available data

Data Format Query Link
Gene annotation {GeneID gene list} HTML Identifier {Keyword} http://www.ncbi.nlm.nih.gov/sites/entrez?db=gene&term=%s
Gene annotation {GeneID gene list} HTML Sequence accession (nucleic acid) http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[accn]
Gene annotation {GeneID gene list} HTML Gene symbol http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[sym]
Gene annotation {GeneID gene list} HTML PubMed ID http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[PMID]
Gene annotation {GeneID gene list} HTML Ontology term name {GO} http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="%s"[GO]
Gene annotation {GeneID gene list} HTML GO term ID http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term="%s"[GO]
Gene annotation {GeneID gene list} HTML Chromosome name; Species name http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s1[CHR]+AND+%s2[ORGN]
Gene annotation {GeneID gene list} HTML EC number http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[EC]
Gene annotation {GeneID gene list} HTML Identifier {Unique ID} http://www.ncbi.nlm.nih.gov/sites/entrez?cmd=search&db=gene&term=%s[uid]

Example queries

Data Format Query Example
Gene annotation {GeneID gene list} HTML Identifier {Keyword} haem
Gene annotation {GeneID gene list} HTML Sequence accession (nucleic acid) M11313
Gene annotation {GeneID gene list} HTML Gene symbol BRCA1
Gene annotation {GeneID gene list} HTML PubMed ID 11331580
Gene annotation {GeneID gene list} HTML Ontology term name {GO} cell+adhesion
Gene annotation {GeneID gene list} HTML EC number 1.9.3.1
Gene annotation {GeneID gene list} HTML Identifier {Unique ID} 4156251
website/geneloc.html0000644000244100017570000000316411606605740014625 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneLoc

GeneLoc map for human chromosomes

An integrated map for each human chromosome, based on data integrated by the GeneLoc algorithm. GeneLoc includes further links to GeneCards, NCBI's Human Genome Sequencing, UniGene, and mapping resources.

IDGeneLoc
Homehttp://genecards.weizmann.ac.il/geneloc/index.shtml
EDAM topicGenomes
EDAM topicChromosomes
TaxonHomo sapiens
website/genenest.html0000644000244100017570000000414611606605740015022 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneNest

GeneNest transcript clusters

GeneNest is a comprehensive visualization of gene indices of various organisms. Each gene is represented by a single cluster of ESTs and/or mRNAs. Further subdivision of a cluster into contigs may be caused by alternative splicing, genomic sequences, or artefacts like chimeric sequences. Consensus sequence derived from GeneNest contigs are a basis for mapping genes onto the genome, and for analysis of splice isoforms.

IDGeneNest
Homehttp://genenest.molgen.mpg.de/
EDAM topicGene structure
EDAM topicNucleic acid classification
EDAM topicSequence clustering
EDAM topicmRNA, EST or cDNA
Taxonall
website/genenote.html0000644000244100017570000000345311606605740015016 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneNote

GeneNote human genes and their expression profiles

A database of human genes and their expression profiles in healthy tissues. It is based on Weizmann Institute of Science DNA array experiments, which were performed on the Affymetrix HG-U95 set A-E.

IDGeneNote
Homehttp://genecards.weizmann.ac.il/genenote/
EDAM topicGene expression and regulation
EDAM topicGene expression profiling
EDAM topicHuman disease
TaxonHomo sapiens
website/genesapiens.html0000644000244100017570000000240211606605740015504 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneSapiens

GeneSapiens human transcriptome database

Human transcriptome database.

IDGeneSapiens
Homehttp://www.genesapiens.org/
EDAM topicGene expression and regulation
TaxonHomo sapiens
website/genesnps.html0000644000244100017570000000546211606605740015036 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneSNPs

SNPs Program at the University of Washington (GeneSNPs)

Gene-centric map of the genome structure, coding sequences, and identified allelic variation in genes being targeted for a role in disease susceptibility by the NIEHS (National Institute of Evironmental Health Sciences). This database provides a graphical view of all available SNP data including allele frequencies and genotypes in select populations. This information is key in selecting the polymorphic sites needed to examine disease risk in human population studies.

IDGeneSNPs
IDaltNIEHS-SNPs
Homehttp://egp.gs.washington.edu/
EDAM topicMutation and polymorphism
EDAM topicGenomes
EDAM topicHuman disease
CategoryPolymorphism databases
TaxonHomo sapiens

Available data

Data Format Query Link
SNP annotation {GeneSNPs entry} HTML GeneSNP ID http://egp.gs.washington.edu/data/%s/
website/genetide.html0000644000244100017570000000251111606605740014770 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneTide

GeneTide database

An automated system for human transcripts (mRNA & ESTs) annotation and elucidation of de-novo genes.

IDGeneTide
Homehttp://genecards.weizmann.ac.il/genetide/
EDAM topicmRNA, EST or cDNA
TaxonHomo sapiens
website/genetree.html0000644000244100017570000000530711606605740015010 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GeneTree

GeneTree

GeneTree

IDGeneTree
AccDB-0162
Homehttp://www.ensemblgenomes.org
EDAM topicGenomes
CategoryPhylogenomic databases
Taxonall

Available data

Data Format Query Link
Gene annotation HTML Identifier {GeneTree} http://www.ensemblgenomes.org/id-genetree/%s

Example queries

Data Format Query Example
Gene annotation HTML Identifier {GeneTree} EMGT00050000006238
website/genevestigator.html0000644000244100017570000000541111606605740016234 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Genevestigator

Genevestigator

Genevestigator

IDGenevestigator
AccDB-0142
Homehttp://www.genevestigator.com/
EDAM topicGenomes
CategoryGene expression databases
Taxonall

Available data

Data Format Query Link
Gene annotation HTML UniProt accession http://www.genevestigator.com/gv/directlink.jsp?geneIDs=%s&geneIDType=SwissPro

Example queries

Data Format Query Example
Gene annotation HTML UniProt accession P48347
website/genolevures.html0000644000244100017570000000323511606605741015547 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Genolevures

Genolevures 18 yeast genomes

Annotated sequence data and classifications for the genomes of eighteen species of hemiascomycete yeasts, including nine complete genomes.

IDGenolevures
Homehttp://www.genolevures.org/
EDAM topicYeast
EDAM topicGenomes
EDAM topicNucleic acid classification
TaxonSaccharomycetales
website/genolist.html0000644000244100017570000001114511606605741015034 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GenoList

GenoList comparative analysis of microbial genomes

An integrated environment for the analysis of microbial genomes.

IDGenoList
AccDB-0157
Homehttp://genolist.pasteur.fr/GenoList
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicComparative genomics
TaxonBacteria

Available data

Data Format Query Link
Gene annotation HTML Gene ID (Genolist) http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/goToGene?accNum=%s
Gene annotation HTML Gene symbol http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/goToGene?geneName=%s
Taxonomic data {GenoList organism(s)} HTML Taxon {GenoList organism} http://genodb.pasteur.fr/cgi-bin/WebObjects/GenoList.woa/wa/goToTaxoRank?level=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID (Genolist) BSU00010
Gene annotation HTML Gene symbol abrB
website/genomereviews.html0000644000244100017570000000607711606605741016077 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GenomeReviews

GenomeReviews database of completely sequenced genomes

Annotated view of the genomic sequence of organisms with completely deciphered genomes. Currently, Genome Reviews contains the genomes of archaea, bacteria, bacteriophages and selected eukaryota.

IDGenomeReviews
IDaltGR
AccDB-0034
Homehttp://www.ebi.ac.uk/GenomeReviews/
EDAM topicGenomes
CategoryGenome annotation databases
Taxonall

Available data

Data Format Query Link
Genome metadata {GenomeReviews entry} HTML GenomeReviews ID http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[GENOMEREVIEWS:%s]+-e

Example queries

Data Format Query Example
Genome metadata {GenomeReviews entry} HTML GenomeReviews ID ab000109_gr
website/genomernai.html0000644000244100017570000000252211606605741015333 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GenomeRNAi

GenomeRNAi database

Phenotypes from systematic RNA interference (RNAi) screens in cultured Drosophila cells.

IDGenomeRNAi
Homehttp://www.dkfz.de/signaling2/rnai/ernai.html
EDAM topicGenotype and phenotype
TaxonDrosophila
website/genomicthreadingdatabase.html0000644000244100017570000000245511606605741020210 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GenomicThreadingDatabase

Genomic threading database

Structural annotations of proteomes, translated from the genomes of key organisms.

IDGenomicThreadingDatabase
Homehttp://bioinf.cs.ucl.ac.uk/GTD/
EDAM topicProteome
Taxonall
website/germlinep53mutations.html0000644000244100017570000000246711606605741017315 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Germlinep53Mutations

Germline p53 Mutations database

Germline p53 mutations

IDGermlinep53Mutations
Homehttp://www.lf2.cuni.cz/projects/germline_mut_p53.htm
EDAM topicCancer
TaxonHomo sapiens
website/germonline.html0000644000244100017570000000602211606605741015345 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GermOnline

Gametogenesis and reproductive tissue expression

High-throughput expression data relevant for germline development and fertility across species.

IDGermOnline
AccDB-0035
Homehttp://www.germonline.org/
EDAM topicGene expression and regulation
CategoryGene expression databases
TaxonEukaryota

Available data

Data Format Query Link
Gene annotation HTML Species name; Gene symbol http://www.germonline.org/%s1/geneview?gene=%s2
Gene annotation HTML Species name; Gene ID (Ensembl) http://www.germonline.org/%s1/geneview?db=core|gene=%s2

Example queries

Data Format Query Example
website/glycatebase.html0000644000244100017570000000251611606605741015475 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GlycateBase

GlycateBase glycation prediction

Glycation of amino groups of lysines in mammalian proteins.

IDGlycateBase
Homehttp://www.cbs.dtu.dk/databases/GlycateBase-1.0/
EDAM topicProtein functional sites
TaxonMammalia
website/glycomedb.html0000644000244100017570000000256611606605741015164 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GlycomeDB

Glycome database

Integrated database of carbohydrate structure and annotations, incorporating data from all freely available databases (CFG , KEGG, GLYCOSCIENCES.de, BCSDB and Carbbank).

IDGlycomeDB
Homehttp://www.glycome-db.org/About.action
EDAM topicCarbohydrates
Taxonall
website/glycosciencesdb.html0000644000244100017570000001152211606605741016347 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GlycosciencesDB

Glycosciences database

Carbohydrate structure database.

IDGlycosciencesDB
IDaltDBGLYCOSCIENCES.de
Homehttp://www.glycosciences.de/sweetdb/index.php
EDAM topicCarbohydrates
Taxon

Available data

Data Format Query Link
Carbohydrate structure report {GLYCOSCIENCES.DB entry} HTML Linucs ID http://www.glycosciences.de/database/start.php?action=explore_linucsid&linucsid=%s
Carbohydrate structure report {GLYCOSCIENCES.de PDB entry} HTML PDB ID http://www.glycosciences.de/database/start.php?action=explore_PDBcode&PDB_code=%s
Carbohydrate conformational map {GlycoMapsDB entry} HTML GlycoMap ID http://www.glycosciences.de/modeling/glycomapsdb/showdetails.php?mapid=%s

Example queries

Data Format Query Example
Carbohydrate structure report {GLYCOSCIENCES.DB entry} HTML Linucs ID 288
Carbohydrate structure report {GLYCOSCIENCES.de PDB entry} HTML PDB ID 1tl0
Carbohydrate conformational map {GlycoMapsDB entry} HTML GlycoMap ID 7147
website/glycosuitedb.html0000644000244100017570000000566411606605741015716 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GlycoSuiteDB

GlycoSuiteDB glycan database

An annotated and curated relational database of glycan structures.

IDGlycoSuiteDB
AccDB-0036
Homehttp://glycosuitedb.expasy.org/
EDAM topicCarbohydrates
CategoryPTM databases
Taxonall

Available data

Data Format Query Link
Carbohydrate structure report {GlycoSuiteDB entry} HTML UniProt accession http://glycosuitedb.expasy.org/glycosuite/results?prot_swissprot=%s;results_index=protein;ig_hist=1

Example queries

Data Format Query Example
Carbohydrate structure report {GlycoSuiteDB entry} HTML UniProt accession P02763
website/goa.html0000644000244100017570000001354411606605741013763 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GOA

Gene ontology annotation database for UniProt (GOA-UniProt)

Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI).

IDGOA
IDaltGOA-UniProt
Homehttp://www.ebi.ac.uk/goa
EDAM topicProteome
EDAM topicAnnotation
Taxonall

Available data

Data Format Query Link
Data reference {GOA-UniProt protein entry} HTML UniProt accession http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein
Data reference {GOA-UniProt protein entry} HTML Protein name http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=Protein
Ontology term HTML GO term ID http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO
Ontology term HTML Ontology term name {GO biological process} http://www.ebi.ac.uk/QuickGO/GSearch?q=%s&what=GO

Example queries

Data Format Query Example
Ontology term HTML Ontology term name {GO biological process} apoptosis
Ontology term HTML GO term ID GO:0006915
Data reference {GOA-UniProt protein entry} HTML Protein name tropomyosin
Data reference {GOA-UniProt protein entry} HTML UniProt accession P06727
website/go.html0000644000244100017570000000547411606605741013625 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GO

Gene ontology

Controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members. THe aim is to standardize representations of gene and gene product attributes across species and databases.

IDGO
AccDB-0037
Homehttp://www.geneontology.org/
EDAM topicOntologies
CategoryOntologies
Taxon

Available data

Data Format Query Link
Ontology term HTML GO term ID http://www.ebi.ac.uk/ego/QuickGO?mode=display&entry=%s

Example queries

Data Format Query Example
Ontology term HTML GO term ID GO:0006915
website/golddb.html0000644000244100017570000000304211606605741014440 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GOLDDB

GOLDDB database of genomics of lipid-associated disorders

GOLDDB integrates disparate information on the function and properties of genes and their protein products that are particularly relevant to the biology, diagnosis management, treatment, and prevention of lipid-associated disorders including non-insulin dependent diabetes, various hyperlipidemias, high blood pressure and atherosclerosis.

IDGOLDDB
Homehttps://gold.tugraz.at/
EDAM topicHuman disease
TaxonHomo sapiens
website/gold.html0000644000244100017570000000237411606605741014141 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GOLD

Genomes database

Information on complete and ongoing genome projects, as well as metagenomes and metadata.

IDGOLD
Homehttp://www.genomesonline.org/
EDAM topicGenomics
Taxonall
website/gopubmed.html0000644000244100017570000000247111606605741015014 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GoPubMed

GoPubMed ontology-based literature search

Ontology-based literature search.

IDGoPubMed
Homehttp://www.gopubmed.org
EDAM topicLiterature and documentation
EDAM topicOntologies
Taxon
website/gpcrdb.html0000644000244100017570000000612511606605741014453 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GPCRDB

Information system for G protein-coupled receptors (GPCRs)

GPCR family profiles, mutation data (in various formats), ligand binding data, sequence annotations and cross-references to other databases.

IDGPCRDB
AccDB-0038
Homehttp://www.gpcr.org/7tm/
EDAM topicMembrane protein
EDAM topicProtein-ligand interactions
CategoryProtein family/group databases
TaxonEukaryota

Available data

Data Format Query Link
Protein report (membrane protein) {GPCRDB entry} HTML Protein family name http://www.gpcr.org/7tm/proteins/%s

Example queries

Data Format Query Example
Protein report (membrane protein) {GPCRDB entry} HTML Protein family name a1kyp5_petma
website/gpcr_nava.html0000644000244100017570000000244611606605741015154 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GPCR_NaVa

GPCR natural variants database

Sequence variants within the family of human G Protein-Coupled Receptors (GPCRs).

IDGPCR_NaVa
Homehttp://nava.liacs.nl/index.html
EDAM topicMembrane protein
TaxonHomo sapiens
website/gpdb.html0000644000244100017570000000275111606605741014127 0ustar jisonindustry Bioinformatics Data Resource Catalogue

gPDB

A database of G-proteins,GPCRs,effectors and their interactions

Relational database of G-proteins and their interactions with GPCRs and effector molecules. The sequences are classified according to a hierarchy of different classes, families and sub-families, based on extensive literature search.

IDgPDB
Homehttp://bioinformatics.biol.uoa.gr/gPDB/
EDAM topicMembrane protein
TaxonEukaryota
website/gramene.html0000644000244100017570000000664011606605741014632 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Gramene

Gramene database for comparative grass genomics

Gramene adds value to public data sets of grass genomes and helps to compare, identify and understand genes, pathways and phenotypes from different grass species.

IDGramene
AccDB-0039
Homehttp://www.gramene.org/
EDAM topicComparative genomics
EDAM topicGenotype and phenotype
EDAM topicOrganism
EDAM topicPathways, networks and models
CategoryOrganism-specific databases
TaxonPoaceae

Available data

Data Format Query Link
Protein report {Gramene entry} HTML UniProt accession http://www.gramene.org//db/protein/protein_search?acc=%s

Example queries

Data Format Query Example
Protein report {Gramene entry} HTML UniProt accession P93436
website/greenphyldb.html0000644000244100017570000000355011606605741015514 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GreenPhylDB

A phylogenomic database for plant comparative genomics

Database for comparative genomic analyses of Arabidopsis thaliana and Oryza sativa full genomes.

IDGreenPhylDB
Homehttp://greenphyl.cirad.fr/cgi-bin/greenphyl.cgi
EDAM topicComparative genomics
EDAM topicPhylogenetics
EDAM topicPhylogenomics
EDAM topicPlant
TaxonSpermatophyta
website/grin.html0000644000244100017570000000411611606605742014150 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GRIN

Germplasm Resources Information Network (GRIN)

GRIN taxonomic data provide the structure and nomenclature for accessions of the National Plant Germplasm System (NPGS). All families and genera of vascular plants and species from throughout the world are represented, especially economic plants and their relatives. Information on scientific and common names, classification, distribution, references, and economic impacts are provided.

IDGRIN
Homehttp://www.ars-grin.gov/cgi-bin/npgs/html/index.pl
EDAM topicPlant
EDAM topicNomenclature
CategoryNot available
TaxonSpermatophyta

Example queries

Data Format Query Example
website/gydb.html0000644000244100017570000000275411606605742014144 0ustar jisonindustry Bioinformatics Data Resource Catalogue

GyDB

Gypsy database of mobile genetic elements

Molecular diversity and evolutionary relationships of mobile genetic elements, viruses and related host genes.

IDGyDB
Homehttp://gydb.uv.es/index.php/Main_Page
EDAM topicVirus
EDAM topicMobile genetic elements
Taxonall
website/haemb.html0000644000244100017570000000252411606605742014266 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HaemB

Haemophilia B Mutation Database

Point mutations and short additions and deletions in the factor IX gene

IDHaemB
Homehttp://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html
EDAM topicHuman disease
TaxonHomo sapiens
website/hamap.html0000644000244100017570000001414111606605742014276 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HAMAP

High-quality automated and manual annotation of microbial proteomes (HAMAP)

A system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is applied to bacterial, archaeal and plastid-encoded proteins.

IDHAMAP
AccDB-0041
Homehttp://www.expasy.org/sprot/hamap/
EDAM topicProteome
EDAM topicProtein families
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
ID list {HAMAP family members} Text HAMAP ID http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=tab&columns=id
Sequence record {HAMAP family sequences} uniprot HAMAP ID http://www.uniprot.org/uniprot/?query=hamap+MF_%s&format=txt
Protein report {HAMAP family rules} HTML HAMAP ID http://www.expasy.org/unirule/MF_%s
Protein report {HAMAP family rules} Text HAMAP ID http://www.expasy.org/unirule/MF_%s.txt

Example queries

Data Format Query Example
ID list {HAMAP family members} Text HAMAP ID 00314
Sequence record {HAMAP family sequences} uniprot HAMAP ID 00314
Protein report {HAMAP family rules} HTML HAMAP ID 00314
Protein report {HAMAP family rules} Text HAMAP ID 00314
website/hamasters.html0000644000244100017570000000250311606605742015176 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HAMASTERS

Haemophilia A FVIII mutation database (HAMASTERS)

Resources for Haemophilia A / factor VIII (FVIII) genetic variation at the DNA and protein level.

IDHAMASTERS
Homehttp://europium.csc.mrc.ac.uk/
EDAM topicHuman disease
TaxonHomo sapiens
website/hcad.html0000644000244100017570000000241511606605742014110 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HCAD

Human chromosome aberration database (HCAD)

Human chromosome aberration database.

IDHCAD
Homehttp://www.pdg.cnb.uam.es/UniPub/HCAD/
EDAM topicChromosomes
TaxonHomo sapiens
website/hepseq.html0000644000244100017570000000262511606605742014501 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HepSeq

HepSeq international repository for Hepatitis B virus strain data

Molecular, clinical and epidemiological database for hepatitis B infection.

IDHepSeq
Homehttp://www.hpa-bioinfodatabases.org.uk/hepatitis_open/main.php
EDAM topicVirus
TaxonHepatitis B virus
website/hervd.html0000644000244100017570000000311311606605742014315 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HERVd

Human endogenous retrovirus database (HERVd)

A database compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects, for screening human genome for HERVs. The HERV database now contains retroviruses from more than 90 % of the human genome.

IDHERVd
Homehttp://herv.img.cas.cz/
EDAM topicVirus
EDAM topicNucleic acid sequences
TaxonHomo sapiens
website/hgdp-ceph.html0000644000244100017570000000250411606605742015047 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HGDP-CEPH

HGDP-CEPH diversity panel database (HGDP-CEPH)

Polymorphic marker genotypes generated by users of the DNAs of the HGDP-CEPH Diversity Panel.

IDHGDP-CEPH
Homehttp://www.cephb.fr/fr/hgdp/
EDAM topicGenetic mapping and linkage
TaxonHomo sapiens
website/hgmd.html0000644000244100017570000000236011606605742014127 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HGMD

Human gene mutation database (HGMD)

Known (published) gene lesions responsible for human inherited disease.

IDHGMD
Homehttp://www.hgmd.org
EDAM topicHuman disease
TaxonHomo sapiens
website/hgnc.html0000644000244100017570000000722211606605742014131 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HGNC

Human gene nomenclature database (HGNC)

Database of unique and meaningful names for all human genes.

IDHGNC
IDaltGenew
AccDB-0042
Homehttp://www.genenames.org/
EDAM topicOrganism
EDAM topicGenomics
EDAM topicNomenclature
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation {HGNC entry} HTML Gene ID (HGNC) http://www.genenames.org/data/hgnc_data.php?hgnc_id=%s

Example queries

Data Format Query Example
Gene annotation {HGNC entry} HTML Gene ID (HGNC) 2041
Gene annotation {HGNC entry} HTML Gene ID (HGNC) HGNC:12849
website/hgt-db.html0000644000244100017570000000360011606605742014353 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HGT-DB

Horizontal gene transfer-database (HGT-DB)

Genomic database that includes statistical parameters such as G+C content, codon and amino-acid usage, as well as information about which genes deviate in these parameters for prokaryotic complete genomes. Under the hypothesis that genes from distantly related species have different nucleotide compositions, these deviated genes may have been acquired by horizontal gene transfer.

IDHGT-DB
Homehttp://genomes.urv.es/HGT-DB/
EDAM topicPhylogenetics
EDAM topicProkaryote
EDAM topicGenomes
Taxonall
website/hgvbaseg2p.html0000644000244100017570000000254711606605742015247 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HGVbaseG2P

Human Genome Variation database of Genotype-to-Phenotype information (HGVbaseG2P)

Centralized compilation of summary level findings from genetic association studies, both large and small.

IDHGVbaseG2P
Homehttp://www.hgvbaseg2p.org
EDAM topicGenotype and phenotype
TaxonHomo sapiens
website/hic-up.html0000644000244100017570000000225411606605742014377 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HIC-Up

Hetero-compound information (HIC-Up)

Structural biology of hetero-compounds ("small molecules").

IDHIC-Up
Homehttp://xray.bmc.uu.se/hicup/
EDAM topicSmall molecules
Taxon
website/h-invdb.html0000644000244100017570000002277111606605742014547 0ustar jisonindustry Bioinformatics Data Resource Catalogue

H-InvDB

H-InvDB integrated database of human genes and transcripts

From extensive analyses of all human transcripts, H-InvDB provides curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats), relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups.

IDH-InvDB
AccDB-0040
Homehttp://www.h-invitational.jp/
EDAM topicGene expression and regulation
EDAM topicGene expression profiling
EDAM topicMutation and polymorphism
EDAM topicMetabolic pathways
EDAM topicHuman disease
EDAM topicOrganism
EDAM topicFunctional RNA
EDAM topicGene structure
EDAM topicProtein targeting and localization
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation (transcript) HTML HIT ID http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=%s
Gene annotation HTML HIX ID http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=%s
Gene annotation (transcript) Text HIT ID http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=%s&status=flat
Gene annotation Text HIX ID http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0005064&status=flat
Gene annotation (transcript) XML HIT ID http://h-invitational.jp/hinv/spsoup/transcript_view?hit_id=HIT000053961&status=xml
Gene annotation XML HIX ID http://h-invitational.jp/hinv/spsoup/locus_view?hix_id=HIX0005064&status=xml

Example queries

Data Format Query Example
Gene annotation (transcript) HTML HIT ID HIT000053961
Gene annotation (transcript) Text HIT ID HIT000053961
Gene annotation (transcript) XML HIT ID HIT000053961
Gene annotation HTML HIX ID HIX0005064
Gene annotation Text HIX ID HIX0005064
Gene annotation XML HIX ID HIX0005064
website/hmdb.html0000644000244100017570000000304411606605743014123 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HMDB

Human Metabolome Database (HMDB)

Information about small molecule metabolites found in the human body. It contains or links three kinds of data: 1) chemical data, 2) clinical data, and 3) molecular biology/biochemistry data.

IDHMDB
Homehttp://www.genpat.uu.se/mtDB
EDAM topicSmall molecules
EDAM topicMetabolites
TaxonHomo sapiens
website/hmtdb.html0000644000244100017570000000273611606605742014315 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HmtDB

Human mitochondrial genomic database (HmtDB)

Human mitochondrial genomic database based on variability studies supporting population genetics and biomedical research.

IDHmtDB
Homehttp://www.hmtdb.uniba.it/
EDAM topicMitochondria
EDAM topicGenomes
TaxonHomo sapiens
website/hogenom.html0000644000244100017570000001355611606605742014655 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HOGENOM

Database of homologous sequences from complete genomes (HOGENOM)

Homologous genes from fully sequenced organisms. It allows selection of sets of homologous genes among species, and visualisation of multiple alignments and phylogenetic trees. It is useful for comparative sequence analysis, phylogeny, molecular evolution studies and to get a view of what is known about a peculiar gene family.

IDHOGENOM
AccDB-0044
Homehttp://pbil.univ-lyon1.fr/databases/hogenom3.html
EDAM topicNucleic acid sequence alignment
EDAM topicGene family or system
EDAM topicPhylogenetics
EDAM topicComparative genomics
EDAM topicPhylogenomics
CategoryPhylogenomic databases
Taxonall

Available data

Data Format Query Link
Phylogenetic tree {Trees and families} HTML UniProt accession http://pbil.univ-lyon1.fr/cgi-bin/acnuc-ac2tree?query=%s&db=HOGENOM
Sequence data {HOGENOM entry} HTML UniProt accession http://pbil.univ-lyon1.fr/cgi-bin/acnuc-search-ac?query=%s&db=HOGENOM
Sequence data {HOGENOM family} HTML UniProt accession http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?query=%s&db=HOGENOM

Example queries

Data Format Query Example
Phylogenetic tree {Trees and families} HTML UniProt accession Q5ZJV9
Sequence data {HOGENOM entry} HTML UniProt accession Q5ZJV9
Sequence data {HOGENOM family} HTML UniProt accession Q5ZJV9
website/hoinvgen.html0000644000244100017570000000424211606605742015026 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HOINVGEN

Homologous invertebrate genes database (HOINVGEN)

Homologous invertebrate genes. It allows selection of sets of homologous genes among invertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family.

IDHOINVGEN
Homehttp://pbil.univ-lyon1.fr/databases/hoinvgen/HOINVGEN.html
EDAM topicGene family or system
EDAM topicNucleic acid sequence alignment
EDAM topicPhylogenetics
EDAM topicComparative genomics
TaxonMetazoa
website/homeoboxpage.html0000644000244100017570000000253411606605742015670 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HomeoboxPage

HomeoboxPage homeobox gene page

Information relevant to homeobox genes, in particular about classification/evolution.

IDHomeoboxPage
Homehttp://www.biosci.ki.se/groups/tbu/homeo.html
EDAM topicGene family or system
TaxonMetazoa
website/homomint.html0000644000244100017570000000310311606605742015036 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HomoMINT

HomoMINT inferred human protein interaction network

Database for extending protein-protein interactions experimentally verified in models organisms, to the orthologous proteins in Homo sapiens.

IDHomoMINT
Homehttp://mint.bio.uniroma2.it/HomoMINT
EDAM topicProtein-protein interactions
EDAM topicPathways, networks and models
TaxonHomo sapiens
website/homstrad.html0000644000244100017570000000303611606605743015033 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HOMSTRAD

Homologous structure alignment database (HOMSTRAD)

A curated database of annotated, structure-based sequence alignments for homologous protein families, from all known protein structure.

IDHOMSTRAD
Homehttp://tardis.nibio.go.jp/homstrad/
EDAM topicProtein sequence alignment
EDAM topicProtein families
Taxonall
website/hoppsigen.html0000644000244100017570000000252311606605743015206 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Hoppsigen

Homologous processed pseudogenes database (Hoppsigen)

Nucleic database of homologous processed pseudogenes.

IDHoppsigen
Homehttp://pbil.univ-lyon1.fr/databases/hoppsigen.html
EDAM topicGene family or system
Taxonall
website/horde.html0000644000244100017570000000347111606605743014316 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HORDE

Human olfactory receptor data explorer (HORDE)

Database of human Olfactory Receptors (ORs), the largest multigene family in multicellular organisms. Information on the OR proteins, their gene structure and their genomic organization. Also available are OR repertoires of other mammalian species.

IDHORDE
Homehttp://bioportal.weizmann.ac.il/HORDE/
EDAM topicSpecific protein
EDAM topicGene family or system
EDAM topicGene structure
TaxonHomo sapiens
website/hotsprint.html0000644000244100017570000000300311606605743015236 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HotSprint

Computational Hot Spots of Protein Interfaces (HotSprint) database

Information about the evolutionary history of the residues on the interface and represents which residues are highly conserved on the interface. In this way, functionally and structurally important residues on the interface can be distinguished.

IDHotSprint
Homehttp://prism.ccbb.ku.edu.tr/hotsprint/
EDAM topicProtein-protein interactions
Taxonall
website/hovergen.html0000644000244100017570000001363711606605742015036 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HOVERGEN

Homologous vertebrate genes database (HOVERGEN)

Homologous vertebrate genes. It allows selection of sets of homologous genes among vertebrate species, and visualisation of multiple alignments and phylogenetic trees. It is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies or more generally, for an overall view of what is known about a peculiar gene family.

IDHOVERGEN
AccDB-0045
Homehttp://pbil.univ-lyon1.fr/databases/hovergen.html
EDAM topicGene family or system
EDAM topicNucleic acid sequence alignment
EDAM topicPhylogenetics
EDAM topicComparative genomics
EDAM topicPhylogenomics
CategoryPhylogenomic databases
TaxonChordata

Available data

Data Format Query Link
Phylogenetic tree {Trees and families} HTML UniProt accession http://pbil.univ-lyon1.fr/cgi-bin/acnuc-ac2tree?query=%s&db=HOVERGEN
Sequence record full {HOVERGEN entry} HTML UniProt accession http://pbil.univ-lyon1.fr/cgi-bin/acnuc-search-ac?query=%s&db=HOVERGEN
Gene annotation {HOVERGEN family} HTML UniProt accession http://pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?query=%s&db=HOVERGEN

Example queries

Data Format Query Example
Phylogenetic tree {Trees and families} HTML UniProt accession Q5ZJV9
Sequence record full {HOVERGEN entry} HTML UniProt accession Q5ZJV9
Gene annotation {HOVERGEN family} HTML UniProt accession Q5ZJV9
website/hpa.html0000644000244100017570000001365311606605743013770 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HPA

Human protein atlas (HPA) of expression and localization of proteins

Expression and localization of proteins in a large variety of normal human tissues, cancer cells and cell lines with the aid of immunohistochemistry (IHC) images and immunofluorescence (IF) confocal microscopy images.

IDHPA
AccDB-0046
Homehttp://www.proteinatlas.org/
EDAM topicGene expression and regulation
EDAM topicCancer
EDAM topicElectron microscopy
EDAM topicOrganism
EDAM topicProtein targeting and localization
EDAM topicProteome
EDAM topicHuman
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation (functional) HTML Gene ID (Ensembl) http://www.proteinatlas.org/gene_info.php?ensembl_gene_id=%s
Gene annotation (functional) HTML Gene name (HGNC) http://www.proteinatlas.org/gene_info.php?hugo_id=%s
Gene annotation (functional) HTML HPA antibody id http://www.proteinatlas.org/gene_info.php?antibody_id=%s

Example queries

Data Format Query Example
Gene annotation (functional) HTML Gene ID (Ensembl) ENSG00000196371
Gene annotation (functional) HTML Gene name (HGNC) FUT4
Gene annotation (functional) HTML HPA antibody id CAB000014
website/hs3d.html0000644000244100017570000000322311606605743014051 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HS3D

Homo sapiens splice sites dataset (HS3D)

Homo Sapiens Exon, Intron and Splice regions extracted from GenBank.

IDHS3D
Homehttp://www.sci.unisannio.it/docenti/rampone/
EDAM topicGene structure
EDAM topicNucleic acid functional sites
EDAM topicRNA splicing
TaxonHomo sapiens
website/hssp.html0000644000244100017570000000556211606605743014175 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HSSP

Homology-derived secondary structure of proteins database (HSSP)

Homology-derived secondary structure of proteins database.

IDHSSP
AccDB-0048
Homehttp://swift.cmbi.kun.nl/swift/hssp/
EDAM topicProtein secondary structure
Category3D structure databases
Taxonall

Available data

Data Format Query Link
Protein features (secondary structure) {HSSP report} HTML PDB ID http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=dssp&id=%s

Example queries

Data Format Query Example
Protein features (secondary structure) {HSSP report} HTML PDB ID 2hva
website/htpselex.html0000644000244100017570000000264511606605743015053 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HTPSELEX

HTPSELEX database of high-throughput SELEX libraries for transcription factor binding sites

Sets of invitro selected transcription factor binding site sequences obtained with SELEX and high-throughput SELEX method.

IDHTPSELEX
Homehttp://www.isrec.isb-sib.ch/htpselex/
EDAM topicTranscription factor and binding site
Taxonall
website/huge.html0000644000244100017570000000612011606605743014137 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HUGE

Human unidentified gene-encoded large proteins database (HUGE)

Database of the human cDNA project at the Kazusa DNA Research Institute, covering various sets of large human proteins of hitherto unidentified functions.

IDHUGE
AccDB-0049
Homehttp://www.kazusa.or.jp/huge/
EDAM topicmRNA, EST or cDNA
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Protein report {HUGE entry} HTML mFLJ/mKIAA number http://www.kazusa.or.jp/tech-cgi/view_direct.cgi?id=%s

Example queries

Data Format Query Example
Protein report {HUGE entry} HTML mFLJ/mKIAA number KIAA0001
website/humanmtdb.html0000644000244100017570000000306511606605743015173 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HumanMtDB

Human mitochondrial genome database (HumanMtDB)

Human mitochondrial genome database.

IDHumanMtDB
Homehttp://www.genpat.uu.se/mtDB
EDAM topicMitochondria
EDAM topicHuman
EDAM topicGenomes
TaxonHomo sapiens
website/humanpax6.html0000644000244100017570000000240111606605743015114 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HumanPAX6

Human PAX6 allelic variant database (HumanPAX6)

Human PAX6 allelic variant database.

IDHumanPAX6
Homehttp://pax6.hgu.mrc.ac.uk/
EDAM topicGenotype and phenotype
TaxonHomo sapiens
website/husida.html0000644000244100017570000000266411606605743014475 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HuSiDa

Human siRNA database

Depository for both sequences of published functional siRNA molecules targeting human genes and important technical details of the corresponding gene silencing experiments.

IDHuSiDa
Homehttp://itb.biologie.hu-berlin.de/~nebulus/sirna/index.htm
EDAM topicsiRNA
TaxonHomo sapiens
website/hvrbase++.html0000644000244100017570000000234711606605743014776 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HvrBase++

HvrBase++ phylogenetic database for primate species

Hypervariable regions database.

IDHvrBase++
Homehttp://www.hvrbase.org
EDAM topicPhylogenetics
TaxonPrimates
website/hypercat.html0000644000244100017570000000333511606605743015033 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HyperCAT

Bacillus cereus group Typing Database (HyperCAT)

Typing databases for the Bacillus cereus group of bacteria, which includes B. cereus, B. anthracis, B. thuringiensis, B. mycoides, B. pseudomycoides, and B. weihenstephanensis. The databases contain MultiLocus Sequence Typing (MLST), MultiLocus Enzyme Electrophoresis (MLEE), and Amplified Fragment Length Polymorphism (AFLP) phylogenetic data.

IDHyperCAT
Homehttp://mlstoslo.uio.no/
EDAM topicMutation and polymorphism
EDAM topicGenotype and phenotype
TaxonBacillus cereus
website/hypercldb.html0000644000244100017570000000277711606605743015201 0ustar jisonindustry Bioinformatics Data Resource Catalogue

HyperCLDB

HyperCLDB cell line database

Cell culture availability extracted from the cell line database of the Interlab Project. HyperCLDB includes links to records of OMIM, the Online Mendelian Inheritance in Man Catalogue and PubMed database of bibliographic biomedical references.

IDHyperCLDB
Homehttp://bioinformatics.istge.it/cldb/indexes.html
EDAM topicCell lines and culture
TaxonHomo sapiens
website/iarctp53.html0000644000244100017570000000251411606605743014644 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IARCTP53

IARC TP53 mutation database

All TP53 gene variations identified in human populations and tumor samples. Data are compiled from the peer-reviewed literature and from generalist databases.

IDIARCTP53
Homehttp://www-p53.iarc.fr/
EDAM topicCancer
TaxonHomo sapiens
website/icd.html0000644000244100017570000000303311606605744013747 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ICD

International Classification of Diseases

The ICD is the international standard diagnostic classification of diseases for all general epidemiological, many health management purposes and clinical use. It is used to classify diseases and other health problems recorded on many types of health and vital records including death certificates and health records.

IDICD
Homehttp://www.who.int/classifications/icd/en/
EDAM topicDisease
Taxonall
website/icds.html0000644000244100017570000000237511606605744014142 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ICDS

Interrupted coding sequences (ICDS)

Interrupted coding sequences.

IDICDS
Homehttp://www-bio3d-igbmc.u-strasbg.fr/ICDS/
EDAM topicGene structure
Taxonall
website/idbases-btkbase.html0000644000244100017570000000604511606605743016240 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IDbases-BTKbase

BTKbase database of X-linked agammaglobulinemia (XLA) mutations

Database of defects in the Bruton tyrosine kinase (BTK) gene causing agammaglobulinemia. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement.

IDIDbases-BTKbase
IDaltBTKbase
Homehttp://bioinf.uta.fi/BTKbase/
EDAM topicHuman disease
TaxonHomo sapiens

Available data

Data Format Query Link
Sequence variation annotation {BTKbase patient entry} Text Sequence accession (nucleic acid) http://bioinf.uta.fi/cgi-bin/fetch_idbase.cgi?gene=BTK&ac=%s&view=full

Example queries

Data Format Query Example
Sequence variation annotation {BTKbase patient entry} Text Sequence accession (nucleic acid) A0625
website/idbases.html0000644000244100017570000000601011606605743014617 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IDbases

IDbases immunodeficiency mutation databases

Locus-specific databases for immunodeficiency-causing mutations.

IDIDbases
Homehttp://bioinf.uta.fi/base_root/
EDAM topicHuman disease
TaxonHomo sapiens

Available data

Data Format Query Link
Sequence variation annotation {IDbase patient entry} Text Gene identifier; Sequence accession (nucleic acid) http://bioinf.uta.fi/cgi-bin/fetch_idbase.cgi?gene=%s1&ac=%s2&view=full

Example queries

Data Format Query Example
Sequence variation annotation {IDbase patient entry} Text Gene identifier; Sequence accession (nucleic acid) BTK;A0625
website/imgt_3dstructure-db.html0000644000244100017570000000310611606605744017103 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IMGT_3Dstructure-DB

IMGT 3D structure database for immunoglobulins (IG), T cell receptors (TR), MHC and RPI

IMGT 3D structure database for immunoglobulins (IG), T cell receptors (TR), MHC and RPI.

IDIMGT_3Dstructure-DB
Homehttp://www.imgt.org/3Dstructure-DB/
EDAM topicImmune-related proteins and peptides
EDAM topicProtein tertiary structure
TaxonChordata
website/imgt_gene-db.html0000644000244100017570000000313211606605744015531 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IMGT_GENE-DB

IMGT gene database for immunoglobulins (IG) and T cell recetors (TR)

IMGT gene database for immunoglobulins (IG) and T cell recetors (TR).

IDIMGT_GENE-DB
Homehttp://www.imgt.org/IMGT_GENE-DB/GENElect?livret=0
EDAM topicImmunoinformatics
TaxonChordata

Example queries

Data Format Query Example
website/imgt_hla.html0000644000244100017570000000604711606605743015003 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IMGT_HLA

IMGT database of human MHC

A specialist database for sequences of the human major histocompatibility complex (HLA) and includes the official sequences for the WHO Nomenclature Committee For Factors of the HLA System.

IDIMGT_HLA
Homehttp://www.ebi.ac.uk/imgt/hla/
EDAM topicImmune-related proteins and peptides
EDAM topicNomenclature
TaxonHomo sapiens

Available data

Data Format Query Link
Protein report {IMGT/HLA entry} HTML IMGT/HLA ID http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-id+1fItl1b_a0N+-e+[IMGTHLA:%27%s%27]+-qnum+1+-enum+1

Example queries

Data Format Query Example
Protein report {IMGT/HLA entry} HTML IMGT/HLA ID HLA00236
website/imgt.html0000644000244100017570000000603411606605743014153 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IMGT

The international immunogenetics database (IMGT)

Database for the immunoglobulins (IG), T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF), major histocompatibility complex superfamily (MhcSF) and related proteins of the immune system (RPI) of human and other vertebrate species.

IDIMGT
AccDB-0050
Homehttp://imgt.cines.fr/
EDAM topicImmune-related proteins and peptides
CategoryProtein family/group databases
TaxonChordata

Available data

Data Format Query Link
Sequence record {IMGT/LIGM-DB flat-file} EMBL format IMGT/HLA ID http://www.imgt.org/services/get?id=%s

Example queries

Data Format Query Example
Sequence record {IMGT/LIGM-DB flat-file} EMBL format IMGT/HLA ID AABR03048499
website/imgt_ligm.html0000644000244100017570000000346011606605744015164 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IMGT_LIGM

IMGT nucleotide sequence database for immunoglobulins (IG) and T cell recetors (TR)

IMGT nucleotide sequence database for immunoglobulins (IG) and T cell recetors (TR).

IDIMGT_LIGM
IDaltLIGM-DB
Homehttp://www.imgt.org/IMGTPrimerDB/
EDAM topicImmune-related proteins and peptides
EDAM topicProtein sequences
TaxonChordata

Example queries

Data Format Query Example
website/imgt_primer-db.html0000644000244100017570000000310211606605744016106 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IMGT_PRIMER-DB

IMGT primer database for immunoglobulins (IG) and T cell recetors (TR)

IMGT primer database for immunoglobulins (IG) and T cell recetors (TR).

IDIMGT_PRIMER-DB
Homehttp://www.imgt.org/cgi-bin/IMGTlect.jv?livret=0
EDAM topicImmune-related proteins and peptides
EDAM topicMolecular probes or primers
TaxonChordata
website/index.html0000644000244100017570000005347211600347104014316 0ustar jisonindustry Bioinformatics Data Resource Catalogue

DRCAT Resource Catalogue

Bioinformatics Web-based Data Resources

  1. Introduction
  2. Resource metadata
  3. Example entries
  4. Browse DRCAT

Introduction

What is DRCAT?

DRCAT (the data resource catalogue) collates metadata on bioinformatics Web-based data resources including databases, ontologies, taxonomies and catalogues. A DRCAT entry includes information such as resource identifier(s), name, description and URL. `Query' lines are defined for each resource that describe what type(s) of data are available, in what format, how (by what identifier) the data can be retrieved and from where (URL).

DRCAT was developed to provide more extensive data integration for EMBOSS, but it has many applications beyond EMBOSS. DRCAT entries (including 'Query' lines) are annotated with terms from the EDAM ontology of common bioinformatics concepts.

Download and Status

An "alpha" version is available:

http://sourceforge.net/projects/drcat/files/

It contains a comprehensive set of resourcs that are fully annotated and a starting point for 'Query' line definition. It includes:

The "alpha" version is intended primarily to solicit feedback. DRCAT is being actively developed: contributions and suggestions are welcome. For further information contact Jon Ison (jison@ebi.ac.uk).

Viewing

DRCAT can be viewed in any text editor. It can also be browsed.

License

DRCAT is made available to all without any constraint or license on its use or redistribution other than:

Contacts

All enquiries to Jon Ison (jison@ebi.ac.uk) cc'ing Peter Rice(pmr@ebi.ac.uk) and Matus Kalas (matus.kalas@bccs.uib.no)

Thanks to Peter Rice and Matus Kalas for valuable discussions and contributions.

Mailing lists

Feel free to subscribe to one or both of the mailing lists:

Once subscribed, you can mail the lists:

drcat-developers is for technical discussions between EDAM developers / contributors. drcat-users is for general discussions and announcements. Traffic will be kept to a minimum.


Resource metadata

Comment lines begin with '#' and can appear anywhere.

Resource identifiers

Resources might be cross-referenced from an EMBL or SwissProt entry. Database identifiers and names are taken (where available) from:

Note that SwissProt identifiers are listed in the the file dbxref.

ID

ID        <ID>

Recommended / official unique identifier.

e.g.

ID      EcID

Value of <ID> is a string (no whitespace). A single ID line is given per entry.

IDalt

IDalt     <ID>

An alternative identifier.

e.g.

IDalt   2DBase-Ecoli

Value of <IDalt> is a string (no whitespace). Multiple IDalt lines may be given per entry (one IDalt / line).

Acc

Acc       <Acc>

Accession number of database.

e.g.

Acc     DB-0115

Value of <Acc> is a string (no whitespace).Values are taken from dbxref (if defined). A single Acc line only is given per entry.

Name

Name      <Text>

Verbose name.

e.g.

Name    Structural classification of proteins (SCOP) database

Values are taken from dbxref (if defined) or otherwise are assigned. A single Name line only is given per entry.

Basic metadata

Desc

Desc      <Text>

Description of resource.

e.g.

Desc    The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

Value of Text is any free text (but typically text from resource home page). A single Desc line only is given per entry.

URL

URL       <URL>

URL of resource server.

e.g.

URL     http://scop.mrc-lmb.cam.ac.uk/scop

Value of <URL> is a resolvable URL. A single URL line only is given per entry.

URLlink

URLlink

URL for instructions on how to link to the database.

e.g.

URLlink http://gene3d.biochem.ucl.ac.uk/Gene3D/linking

Value of <URLlink> is a resolvable URL. A single URLlink line only is given per entry.

URLrest

URLrest

URL of documentation on REST-based interface (if available).

e.g.

URLrest http://www.ebi.ac.uk/pride/prideMartWebService.do

Value of <URLrest> is a resolvable URL. A single URLrest line only is given per entry.

URLsoap

URLsoap

URL of documentation on SOAP-based interface (if available).

e.g.

URLsoap http://api.cathdb.info/api/soap/dataservices/wsdl

Value of <URLsoap> is a resolvable URL. Single URLsoap line per entry.

Annotation

Cat

Cat       <Cat>

Database category.

e.g.

Cat     2D gel databases

Values taken from dbxref.txt (if defined).

A single Cat line only is given per entry.

Taxon

Taxon    <tax_id> | <scientific_name>

Annotation of the taxonomic scope of the resource.

e.g.

Taxon   562 | Escherichia coli

Values of <tax_id> and <scientific_name> are the taxonomic ID and scientific name of an organism taken from the NCBI Taxonomy. Multiple Taxon lines may be given.

EDAMdat

EDAMdat   <EDAM_id> | <EDAM_term>

EDAM annotation of the data returned by a query.

e.g.

EDAMdat 0001554 | SCOP node

Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Data" branch. Multiple EDAMdat lines may be given.

EDAMfmt

EDAMfmt   <EDAM_id> | <EDAM_term>

EDAM annotation of the format of data returned by a query.

e.g.

EDAMfmt 0001929 | FASTA format

Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Format" branch. Multiple EDAMfmt lines may be given.

EDAMid

EDAMid    <EDAM_id> | <EDAM_term>

EDAM annotation of the data identifier used as a query.

e.g.

EDAMid  0001033 | Gene ID (Ensembl)

Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Identifier" branch. Multiple EDAMid lines may be given.

EDAMtpc

EDAMtpc   <EDAM_id> | <EDAM_term>

EDAM annotation of the resource itself.

e.g.

EDAMtpc 0000147 | Protein-protein interactions

Values of <EDAM_id> and <EDAM_term> are a unique identifier and term name for a concept from the EDAM ontology "Topic" branch. Multiple EDAMtpc lines may be given.

Cross-references

Xref

Xref      <token> | <ID1;ID2>

Nature of cross-reference from a SwissProt or EMBL database entry.

e.g.

Xref    SP_explicit | UniProt accession

Where <token> is one of:

ID1, ID2 etc. give the type of identifier(s), i.e. term names from the EDAM "Identifier" branch, used in the cross-reference, e.g.

SP_explicit | EC number;OrganismID

Multiple Xref lines may be given. UniProt/SwissProt xrefs are described in detail in the UniProt userman.htm file.

SP_explicit

SP_explicit links are generally of the form:

DR database_name; primary_id; secondary_id

primary_id is usually an accession and secondary_id usually complements the first, e.g. entry name or version number.

SP_implicit

SP_implicit links are to databases that (typically) lack their own accession number scheme, but may be cross-referenced by 1) SP primary accession number or 2) some other identifier used by SP, e.g. gene name in the GN line. In both cases no extra DR line is present.

SP_CC

SP_CC links are to databases that (typically) are accessed via one URL, not by individual accessions.

SP_FT

SP_FTlinks are provided where the link concerns a feature.

SP_lit

SP_lit links the RX line provides the Medline or PubMed identifier.

Other

Other links include e.g. taxonomy identifier (Tax_id) that uniquely identifies an organism in NCBI taxonomy classification, and Enzyme EC numbers which are found in SP description (DE) lines.

Queryable data

Query

Query     <Data_type> {<comment>} | <Data_format> {<comment>} | <Data_identifier> {<comment>} | <URL>

Specification of data resource query.

e.g.

Query   SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Query   Fungi annotation | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2
Query   Fungi annotation (anamorph) | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2__(anamorph)

<Data_type>, <Data_format>, <Data_identifier> are term names from the EDAM ontology ("Data", "Format" and "Identifier" branches respectively). For each one, a corresponding EDAMdat, EDAMfmt or EDAMid annotation is given:

Query lines may employ two or more data identifiers. In such cases identifiers are separated by a ';' and the URL should use %s1, %s2, %s3 etc (for first, second, third identifiers etc.). In the rare cases where the same ID is used twice in the URL then (e.g.) %s1 %s1 is used (for two uses of the first id) and %s2, %s3 etc (for second, third identifiers).

Multiple Query lines may be given. Note an optional comment may be given after <Datatype>, <Data_format> or <Data_identifier> and can be used for a provider-supplied names or comments for that type, format or identifier.

Example

Example   <Data_identifier> | <Example>

Example identifiers used in Query lines.

e.g.

Example Genus name | Aspergillus
Example Species name | giganteus

<Data_identifier> is a term name from the EDAM ontology ("Identifier" branch) as used in one or more Query lines. <Example> is valid value of the identifier for use in a query. Multiple Example lines may be given.

Example entries

ID      AFTOL
Name    Assembling the Fungal Tree of Life (AFTOL) database
Desc    Fungal structural and biochemical database.
URL     http://www.aftol.org/index.php
Cat     Not available
Taxon   4751 | Fungi
EDAMtpc 0000782 | Fungal
EDAMid  0001045 | Species name
EDAMid  0001870 | Genus name
EDAMdat 0002395 | Fungi annotation
EDAMdat 0002396 | Fungi annotation (anamorph)
EDAMfmt 0002331 | HTML
Xref    SP_FT | None
Query   Fungi annotation | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2
Query   Fungi annotation (anamorph) | HTML | Genus name;Species name | http://aftol.umn.edu/species/%s1_%s2__(anamorph)
Example Genus name | Aspergillus
Example Species name | giganteus

ID      ANU-2DPAGE
Acc     DB-0002
Name    Australian National University 2-DE database (ANU-2DPAGE)
Desc    2-DE PAGE database.
URL     http://semele.anu.edu.au
Cat     2D gel databases
Taxon   1 | all
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMid  0003021 | UniProt accession
EDAMdat 0002364 | Experiment annotation (2D PAGE)
EDAMfmt 0002331 | HTML
Xref    SP_explicit | UniProt accession
Query   Experiment annotation (2D PAGE) | HTML | UniProt accession | http://semele.anu.edu.au/cgi-bin/get-2d-entry?%s
Example UniProt accession | P02930
Example UniProt accession | Q9SIB9

ID      SCOP
Name    Structural classification of proteins (SCOP) database
Desc    The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.
URL     http://scop.mrc-lmb.cam.ac.uk/scop
Taxon   1 | all
EDAMtpc 0000736 | Protein domains
EDAMdat 0001554 | SCOP node
EDAMdat 0002093 | Data reference
EDAMid  0001042 | SCOP sunid
EDAMid  0001127 | PDB ID
EDAMid  0000842 | Identifier
EDAMfmt 0002331 | HTML
Query   SCOP node | HTML | SCOP sunid | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Query   Data reference {PDB Entry search} | HTML | PDB ID | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?PDB=%s
Query   Data reference | HTML | Identifier {Keyword} | http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s
Example SCOP sunid | 47718
Example PDB ID | 1djh
Example Identifier {Keyword} | immunoglobulin

ID      ECO2DBASE
IDalt   2DBase-Ecoli
IDalt   EC-2D-GEL
Acc     DB-0115
Name    2D-PAGE database of Escherichia coli
Desc    This Database currently contains 12 gels consisting of 1185 protein spots information in which 723 proteins where identified and annotated. Individual protein spots in the existing gels can be displayed, queried, analysed and compared in a tabular format based on varios functional categories enabling quick and subsequent analysis.
URL     http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi
Cat     2D gel databases
Taxon   562 | Escherichia coli
EDAMtpc 0000133 | Two-dimensional gel electrophoresis
EDAMdat 0002364 | Experiment annotation (2D PAGE)
EDAMid  0003021 | UniProt accession
EDAMfmt 0002331 | HTML
Xref    SP_explicit | None
Query   Experiment annotation (2D PAGE) {ECO2DBASE entry} | HTML | UniProt accession | http://2dbase.techfak.uni-bielefeld.de/cgi-bin/2d/2d.cgi?%s
Example UniProt accession | P02930
Example UniProt accession | P52697

ID      Ensembl
Acc     DB-0023
Name    Ensembl eukaryotic genome annotation project
Desc    Genome databases for vertebrates and other eukaryotic species.
URL     http://www.ensembl.org/
Cat     Genome annotation databases
Taxon   33208 | Metazoa
EDAMtpc 0000643 | Genomes
EDAMtpc 0002818 | Eukaryote
EDAMtpc 0000643 | Genomes
EDAMdat 0000849 | Sequence record
EDAMdat 0000916 | Gene annotation
EDAMid  0001033 | Gene ID (Ensembl)
EDAMid  0002725 | Transcript ID (Ensembl)
EDAMfmt 0001929 | FASTA format
EDAMfmt 0002331 | HTML
Xref    SP_explicit | None
Xref    SP_FT | None
Query   Gene annotation | HTML | Gene ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Summary?g=%s
Query   Sequence record | FASTA format | Gene ID (Ensembl);Transcript ID (Ensembl) | http://www.ensembl.org/Homo_sapiens/Gene/Export?db=core;g=%s1;output=fasta;r=13:31787617-31871809;strand=feature;t=%s2;time=1244110856.85314;st=cdna;st=coding;st=peptide;st=utr5;st=utr3;st=exons;st=introns;genomic=unmasked;_format=Text
Example Gene ID (Ensembl);Transcript ID (Ensembl) | ENSG00000139618;ENST00000380152
website/infevers.html0000644000244100017570000000253211606605744015034 0ustar jisonindustry Bioinformatics Data Resource Catalogue

INFEVERS

Familial mediterranean fever (FMF) mutations database (INFEVERS)

The registry of familial mediterranean fever (FMF) and hereditary auto-inflammatory disorders mutations.

IDINFEVERS
Homehttp://fmf.igh.cnrs.fr/infevers
EDAM topicHuman disease
TaxonHomo sapiens
website/inparanoid.html0000644000244100017570000000245711606605744015345 0ustar jisonindustry Bioinformatics Data Resource Catalogue

InParanoid

Inparanoid orthologs database

Eukaryotic orthholog groups.

IDInParanoid
AccDB-0146
Homehttp://InParanoid.sbc.su.se
EDAM topicNucleic acid classification
Taxonall
website/intact.html0000644000244100017570000000560211606605744014476 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IntAct

IntAct protein interaction database and analysis system

Protein interaction database and analysis system.

IDIntAct
AccDB-0051
Homehttp://www.ebi.ac.uk/intact/
EDAM topicProtein-protein interactions
CategoryProtein-protein interaction databases
Taxonall

Available data

Data Format Query Link
Protein interaction report {IntAct entry} HTML UniProt accession http://www.ebi.ac.uk/intact/binary-search/faces/search.xhtml?query=%s

Example queries

Data Format Query Example
Protein interaction report {IntAct entry} HTML UniProt accession P32234
website/integr8.html0000644000244100017570000000342011606605744014570 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Integr8

Integr8 genome and proteome database

Integrated information about deciphered genomes and their corresponding proteomes. Available data includes DNA sequences (from databases including the EMBL Nucleotide Sequence Database, Genome Reviews, and Ensembl); protein sequences (from databases including the UniProt Knowledgebase and IPI); statistical genome and proteome analysis (performed using InterPro, CluSTr, and GOA); and information about orthology, paralogy, and synteny.

IDIntegr8
Homehttp://www.ebi.ac.uk/integr8/
EDAM topicProteome
EDAM topicGenomes
Taxonall
website/integrall.html0000644000244100017570000000240011606605744015166 0ustar jisonindustry Bioinformatics Data Resource Catalogue

INTEGRALL

INTEGRALL integron integrases and gene cassettes

Database of DNA sequences and genetic arrangements.

IDINTEGRALL
Homehttp://integrall.bio.ua.pt/
EDAM topicGene structure
Taxonall
website/intenz.html0000644000244100017570000000306311606605744014522 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IntEnz

Integrated relational enzyme database (IntEnz)

IntEnz contains the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB) on the nomenclature and classification of enzyme-catalysed reactions.

IDIntEnz
Homehttp://www.ebi.ac.uk/intenz
EDAM topicEnzymes
EDAM topicNomenclature
Taxonall
website/interpro.html0000644000244100017570000000637011606605744015061 0ustar jisonindustry Bioinformatics Data Resource Catalogue

InterPro

InterPro integrated database of protein families, domains, regions, repeats and functional sites

Protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences.

IDInterPro
AccDB-0052
Homehttp://www.ebi.ac.uk/interpro/
EDAM topicProtein families
EDAM topicProtein functional sites
EDAM topicRepeat sequence
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Protein signature HTML InterPro accession http://www.ebi.ac.uk/interpro/IEntry?ac=%s

Example queries

Data Format Query Example
Protein signature HTML InterPro accession IPR000059
website/ipd-estdab.html0000644000244100017570000000317011606605744015226 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IPD-ESTDAB

Immuno polymorphism EST database (IPD-ESTDAB)

Searchable database of tumour cell lines.

IDIPD-ESTDAB
Homehttp://www.ebi.ac.uk/ipd/estdab/index.html
EDAM topicCancer
EDAM topicMutation and polymorphism
EDAM topicmRNA, EST or cDNA
TaxonChordata
website/ipd-hpa.html0000644000244100017570000000247711606605744014545 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IPD-HPA

Immuno polymorphism human platelet antigens database (IPD-HPA)

Information on human platelet antigens (HPA).

IDIPD-HPA
Homehttp://www.ebi.ac.uk/ipd/hpa/index.html
EDAM topicMutation and polymorphism
TaxonHomo sapiens
website/ipd.html0000644000244100017570000000265411606605744013774 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IPD

Immuno polymorphism database (IPD)

Database for the study of polymorphism in genes of the immune system.

IDIPD
Homehttp://www.ebi.ac.uk/ipd/
EDAM topicMutation and polymorphism
EDAM topicImmunoinformatics
TaxonChordata
website/ipd-kir.html0000644000244100017570000000330711606605744014553 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IPD-KIR

Immuno polymorphism killer-cell Immunoglobulin-like receptor database (IPD-KIR)

Sequences of human Killer-cell Immunoglobulin-like Receptors (KIR).

IDIPD-KIR
Homehttp://www.ebi.ac.uk/ipd/kir/index.html
EDAM topicMutation and polymorphism
EDAM topicImmune-related proteins and peptides
EDAM topicProtein sequences
TaxonHomo sapiens
website/ipd-mhc.html0000644000244100017570000000250411606605744014533 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IPD-MHC

Immuno polymorphism major histocompatibility complex database (IPD-MHC)

Sequences of the the major histocompatibility complex in a number of species.

IDIPD-MHC
Homehttp://www.ebi.ac.uk/ipd/mhc
EDAM topicMutation and polymorphism
TaxonChordata
website/ipi.html0000644000244100017570000000620011606605744013770 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IPI

International protein index (IPI)

Provides a top level guide to the main databases that describe the proteomes of higher eukaryotic organisms. IPI effectively maintains a database of cross references between the primary data sources, provides minimally redundant yet maximally complete sets of proteins for featured species (one sequence per transcript) and maintains stable identifiers (with incremental versioning) to allow the tracking of sequences in IPI between IPI releases.

IDIPI
AccDB-0132
Homehttp://www.ebi.ac.uk/IPI
EDAM topicProteome
CategorySequence databases
Taxonall

Available data

Data Format Query Link
Sequence record {IPI entry} HTML IPI protein ID http://www.ebi.ac.uk/cgi-bin/dbfetch?db=IPI&id=%s

Example queries

Data Format Query Example
Sequence record {IPI entry} HTML IPI protein ID IPI00177866
website/irefindex.html0000644000244100017570000000311711606605744015170 0ustar jisonindustry Bioinformatics Data Resource Catalogue

iRefIndex

iRefIndex index of consolidated protein interactions

An index of protein interactions available in a number of primary interaction databases including BIND, BioGRID, CORUM, DIP, HPRD, IntAct, MINT, MPact, MPPI and OPHID. This index includes multiple interaction types including physical and genetic (mapped to their corresponding protein products) as determined by a multitude of methods.

IDiRefIndex
Homehttp://irefindex.uio.no/wiki/iRefIndex
EDAM topicProtein-protein interactions
Taxonall
website/iresdb.html0000644000244100017570000000271511606605744014466 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IRESdb

Internal ribosome entry site database (IRESdb)

Internal ribosome entry sites.

IDIRESdb
Homehttp://ifr31w3.toulouse.inserm.fr/IRESdatabase/
EDAM topicNucleic acid functional sites
EDAM topicRibosomes
Taxonall
website/iresite.html0000644000244100017570000000322311606605744014655 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IRESite

Database of experimentally verified IRES structures (IRESite)

Information about the experimentally studied IRES (Internal Ribosome Entry Site) segments. IRES regions are known to attract eukaryotic ribosomal translation initiation complex and thus promote translation initiation independently of the presence of the commonly utilized 5'-terminal 7mG cap structure.

IDIRESite
Homehttp://www.iresite.org
EDAM topicRibosomes
EDAM topicTranscription
Taxonall
website/isfinder.html0000644000244100017570000000321611606605745015017 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ISfinder

Insertion sequence elements database (ISfinder)

A database of insertion sequences isolated from eubacteria and archae. It is organised into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequences.

IDISfinder
Homehttp://www-is.biotoul.fr
EDAM topicMobile genetic elements
Taxonall

Example queries

Data Format Query Example
website/isola.html0000644000244100017570000000304211606605745014320 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ISOLA

Italian Solanaceae genome resource (ISOLA)

Solanaceae genome resource.

IDISOLA
Homehttp://biosrv.cab.unina.it/isola
EDAM topicPlant
EDAM topicGenomes
EDAM topicPlant
TaxonSolanaceae
website/its2.html0000644000244100017570000000334611606605745014101 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ITS2

Internal transcribed spacer 2 sequences (ITS2)

Optimal global pairwise alignments from about 200,000 internal transcribed spacer 2 (ITS2) sequences - all against all - have been generated in order to model ITS2 secondary structures based on sequences with known structures.

IDITS2
Homehttp://its2.bioapps.biozentrum.uni-wuerzburg.de/cgi-bin/index.pl?about
EDAM topicNucleic acid sequence alignment
EDAM topicRNA structure and alignment
Taxonall
website/ittaca.html0000644000244100017570000000336611606605745014467 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ITTACA

Integrated tumor transcriptome array and clinical data analysis (ITTACA)

Database created for Integrated Tumor Transcriptome Array and Clinical data Analysis. ITTACA centralizes public datasets containing both gene expression and clinical data and currently focuses on the types of cancer that are of particular interest to the Institut Curie: breast carcinoma, bladder carcinoma, and uveal melanoma.

IDITTACA
Homehttp://bioinfo-out.curie.fr/ittaca/
EDAM topicGene expression and regulation
EDAM topicCancer
TaxonHomo sapiens
website/iupac.html0000644000244100017570000000230311606605745014311 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IUPAC

IUPAC nomenclature database

Recommendations on Organic & Biochemical Nomenclature, Symbols & Terminology etc.

IDIUPAC
Homehttp://www.chem.qmul.ac.uk/iupac/
EDAM topicNomenclature
Taxon
website/iuphar-db.html0000644000244100017570000000273611606605745015075 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IUPHAR-DB

IUPHAR database

Official database of the IUPHAR Committee on Receptor Nomenclature and Drug Classification, incorporating the IUPHAR Database of G Protein-Coupled Receptors and the IUPHAR Database of Voltage-Gated and Ligand-Gated Ion Channels.

IDIUPHAR-DB
Homehttp://www.iuphar-db.org
EDAM topicDrugs and targets
EDAM topicNomenclature
Taxon
website/ixdb.html0000644000244100017570000000240511606605745014141 0ustar jisonindustry Bioinformatics Data Resource Catalogue

IXDB

Integrated X chromosome database (IXDB)

Integrated X chromosome database.

IDIXDB
Homehttp://ixdb.mpimg-berlin-dahlem.mpg.de
EDAM topicChromosomes
TaxonHomo sapiens
website/jail.html0000644000244100017570000000305211606605745014131 0ustar jisonindustry Bioinformatics Data Resource Catalogue

JAIL

JAIL structure-based interface library for macromolecules

JAIL classifies not only the interfaces between domain architectures but also those between protein chains and those between proteins and nucleic acids.

IDJAIL
Homehttp://bioinformatics.charite.de/jail/
EDAM topicProtein interactions
EDAM topicStructure
Taxonall
website/jaspar.html0000644000244100017570000000272011606605745014473 0ustar jisonindustry Bioinformatics Data Resource Catalogue

JASPAR

JASPAR eukaryotic transcription factor binding profiles

High-quality transcription factor binding profile database.

IDJASPAR
Homehttp://jaspar.cgb.ki.se/
EDAM topicTranscription factor and binding site
EDAM topicSequence profiles and HMMs
TaxonEukaryota
website/jcm.html0000644000244100017570000000305411606605745013765 0ustar jisonindustry Bioinformatics Data Resource Catalogue

JCM

Japan collection of microorganisms

Japan collection of microorganisms.

IDJCM
Homehttp://www.jcm.riken.go.jp/JCM/catalogue.shtml
EDAM topicTaxonomy
CategoryNot available
TaxonBacteria

Example queries

Data Format Query Example
website/jenalib.html0000644000244100017570000000304411606605745014617 0ustar jisonindustry Bioinformatics Data Resource Catalogue

JenaLib

Jena library of biological macromolecules (JenaLib)

Information on three-dimensional biopolymer structures with an emphasis on visualization and analysis. JenaLib provides access to all structure entries deposited at the Protein Data Bank (PDB) or at the Nucleic Acid Database (NDB). In addition, basic information on the architecture of biopolymer structures is available.

IDJenaLib
Homehttp://www.fli-leibniz.de/IMAGE.html
EDAM topicStructure
Taxonall
website/jpgv.html0000644000244100017570000000234511606605745014164 0ustar jisonindustry Bioinformatics Data Resource Catalogue

JPGV

Jena prokaryotic genome viewer (JPGV)

Visualization and analysis of prokaryotic genomes.

IDJPGV
Homehttp://jpgv.fli-leibniz.de
EDAM topicGenomes
TaxonBacteria
website/jws.html0000644000244100017570000000300111606605745014007 0ustar jisonindustry Bioinformatics Data Resource Catalogue

JWS

JWS Online

JWS Online aims to provide a service to the Systems Biology community by 1) giving access to a database of curated models of biological systems, and 2) allowing the users to run these models in a web browser via an easy to use interface, and 3) helping in reviewing of manuscripts containing kinetic models.

IDJWS
Homehttp://jjj.biochem.sun.ac.za/index.html
EDAM topicPathways, networks and models
Taxonall
website/karyotypedb.html0000644000244100017570000000307511606605745015554 0ustar jisonindustry Bioinformatics Data Resource Catalogue

KaryotypeDB

Karyotype features from different animals and plants

Karyotype and chromosome information like chromosome number, length, karyotype features, idiograms, physical localizations of DNA sequences by fluorescence in situ hybridizion (FISH), and cell material for metaphase chromosomes and polytene chromosomes from different animal and plant species together with literature references and links.

IDKaryotypeDB
Homehttp://www.nenno.it/karyotypedb/
EDAM topicChromosomes
TaxonEukaryota
website/kdd.html0000644000244100017570000000251211606605745013754 0ustar jisonindustry Bioinformatics Data Resource Catalogue

KDD

Kidney development database

Data from a large number of developmental studies that have a bearing on the study of kidney development.

IDKDD
Homehttp://golgi.ana.ed.ac.uk/kidhome.html
EDAM topicCell cycle and development
TaxonChordata
website/kegg.html0000644000244100017570000001200611606605745014126 0ustar jisonindustry Bioinformatics Data Resource Catalogue

KEGG

Kyoto encyclopedia of genes and genomes (KEGG)

Encyclopedia of genes and genomes.

IDKEGG
AccDB-0053
Homehttp://www.genome.jp/kegg/
EDAM topicGenomes
EDAM topicGene family or system
EDAM topicGenomics
CategoryGenome annotation databases
Taxonall

Available data

Data Format Query Link
Pathway or network report HTML Pathway ID (KEGG) http://www.kegg.jp/pathway/%s
Hierarchy annotation {Brite hierarchy} HTML Biological model accession {Brite hierarchy ID} http://www.kegg.jp/brite/%s
Metadata and annotation {KEGG entry} HTML KEGG object identifier http://www.kegg.jp/dbget-bin/www_bget?%s

Example queries

Data Format Query Example
Metadata and annotation {KEGG entry} HTML KEGG object identifier tpv:TP04_0437
Pathway or network report HTML Pathway ID (KEGG) map00010
Hierarchy annotation {Brite hierarchy} HTML Biological model accession {Brite hierarchy ID} ko00001
website/kinmutbase.html0000644000244100017570000000252411606605745015357 0ustar jisonindustry Bioinformatics Data Resource Catalogue

KinMutBase

KinMutBase registry of disease-causing mutations in protein kinase domains database

Disease-causing mutations in protein kinase domains.

IDKinMutBase
Homehttp://www.uta.fi/imt/bioinfo/KinMutBase/
EDAM topicCancer
TaxonHomo sapiens
website/kinomer.html0000644000244100017570000000331411606605745014657 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Kinomer

Kinomer database

A multilevel HMM library that models these protein kinase groups. It allows accurate identification of protein kinases and classification to the appropriate kinase group.

IDKinomer
Homehttp://www.compbio.dundee.ac.uk/kinomer
EDAM topicProtein functional sites
EDAM topicSequence motifs
EDAM topicSpecific protein
Taxonall
website/knottin.html0000644000244100017570000000314011606605745014676 0ustar jisonindustry Bioinformatics Data Resource Catalogue

KNOTTIN

KNOTTIN database

Database of knottins; intriguing miniproteins with strong potential in drug design.

IDKNOTTIN
Homehttp://knottin.cbs.cnrs.fr
EDAM topicPharmacoinformatics
EDAM topicProtein tertiary structure
EDAM topicSpecific protein
TaxonHomo sapiens
website/l1base.html0000644000244100017570000000276211606605745014370 0ustar jisonindustry Bioinformatics Data Resource Catalogue

L1Base

LINE-1 human and rodent

Putatively active LINE-1 (L1) insertions residing in human and rodent genomes: a) intact in the two ORFs, full length L1s (FLI-L1s) and b) L1s with intact ORF2 but disrupted ORF1 (ORF2-L1s). In addition, due to their regulatory potential, the full length (>6000bp) non-intact L1s (FLnI-L1s) were also included.

IDL1Base
Homehttp://line1.molgen.mpg.de
EDAM topicMobile genetic elements
TaxonEutheria
website/leger.html0000644000244100017570000000405411606605745014313 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LEGER

LEGER genome database for Listeria research

LEGER links requirements of listerial research projects with knowledge derived from functional genome studies. LEGER provides information on gene functions, protein expression levels, subcellular localization of proteins and the biological meaning of genes and proteins based on KEGG, InterPro and Gene Ontology.

IDLEGER
Homehttp://leger2.gbf.de/cgi-bin/expLeger.pl
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicGene expression and regulation
EDAM topicProtein targeting and localization
TaxonListeria
website/legiolist.html0000644000244100017570000001014611606605746015210 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LegioList

Legionella pneumophila genome database

Legionella pneumophila genome database.

IDLegioList
AccDB-0054
Homehttp://genolist.pasteur.fr/LegioList/
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonLegionella

Available data

Data Format Query Link
Gene annotation HTML Sequence accession (nucleic acid) http://genolist.pasteur.fr/LegioList/genome.cgi?external_query+%s
Gene annotation HTML Gene symbol http://genolist.pasteur.fr/LegioList/genome.cgi?external_query+%s

Example queries

Data Format Query Example
Gene annotation HTML Sequence accession (nucleic acid) LPC_2308
Gene annotation HTML Gene symbol aacA4
website/leproma.html0000644000244100017570000001013311606605746014650 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Leproma

Mycobacterium leprae genome database

Mycobacterium leprae genome database.

IDLeproma
AccDB-0055
Homehttp://genolist.pasteur.fr/Leproma/
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonMycobacterium leprae

Available data

Data Format Query Link
Gene annotation HTML Sequence accession (nucleic acid) http://genolist.pasteur.fr/Leproma/genome.cgi?external_query+%s
Gene annotation HTML Gene symbol http://genolist.pasteur.fr/Leproma/genome.cgi?external_query+%s

Example queries

Data Format Query Example
Gene annotation HTML Sequence accession (nucleic acid) ML0981
Gene annotation HTML Gene symbol 35kd_ag
website/lgicdb.html0000644000244100017570000001035411606605746014442 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LGICdb

Ligand-gated ion channel database (LGICdb)

Nucleic and proteic sequences of the subunits. Multiple sequence alignments can be generated, and some phylogenetic studies of the superfamilies are provided. Finally, the atomic coordinates of subunits, or portion of subunits, are provided when available.

IDLGICdb
Homehttp://www.ebi.ac.uk/compneur-srv/LGICdb/LGICdb.php
EDAM topicSequence alignment
EDAM topicPhylogenetics
Taxonall

Available data

Data Format Query Link
Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} HTML Protein ID (LGICdb) http://www.ebi.ac.uk/compneur-srv/LGICdb/HTML/%s.php
Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} XML Protein ID (LGICdb) http://www.ebi.ac.uk/compneur-srv/LGICdb/XML/%s.xml

Example queries

Data Format Query Example
Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} HTML Protein ID (LGICdb) 5HT3Arano
Protein report (membrane protein) {Ligand-Gated Ion Channel database entry} XML Protein ID (LGICdb) 5HT3Arano
website/ligasite.html0000644000244100017570000000302411606605746015013 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LigAsite

Ligand attachment site database (LigAsite)

A gold-standard dataset of biologically relevant binding sites in protein structures.

IDLigAsite
Homehttp://www.scmbb.ulb.ac.be/Users/benoit/LigASite
EDAM topicProtein functional sites
EDAM topicProtein-ligand interactions
Taxonall
website/lipaseengineering.html0000644000244100017570000000256011606605746016706 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LipaseEngineering

Lipase engineering database

Integrates information on sequence and structure of lipases and related proteins sharing the same a/b hydrolase fold to facilitate protein engineering.

IDLipaseEngineering
Homehttp://www.led.uni-stuttgart.de/
EDAM topicSpecific protein
Taxonall
website/lipidbank.html0000644000244100017570000000243011606605746015147 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LipidBank

LipidBank

A database of natural lipids including fatty acids, glycerolipids, sphingolipids, steroids, and various vitamins.

IDLipidBank
Homehttp://lipidbank.jp/index.html
EDAM topicLipids
Taxonall
website/lmsd.html0000644000244100017570000000245711606605746014162 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LMSD

LIPID MAPS Structure Database (LMSD)

Structures and annotations of biologically relevant lipids.

IDLMSD
Homehttp://www.lipidmaps.org/data/structure/index.html
EDAM topicLipids
Taxonall
website/lumbribase.html0000644000244100017570000000275411606605746015350 0ustar jisonindustry Bioinformatics Data Resource Catalogue

LumbriBASE

Lumbricus rubellus genome project database

Genome database for the earthworm, Lumbricus rubellus.

IDLumbriBASE
Homehttp://xyala.cap.ed.ac.uk/Lumbribase/index.shtml
EDAM topicInvertebrate
EDAM topicGenomes
TaxonLumbricus rubellus
website/macie.html0000644000244100017570000000277211606605746014301 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MACiE

Mechanism, annotation and classification in enzymes (MACiE) database

A database of enzyme reaction mechanisms, detailing the chemical compounds involved, individual reaction stages, mechanisms, alternative mechanisms, amino acids involved as well as the species name in which the reaction occurs.

IDMACiE
Homehttp://www.ebi.ac.uk/thornton-srv/databases/MACiE/
EDAM topicEnzymes
Taxonall
website/maizegdb.html0000644000244100017570000000633211606605746015001 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MaizeGDB

Maize genetics and genomics database (MaizeGDB)

Biological information about the crop plant Zea mays ssp. mays. The following datatypes are accessible through this site: genetic, genomic, sequence, gene product, functional characterization, literature reference, and person/organization contact information.

IDMaizeGDB
IDaltMaizeDB
AccDB-0058
Homehttp://www.maizegdb.org/
EDAM topicPlant
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonZea mays

Available data

Data Format Query Link
Gene annotation (clone or EST) {MaizeGDB entry} HTML MaizeDB ID http://www.maizegdb.org/cgi-bin/id_search.cgi?id=%s

Example queries

Data Format Query Example
Gene annotation (clone or EST) {MaizeGDB entry} HTML MaizeDB ID 635633
website/mamep.html0000644000244100017570000000245611606605746014321 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MAMEP

Molecular anatomy of mouse embryo project (MAMEP)

Functional analysis of pattern formation, tissue development and organogenesis in mouse.

IDMAMEP
Homehttp://mamep.molgen.mpg.de/
EDAM topicCell cycle and development
TaxonMus
website/mampol.html0000644000244100017570000000241211606605746014477 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MamPol

Mammalia polymorphism database (MamPol)

A collection of all the existing polymorphic sequences in the Mammalia group.

IDMamPol
Homehttp://mampol.uab.es
EDAM topicMutation and polymorphism
TaxonMammalia
website/mapu.html0000644000244100017570000000260611606605746014161 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MAPU

Max-Planck unified proteome database (MAPU)

Body fluid proteomes including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth.

IDMAPU
Homehttp://www.mapuproteome.com/
EDAM topicProteome
Taxonall
website/matdb.html0000644000244100017570000000314511606605746014305 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MAtDB

Arabadopsis genome database (MAtDB)

A repository for genome sequence data in the European Scientists Sequencing Arabidopsis (ESSA) project.

IDMAtDB
Homehttp://mips.gsf.de/proj/thal/db
EDAM topicPlant
EDAM topicGenomes
EDAM topicPlant
TaxonArabidopsis
website/matrixdb.html0000644000244100017570000000236511606605746015033 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MatrixDB

MatrixDB

A database of interactions established by extracellular proteins and polysaccharides.

IDMatrixDB
Homehttp://matrixdb.ibcp.fr/
EDAM topicProtein interactions
Taxonall
website/medobis.html0000644000244100017570000000237011606605746014637 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MedOBIS

Mediterranean ocean biogeographic information system (MedOBIS)

Regional repository of marine biodiversity data.

IDMedOBIS
Homehttp://www.medobis.org
EDAM topicEcoinformatics
Taxonall
website/megx.html0000644000244100017570000000246411606605746014161 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MeGX

MeGX marine microbial ecological genomics database

Specialized database for genome-wide analysis of marine bacteria and metagenomics.

IDMeGX
IDaltMegDB
Homehttp://www.megx.net
EDAM topicEcoinformatics
Taxonall
website/mepd.html0000644000244100017570000000246011606605746014142 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MEPD

Medaka expression pattern database (MEPD)

Medaka gene expression data examined through whole mount in situ hybridization.

IDMEPD
Homehttp://ani.embl.de:8080/mepd/
EDAM topicGene expression and regulation
TaxonOryzias latipes
website/merops.html0000644000244100017570000001030111606605746014513 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MEROPS

MEROPS peptidase database

Information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them. Information includes the classification and nomenclature of the peptidase and links to supplementary pages showing sequence identifiers, the structure if known, literature references and more.

IDMEROPS
AccDB-0059
Homehttp://merops.sanger.ac.uk/
EDAM topicEnzymes
EDAM topicNomenclature
CategoryProtein family/group databases
Taxonall

Available data

Data Format Query Link
Protein report {MEROPS page} HTML Identifier {Clan} http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Protein report {MEROPS page} HTML Identifier {Family} http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary
Protein report {MEROPS page} HTML Enzyme ID (MEROPS) http://merops.sanger.ac.uk/cgi-bin/merops.cgi?id=%s;action=summary

Example queries

Data Format Query Example
Protein report {MEROPS page} HTML Enzyme ID (MEROPS) A01.001
website/metacrop.html0000644000244100017570000000305011606605746015023 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MetaCrop

MetaCrop database of metabolic pathways in crop plants

Diverse information about metabolic pathways in crop plants and allows automatic export of information for the creation of detailed metabolic models.

IDMetaCrop
Homehttp://metacrop.ipk-gatersleben.de
EDAM topicMetabolic pathways
EDAM topicPlant
TaxonSpermatophyta
website/metagrowth.html0000644000244100017570000000254411606605747015402 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MetaGrowth

MetaGrowth database of culture conditions of obligate parasitic bacteria

Evidence and hypotheses for the study of culture conditions of obligate parasitic bacteria.

IDMetaGrowth
Homehttp://www.igs.cnrs-mrs.fr/axenic/
EDAM topicCell lines and culture
TaxonBacteria
website/metal-macie.html0000644000244100017570000000264511606605747015401 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Metal-MACiE

Metal-MACiE database of metals involved in biological catalysis

Properties and functions of the metal ions involved in the catalytic reactions of enzymes.

IDMetal-MACiE
Homehttp://www.ebi.ac.uk/thornton-srv/databases/Metal_MACiE/home.html
EDAM topicEnzymes
Taxonall
website/methdb.html0000644000244100017570000000231311606605747014456 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MethDB

MethDB DNA methylation database

DNA methylation and environmental epigenetic effects.

IDMethDB
Homehttp://www.methdb.de
EDAM topicDNA
Taxonall
website/mfungd.html0000644000244100017570000000567311606605747014507 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MfunGD

MIPS mouse functional genome database (MfunGD)

Mouse genome database including DNA and protein sequences, annotation, gene models and mapping etc.

IDMfunGD
Homehttp://mips.gsf.de/genre/proj/mfungd/
EDAM topicVertebrate
EDAM topicGenomes
TaxonMus

Available data

Data Format Query Link
Gene annotation {Mfungd Entry} HTML Gene ID (MfunGD) http://mips.helmholtz-muenchen.de/genre/proj/mfungd/singleGeneReport.html?entry=%s

Example queries

Data Format Query Example
Gene annotation {Mfungd Entry} HTML Gene ID (MfunGD) mc1000056
website/mgi.html0000644000244100017570000000661611606605747014001 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MGI

Mouse genome database (MGD) from Mouse Genome Informatics (MGI)

Integrated genetic, genomic, and biological data for mouse.

IDMGI
IDaltMGD
AccDB-0060
Homehttp://www.informatics.jax.org/
EDAM topicVertebrate
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonMus
Linkinghttp://www.informatics.jax.org/mgihome/other/link_instructions.shtml

Available data

Data Format Query Link
Data reference {MGI entry} HTML Gene name (MGD) http://www.informatics.jax.org/searches/accession_report.cgi?id=%s

Example queries

Data Format Query Example
Data reference {MGI entry} HTML Gene name (MGD) 1894891
website/micado.html0000644000244100017570000000636611606605747014463 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Micado

Microbial advanced database organisation (Micado)

Microbial genome and functional analysis of Bacillus subtilis.

IDMicado
AccDB-0061
Homehttp://genome.jouy.inra.fr/cgi-bin/micado/index.cgi
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonBacillus subtilis

Available data

Data Format Query Link
Data reference {Micado entry} HTML Gene symbol http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi?species=Bacillus+subtilis&gene=%s

Example queries

Data Format Query Example
Data reference {Micado entry} HTML Gene symbol ypuD
website/mim.html0000644000244100017570000000676211606605747014011 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MIM

Online Mendelian inheritance in Man (OMIM)

Compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.

IDMIM
IDaltOMIM
AccDB-0062
Homehttp://www.ncbi.nlm.nih.gov/omim/
EDAM topicHuman disease
EDAM topicOrganism
EDAM topicGenotype and phenotype
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Genotype/phenotype annotation {OMIM entry} HTML OMIM ID http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=OMIM&dopt=Detailed&tmpl=dispomimTemplate&list_uids=%s

Example queries

Data Format Query Example
Genotype/phenotype annotation {OMIM entry} HTML OMIM ID 125700
website/mint.html0000644000244100017570000000551711606605747014173 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MINT

Molecular interaction Database (MINT)

Experimentally verified protein-protein interactions mined from the scientific literature by expert curators.

IDMINT
AccDB-0158
Homehttp://mint.bio.uniroma2.it/mint/
EDAM topicProtein-protein interactions
Taxonall

Available data

Data Format Query Link
Protein-protein interaction {MINT interaction} HTML MINT ID http://mint.bio.uniroma2.it/mint/search/interaction.do?ac=MINT-%s

Example queries

Data Format Query Example
Protein-protein interaction {MINT interaction} HTML MINT ID 3979570
website/mipsplantsdb.html0000644000244100017570000000347311606605747015723 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MIPSPlantsDB

MIPS plants database

Data for individual plant species and a platform for integrative and comparative plant genome research.

IDMIPSPlantsDB
Homehttp://mips.gsf.de/proj/plant/jsf/genomes.jsp
EDAM topicPlant
EDAM topicGenomes
EDAM topicComparative genomics
EDAM topicPlant
TaxonSpermatophyta
website/mirbase.html0000644000244100017570000000307011606605747014636 0ustar jisonindustry Bioinformatics Data Resource Catalogue

miRBase

miRBase database

Database of all published miRNA sequences, genomic locations and associated annotation, predicted miRNA target genes and a confidential service assigning official names for novel miRNA genes prior to publication of their discovery.

IDmiRBase
Homehttp://microrna.sanger.ac.uk/
EDAM topicmiRNA
EDAM topicGene family or system
Taxonall
website/miriam.html0000644000244100017570000000247611606605747014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

miriam

MIRIAM resources

Catalogue of data types (these can be controlled vocabularies or databases), their URIs and the corresponding physical URLs or resources. Access to this data is made available via exports (XML) and Web Services (SOAP).

IDmiriam
Homehttp://www.ebi.ac.uk/miriam/
EDAM topicData types and objects
Taxon
website/mirortho.html0000644000244100017570000000261711606605747015065 0ustar jisonindustry Bioinformatics Data Resource Catalogue

miROrtho

miROrtho animal microRNA database

Catalogue of animal microRNA genes.

IDmiROrtho
Homehttp://cegg.unige.ch/mirortho
EDAM topicmiRNA
EDAM topicGene family or system
TaxonMetazoa
website/mitodrome.html0000644000244100017570000000411711606605747015216 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MitoDrome

OXPHOS genes in Drosophila

Annotation for Drosophila melanogaster nuclear genes encoding for mitochondrial proteins in order to contribute to their functional characterization. The data collected in MitoDrome derive from the comparison of Human mitochondrial proteins available in SWISSPROT vs. the Drosophila genome, ESTs and cDNA sequences available in the FlyBase database. According to the results, each Drosophila gene sharing significant homology with a human mitochondrial protein was classified as a putative Drosophila mitochondrial gene and annotated in MitoDrome.

IDMitoDrome
Homehttp://www2.ba.itb.cnr.it/MitoDrome/
EDAM topicMitochondria
EDAM topicGene family or system
EDAM topicmRNA, EST or cDNA
TaxonDrosophila
website/mitop2.html0000644000244100017570000000307111606605747014427 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MITOP2

Mitochondrial proteome database

Mitochondria-related genes, proteins and diseases.

IDMITOP2
Homehttp://www.mitop.de:8080/mitop2/
EDAM topicMitochondria
EDAM topicProteome
EDAM topicDisease
TaxonEukaryota
website/mitores.html0000644000244100017570000000272011606605747014677 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MitoRes

MitoRes resource for mitochondria-related genes, transcripts and proteins

Mitochondria-related genes, transcripts and proteins

IDMitoRes
Homehttp://www2.ba.itb.cnr.it/MitoNuc/
EDAM topicMitochondria
EDAM topicProteome
TaxonEukaryota
website/mlvabank.html0000644000244100017570000000234711606605747015015 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MLVAbank

Bacterial MLVA-genotyping service (MLVAbank)

Bacterial MLVA-genotyping service.

IDMLVAbank
Homehttp://mlva.u-psud.fr/
EDAM topicGenotype and phenotype
TaxonBacteria
website/mmdb.html0000644000244100017570000000306011606605747014132 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MMDB

Molecular Modeling DataBase (MMDB)

A database of experimentally determined structures obtained from the RCSB Protein Data Bank (PDB). Useful features are added that facilitate computation on the data and link them to many other data types in the Entrez system.

IDMMDB
IDaltEntrez Structure
Homehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=structure
EDAM topicProtein tertiary structure
Taxonall
website/mmmp.html0000644000244100017570000000373011606605746014164 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MMMP

Melanoma Molecular Map Project (MMMP) i

A multidatabase dedicated to research on melanoma biology and therapy. It collects and integrates published data including melanoma-related molecular (or cellular) pathways of interest (Biomaps), structured and standardized information on single melanoma-related molecules of interest (Biocards), molecular derangements demonstrated in human melanoma (Melanoma Molecular Profile), preclinical and clinical information regarding drugs tested for melanoma treatment (Drug Development Database), Results form clinical trials (with therapeutic and/or, prognostic/predictive purposes), epidemiological studies, and meta-analyses (clinical Trial Database), key terms (or expressions, concepts) used in the MMMP site (Glossary).

IDMMMP
Homehttp://www.mmmp.org/MMMP/import.mmmp?page=aims_org.mmmp
EDAM topicCancer
Taxonall
website/mmruv.html0000644000244100017570000000260511606605747014365 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MMRUV

MMR Gene Unclassified Variants Database

Database of mismatch repair gene unclassified variants: information from functional assays and other type of data to support the interpretation of MMR gene unclassified variants.

IDMMRUV
Homehttp://www.mmrmissense.net/
EDAM topicMutation and polymorphism
TaxonHomo sapiens
website/mmsinc.html0000644000244100017570000000225611606605747014507 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MMsINC

MMsINC chemoinformatics database

Chemoinformatics database.

IDMMsINC
Homehttp://mms.dsfarm.unipd.it/MMsINC/search/
EDAM topicSmall molecules
Taxon
website/mncdb.html0000644000244100017570000000324111606605750014271 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MNCDB

MNCDB Neurospora crassa genome database

Molecular structure and functional network of the entirely sequenced, filamentous fungus Neurospora crassa.

IDMNCDB
Homehttp://mips.gsf.de/genre/proj/ncrassa/
EDAM topicPathways, networks and models
EDAM topicFungal
EDAM topicGenomes
TaxonNeurospora crassa
website/modbase.html0000644000244100017570000001214411606605750014622 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ModBase

ModBase database of comparative protein structure models

Three-dimensional protein models calculated by comparative modelling.

IDModBase
AccDB-0063
Homehttp://modbase.compbio.ucsf.edu/modbase-cgi/index.cgi
EDAM topicProtein tertiary structure
Category3D structure databases
Taxonall

Available data

Data Format Query Link
Protein structure report HTML UniProt accession http://salilab.org/modbase/searchbyid?databaseID=%s
SNP annotation {all SNPs} HTML UniProt accession http://salilab.org/modbase/searchbyid?databaseID=%s&displaymode=snpview
SNP annotation {specific SNP} HTML UniProt accession; dbSNP ID http://salilab.org/modbase/searchbyid?databaseID=%s1&dbsnpID=%s2

Example queries

Data Format Query Example
Protein structure report HTML UniProt accession P43632
SNP annotation {all SNPs} HTML UniProt accession P43632
SNP annotation {specific SNP} HTML UniProt accession; dbSNP ID P43632;rs1143507
website/modeldb.html0000644000244100017570000000234311606605747014624 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ModelDB

ModelDB

Computational neuroscience models.

IDModelDB
Homehttp://senselab.med.yale.edu/ModelDB/
EDAM topicBiological models
Taxonall
website/modomics.html0000644000244100017570000000240711606605750015023 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MODOMICS

Database of RNA modification pathways

Database of RNA modification pathways.

IDMODOMICS
Homehttp://www.genesilico.pl/modomics
EDAM topicPathways, networks and models
Taxonall
website/moka.html0000644000244100017570000000301511606605750014134 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MoKA

MoKCa database of mutations of kinases in cancer

Structural and functional annotation on the phenotypic consequences of mutations in protein kinases implicated in cancer.

IDMoKA
Homehttp://strubiol.icr.ac.uk/extra/mokca/
EDAM topicCancer
EDAM topicGenotype and phenotype
TaxonHomo sapiens
website/molligen.html0000644000244100017570000000240611606605750015016 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MolliGen

MolliGen Mollicutes database

Comparative genomics of Mollicutes.

IDMolliGen
Homehttp://cbi.labri.fr/outils/molligen/
EDAM topicComparative genomics
TaxonMollicutes
website/monosaccharidedb.html0000644000244100017570000000522711606605747016507 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MonosaccharideDB

Monosaccharide database

Information on the residues used in glycan databases.

IDMonosaccharideDB
Homehttp://www.monosaccharidedb.org/
EDAM topicCarbohydrates
Taxon

Available data

Data Format Query Link
Carbohydrate structure report {MonosaccharideDB entry} HTML MonosaccharideDB ID http://www.monosaccharidedb.org/display_monosaccharide.action?id=%s

Example queries

Data Format Query Example
Carbohydrate structure report {MonosaccharideDB entry} HTML MonosaccharideDB ID 1
website/mosaic.html0000644000244100017570000000242211606605750014461 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MOSAIC

MOSAIC bacterial genome comparison database

Comparison of closely related bacterial genomes.

IDMOSAIC
Homehttp://genome.jouy.inra.fr/mosaic/
EDAM topicComparative genomics
TaxonBacteria
website/mosdb.html0000644000244100017570000000315311606605750014314 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MOsDB

MOsDB rice genome database

Publicly available sequences of the rice (Oryza sativa L.) genome.

IDMOsDB
Homehttp://mips.gsf.de/proj/plant/jsf/rice/index.jsp
EDAM topicPlant
EDAM topicGenomes
EDAM topicPlant
TaxonOryza sativa
website/mousebook.html0000644000244100017570000000264011606605750015213 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MouseBook

MouseBook data from MRC Harwell

All the data from MRC Harwell. This includes mouse stocks in FESA (Frozen Embryo and Sperm Archive), mutants from the mutagenesis screen, the ENU DNA archive, standardized phenotyping procedures, imprinting genes and chromosome anomalies.

IDMouseBook
Homehttp://www.mousebook.org
EDAM topicOrganism
TaxonMus
website/mousesage.html0000644000244100017570000000277211606605750015206 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MouseSAGE

MouseSAGE serial analysis of gene expression database

Collection of public available SAGE libraries generated from various mouse tissues and cell lines. The libraries were collected from GEO repository as well as from individual laboratories that made the libraries freely available on the Internet or in their publications.

IDMouseSAGE
Homehttp://mouse.img.cas.cz/sage/
EDAM topicGene expression and regulation
TaxonMus
website/mpact.html0000644000244100017570000000246411606605750014320 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Mpact

MPact: Representation of Interaction Data at MIP

Protein interaction resources from MIPS, designed to support the PSI-MI standard.

IDMpact
Homehttp://mips.gsf.de/genre/proj/mpact
EDAM topicProtein interactions
Taxonall
website/mtrdb.html0000644000244100017570000000236411606605747014331 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MTRDB

Microorganisms tandem repeats database

Microorganisms tandem repeats database.

IDMTRDB
Homehttp://minisatellites.u-psud.fr
EDAM topicRepeat sequence
TaxonBacteria
website/mugen.html0000644000244100017570000000265011606605750014324 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Mugen

MUGEN mouse database

Database of murine models of immune processes and immunological diseases.

IDMugen
Homehttp://www.mugen-noe.org/database
EDAM topicImmunoinformatics
EDAM topicDisease
TaxonMus
website/mumdb.html0000644000244100017570000000323611606605750014316 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MUMDB

MIPS Ustilago maydis Database (MUMDB)

Molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis.

IDMUMDB
Homehttp://mips.gsf.de/genre/proj/ustilago/
EDAM topicPathways, networks and models
EDAM topicFungal
EDAM topicGenomes
TaxonUstilago maydis
website/myhits.html0000644000244100017570000000376211606605750014533 0ustar jisonindustry Bioinformatics Data Resource Catalogue

MyHits

MyHits protein domains database

Protein domain database for investigating the relationships between protein sequences and motifs described on them. These motifs are defined by an heterogeneous collection of predictors, which currently includes regular expressions, generalized profiles and hidden Markov models.

IDMyHits
Homehttp://myhits.isb-sib.ch/cgi-bin/index
EDAM topicProtein functional sites
EDAM topicSequence motifs
EDAM topicProtein domains
EDAM topicSequence profiles and HMMs
Taxonall
website/naproc-13.html0000644000244100017570000000254211606605750014714 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NAPROC-13

NAPROC-13 natural products 13C NMR database

Natural products 13C NMR, for the dereplication of natural product mixtures in bioassay-guided protocols.

IDNAPROC-13
Homehttp://c13.usal.es
EDAM topicSmall molecules
EDAM topicNMR
Taxon
website/narcisse.html0000644000244100017570000000240111606605750015012 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Narcisse

Narcisse mirror view of conserved synteny

Mirror view of conserved synteny.

IDNarcisse
Homehttp://narcisse.toulouse.inra.fr
EDAM topicGenetic mapping and linkage
Taxonall
website/nbrc.html0000644000244100017570000000256211606605750014137 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NBRC

NITE biological resource center

Microbial culture catalogue.

IDNBRC
IDaltNITE-BRC
Homehttp://www.nbrc.nite.go.jp/e/index.html
EDAM topicCell lines and culture
CategoryNot available
Taxonall
website/ncl.html0000644000244100017570000000277311606605750013773 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NCL

NCL Mutation Database

Published mutations and polymorphisms in the NCL genes together with unpublished data included with permission.

IDNCL
Homehttp://www.ucl.ac.uk/ncl/mutation.shtml
EDAM topicGene family or system
EDAM topicMutation and polymorphism
TaxonHomo sapiens
website/ncrnas.html0000644000244100017570000000275011606605750014476 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ncRNAs

ncRNAs database

Sequences and functions of transcripts which do not code for proteins, but perform regulatory roles in the cell.

IDncRNAs
Homehttp://biobases.ibch.poznan.pl/ncRNA/
EDAM topicGene expression and regulation
EDAM topicFunctional RNA
Taxonall
website/nembase.html0000644000244100017570000000243611606605750014625 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NEMBASE

NEMBASE database for analysis of nematode ESTs

Nematode EST datasets.

IDNEMBASE
Homehttp://www.nematodes.org/nembase3/index.shtml
EDAM topicmRNA, EST or cDNA
TaxonNematoda
website/nesbase.html0000644000244100017570000000261511606605750014632 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NESbase

NESbase database of leucine-rich nuclear export signals

Database of proteins in which the presence of Leucine-rich nuclear export signal (NES) has been experimentally verified. It is curated from literature.

IDNESbase
Homehttp://www.cbs.dtu.dk/databases/NESbase
EDAM topicSpecific protein
Taxonall
website/neuromorpho.html0000644000244100017570000000256511606605750015573 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NeuroMorpho

NeuroMorpho

NeuroMorpho.Org is a centrally curated inventory of digitally reconstructed neurons and associated metadata from peer-reviewed publications.

IDNeuroMorpho
Homehttp://neuromorpho.org/neuroMorpho/index.jsp
EDAM topicCell biology informatics
Taxonall
website/neurondb.html0000644000244100017570000000310411606605751015021 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NeuronDB

NeuronDB

NeuronDB provides a dynamically searchable database of three types of neuronal properties: voltage gated conductances, neurotransmitter receptors, and neurotransmitter substances. It contains tools that provide for integration of these properties in a given type of neuron and compartment, and for comparison of properties across different types of neurons and compartments.

IDNeuronDB
Homehttp://senselab.med.yale.edu/NeuronDB/
EDAM topicCell biology informatics
Taxonall
website/nextbio.html0000644000244100017570000000664111606605751014666 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NextBio

NextBio gene-centric data for human, mouse, rat, fly, worm and yeast

NextBio gene-centric data for human, mouse, rat, fly, worm and yeast

IDNextBio
AccDB-0128
Homehttp://www.nextbio.com/
EDAM topicGenomes
EDAM topicComparative genomics
CategoryOther
TaxonHomo sapiens, Mus, Rattus, Caenorhabditis elegans, Drosophila, Saccharomyces cerevisiae

Available data

Data Format Query Link
Gene annotation HTML Identifier {NextBio} http://www.nextbio.com/b/home/home.nb?id=%s&type=feature

Example queries

Data Format Query Example
Gene annotation HTML Identifier {NextBio} 797758
website/nextdb.html0000644000244100017570000000305011606605751014471 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NextDB

Nematode expression pattern dataBase (NextDB)

Nematode expression pattern dataBase.

IDNextDB
Homehttp://nematode.lab.nig.ac.jp/
EDAM topicGene expression and regulation
CategoryNot available
TaxonNematoda

Example queries

Data Format Query Example
website/nextprot.html0000644000244100017570000000535311606605751015100 0ustar jisonindustry Bioinformatics Data Resource Catalogue

neXtProt

neXtProt; the human protein knowledge platform

neXtProt; the human protein knowledge platform

IDneXtProt
AccDB-0161
Homehttp://www.nextprot.org/
EDAM topicGenomes
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation HTML Identifier {neXtProt} http://www.nextprot.org/entry/%s

Example queries

Data Format Query Example
Gene annotation HTML Identifier {neXtProt} NX_P31946
website/niaest.html0000644000244100017570000000277511606605751014505 0ustar jisonindustry Bioinformatics Data Resource Catalogue

niaEST

NIA mouse cDNA project

NIA mouse cDNA project

IDniaEST
Homehttp://lgsun.grc.nia.nih.gov/cDNA/
EDAM topicmRNA, EST or cDNA
CategoryNot available
TaxonMus

Example queries

Data Format Query Example
website/nmpdr.html0000644000244100017570000001173511606605751014336 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NMPDR

National microbial pathogen

Curated annotations in an environment for comparative analysis of genomes and biological subsystems, with an emphasis on the food-borne pathogens Campylobacter, Listeria, Staphylococcus, Streptococcus, and Vibrio as well as the STD pathogens Chlamydiaceae, Haemophilus, Mycoplasma, Neisseria, Treponema, and Ureaplasma.

IDNMPDR
AccDB-0125
Homehttp://www.nmpdr.org
EDAM topicGenomes
EDAM topicPathogen
EDAM topicComparative genomics
CategoryGenome annotation databases
TaxonBacteria
Linkinghttp://www.nmpdr.org/FIG/wiki/view.cgi/FIG/LinkingToTheGenomeViewer

Available data

Data Format Query Link
Gene annotation HTML NCBI taxonomy ID http://www.nmpdr.org/linkin.cgi?genome=%s
Gene annotation {Protein encoding gene or other feature} HTML FIG ID http://www.nmpdr.org/linkin.cgi?id=%s

Example queries

Data Format Query Example
Gene annotation HTML NCBI taxonomy ID 83333.1
Gene annotation {Protein encoding gene or other feature} HTML FIG ID 83333.1.peg.123
Gene annotation {Protein encoding gene or other feature} HTML FIG ID 83333.1.rna.1
website/nmrshift.html0000644000244100017570000000262311606605751015044 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NMRShift

NMRShift database of organic structure NMR spectra

An NMR database for organic structures and their nuclear magnetic resonance (nmr) spectra. It allows for spectrum prediction (13C, 1H and other nuclei) as well as for searching spectra, structures and other properties. It features peer-reviewed submission of datasets by its users.

IDNMRShift
Homehttp://nmrshiftdb.ice.mpg.de/
EDAM topicNMR
Taxon
website/nopdb.html0000644000244100017570000000263011606605751014312 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NOPDB

Nucleolar proteome database (NOPDB)

Data from LamondLab proteomic analysis of human nucleoli. High sensitivity mass spectrometry and stringent criteria is used to identify peptides from human proteins from purified nucleoli.

IDNOPDB
Homehttp://www.lamondlab.com/NOPDB3.0/
EDAM topicMass spectrometry
TaxonHomo sapiens
website/norine.html0000644000244100017570000000236411606605751014506 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NORINE

NORINE database of nonribosomal peptides

Database of nonribosomal peptides.

IDNORINE
Homehttp://bioinfo.lifl.fr/norine/
EDAM topicPeptides and amino acids
Taxonall
website/npc-db.html0000644000244100017570000000234111606605751014352 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NPC-db

Niemann-Pick Type C mutations

Niemann-Pick type C disease gene variation database (NPC-db).

IDNPC-db
Homehttp://npc.fzk.de/
EDAM topicHuman disease
TaxonHomo sapiens
website/npd.html0000644000244100017570000000322111606605751013766 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NPD

Nuclear protein database (NPD)

Information on vertebrate proteins (mainly those from mouse and human) that are thought to, or known to, be localised to the cell nucleus. Where known, the sub-nuclear compartment where the proteins have been found are reported. Also stored is information on the amino acid sequence, predicted protein size and isoelectric point, as well as any repeats, motifs or domains within the protein sequence. Biological and molecular functions of the proteins are described using GO terms.

IDNPD
Homehttp://npd.hgu.mrc.ac.uk
EDAM topicSpecific protein
TaxonChordata
website/nrestdb.html0000644000244100017570000000302311606605751014646 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NRESTdb

Natural rubber EST database (NRESTdb)

Natural rubber EST database.

IDNRESTdb
Homehttp://genome.ukm.my/nrestdb/
EDAM topicmRNA, EST or cDNA
CategoryNot available
TaxonHevea brasiliensis

Example queries

Data Format Query Example
website/nrsub.html0000644000244100017570000000276011606605751014345 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NRSub

Non-Redundant B.subtilis database (NRSub)

Complete genome of Bacillus subtilis, plus additional data on gene mapping and codon usage.

IDNRSub
Homehttp://pbil.univ-lyon1.fr/nrsub/nrsub.html
EDAM topicGenomes
EDAM topicProkaryote
TaxonBacillus subtilis
website/nurebase.html0000644000244100017570000000247511606605751015023 0ustar jisonindustry Bioinformatics Data Resource Catalogue

NUREBASE

Nuclear receptor database (NUREBASE)

Nuclear receptor database

IDNUREBASE
Homehttp://www.ens-lyon.fr/LBMC/laudet/nurebase/nurebase.html
EDAM topicSpecific protein
TaxonEukaryota
website/oglycbase.html0000644000244100017570000000353711606605751015167 0ustar jisonindustry Bioinformatics Data Resource Catalogue

OGLYCBASE

O-GlycBase database

Database of O- and C-glycosylated proteins. The criteria for inclusion are at least one experimentally verified O- or C-glycosylation site. The terminal sugar linked to serine or threonine is cited when known. The database is non-redundant in the sense that it contains no identical sequences, unless there is conflicting glycosylation data. Mucins have tandem repeat sequences, which are O-glycosylated. This result in some redundancy of the O-glycosylation sites.

IDOGLYCBASE
Homehttp://www.cbs.dtu.dk/databases/OGLYCBASE/
EDAM topicProtein functional sites
EDAM topicSpecific protein
Taxonall
website/ogp.html0000644000244100017570000000561211606605751014000 0ustar jisonindustry Bioinformatics Data Resource Catalogue

OGP

Oxford glycoProteomics 2-DE database (OGP)

Two-dimensional polyacrylamide gel electrophoresis database.

IDOGP
AccDB-0067
Homehttp://proteomewww.bioch.ox.ac.uk/2d/2d.html
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) {OGP entry} HTML UniProt accession http://proteomewww.glycob.ox.ac.uk/cgi-bin/2d-search-ac?%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) {OGP entry} HTML UniProt accession P04406
website/oma.html0000644000244100017570000000620511606605751013766 0ustar jisonindustry Bioinformatics Data Resource Catalogue

OMA

Identification of orthologs from complete genome data (OMA database)

Identification of orthologs from complete genome data.

IDOMA
AccDB-0137
Homehttp://www.omabrowser.org
EDAM topicNucleic acid classification
EDAM topicPhylogenetics
EDAM topicPhylogenomics
CategoryPhylogenomic databases
Taxonall

Available data

Data Format Query Link
Data reference HTML Protein identifier {OMA} http://omabrowser.org/cgi-bin/gateway.pl?f=DisplayGroup&p1=%s

Example queries

Data Format Query Example
Data reference HTML Protein identifier {OMA} FDVARTG
website/optic.html0000644000244100017570000000257411606605751014335 0ustar jisonindustry Bioinformatics Data Resource Catalogue

OPTIC

Orthologous and paralogous transcripts in clades (OPTIC) database

Orthologous and paralogous transcripts in clades, from anaylsis of complete genomes (flies, nematodes, amniota, yeasts) in several clades.

IDOPTIC
Homehttp://genserv.anat.ox.ac.uk/
EDAM topicNucleic acid classification
TaxonEukaryota
website/orenza.html0000644000244100017570000000243611606605751014512 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ORENZA

Database of orphan enzyme activities (ORENZA)

Enzyme Activities for which no sequences are available in the main sequence protein databases.

IDORENZA
Homehttp://www.orenza.u-psud.fr/
EDAM topicEnzymes
Taxonall
website/orphanet.html0000644000244100017570000000606511606605751015036 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Orphanet

Orphanet portal for rare diseases and orphan drugs

Information on rare diseases and orphan drugs.

IDOrphanet
AccDB-0068
Homehttp://www.orpha.net/consor/cgi-bin/home.php?Lng=GB
EDAM topicDrugs and targets
EDAM topicDisease
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Disease annotation {Orphanet entry} HTML Orpha number http://www.orpha.net//consor/cgi-bin/OC_Exp.php?Lng=GB&Expert=%s

Example queries

Data Format Query Example
Disease annotation {Orphanet entry} HTML Orpha number 69739
website/orthodb.html0000644000244100017570000000274511606605751014660 0ustar jisonindustry Bioinformatics Data Resource Catalogue

OrthoDB

Orthologous groups database (OrthoDB)

Orthologous groups database.

IDOrthoDB
AccDB-0143
Homehhttp://cegg.unige.ch/orthodb2
EDAM topicNucleic acid classification
EDAM topicGene family or system
Taxonall
website/orygenesdb.html0000644000244100017570000000341211606605751015350 0ustar jisonindustry Bioinformatics Data Resource Catalogue

OryGenesDB

Database for rice reverse genetics (OryGenesDB)

Oryza sativa database of sequence information, such as the T-DNA and Ds flanking sequence tags (FSTs), plus related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data etc).

IDOryGenesDB
Homehttp://orygenesdb.cirad.fr/
EDAM topicmRNA, EST or cDNA
EDAM topicNucleic acid sequences
EDAM topicPlant
TaxonOryza sativa
website/oryza.html0000644000244100017570000000343211606605752014356 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Oryza

Oryza tag line

Database for the functional analyis of the rice genome. Phenotypic data from evaluation of the Genoplante rice insertion line library. Sequence information (Flanking Sequence Tags) from the molecular characterization of the mutagen insertion sites.

IDOryza
Homehttp://urgi.versailles.inra.fr/OryzaTagLine/
EDAM topicGenotype and phenotype
EDAM topicPlant
EDAM topicGenomes
TaxonOryza sativa
website/osteogenesis.html0000644000244100017570000001363511606605752015727 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Osteogenesis

Osteogenesis imperfecta and type III collagen mutations

All published accounts of variants resulting in osteogenesis imperfecta. Such variants occur in the COL1A1, COL1A2, CRTAP and LEPRE1 genes.

IDOsteogenesis
Homehttps://oi.gene.le.ac.uk
EDAM topicHuman disease
TaxonHomo sapiens

Available data

Data Format Query Link
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) http://oi.gene.le.ac.uk/home.php?select_db=%s

Example queries

Data Format Query Example
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) COL1A1
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) COL1A2
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) CRTAP
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) FKBP10
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) LEPRE1
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) PPIB
Sequence variation annotation {Sequence variants} HTML Database name (Osteogenesis) SERPINH1
website/p53famtag.html0000644000244100017570000000301111606605752014772 0ustar jisonindustry Bioinformatics Data Resource Catalogue

p53FamTaG

p53FamTaG direct target genes

A resource of human p53, p63, p73 direct target genes combining in silico prediction and microarray analysis.

IDp53FamTaG
Homehttp://www2.ba.itb.cnr.it/p53FamTaG/
EDAM topicGene family or system
EDAM topicGene expression and regulation
TaxonHomo sapiens
website/pairsdb.html0000644000244100017570000000260611606605752014640 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PairsDB

PairsDB BLAST and PSI-BLAST alignments

Collection of protein sequences and the BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually, results can be retrieved from a database of pre-computed alignments.

IDPairsDB
Homehttp://pairsdb.csc.fi
EDAM topicProtein sequence alignment
Taxonall
website/pandit.html0000644000244100017570000000251411606605752014471 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PANDIT

Protein and associated nucleotide domains with inferred trees (PANDIT)

Protein and associated nucleotide domains with inferred trees.

IDPANDIT
Homehttp://www.ebi.ac.uk/goldman-srv/pandit/
EDAM topicProtein functional sites
Taxonall
website/pandora.html0000644000244100017570000000244311606605752014637 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PANDORA

PANDORA visualization and annotation for protein sets

Keyword-based analysis of protein sets by integration of annotation sources.

IDPANDORA
Homehttp://www.pandora.cs.huji.ac.il
EDAM topicProteins
Taxonall
website/panther.html0000644000244100017570000001224111606605752014651 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PANTHER

Protein analysis through evolutionary relationships (PANTHER)

Classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence. Proteins are classified by expert biologists into families and subfamilies of shared function, which are then categorized by molecular function and biological process ontology terms. PANTHER includes "PANTHER Genes" (genes, transcripts and proteins in Human, Mouse, Rat, and Drosophila melanogaster), PANTHER Families (Protein families and subfamilies and associated data such as phylogenetic trees, multiple sequence alignments and HMMs), "PANTHER Pathways" (expert-curated signaling and metabolic pathways mapped to protein sequences in PANTHER Library) and "PANTHER Ontologies".

IDPANTHER
AccDB-0069
Homehttp://www.pantherdb.org/
EDAM topicPathways, networks and models
EDAM topicProtein families
EDAM topicGene family or system
EDAM topicPhylogenetics
CategoryFamily and domain databases
CategoryProtein sequence classification database
Taxonall

Available data

Data Format Query Link
Protein family annotation {PANTHER Family} HTML Protein family ID (PANTHER) http://www.pantherdb.org/panther/family.do?clsAccession=%s
Pathway or network report HTML Pathway ID (Panther) http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=%s

Example queries

Data Format Query Example
Protein family annotation {PANTHER Family} HTML Protein family ID (PANTHER) PTHR12649:SF6
Pathway or network report HTML Pathway ID (Panther) P00002
website/parameciumdb.html0000644000244100017570000000312311606605752015640 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ParameciumDB

Database for the model organism Paramecium tetraurelia (ParameciumDB)

Macronuclear genome sequence and annotations, linked to available genetic data (RNA interference data and stock collection) for the model organism, Paramecium tetraurelia.

IDParameciumDB
Homehttp://paramecium.cgm.cnrs-gif.fr
EDAM topicUnicellular eukaryote
EDAM topicGenomes
TaxonParamecium
website/pathema.html0000644000244100017570000000355011606605752014632 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Pathema

Pathema: a clade-specific bioinformatics resource

Genome database for six clades of Category A-C pathogens — Bacillus anthracis, Clostridium botulinum, Burkholderia mallei, Burkholderia pseudomallei, Clostridium perfringens, Entamoeba histolytica.

IDPathema
Homehttp://www.jcvi.org/cms/research/projects/pathema/overview/
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicPathogen
CategoryNot available
Taxonall
website/pathoplant.html0000644000244100017570000000421411606605752015363 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PathoPlant

PathoPlant database of plant-pathogen interactions and Arabidopsis expression

Plant-pathogen interactions and components of signal transduction pathways related to plant pathogenesis. Also harbors gene expression data from Arabidopsis thaliana microarray experiments to enable searching for specific genes regulated upon pathogen infection or elicitor treatment.

IDPathoPlant
Homehttp://www.pathoplant.de
EDAM topicGene expression and regulation
EDAM topicPlant
EDAM topicSignalling pathways
EDAM topicPlant
EDAM topicPathogen
Taxonall
website/pathway_interaction_db.html0000644000244100017570000000573511606605752017743 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Pathway_Interaction_DB

NCI-Nature pathway interaction database

Biomolecular interactions and cellular processes assembled into human signaling pathways.

IDPathway_Interaction_DB
AccDB-0134
Homehttp://pid.nci.nih.gov/
EDAM topicSignalling pathways
CategoryEnzyme and pathway databases
TaxonHomo sapiens

Available data

Data Format Query Link
Pathway or network report HTML Pathway ID (NCI-Nature) http://pid.nci.nih.gov/search/pathway_landing.shtml?pathway_id=%s&source=NATURE&what=graphic&jpg=on&ppage=1

Example queries

Data Format Query Example
Pathway or network report HTML Pathway ID (NCI-Nature) 200034
website/pdbe.html0000644000244100017570000000233511606605752014125 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDBe

PDBe protein structure database in Europe

PDBe protein structure database in Europe

IDPDBe
Homehttp://www.ebi.ac.uk/PDBe/
EDAM topicStructure
Taxonall
website/pdbfinder.html0000644000244100017570000000636011606605752015152 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDBFINDER

PDBFINDER reformatted PDB files

The PDBFINDER holds for each PDB file a structured, search-engine-friendly-formatted entry that holds the data-items most likely needed for people search for certain types of PDB entries. The PDBFINDER is not useful to search in atomic coordinates: it is meant to ad searches in the administrative records of PDB files.

IDPDBFINDER
Homehttp://swift.cmbi.ru.nl/gv/PDBfinder/
EDAM topicProtein structure
Taxonall
RESThttp://mrs.cmbi.ru.nl/mrsws/search/rest/GetEntry/db/PDBfinder2/id/%s
SOAPhttp://mrs.cmbi.ru.nl/mrsws/wsdl

Available data

Data Format Query Link
Structure report {PDBFinder report} HTML PDB ID http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=PDBfinder2&id=%s

Example queries

Data Format Query Example
Structure report {PDBFinder report} HTML PDB ID 2hva
website/pdbfun.html0000644000244100017570000000235311606605752014471 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDBfun

PDBfun annotated protein structures

Database of annotated residues in proteins from PDB.

IDPDBfun
Homehttp://PDBfun.uniroma2.it
EDAM topicProtein structure
Taxonall
website/pdb.html0000644000244100017570000001252511606605752013762 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDB

The RCSB Protein Data Bank

A repository for 3D biological macromolecular structure data.

IDPDB
AccDB-0070
Homehttp://www.rcsb.org/PDB/
EDAM topicStructure
Category3D structure databases
Taxonall

Available data

Data Format Query Link
Structure report HTML PDB ID http://www.PDB.org/PDB/explore/explore.do?structureId=%s
Structure PDB format PDB ID http://www.PDB.org/PDB/files/%s.PDB
Structure mmCIF PDB ID http://www.PDB.org/PDB/files/%s.cif
Structure PDBML PDB ID http://www.PDB.org/PDB/files/%s.xml

Example queries

Data Format Query Example
Structure report HTML PDB ID 1rbp
Structure PDB format PDB ID 1rbp
Structure mmCIF PDB ID 1rbp
Structure PDBML PDB ID 1rbp
website/pdb-redo.html0000644000244100017570000000462511606605752014713 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDB-redo

PDB-redo database of re-refined PDB entries

Re-refined macromolecular X-ray diffraction structures.

IDPDB-redo
Homehttp://swift.cmbi.ru.nl/PDBredo/index.html
EDAM topicStructure
Taxonall

Available data

Data Format Query Link
Structure {PDB-redo} HTML PDB ID http://www.cmbi.ru.nl/PDB_redo/yg/%s/index.html
Structure {PDB-redo} HTML PDB ID http://www.cmbi.ru.nl/PDB_redo/yg/1ygb/index.html
website/pdbreport.html0000644000244100017570000000264211606605752015215 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDBREPORT

Structure validation reports for PDB entries (PDBREPORT)

Reports describing structural problems in PDB entries that have been determined using X-ray diffraction or NMR techniques. There are many more than ten million diagnostics.

IDPDBREPORT
Homehttp://swift.cmbi.ru.nl/gv/PDBreport/
EDAM topicProtein structure
Taxonall
website/pdbselect.html0000644000244100017570000000246511606605752015164 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDBselect

PDBselect database of representative PDB chains

Selection of a representative set of PDB chains.

IDPDBselect
Homehttp://bioinfo.tg.fh-giessen.de/PDBselect/
EDAM topicProtein tertiary structure
Taxonall
website/pdbsum.html0000644000244100017570000000564611606605752014515 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDBsum

PDBsum overview of macromolecular structures

At-a-glance overview of every macromolecular structure deposited in the Protein Data Bank (PDB), giving schematic diagrams of the molecules in each structure and of the interactions between them.

IDPDBsum
AccDB-0119
Homehttp://www.ebi.ac.uk/PDBsum
EDAM topicProtein structure
Category3D structure databases
Taxonall

Available data

Data Format Query Link
Structure report {PDBSum entry} HTML PDB ID http://srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e

Example queries

Data Format Query Example
Structure report {PDBSum entry} HTML PDB ID 1kfv
website/pdbtm.html0000644000244100017570000000235611606605752014324 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PDBTM

Transmembrane proteins from PDB (PDBTM)

Transmembrane protein selection of the Protein Data Bank (PDB).

IDPDBTM
Homehttp://PDBtm.enzim.hu/
EDAM topicMembrane protein
Taxonall
website/pedant.html0000644000244100017570000000374611606605753014476 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PEDANT

PEDANT3 protein extraction, description and analysis tool

Automatic analysis of genomic sequences by a large variety of bioinformatics tools. For example the following pre-computed analyses are available to analyse protein function: Blast similarity searches against the non-redundant protein sequence database, motif searches against the Pfam, BLOCKS and PROSITE databases. Prediction of cellular roles and functions are made based on high stringency BLAST searches against protein sequences with manually assigned functional categories according to the Functional Catalogue (FunCat) developed by MIPS and Biomax AG. Protein structure analysis includes the similarity-based identification of known 3D structures and structural domains, by searching against the PDB and SCOP databases, and predictions of transmembrane regions, low similarity regions and non-globular domains.

IDPEDANT
Homehttp://pedant.gsf.de
EDAM topicGenomes
Taxonall
website/ped.html0000644000244100017570000000310711606605753013762 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PED

Pancreatic expression database (PED)

Database for cancer pathogenesis, allowing query by cancer tissue and type, a wide range of sequence types, SNP selection for candidate gene screening and disease links, as well as cross-species analyses.

IDPED
Homehttp://www.pancreasexpression.org
EDAM topicCancer
EDAM topicGene expression and regulation
TaxonEutheria
website/pepseeker.html0000644000244100017570000000262711606605753015203 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PepSeeker

PepSeeker database of proteome peptide identifications for investigating fragmentation patterns

Proteome peptide identifications for investigating fragmentation patterns.

IDPepSeeker
Homehttp://www.ispider.manchester.ac.uk/pepseeker/
EDAM topicPeptide identification and proteolysis
Taxonall
website/peptaibol.html0000644000244100017570000000263411606605753015175 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Peptaibol

Peptaibol database of natural fungal peptides

Natural fungal peptides.

IDPeptaibol
Homehttp://peptaibol.cryst.bbk.ac.uk
EDAM topicPeptides and amino acids
EDAM topicFungal
TaxonFungi
website/peptideatlas.html0000644000244100017570000002357511606605753015704 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PeptideAtlas

PeptideAtlas peptide database

A multi-organism compendium of peptides identified in a large set of tandem mass spectrometry proteomics experiments. Mass spectrometer output files are collected for human, mouse, yeast, and several other organisms, and searched using the latest search engines and protein sequences.

IDPeptideAtlas
AccDB-0071
Homehttp://www.peptideatlas.org
EDAM topicPeptides and amino acids
EDAM topicPeptide identification and proteolysis
CategoryProteomic databases
CategoryPeptide identification database
CategoryMass spectrometry database
Taxonall

Available data

Data Format Query Link
Peptide identification HTML Protein ID (Ensembl) http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY
Peptide identification XML Protein ID (Ensembl) http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=xml
Peptide identification Text Protein ID (Ensembl) http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetPeptides?row_limit=5000&atlas_build_id=182&display_options=ShowMappings%2CShowModifications&organism_id=2&biosequence_name_constraint=%s&QUERY_NAME=AT_GetPeptides&apply_action=QUERY&output_mode=tsv
Mass spectrometry data {Recommended transitions for human protein} HTML Protein ID (Ensembl) http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/ViewMRMList?protein_name_constraint=%s&atlas_build_id=182&consensus_library_id=9&action=QUERY
Protein report {PeptideAtlas entry} HTML IPI protein ID http://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/GetProtein?atlas_build_id=242&protein_name=%s&action=QUERY
Protein report {PeptideAtlas entry} HTML Protein identifier {PeptideAtlas} https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/Search?action=GO&search_key=%s

Example queries

Data Format Query Example
Peptide identification HTML Protein ID (Ensembl) ENSP00000374576
Peptide identification XML Protein ID (Ensembl) ENSP00000374576
Peptide identification Text Protein ID (Ensembl) ENSP00000374576
Mass spectrometry data {Recommended transitions for human protein} HTML Protein ID (Ensembl) ENSP00000374576
Protein report {PeptideAtlas entry} HTML IPI protein ID IPI00795032
Protein report {PeptideAtlas entry} HTML Protein identifier {PeptideAtlas} P62258
website/peptidedb.html0000644000244100017570000000317111606605753015153 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PeptideDB

PeptideDB database of bioactive signaling peptides

Naturally occurring signalling peptides from animal source, which are derived by cleavage from prepropeptide precursor proteins. It includes cytokine and growth factor, peptide hormones, antimicrobial peptides, toxins and venom peptides, and antifreeze proteins.

IDPeptideDB
Homehttp://www.peptides.be/
EDAM topicSpecific protein
EDAM topicPeptides and amino acids
Taxonall
website/peroxibase.html0000644000244100017570000000563711606605753015365 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PeroxiBase

PeroxiBase peroxidase family database

Sequences from peroxidase superfamilies with annotation on putative functions and transcription regulation.

IDPeroxiBase
AccDB-0072
Homehttp://peroxibase.isb-sib.ch/index.php
EDAM topicSpecific protein
CategoryProtein family/group databases
Taxonall

Available data

Data Format Query Link
Protein report {PeroxiBase entry} HTML Protein ID (PeroxiBase) http://peroxibase.isb-sib.ch/listing.php?action=view&id=%s

Example queries

Data Format Query Example
Protein report {PeroxiBase entry} HTML Protein ID (PeroxiBase) 6846
website/peroxisomedb.html0000644000244100017570000000350411606605753015713 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PeroxisomeDB

Peroxisome database (PeroxisomeDB)

Curated information on peroxisomal genes, their encoded proteins, their molecular function and metabolic pathway they belong to, and their related disorders. PeroxisomeDB contains the complete peroxisomal proteome of Homo sapiens (encoded by 85 genes) and Saccaromyces cerevisiae (encoded by 61 genes).

IDPeroxisomeDB
Homehttp://www.peroxisomeDB.org
EDAM topicMetabolic pathways
EDAM topicSpecific protein
EDAM topicProteome
TaxonEukaryota
website/pespotdb.html0000644000244100017570000000256711606605753015043 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PespotDB

Pepspot database (PespotDB) of peptide chip data

Repository for the storage and the analysis of data coming from interaction assays exploiting peptide chip technology.

IDPespotDB
Homehttp://mint.bio.uniroma2.it/PepspotDB
EDAM topicPeptide identification and proteolysis
Taxonall
website/pfam.html0000644000244100017570000001434711606605753014145 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Pfam

Pfam protein domain database

Large collection of protein families, each represented by multiple sequence alignments and hidden Markov models (HMMs).

IDPfam
AccDB-0073
Homehttp://pfam.sanger.ac.uk/
EDAM topicProtein sequence alignment
EDAM topicSequence profiles and HMMs
EDAM topicProtein families
EDAM topicProtein domains
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Protein family annotation {Pfam entry} HTML Sequence accession (protein) http://pfam.sanger.ac.uk/protein/acc=%s
Protein family annotation {Pfam entry} HTML Pfam accession number http://pfam.sanger.ac.uk/family?acc=%s
Protein family annotation {Pfam entry} HTML Pfam clan ID http://pfam.sanger.ac.uk/clan?acc=%s
Protein family annotation {Pfam entry} HTML NCBI taxonomy ID http://pfam.sanger.ac.uk/proteome?taxId=%s

Example queries

Data Format Query Example
Protein family annotation {Pfam entry} HTML Sequence accession (protein) VAV_HUMAN
Protein family annotation {Pfam entry} HTML Pfam accession number PF07388
Protein family annotation {Pfam entry} HTML Pfam clan ID CL0247
Protein family annotation {Pfam entry} HTML NCBI taxonomy ID 349163
website/pgn.html0000644000244100017570000000317311606605753014001 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PGN

Plant Genome Network (PGN)

A general purpose EST analysis pipeline/website that can be readily used as a "front end" for EST sequencing projects. All data in PGN is directly derived from chromatograms and all original and intermediate data are stored in the database.

IDPGN
Homehttp://pgn.cornell.edu/
EDAM topicmRNA, EST or cDNA
EDAM topicPlant
CategoryNot available
TaxonSpermatophyta
website/pharmgkb.html0000644000244100017570000000673211606605753015014 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PharmGKB

The pharmacogenetics and pharmacogenomics knowledge base (PharmGKB)

Database on the impact of human genetic variations on drug response. PharmGKB curates primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.

IDPharmGKB
AccDB-0074
Homehttp://www.pharmgkb.org
EDAM topicGenotype and phenotype
EDAM topicPharmacoinformatics
EDAM topicPharmacogenomics
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation HTML PharmGKB ID http://www.pharmgkb.org/do/serve?objId=%s&objCls=Gene

Example queries

Data Format Query Example
Gene annotation HTML PharmGKB ID PA356
website/phci-2dpage.html0000644000244100017570000000552711606605753015305 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PHCI-2DPAGE

Parasite host cell interaction 2D-PAGE database (PHCI-2DPAGE)

Two-dimensional polyacrylamide gel electrophoresis database.

IDPHCI-2DPAGE
AccDB-0075
Homehttp://www.gram.au.dk/2d/2d.html
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML UniProt accession http://www.gram.au.dk/cgi-bin/get-2d-entry?%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML UniProt accession P17821
website/phenomicdb.html0000644000244100017570000000301611606605753015321 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhenomicDB

PhenomicDB cross-species genotype/phenotype database

A multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indexes (NCBI Gene) and orthologues (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously.

IDPhenomicDB
Homehttp://www.phenomicdb.de
EDAM topicGenotype and phenotype
TaxonEukaryota
website/phi-base.html0000644000244100017570000000304011606605753014676 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PHI-base

PHI-base pathogen host interactions database

Curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. Information is also given on the target sites of some anti-infective chemistries.

IDPHI-base
Homehttp://www.phibase.org
EDAM topicGene family or system
EDAM topicPathogen
Taxonall
website/phosphat.html0000644000244100017570000000401211606605753015034 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhosPhAt

Arabidopsis experimental phosphorylation sites database (PhosPhAt)

Arabidopsis phosphorylation sites which were identified by mass spectrometry in large scale experiments from different research groups. Specific information on the peptide properties as well as on the experimental and analytical context is given.

IDPhosPhAt
Homehttp://phosphat.mpimp-golm.mpg.de/app.html
EDAM topicPhosphorylation
EDAM topicPlant
EDAM topicMass spectrometry
EDAM topicPeptide identification and proteolysis
TaxonArabidopsis
website/phospho3d.html0000644000244100017570000000343711606605753015127 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PHOSPHO3D

PHOSPHO3D structures of phosphorylation sites

Three-dimensional structures of phosphorylation sites which stores information retrieved from the phospho.ELM database and which is enriched with structural information and annotations at the residue level. The database also collects the results of a large-scale structural comparison procedure providing clues for the identification of new putative phosphorylation sites.

IDPHOSPHO3D
Homehttp://bioinformatica.uniroma2.it/phospho3d
EDAM topicPhosphorylation
EDAM topicProtein tertiary structure
Taxonall
website/phosphoelm.html0000644000244100017570000001044511606605753015373 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhosphoELM

PhosphoELM database of S/T/Y phosphorylation sites

Experimentally verified phosphorylation sites in eukaryotic proteins.

IDPhosphoELM
Homehttp://phospho.elm.eu.org/
EDAM topicPhosphorylation
Taxonall

Available data

Data Format Query Link
Sequence motif (protein) {Phospho-ELM report} HTML Protein name {Substrate} http://phospho.elm.eu.org/cgimodel.py?fun=Search&substrate=%s
Sequence motif (protein) {Phospho-ELM report} HTML Sequence accession (protein) http://phospho.elm.eu.org/cgimodel.py?fun=Search&accession=%s
Sequence motif (protein) {Phospho-ELM report} HTML Kinase name http://phospho.elm.eu.org/cgimodel.py?fun=Search&kinase=%s

Example queries

Data Format Query Example
Sequence motif (protein) {Phospho-ELM report} HTML Sequence accession (protein) Q9H0E9
Sequence motif (protein) {Phospho-ELM report} HTML Protein name {Substrate} Src substrate cortactin
website/phosphopep.html0000644000244100017570000000263511606605753015404 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhosphoPep

PhosphoPep database of MS-derived phosphorylation data from 4 organisms

MS-derived phosphorylation data from 4 different organisms: the fly (Drosophila melanogaster), human (Homo sapiens), worm (Caenorhabditis elegans), and yeast (Saccharomyces cerevisiae).

IDPhosphoPep
Homehttp://www.phosphopep.org/
EDAM topicPhosphorylation
Taxonall
website/phosphosite.html0000644000244100017570000000610311606605753015556 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhosphoSite

Phosphorylation site database

A curated, sequence-oriented protein database dedicated to in vivo phosphorylation sites. Information in PhosphoSite version 1.0 includes the phosphorylated residue and its surrounding sequence, orthologous sites in other species, the location within domains and motifs, links to other online resources and literature references.

IDPhosphoSite
AccDB-0123
Homehttp://www.phosphosite.org
EDAM topicPhosphorylation
CategoryPTM databases
Taxonall

Available data

Data Format Query Link
Sequence motif (protein) {PhosphoSite entry} HTML UniProt accession http://www.phosphosite.org/uniprotAccAction.do?id=%s

Example queries

Data Format Query Example
Sequence motif (protein) {PhosphoSite entry} HTML UniProt accession Q92844
website/phossite.html0000644000244100017570000000576311606605753015062 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhosSite

Phosphorylation site database for Archaea and Bacteria

Phosphorylation site database for Archaea and Bacteria

IDPhosSite
AccDB-0076
Homehttp://www.phosphorylation.biochem.vt.edu/
EDAM topicPhosphorylation
CategoryPTM databases
TaxonBacteria, Archaea

Available data

Data Format Query Link
Sequence motif (protein) {PhosSite entry} HTML UniProt accession http://www.phosphorylation.biochem.vt.edu/xpd2.cfm?extf=uniprot&extref=%s

Example queries

Data Format Query Example
Sequence motif (protein) {PhosSite entry} HTML UniProt accession P36683
website/phylomedb.html0000644000244100017570000000325011606605754015175 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhylomeDB

PhylomeDB database of phylogenetic trees for all proteins

A collection of gene phylogenies (phylomes) including phylogenetic trees, multiple sequence alignments and genome-wide orthology and paralogy predictions based on the analysis of the phylogenetic trees.

IDPhylomeDB
AccDB-0144
Homehttp://phylomedb.bioinfo.cipf.es
EDAM topicProtein sequence alignment
EDAM topicPhylogenetics
Taxonall
website/phylopat.html0000644000244100017570000000267311606605754015062 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhyloPat

PhyloPat database of phylogenetic patterns

Database for the analysis of where in evolution some phylogenetic lineages were started and over which species they were contained. PhyloPat uses the latest release of EnsMartand their one-to-one, one-to-many and many-to-many orthologies.

IDPhyloPat
Homehttp://www.cmbi.ru.nl/phylopat
EDAM topicPhylogenetics
Taxonall
website/phytoprot.html0000644000244100017570000000317311606605754015266 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PhytoProt

PhytoProt protein clusters database

Database built from "all-by-all" comparison of (putative) protein sequences and sequence clustering. Relationships between sequences in a cluster and help identify annotation errors (fused genes, missing exons, frameshifts, etc).

IDPhytoProt
Homehttp://urgi.versailles.inra.fr/phytoprot/
EDAM topicProtein families
EDAM topicSequence clustering
Taxonall
website/pips.html0000644000244100017570000000245411606605754014172 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PIPs

Human protein-protein interaction prediction (PIPs)

Predicted human protein interactions.

IDPIPs
Homehttp://www.compbio.dundee.ac.uk/www-pips
EDAM topicProtein-protein interactions
TaxonHomo sapiens
website/pir.html0000644000244100017570000000553511606605754014014 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PIR

Protein sequence database of the Protein Information Resource (PIR)

Integrated protein informatics resource for genomic, proteomic and systems biology research.

IDPIR
AccDB-0078
Homehttp://pir.georgetown.edu/
EDAM topicProtein sequences
CategorySequence databases
Taxonall

Available data

Data Format Query Link
Sequence record full HTML Protein identifier {PIR accession} http://pir.georgetown.edu/cgi-bin/nbrfget?uid=%s

Example queries

Data Format Query Example
Sequence record full HTML Protein identifier {PIR accession} S12345
website/pirsf.html0000644000244100017570000000642611606605754014345 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PIRSF

PIRSF whole-protein classification database

Non-overlapping clustering of UniProtKB sequences into a hierarchical order to reflect their evolutionary relationships. The PIRSF classification system is based on whole proteins rather than on the component domains therefore, it allows annotation of generic biochemical and specific biological functions, as well as classification of proteins without well-defined domains.

IDPIRSF
AccDB-0079
Homehttp://pir.georgetown.edu/pirsf/
EDAM topicSequence clustering
EDAM topicProtein families
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Protein family annotation {PIRSF entry} HTML PIRSF ID http://pir.georgetown.edu/cgi-bin/ipcSF?id=%s

Example queries

Data Format Query Example
Protein family annotation {PIRSF entry} HTML PIRSF ID SF000186
website/plantcare.html0000644000244100017570000000344511606605754015171 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PlantCARE

Plant cis acting element

A database of different names of plant transcription sites (monocots, dicots and other) describing plant promoters, with plant transcription sites, consensus sequences and matrices.

IDPlantCARE
Homehttp://bioinformatics.psb.ugent.be/webtools/plantcare/html/
EDAM topicNucleic acid functional sites
EDAM topicTranscription
EDAM topicPlant
TaxonSpermatophyta
website/plantdnac-values.html0000644000244100017570000000326011606605754016454 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PlantDNAC-values

Plant DNA C-values database (PlantDNAC-values)

The DNA amount in the unreplicated gametic nucleus of an organism is referred to as its C-value, irrespective of the ploidy level of the taxon. The Plant DNA C-values Database currently contains data for different plant species. It combines data from the Angiosperm DNA C-values Database, Gymnosperm DNA C-values Database, the Pteridophyte DNA C-values Database, the Bryophyte DNA C-values Database, together with the addition of the Algae DNA C-values database.

IDPlantDNAC-values
Homehttp://data.kew.org/cvalues/
EDAM topicPlant
TaxonSpermatophyta
website/plantmarkers.html0000644000244100017570000000265711606605754015727 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PlantMarkers

PlantMarkers database of predicted molecular markers from plants

Predicted molecular markers from plants.

IDPlantMarkers
Homehttp://markers.btk.fi
EDAM topicGenetic mapping and linkage
EDAM topicPlant
TaxonSpermatophyta
website/plant-pis.html0000644000244100017570000000303711606605754015124 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PLANT-Pis

PLANT-Pis database for protease inhibitors and their genes in higher plants

Information on the distribution and functional properties of protease inhibitors (PIs) in higher plants.

IDPLANT-Pis
Homehttp://bighost.area.ba.cnr.it/PLANT-Pis
EDAM topicSpecific protein
EDAM topicPlant
TaxonSpermatophyta
website/plantprom.html0000644000244100017570000000351711606605754015234 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PlantProm

PlantProm database of experimental plant promoter and transcription start site

An annotated, non-redundant collection of proximal promoter sequences for RNA polymerase II with experimentally determined transcription start site(s), TSS, from various plant species.

IDPlantProm
Homehttp://mendel.cs.rhul.ac.uk/mendel.php?topic=plantprom
EDAM topicNucleic acid functional sites
EDAM topicTranscription
EDAM topicPlant
TaxonSpermatophyta
website/plantsnorna.html0000644000244100017570000000270111606605754015551 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PlantsnoRNA

Plant snoRNA database

Plant snoRNA database.

IDPlantsnoRNA
Homehttp://bioinf.scri.sari.ac.uk/cgi-bin/plant_snorna/home
EDAM topicsnoRNA
EDAM topicPlant
TaxonSpermatophyta
website/plasmodraft.html0000644000244100017570000000340711606605754015532 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PlasmoDraft

Predictions of Plasmodium falciparum gene function

Gene Ontology (GO) annotation predictions for the genes of Plasmodium falciparum. It involves both the ~60% of genes that lake GO annotation, and the genes that are already annotated in GeneDB. Predictions of PlasmoDraft are based on transcriptome, proteome, and interactome data, and are thus complementary to predictions achieved by sequence homology.

IDPlasmoDraft
Homehttp://www.atgc-montpellier.fr/PlasmoDraft/
EDAM topicAnnotation
EDAM topicGenomes
TaxonPlasmodium
website/plmitrna.html0000644000244100017570000000344111606605754015042 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PLMItRNA

PLMItRNA database of tRNAs in plant mitochondria

A database for tRNA molecules and genes in mitochondria of photosynthetic eukaryotes.

IDPLMItRNA
Homehttp://www.ba.itb.cnr.it/PLMItRNA/
EDAM topicMitochondria
EDAM topictRNA
EDAM topicGene family or system
EDAM topicPlant
TaxonSpermatophyta
website/plprot.html0000644000244100017570000000353411606605754014537 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Plprot

Plastid proteins database (Plprot)

Integrates data from large scale proteome analyses of different plastid types. These include etioplasts, chloroplasts, chromoplasts and the undifferentiated proplastid-like organelles of tobacco BY2 cells. This comparison yields a core proteome common to all plastid types and provides furthermore information about plastid type-specific functions.

IDPlprot
Homehttp://www.plprot.ethz.ch/
EDAM topicSpecific protein
EDAM topicProteome
EDAM topicOrganelles
TaxonEukaryota
website/pmap-cutdb.html0000644000244100017570000000537511606605754015260 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PMAP-CutDB

PMAP-CutDB proteolytic event database

Curated proteolytic events and pathways from the literature.

IDPMAP-CutDB
AccDB-0138
Homehttp://www.proteolysis.org/
EDAM topicPathways, networks and models
CategoryOther
Taxonall

Available data

Data Format Query Link
Data reference HTML UniProt accession http://substrate.burnham.org/lookup/uniprot/%s

Example queries

Data Format Query Example
Data reference HTML UniProt accession P05067
website/pmdb.html0000644000244100017570000000254111606605754014136 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PMDB

Protein model database (PMDB)

Three dimensional protein models from structure prediction methods. The database currently stores all models submitted to the last four editions of the CASP experiment.

IDPMDB
Homehttp://www.caspur.it/PMDB/
EDAM topicProtein tertiary structure
Taxonall
website/pmma-2dpage.html0000644000244100017570000000551311606605756015312 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PMMA-2DPAGE

Purkyne Military Medical Academy 2D-PAGE database

Purkyne Military Medical Academy 2D-PAGE database

IDPMMA-2DPAGE
AccDB-0080
Homehttp://www.pmma.pmfhk.cz/2d/2d.html
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonHomo sapiens

Available data

Data Format Query Link
2D PAGE spot annotation HTML UniProt accession http://www.pmma.pmfhk.cz/cgi-bin/get-2d-entry?%s

Example queries

Data Format Query Example
2D PAGE spot annotation HTML UniProt accession P63101
website/polymorphix.html0000644000244100017570000000250211606605754015603 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Polymorphix

Polymorphix intraspecific sequence polymorphism database

Families of polymorphic sequences.

IDPolymorphix
Homehttp://pbil.univ-lyon1.fr/polymorphix/query.php
EDAM topicMutation and polymorphism
Taxonall
website/pomamo.html0000644000244100017570000000236411606605754014507 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PoMaMo

PoMaMo potato maps database

Potato sequences, mapping info, SNPs etc.

IDPoMaMo
Homehttps://gabi.rzpd.de/PoMaMo.html
EDAM topicGenomes
TaxonSolanum tuberosum
website/ppd.html0000644000244100017570000000241411606605754013776 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PPD

PPD protein pKa values database

Protein pKa values.

IDPPD
Homehttp://www.darrenflower.info/PPD/pKahomepage.htm
EDAM topicProtein physicochemistry
Taxonall
website/ppnema.html0000644000244100017570000000265411606605754014501 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PPNEMA

rRNA genes from plant-parasitic nematodes (PPNEMA)

Plant-parasitic nematodes multialigned ribosomal cistrons.

IDPPNEMA
Homehttp://www.ppnema.uniba.it/
EDAM topicrRNA
EDAM topicGene family or system
TaxonNematoda
website/pptasedb.html0000644000244100017570000000556311606605754015025 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PptaseDB

Prokaryotic protein phosphatase database (PptaseDB)

Prokaryotic protein phosphatases.

IDPptaseDB
AccDB-0081
Homehttp://vigen.biochem.vt.edu/p3d/p3d.htm
EDAM topicSpecific protein
CategoryProtein family/group databases
TaxonBacteria

Available data

Data Format Query Link
Protein report {PptaseDB entry} HTML Protein identifier http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=accession&extref=%s

Example queries

Data Format Query Example
Protein report {PptaseDB entry} HTML Protein identifier P3D0409136
website/predict.html0000644000244100017570000000235611606605755014653 0ustar jisonindustry Bioinformatics Data Resource Catalogue

preDiCT

preDiCT database of drug effects on the heart

Drug effects on the heart.

IDpreDiCT
Homehttp://www.vph-predict.eu/
EDAM topicPharmacoinformatics
TaxonHomo sapiens
website/pride.html0000644000244100017570000000660211606605755014322 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PRIDE

PRIDE proteomics identifications database

Standards compliant, public data repository for proteomics data, protein and peptide identifications together with the evidence supporting these identifications.

IDPRIDE
AccDB-0130
Homehttp://www.ebi.ac.uk/pride
EDAM topicPeptide identification and proteolysis
EDAM topicProteomics
CategoryProteomic databases
Taxonall
RESThttp://www.ebi.ac.uk/pride/prideMartWebService.do

Available data

Data Format Query Link
Mass spectrometry data {PRIDE entry} HTML UniProt accession http://www.ebi.ac.uk/pride/searchSummary.do?queryTypeSelected=identification%20accession%20number&identificationAccessionNumber=%s

Example queries

Data Format Query Example
Mass spectrometry data {PRIDE entry} HTML UniProt accession P29375
website/prints.html0000644000244100017570000000662411606605755014542 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PRINTS

PRINTS protein motif fingerprint database

A compendium of protein fingerprints, or group of conserved motifs used to characterise a protein family.

IDPRINTS
AccDB-0082
Homehttp://umber.sbs.man.ac.uk/dbbrowser/PRINTS/
EDAM topicProtein families
EDAM topicProtein functional sites
EDAM topicSequence motifs
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Protein signature {PRINTS entry} HTML PRINTS code http://www.bioinf.manchester.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=pr00018

Example queries

Data Format Query Example
Protein signature {PRINTS entry} HTML PRINTS code pr00018
website/prism.html0000644000244100017570000000246511606605755014354 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Prism

Prism protein interaction by structural matching

Database to explore protein interfaces and predict protein-protein interactions.

IDPrism
Homehttp://prism.ccbb.ku.edu.tr/prism
EDAM topicProtein-protein interactions
Taxonall
website/probebase.html0000644000244100017570000000272011606605755015156 0ustar jisonindustry Bioinformatics Data Resource Catalogue

probeBase

probeBase database of rRNA-targeted oligonucleotide probes

rRNA-targeted oligonucleotide probes.

IDprobeBase
Homehttp://www.microbial-ecology.net/probebase
EDAM topicMolecular probes or primers
EDAM topicrRNA
Taxonall
website/procmd.html0000644000244100017570000000344211606605755014502 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProCMD

ProCMD 3D protein C mutations database

Database for molecular aspects of thrombophilic disease. It integrates clinical and phenotypical descriptions with functional and structural data obtained by computational approach to help to elucidate the chain of events leading from the molecular defect to disease.

IDProCMD
Homehttp://www.itb.cnr.it/procmd/
EDAM topicHuman disease
EDAM topicDisease
EDAM topicGenotype and phenotype
TaxonHomo sapiens
website/procognate.html0000644000244100017570000000422511606605755015357 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PROCOGNATE

PROCOGNATE ligand domain mapping for enzymes

Cognate ligands for the domains of enzyme structures in CATH, SCOP and Pfam. The database contains an assignment of PDB ligands to the domains of structures as classified by the CATH, SCOP and Pfam databases. Cognate ligands have been identified using data from the ENZYME and KEGG databases and compared to the PDB ligand using graph matching to assess chemical similarity. Cognate ligands from the known reactions in ENZYME and KEGG for a particular enzyme are then assigned to enzymes structures which have EC numbers.

IDPROCOGNATE
Homehttp://www.ebi.ac.uk/thornton-srv/databases/procognate/index.html
EDAM topicEnzymes
EDAM topicProtein-ligand interactions
EDAM topicSmall molecules
Taxonall
website/prodom.html0000644000244100017570000001660511606605755014523 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProDom

ProDom protein domain database

A comprehensive set of protein domain families automatically generated from the UniProt Knowledge Database.

IDProDom
AccDB-0083
Homehttp://prodom.prabi.fr/prodom/current/html/home.php
EDAM topicProtein families
EDAM topicProtein domains
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Protein family annotation {ProDom entry} HTML ProDom accession number http://prodom.prabi.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query=%s
Sequence alignment (protein) {ProDom family alignment} HTML ProDom accession number http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent1=%s&wanted=align
Phylogenetic tree HTML ProDom accession number http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent1=%s&wanted=tree
Sequence features (motifs) {ProDom domain image} HTML ProDom accession number http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?CG=0&question=DBLI&query=%s
Sequence alignment (protein) {ProDom family alignment} Text ProDom accession number http://prodom.prabi.fr/prodom/2006.1/cgi-bin/request.pl?db_ent0=%s

Example queries

Data Format Query Example
Protein family annotation {ProDom entry} HTML ProDom accession number PD000023
Sequence alignment (protein) {ProDom family alignment} HTML ProDom accession number PD000023
Phylogenetic tree HTML ProDom accession number PD000023
Sequence features (motifs) {ProDom domain image} HTML ProDom accession number PD000023
Sequence alignment (protein) {ProDom family alignment} Text ProDom accession number PD000023
website/prodoric.html0000644000244100017570000000307011606605755015034 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PRODORIC

PRODORIC prokaryotic database of gene regulation

Comprehensive database about gene regulation and gene expression in prokaryotes. It includes a manually curated and unique collection of transcription factor binding sites.

IDPRODORIC
Homehttp://www.prodoric.de
EDAM topicGene expression and regulation
EDAM topicTranscription factor and binding site
TaxonBacteria
website/promec.html0000644000244100017570000000274011606605755014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PromEC

PromEC verified E. coli promoters

E. coli mRNA promoters with experimentally identified transcriptional start sites.

IDPromEC
Homehttp://margalit.huji.ac.il/promec/
EDAM topicNucleic acid functional sites
EDAM topicTranscription
TaxonEscherichia coli
website/promex.html0000644000244100017570000000734111606605755014532 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProMEX

ProMEX protein mass spectral library

A mass spectral library consisting of tryptic peptide product ion spectra generated by liquid chromatography coupled to ion trap mass spectrometry (LC-ITMS). Developed using samples derived from Arabidopsis thaliana and Medicago truncatula. The database serves as a reference and can be used for protein identification in uncharacterized samples. Protein identification by ProMEX is linked to other molecular levels of biological organization such as metabolite, pathway and transcript data.

IDProMEX
AccDB-0124
Homehttp://promex.mpimp-golm.mpg.de/
EDAM topicPeptide identification and proteolysis
EDAM topicMass spectrometry
EDAM topicPlant
CategoryProteomic databases
TaxonArabidopsis, Medicago trunculata

Available data

Data Format Query Link
Mass spectrometry spectra {ProMEX entry} HTML Locus ID (AGI) http://promex.mpimp-golm.mpg.de/cgi-bin/peplib.pl?action=11&txt_query=%s

Example queries

Data Format Query Example
Mass spectrometry spectra {ProMEX entry} HTML Locus ID (AGI) At5g50600
website/prophecy.html0000644000244100017570000000302711606605755015046 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PROPHECY

PROPHECY profiling of phenotypic characteristics in yeast

Quantitative information about phenotypes for the complete collection of deletion strains in yeast (Saccharomyces cerevisiae).

IDPROPHECY
Homehttp://prophecy.lundberg.gu.se
EDAM topicGenotype and phenotype
EDAM topicFungal
TaxonSaccharomyces cerevisiae
website/prorule.html0000644000244100017570000000374211606605755014711 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProRule

ProRule collection of rules based on PROSITE predictors

ProRule section of PROSITE is constituted of manually created rules that increase the discriminatory power of PROSITE motifs (generally profiles) by providing additional information about functionally and/or structurally critical amino acids and can automatically generate annotation based on PROSITE motifs in the UniProtKB/Swiss-Prot format. Each ProRule is defined in the UniRule format.

IDProRule
Homehttp://www.expasy.org/prosite/prorule.html
EDAM topicProtein functional sites
EDAM topicSequence motifs
EDAM topicSequence profiles and HMMs
Taxonall
website/prosas.html0000644000244100017570000000323611606605755014526 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProSAS

Protein Structure and Alternative Splicing database (ProSAS)

Unified resource to analyze the effects of alternative splicing events on the structure of the resulting protein isoforms. Annotates protein structures for several Ensembl genomes. Alternative transcripts can be analyzed on the protein structure and protein function level.

IDProSAS
Homehttp://www.bio.ifi.lmu.de/ProSAS/
EDAM topicGene structure
EDAM topicProtein structure
Taxonall
website/prosat2.html0000644000244100017570000000251011606605755014603 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PROSAT2

PROSAT2 protein structure annotation tool

Tool to map SwissProt features and Prosite patterns on to a 3D structure of a protein.

IDPROSAT2
Homehttp://projects.villa-bosch.de/dbase/PDBa/
EDAM topicProtein structure
Taxonall
website/prosite.html0000644000244100017570000001113611606605755014702 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PROSITE

A Database of protein domains, families and functional sites

Documentation for protein domains, families and functional sites as well as associated patterns and profiles to identify them.

IDPROSITE
AccDB-0084
Homehttp://www.expasy.org/prosite/
EDAM topicProtein families
EDAM topicProtein domains
EDAM topicProtein functional sites
EDAM topicSequence motifs
EDAM topicSequence profiles and HMMs
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Sequence motif (protein) {PROSITE entry} Text Prosite accession number http://www.expasy.org/cgi-bin/get-prosite-raw.pl?%s
Sequence motif (protein) {PROSITE entry} HTML Prosite accession number http://www.expasy.org/cgi-bin/prosite-search-ac?%s

Example queries

Data Format Query Example
Sequence motif (protein) {PROSITE entry} Text Prosite accession number PDOC00022
Sequence motif (protein) {PROSITE entry} HTML Prosite accession number PDOC00022
website/protclustdb.html0000644000244100017570000000615011606605755015562 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProtClustDB

Entrez Protein Clusters

Entrez Protein Clusters

IDProtClustDB
AccDB-0154
Homehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=proteinclusters
EDAM topicProtein families
EDAM topicSequence clustering
CategoryPhylogenomic databases
Taxonall

Available data

Data Format Query Link
Protein family annotation HTML Protein family identifier {ProtClustDB} http://www.ncbi.nlm.nih.gov/sites/entrez?Db=proteinclusters&Cmd=DetailsSearch&Term=%u

Example queries

Data Format Query Example
Protein family annotation HTML Protein family identifier {ProtClustDB} CLSP2511638
website/proteinmodelportal.html0000644000244100017570000000553011606605755017141 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProteinModelPortal

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

Protein Model Portal of the PSI-Nature Structural Biology Knowledgebase

IDProteinModelPortal
AccDB-0159
Homehttp://www.proteinmodelportal.org/
EDAM topicProtein domains
Category3D structure databases
Taxonall

Available data

Data Format Query Link
Protein report HTML UniProt accession http://www.proteinmodelportal.org/query/uniprot/%s

Example queries

Data Format Query Example
Protein report HTML UniProt accession Q91G65
website/protepedia.html0000644000244100017570000000252311606605755015351 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Protepedia

Protepedia collaborative 3D protein encyclopedia

Free, collaborative 3D encyclopedia of proteins & other molecules.

IDProtepedia
Homehttp://www.proteopedia.org/wiki/index.php/Main_Page
EDAM topicProteins
Taxonall
website/proteus.html0000644000244100017570000000306111606605755014714 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProTeus

Protein terminus short linear sequences

Tool for identification of short linear signatures in protein termini, based on a positional-based search method for revealing short significant signatures in termini of proteins.

IDProTeus
Homehttp://www.proteus.cs.huji.ac.il
EDAM topicProtein functional sites
EDAM topicSequence motifs
Taxonall
website/protonet.html0000644000244100017570000000755111606605755015075 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ProtoNet

ProtoNet automatic hierarchical classification of proteins

Automatic hierarchical classification of protein sequences.

IDProtoNet
AccDB-0085
Homehttp://www.protonet.cs.huji.ac.il/
EDAM topicProtein families
CategoryOther
Taxonall

Available data

Data Format Query Link
Protein family annotation {ProtoNet entry} HTML UniProt accession http://www.protonet.cs.huji.ac.il/sp.php?prot=%s
Protein family annotation {ProtoNet entry} DASGFF UniProt accession http://www.protonet.cs.huji.ac.il/das/protonet/features?segment=%s

Example queries

Data Format Query Example
Protein family annotation {ProtoNet entry} HTML UniProt accession P01011
Protein family annotation {ProtoNet entry} DASGFF UniProt accession P01011
website/pseudobase.html0000644000244100017570000000244311606605756015351 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PseudoBase

PseudoBase RNA pseudoknots database

Collection of RNA pseudoknots.

IDPseudoBase
Homehttp://www.ekevanbatenburg.nl/PKBASE/PKB.HTML
EDAM topicRNA structure and alignment
Taxonall
website/pseudocap.html0000644000244100017570000000775311606605756015213 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PseudoCAP

PseudoCAP pseudomonas genome database

Pseudomonas genome database.

IDPseudoCAP
AccDB-0086
Homehttp://www.pseudomonas.com/
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonPseudomonas

Available data

Data Format Query Link
Gene annotation HTML Locus ID (PseudoCAP) http://www.pseudomonas.com/getAnnotation.do?locusID=%s
Gene annotation HTML GI number http://www.pseudomonas.com/getAnnotation.do?gi=%s

Example queries

Data Format Query Example
Gene annotation HTML Locus ID (PseudoCAP) PA0006
Gene annotation HTML GI number 15596473
website/pstiing.html0000644000244100017570000000407711606605756014701 0ustar jisonindustry Bioinformatics Data Resource Catalogue

pSTIING

Protein, signalling, transcriptional interactions and inflammation networks gateway (pSTIING)

Protein-protein, protein-lipid, protein-small molecules, ligand-receptor interactions, receptor-cell type information, transcriptional regulatory and signal transduction modules relevant to inflammation, cell migration and tumourigenesis. It integrates in-house curated information from the literature, biochemical experiments, functional assays and in vivo studies, with publicly available information from multiple and diverse sources across human, rat, mouse, fly, worm and yeast.

IDpSTIING
Homehttp://pstiing.licr.org/
EDAM topicGene regulatory networks
EDAM topicProtein interactions
EDAM topicPathways, networks and models
TaxonMetazoa
website/ptch.html0000644000244100017570000000340311606605756014152 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PTCH

PTCH mutation database

Information on mutations and polymorphisms in the PTCH1 gene. The human homologue of Drosophila patched, PTCH1, has been identified as the gene underlying the cancer predisposition syndrome Nevoid Basal Cell Carcinoma Syndrome (NBCCS, OMIM 109400). This syndrome is also known as Gorlin's syndrome or Basal Cell Nevus Syndrome.

IDPTCH
Homehttp://www.cybergene.se/cgi-bin/w3-msql/ptchbase/index.html
EDAM topicMutation and polymorphism
EDAM topicCancer
TaxonHomo sapiens
website/pubchem.html0000644000244100017570000000245411606605756014644 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PubChem

PubChem

Information on the biological activities of small molecules, including bioassay records, chemical structures and substances.

IDPubChem
Homehttp://pubchem.ncbi.nlm.nih.gov/
EDAM topicSmall molecules
Taxonall
website/pubmeth.html0000644000244100017570000001017011606605756014657 0ustar jisonindustry Bioinformatics Data Resource Catalogue

PubMeth

PubMeth reviewed methylation database in cancer

An annotated and reviewed database of methylation in cancer. It is based on automated textmining of literature and is afterwards manually curated and annotated.

IDPubMeth
Homehttp://www.pubmeth.org
EDAM topicCancer
EDAM topicDNA
TaxonEukaryota

Available data

Data Format Query Link
Gene annotation {PubMeth gene entry} HTML Gene symbol http://matrix.ugent.be/temp/static/%s.html
Gene annotation {PubMeth gene entry (cancer record)} HTML Gene symbol; Identifier (typed) {Cancer type} http://matrix.ugent.be/temp/static/%s1_%s2.html

Example queries

Data Format Query Example
Gene annotation {PubMeth gene entry} HTML Gene symbol CDKN2A
Gene annotation {PubMeth gene entry (cancer record)} HTML Gene symbol; Identifier (typed) {Cancer type} CDKN2A;lung
website/rat-heart-2dpage.html0000644000244100017570000000572411606605756016253 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Rat-heart-2DPAGE

2-DE database of rat heart, at German Heart Institute Berlin, Germany

2-DE database of rat heart, at German Heart Institute Berlin, Germany

IDRat-heart-2DPAGE
AccDB-0087
Homehttp://www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d/
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonHomo sapiens

Available data

Data Format Query Link
2D PAGE spot annotation HTML UniProt accession http://www.mpiib-berlin.mpg.de/mpiib-cgi/RAT-HEART/get-2d-entry?%s

Example queries

Data Format Query Example
2D PAGE spot annotation HTML UniProt accession P62738
website/ratmap.html0000644000244100017570000000317211606605756014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RATMAP

RATMAP rat genome database

Rat genome database.

IDRATMAP
Homehttp://ratmap.gen.gu.se/
EDAM topicVertebrate
EDAM topicGenomes
CategoryNot available
TaxonRattus

Example queries

Data Format Query Example
website/rb1genemutation.html0000644000244100017570000000240711606605756016323 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RB1GeneMutation

RB1 gene mutation database (RB1GeneMutation)

Retinoblastoma genetics database.

IDRB1GeneMutation
Homehttp://www.verandi.de/joomla/
EDAM topicHuman disease
TaxonHomo sapiens
website/rdg.html0000644000244100017570000000260611606605756013774 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RDG

Rat genome database (RDG)

Rat genome database.

IDRDG
Homehttp://rgd.mcw.edu/
EDAM topicVertebrate
EDAM topicGenomes
CategoryNot available
TaxonRattus
website/reactome.html0000644000244100017570000002700311606605756015015 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Reactome

Reactome knowledgebase of biological pathways

Curated knowledgebase of biological pathways and processes.

IDReactome
AccDB-0088
Homehttp://www.reactome.org/
EDAM topicPathways, networks and models
CategoryEnzyme and pathway databases
Taxonall
Linkinghttp://www.reactome.org/referring2GK.html
SOAPhttp://www.reactome.org/download/index.html

Available data

Data Format Query Link
Pathway or network report HTML Pathway ID (reactome) http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID=%s&ZOOM=2
Pathway or network report XML Pathway ID (reactome) http://www.reactome.org/cgi-bin/sbml_export?DB=gk_current&ID=%s
Protein report {Reactome entry} HTML Database name; Protein identifier http://www.reactome.org/cgi-bin/link?SOURCE=%s1&ID=%s2
Protein report {Reactome entry} HTML UniProt accession http://www.reactome.org/cgi-bin/link?SOURCE=UNIPROT&ID=%s
Protein report {Reactome entry} HTML ChEBI ID http://www.reactome.org/cgi-bin/link?SOURCE=CHEBI&ID=%s
Protein report {Reactome entry} HTML Compound name http://www.reactome.org/cgi-bin/link?SOURCE=COMPOUND&ID=%s
Protein report {Reactome entry} HTML GO term ID http://www.reactome.org/cgi-bin/link?SOURCE=GO&ID=%s
Protein report {Reactome entry} HTML EC number http://www.reactome.org/cgi-bin/link?SOURCE=EC&ID=%s
Protein report {Reactome entry} HTML Gene ID (NCBI) http://www.reactome.org/cgi-bin/link?SOURCE=Entrez+Gene&ID=%s
Protein report {Reactome entry} HTML Pathway ID (reactome) http://www.reactome.org/cgi-bin/link?SOURCE=Reactome&ID=%s

Example queries

Data Format Query Example
Protein report {Reactome entry} HTML UniProt accession P30304
Protein report {Reactome entry} HTML ChEBI ID 15422
Protein report {Reactome entry} HTML Compound name C00002
Protein report {Reactome entry} HTML GO term ID 0030060
Protein report {Reactome entry} HTML EC number 1.1.1.37
Protein report {Reactome entry} HTML Gene ID (NCBI) 4171
Pathway or network report HTML Pathway ID (reactome) REACT_1
Pathway or network report XML Pathway ID (reactome) REACT_1
Protein report {Reactome entry} HTML Pathway ID (reactome) REACT_1
website/rebase.html0000644000244100017570000000723011606605756014457 0ustar jisonindustry Bioinformatics Data Resource Catalogue

REBASE

REBASE restriction enzymes and methylases database

Restriction enzymes and methylases database.

IDREBASE
AccDB-0089
Homehttp://rebase.neb.com/
EDAM topicEnzymes
CategoryProtein family/group databases
Taxonall

Available data

Data Format Query Link
Protein report (enzyme) HTML Enzyme name http://rebase.neb.com/rebase/enz/%s.html
Protein report (enzyme) HTML REBASE enzyme number http://rebase.neb.com/rebase/enz/%s.html

Example queries

Data Format Query Example
Protein report (enzyme) HTML Enzyme name EcoRI
Protein report (enzyme) HTML REBASE enzyme number 993
website/redidb.html0000644000244100017570000001370711606605756014455 0ustar jisonindustry Bioinformatics Data Resource Catalogue

REDIdb

RNA editing database (REDIdb)

Sequences post-transcriptionally modified by RNA editing from primary databases and literature. All editing information such as substitutions, insertions and deletions occurring in a wide range of organisms is stored.

IDREDIdb
Homehttp://biologia.unical.it/py_script/overview.html
EDAM topicGene structure
Taxonall

Available data

Data Format Query Link
Sequence record lite {REDIdb entry} HTML REDIdb ID http://biologia.unical.it/py_script/cgi-bin/retrieve.py?query=%s
Sequence record lite {REDIdb fasta} FASTA-HTML REDIdb ID http://biologia.unical.it/py_script/cgi-bin/fasta.py?query=%s
Sequence alignment (nucleic acid) {REDIdb overview} HTML REDIdb ID http://biologia.unical.it/py_script/cgi-bin/display.py?query=%s
Sequence alignment (nucleic acid) {REDIdb alignment} HTML REDIdb ID http://biologia.unical.it/py_script/cgi-bin/align.py?query=%s

Example queries

Data Format Query Example
Sequence record lite {REDIdb entry} HTML REDIdb ID EDI_000000002
Sequence record lite {REDIdb fasta} FASTA-HTML REDIdb ID EDI_000000002
Sequence alignment (nucleic acid) {REDIdb overview} HTML REDIdb ID EDI_000000002
Sequence alignment (nucleic acid) {REDIdb alignment} HTML REDIdb ID EDI_000000002
website/refseq.html0000644000244100017570000000642311606605756014506 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RefSeq

NCBI reference sequences

A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. Provides a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.

IDRefSeq
AccDB-0117
Homehttp://www.ncbi.nlm.nih.gov/RefSeq/
EDAM topicSequence
EDAM topicComparative genomics
CategorySequence databases
Taxonall

Available data

Data Format Query Link
Sequence record {RefSeq entry} HTML Protein identifier {Refseq} http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&id=%s

Example queries

Data Format Query Example
Sequence record {RefSeq entry} HTML Protein identifier {Refseq} YP_654574.1
website/repairtoire.html0000644000244100017570000000273311606605756015546 0ustar jisonindustry Bioinformatics Data Resource Catalogue

REPAIRtoire

REPAIRtoire DNA repair pathways

Components involved in the repair mechanisms for all kinds of cellular DNA lesions. Four repair pathways (from H.sapiens, E.coli and S.cerevisiae) are contained, together with their protein components and molecular events that trigger those pathways.

IDREPAIRtoire
Homehttp://repairtoire.genesilico.pl/
EDAM topicPathways, networks and models
Taxonall
website/reproduction-2dpage.html0000644000244100017570000000762311606605756017101 0ustar jisonindustry Bioinformatics Data Resource Catalogue

REPRODUCTION-2DPAGE

REPRODUCTION-2DPAGE database

REPRODUCTION-2DPAGE 2D gel protein database.

IDREPRODUCTION-2DPAGE
IDaltREPRODUCTION2DPAGE
AccDB-0090
Homehttp://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML UniProt accession http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s&format=text
Experiment annotation (2D PAGE) Text UniProt accession http://reprod.njmu.edu.cn/cgi-bin/2d/2d.cgi?ac=%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML UniProt accession P00352
Experiment annotation (2D PAGE) Text UniProt accession P00352
website/resid.html0000644000244100017570000000546411606605756014333 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RESID

RESID database of protein modifications

A comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

IDRESID
Homehttp://www.ebi.ac.uk/RESID/
EDAM topicProtein modifications
Taxonall

Available data

Data Format Query Link
Protein modification annotation {RESID entry} XML RESID ID http://www.ebi.ac.uk/ontology-lookup/RESIDService?resid_id=%s

Example queries

Data Format Query Example
Protein modification annotation {RESID entry} XML RESID ID AA0002
website/retroryza.html0000644000244100017570000000267411606605756015266 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RetrOryza

RetrOryza database of rice LTR retrotransposons

Information and resources related to LTR-retrotransposons in rice genome.

IDRetrOryza
Homehttp://www.retroryza.org
EDAM topicMobile genetic elements
EDAM topicPlant
TaxonOryza sativa
website/rfam.html0000644000244100017570000001353511606605756014150 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RFAM

RNA families database of alignments and CMs

Collection of multiple sequence alignments and covariance models covering many common non-coding RNA families. The main use of Rfam is as a source of RNA multiple alignments with consensus secondary structure annotation in a consistent format.

IDRFAM
IDaltRFam
Homehttp://rfam.sanger.ac.uk/
EDAM topicNucleic acid sequence alignment
EDAM topicRNA structure and alignment
CategoryNot available
Taxonall

Available data

Data Format Query Link
RNA family annotation HTML RFAM accession http://rfam.sanger.ac.uk/family?acc=%s
RNA family annotation HTML RFAM name http://rfam.sanger.ac.uk/family?acc=%s
RNA family annotation XML RFAM accession http://rfam.sanger.ac.uk/family?acc=%s&output=xml
RNA family annotation XML RFAM name http://rfam.sanger.ac.uk/family?acc=%s&output=xml

Example queries

Data Format Query Example
RNA family annotation HTML RFAM accession RF00522
RNA family annotation XML RFAM accession RF00522
RNA family annotation HTML RFAM name PreQ1
RNA family annotation XML RFAM name PreQ1
website/rgd.html0000644000244100017570000001054111606605756013771 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RGD

Rat genome database

Rat genome database (RGD) goal is to collect, consolidate, and integrate data generated from ongoing rat genetic and genomic research efforts and make these data widely available to the scientific community. A secondary, but critical goal is to provide curation of mapped positions for quantitative trait loci, known mutations and other phenotypic data.

IDRGD
AccDB-0091
Homehttp://rgd.mcw.edu/
EDAM topicVertebrate
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonRattus

Available data

Data Format Query Link
Gene annotation {RGD report} HTML RGD ID http://rgd.mcw.edu/generalSearch/RgdSearch.jsp?quickSearch=1&searchKeyword=[%s]
Gene annotation {RGD report} XML RGD ID http://rgd.mcw.edu/rgdweb/search/genes.html?term=%s&speciesType=3&fmt=6

Example queries

Data Format Query Example
Gene annotation {RGD report} HTML RGD ID 620528
Gene annotation {RGD report} XML RGD ID 620528
website/rhea.html0000644000244100017570000000276311606605757014144 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Rhea

Rhea

A reaction database, where all reaction participants (reactants and products) are linked to the ChEBI database (Chemical Entities of Biological Interest) which provides detailed information about structure, formula and charge. Rhea provides built-in validations that ensure both elemental and charge balance of the reactions.

IDRhea
Homehttp://www.ebi.ac.uk/rhea/about.xhtml
EDAM topicEnzymes
Taxonall
website/rissc.html0000644000244100017570000000246711606605757014351 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RISSC

Ribosomal internal spacer sequence collection (RISSC)

Ribosomal 16S-23S spacer sequences intended mainly for molecular biology studies in typing, phylogeny and population genetics.

IDRISSC
Homehttp://egg.umh.es/rissc
EDAM topicRibosomes
Taxonall
website/rna-frabase.html0000644000244100017570000000260411606605757015400 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RNA-FRABASE

RNA FRABASE database

Database to search the three-dimensional fragments within 3D RNA structures using as an input the sequence(s) and / or secondary structure(s) given in the dot-bracket notation.

IDRNA-FRABASE
Homehttp://rnafrabase.ibch.poznan.pl/
EDAM topicRNA structure and alignment
Taxonall
website/rnavirusdb.html0000644000244100017570000000540311606605757015376 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RNAVirusDB

RNA virus genome database (RNAVirusDB)

RNA virus genome database.

IDRNAVirusDB
Homehttp://tree.bio.ed.ac.uk/rnavirusdb
EDAM topicVirus
EDAM topicGenomes
TaxonViruses

Available data

Data Format Query Link
Virus annotation HTML RNAVirusDB ID http://tree.bio.ed.ac.uk/rnavirusdb/virus.php?id=%s

Example queries

Data Format Query Example
Virus annotation HTML RNAVirusDB ID 56486
website/rnrdb.html0000644000244100017570000000326711606605757014334 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RNRdb

Ribonucleotide reductase database (RNRdb)

Compilation of all published 3D structures of different RNR proteins as well as a compilation of all mutant proteins constructed including links to the relevant publication(s). It is used to retrieve RNR protein sequences from any organism that have been either experimentally characterised or predicted from genome sequence data.

IDRNRdb
Homehttp://rnrdb.molbio.su.se/
EDAM topicSpecific protein
EDAM topicProtein tertiary structure
Taxonall
website/rouge.html0000644000244100017570000000632111606605757014340 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Rouge

Rodent unidentified gene-encoded large proteins database (Rouge)

A sister database of HUGE protein database which has accumulated the results of comprehensive sequence analysis of human long cDNAs (KIAA cDNAs). The ROUGE protein database has been created to publicize the information obtained from mouse homologues of the KIAA cDNAs (mKIAA cDNAs).

IDRouge
AccDB-0092
Homehttp://www.kazusa.or.jp/rouge/
EDAM topicProtein sequences
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonMus

Available data

Data Format Query Link
Gene annotation (functional) {Rouge entry} HTML mFLJ/mKIAA number http://www.kazusa.or.jp/rouge/gfpage/%s

Example queries

Data Format Query Example
Gene annotation (functional) {Rouge entry} HTML mFLJ/mKIAA number mFLJ00002
website/rsitedb.html0000644000244100017570000000341311606605757014652 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RsiteDB

RNA binding site database (RsiteDB)

Interactions of extruded, unpaired RNA nucleotide bases. It presents and classifies the protein binding pockets that accommodate them. It allows the recognition of similar protein binding patterns involved in interactions with different RNA molecules. Given an unbound structure of a target protein it allows the prediction of its RNA nucleotide binding sites.

IDRsiteDB
Homehttp://bioinfo3d.cs.tau.ac.il/RsiteDB/
EDAM topicNucleic acid functional sites
EDAM topicProtein-nucleic acid interactions
Taxonall
website/rtkdb.html0000644000244100017570000000237211606605757014327 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RTKdb

Receptor tyrosine kinase database (RTKdb)

Receptor tyrosine kinase database.

IDRTKdb
Homehttp://pbil.univ-lyon1.fr/RTKdb/
EDAM topicSpecific protein
TaxonEukaryota
website/rtprimerdb.html0000644000244100017570000000306511606605757015373 0ustar jisonindustry Bioinformatics Data Resource Catalogue

RTPrimerDB

PCR primers and probes database (RTPrimerDB)

Database of primer and probe sequences used in real-time PCR assays employing popular chemistries (SYBR Green I, Taqman, Hybridisation Probes, Molecular Beacon) to prevent time-consuming primer design and experimental optimisation, and to introduce a certain level of uniformity and standardisation among different laboratories.

IDRTPrimerDB
Homehttp://medgen.ugent.be/rtprimerdb/
EDAM topicMolecular probes or primers
Taxonall
website/s4.html0000644000244100017570000000256411606605757013552 0ustar jisonindustry Bioinformatics Data Resource Catalogue

S4

S4 structure-based sequence alignments of SCOP superfamilies

An automatically generated database of multiple structure-based sequence alignments of protein superfamilies in the SCOP database.

IDS4
Homehttp://compbio.mds.qmw.ac.uk/S4.html
EDAM topicProtein sequence alignment
Taxonall
website/sabio-rk.html0000644000244100017570000001122511606605757014725 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SABIO-RK

Database for biochemical reactions and their kinetics.

Biochemical pathways and reaction kinetics.

IDSABIO-RK
Homehttp://sabio.villa-bosch.de/SABIORK
EDAM topicPathways, networks and models
Taxonall

Available data

Data Format Query Link
Reaction annotation {SABIO-RK reaction} HTML Reaction ID (SABIO-RK) http://sabio.h-its.org/index2.jsp?reac=%s
Enzyme kinetics data {SABIO-RK Kinetic Record} HTML Reaction kinetics ID (SABIO-RK) http://sabio.h-its.org/kineticLawEntry.jsp?kinlawid=%s
Data reference {SABIO-RK EC code} HTML EC number http://sabio.h-its.org/index2.jsp?EC=%s

Example queries

Data Format Query Example
Reaction annotation {SABIO-RK reaction} HTML Reaction ID (SABIO-RK) 75
Enzyme kinetics data {SABIO-RK Kinetic Record} HTML Reaction kinetics ID (SABIO-RK) 5046
Data reference {SABIO-RK EC code} HTML EC number 2.1.1.45
website/saffron_genes.html0000644000244100017570000000265411606605757016043 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Saffron_Genes

Saffron genes database

EST sequences from saffron (Crocus sativus) stigmas.

IDSaffron_Genes
Homehttp://www.saffrongenes.org
EDAM topicmRNA, EST or cDNA
EDAM topicGene family or system
TaxonCrocus sativus
website/scop.html0000644000244100017570000001163311606605757014165 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SCOP

Structural classification of proteins (SCOP) database

The SCOP database, created by manual inspection and abetted by a battery of automated methods, aims to provide a detailed and comprehensive description of the structural and evolutionary relationships between all proteins whose structure is known. As such, it provides a broad survey of all known protein folds, detailed information about the close relatives of any particular protein, and a framework for future research and classification.

IDSCOP
Homehttp://scop.mrc-lmb.cam.ac.uk/scop
EDAM topicProtein domains
Taxonall

Available data

Data Format Query Link
SCOP node HTML SCOP sunid http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?sunid=%s
Data reference {PDB Entry search} HTML PDB ID http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?PDB=%s
Data reference HTML Identifier {Keyword} http://scop.mrc-lmb.cam.ac.uk/scop/search.cgi?key=%s

Example queries

Data Format Query Example
SCOP node HTML SCOP sunid 47718
Data reference {PDB Entry search} HTML PDB ID 1djh
Data reference HTML Identifier {Keyword} immunoglobulin
website/scoppi.html0000644000244100017570000000271311606605757014515 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SCOPPI

Structural Classification of Protein-Protein Interfaces (SCOPPI)

Domain-domain interactions and their interfaces derived from PDB structure files and SCOP domain definitions. Interfaces are classified according to the geometry of the domain associations and are annotated with various interaction characteristics.

IDSCOPPI
Homehttp://www.scoppi.org
EDAM topicProtein-protein interactions
Taxonall
website/scowl.html0000644000244100017570000000640111606605757014345 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SCOWL

Structural characterization of water, ligands and proteins (SCOWL)

PDB interface interactions at atom, residue and domain level. The database contains protein interfaces and residue-residue interactions formed by structural units and interacting solvent.

IDSCOWL
Homehttp://www.scowlp.org
EDAM topicProtein interactions
Taxonall

Available data

Data Format Query Link
Domain-domain interaction HTML PDB ID http://www.scowlp.org/scowlp/PDB.action?show=&PDBId=%s
Domain-domain interaction HTML SCOP sunid {SCOP family id} http://www.scowlp.org/scowlp/Search.action?childs=¤tChoice=SCOP_FAMILY%s

Example queries

Data Format Query Example
Domain-domain interaction HTML PDB ID 1fxk
website/seattlesnps.html0000644000244100017570000000625311606605757015570 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SeattleSNPs

SeattleSNPs variation discovery resource

Database for identifying, genotyping, and modelling the associations between single nucleotide polymorphisms (SNPs) in candidate genes and pathways that underlie inflammatory responses in humans.

IDSeattleSNPs
Homehttp://pga.gs.washington.edu/
EDAM topicMutation and polymorphism
EDAM topicPathways, networks and models
EDAM topicGenotype and phenotype
CategoryPolymorphism databases
TaxonHomo sapiens

Available data

Data Format Query Link
Gene annotation HTML Gene name (HGNC) http://pga.gs.washington.edu/data/%s/

Example queries

Data Format Query Example
Gene annotation HTML Gene name (HGNC) a4galt
website/sebida.html0000644000244100017570000000320611606605757014445 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Sebida

Sebida sex-biased genes

Functional and evolutionary analysis of sex-biased genes. Sebida integrates data from multiple microarray studies comparing male versus female gene expression in D. melanogaster, D. simulans, and A. gambiae.

IDSebida
Homehttp://www.sebida.de
EDAM topicGene family or system
EDAM topicGene expression and regulation
TaxonAnophelea, Drosophila
website/seed.html0000644000244100017570000001110511606605757014133 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SEED

The SEED genome comparison environment

Environment for comparative genome analysis.

IDSEED
Homehttp://www.theseed.org/
EDAM topicComparative genomics
CategoryNot available
Taxonall

Available data

Data Format Query Link
Genome metadata HTML FIG ID {Genome fig} http://www.theseed.org/linkin.cgi?genome=fig|%s
Gene annotation (functional) HTML FIG ID {PEG ID} http://www.theseed.org/linkin.cgi?id=fig|%s
Gene annotation {RNA feature} HTML FIG ID {RNA fig} http://www.theseed.org/linkin.cgi?id=fig|%s

Example queries

Data Format Query Example
Genome metadata HTML FIG ID {Genome fig} 83333.1
Gene annotation (functional) HTML FIG ID {PEG ID} 83333.1.peg.123
Gene annotation {RNA feature} HTML FIG ID {RNA fig} 83333.1.rna.1
website/selectome.html0000644000244100017570000002277411606605757015211 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Selectome

Selectome database of positive selection

Database of positive selection based on a rigorous branch-site specific likelihood test.

IDSelectome
Homehttp://bioinfo.unil.ch/selectome/
EDAM topicPhylogenetics
EDAM topicGene family or system
Taxonall

Available data

Data Format Query Link
Phylogenetic tree {Selectome entry} HTML Identifier {Selectome identifier}; Protein family name; Taxon http://bioinfo.unil.ch/cgi-bin/selectome/subfamily.cgi?ac=%s1&sub=%s2&taxon=%s3
Gene annotation {Selectome family} HTML Identifier {Selectome identifier} http://bioinfo.unil.ch/cgi-bin/selectome/getFamily.cgi?query=%s
Data reference {Selectome Xref} HTML Protein identifier {Cross-reference} http://bioinfo.unil.ch/cgi-bin/selectome/getXref.cgi?query=%s
Data reference {Selectome Xref} HTML PDB ID {Cross-reference} http://bioinfo.unil.ch/cgi-bin/selectome/getXref.cgi?query=%s
Data reference {Selectome genes} HTML Identifier {Keyword} http://bioinfo.unil.ch/cgi-bin/selectome/getGene.cgi?query=%s
Data reference {Selectome gene family} HTML Identifier {Keyword} http://bioinfo.unil.ch/cgi-bin/selectome/getGeneFamily.cgi?query=%s

Example queries

Data Format Query Example
Gene annotation {Selectome family} HTML Identifier {Selectome identifier} TF105041
Phylogenetic tree {Selectome entry} HTML Identifier {Selectome identifier}; Protein family name; Taxon TF105041;1;v
Data reference {Selectome genes} HTML Identifier {Keyword} kidney
Data reference {Selectome gene family} HTML Identifier {Keyword} kidney
Data reference {Selectome genes} HTML Identifier {Keyword} Ascc3_F2
Data reference {Selectome gene family} HTML Identifier {Keyword} Ascc3_F2
Data reference {Selectome genes} HTML Identifier {Keyword} BRCA2
Data reference {Selectome gene family} HTML Identifier {Keyword} BRCA2
website/sgd.html0000644000244100017570000001231211606605757013771 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SGD

Saccharomyces genome database (SGD)

Database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

IDSGD
AccDB-0095
Homehttp://www.yeastgenome.org/
EDAM topicYeast
EDAM topicGenomes
EDAM topicFungal
CategoryOrganism-specific databases
TaxonSaccharomyces cerevisiae

Available data

Data Format Query Link
Gene annotation {Locus Summary page (gene page)} HTML Locus ID (SGD) http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=%s
Gene annotation {Locus Summary page (gene page)} HTML ORF name http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=%s
Gene annotation {Locus Summary page (gene page)} HTML Gene symbol http://www.yeastgenome.org/cgi-bin/locus.fpl?locus=%s

Example queries

Data Format Query Example
Gene annotation {Locus Summary page (gene page)} HTML Locus ID (SGD) S000000981
Gene annotation {Locus Summary page (gene page)} HTML ORF name YER179W
Gene annotation {Locus Summary page (gene page)} HTML Gene symbol DMC1
website/siena-2dpage.html0000644000244100017570000000566311606605757015466 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Siena-2DPAGE

2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy

2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy

IDSiena-2DPAGE
AccDB-0096
Homehttp://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonHomo sapiens

Available data

Data Format Query Link
2D PAGE spot annotation HTML UniProt accession http://www.bio-mol.unisi.it/cgi-bin/2d/2d.cgi?%s

Example queries

Data Format Query Example
2D PAGE spot annotation HTML UniProt accession P31937
website/signalinggateway.html0000644000244100017570000000275611606605760016556 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SignalingGateway

UCSD-Nature Signaling Gateway Molecule Pages

Information on over 4000 proteins involved in cellular signaling. Each 'molecule page' contains regularly updated information derived from public data sources as well as sequence analysis, references and links to other databases.

IDSignalingGateway
Homehttp://www.signaling-gateway.org/molecule/
EDAM topicSignalling pathways
Taxonall
website/silva-lsu.html0000644000244100017570000000602411606605760015130 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SILVA-LSU

SILVA ribosomal RNA sequence data (large subunit)

SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

IDSILVA-LSU
Homehttp://www.arb-silva.de
EDAM topicrRNA
EDAM topicNucleic acid sequences
Taxonall

Available data

Data Format Query Link
Sequence metadata {SILVA database entry 23S/28S} HTML Sequence accession (nucleic acid) http://www.arb-silva.de/browser/lsu/%s

Example queries

Data Format Query Example
Sequence metadata {SILVA database entry 23S/28S} HTML Sequence accession (nucleic acid) AB426552
website/silva-ssu.html0000644000244100017570000000600411606605760015135 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SILVA-SSU

SILVA ribosomal RNA sequence data (small subunit)

SILVA provides comprehensive, quality checked and regularly updated databases of aligned small (16S/18S, SSU) and large subunit (23S/28S, LSU) ribosomal RNA (rRNA) sequences for all three domains of life (Bacteria, Archaea and Eukarya).

IDSILVA-SSU
Homehttp://www.arb-silva.de
EDAM topicrRNA
EDAM topicNucleic acid sequences
Taxonall

Available data

Data Format Query Link
Sequence metadata {SILVA database entry} HTML Sequence accession (nucleic acid) http://www.arb-silva.de/browser/ssu/%s

Example queries

Data Format Query Example
Sequence metadata {SILVA database entry} HTML Sequence accession (nucleic acid) AB426552
website/simap.html0000644000244100017570000001342111606605760014321 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SIMAP

Similarity matrix of proteins (SIMAP)

Pre-calculated protein similarities. It contains published protein sequences and is continuously updated.

IDSIMAP
Homehttp://boinc.bio.wzw.tum.de/boincsimap/
EDAM topicProtein families
Taxonall

Available data

Data Format Query Link
Protein report HTML Identifier {md5 hash of sequence} http://webclu.bio.wzw.tum.de/portal/web/simap/link?p_p_id=LinkPortlet_WAR_SIMAP&p_p_action=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-2&p_p_col_count=2&method=proteinReport&md5=%s
Database hits (sequence) {SIMAP sequence similarities} HTML Identifier {md5 hash of sequence} http://webclu.bio.wzw.tum.de/portal/web/simap/link?p_p_id=LinkPortlet_WAR_SIMAP&p_p_action=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-2&p_p_col_count=2&method=sequenceHomologs&md5=%s
Protein report {SIMAP domain architecture similarities} HTML Identifier {md5 hash of sequence} http://webclu.bio.wzw.tum.de/portal/web/simap/link?p_p_id=LinkPortlet_WAR_SIMAP&p_p_action=1&p_p_state=normal&p_p_mode=view&p_p_col_id=column-2&p_p_col_count=2&method=domainHomologs&md5=%s

Example queries

Data Format Query Example
Protein report HTML Identifier {md5 hash of sequence} 5bd410d0d1f3fa2c0607eb453835857f
Database hits (sequence) {SIMAP sequence similarities} HTML Identifier {md5 hash of sequence} 5bd410d0d1f3fa2c0607eb453835857f
Protein report {SIMAP domain architecture similarities} HTML Identifier {md5 hash of sequence} 5bd410d0d1f3fa2c0607eb453835857f
website/sirnadb.html0000644000244100017570000000233211606605760014631 0ustar jisonindustry Bioinformatics Data Resource Catalogue

siRNAdb

siRNAdb database

siRNAdb database

IDsiRNAdb
Homehttp://sirna.sbc.su.se/sirnadb_050915.txt
EDAM topicsiRNA
Taxonall
website/sisyphus.html0000644000244100017570000000542711606605760015106 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SISYPHUS

SISYPHUS database of protein structure alignments

Structural alignments for proteins with non-trivial relationships.

IDSISYPHUS
Homehttp://sisyphus.mrc-cpe.cam.ac.uk
EDAM topicProtein structure alignment
Taxonall

Available data

Data Format Query Link
Structure alignment (protein) {SISYPHUS alignment} XML SISYPHUS ID http://sisyphus.mrc-cpe.cam.ac.uk/sisyphus/das/alignments/alignment?query=%s

Example queries

Data Format Query Example
Structure alignment (protein) {SISYPHUS alignment} XML SISYPHUS ID AL00050692
website/sitesbase.html0000644000244100017570000000366011606605760015176 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SitesBase

SitesBase database

Known ligand binding sites within PDB navigable by PDB identifier or ligand 3 letter code e.g. NAD. Each binding site has a frequently updated register of structurally similar binding sites sharing atomic similarity detected by geometric hashing. Multiple alignments, structural superpositions and links to other structural databases are also available enabling further analysis.

IDSitesBase
Homehttp://www.modelling.leeds.ac.uk/sb/
EDAM topicProtein functional sites
EDAM topicProtein-ligand interactions
EDAM topicProtein sequence alignment
Taxonall
website/s_martdb.html0000644000244100017570000000273711606605757015021 0ustar jisonindustry Bioinformatics Data Resource Catalogue

S_MARtDB

The S/MAR transaction database (S/MARtDB)

Information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human.

IDS_MARtDB
Homehttp://smartdb.bioinf.med.uni-goettingen.de/
EDAM topicSpecific protein
TaxonEukaryota
website/smart.html0000644000244100017570000001001111606605760014326 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SMART

Simple modular architecture research tool (SMART)

SMART protein domain database.

IDSMART
AccDB-0097
Homehttp://smart.embl.de/
EDAM topicProtein families
EDAM topicProtein domains
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Protein structure report (domain) {SMART entry} HTML SMART domain name http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY
Protein structure report (domain) {SMART entry} HTML SMART accession number http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s&BLAST=DUMMY

Example queries

Data Format Query Example
Protein structure report (domain) {SMART entry} HTML SMART domain name KISc
Protein structure report (domain) {SMART entry} HTML SMART accession number SM00129
website/smpdb.html0000644000244100017570000000340511606605760014316 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SMPDB

Small Molecule Pathway Database (SMPDB)

Small molecule pathways found in humans. It provides detailed, fully searchable, hyperlinked diagrams of human metabolic pathways, metabolic disease pathways, metabolite signaling pathways and drug-action pathways. All SMPDB pathways include information on the relevant organs, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures.

IDSMPDB
Homehttp://www.smPDB.ca/
EDAM topicPathways, networks and models
EDAM topicMetabolites
TaxonHomo sapiens
website/smr.html0000644000244100017570000000566611606605760014025 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SMR

A database of annotated 3D protein structure models

Annotated three-dimensional comparative protein structure models generated by the fully automated homology-modelling pipeline SWISS-MODEL.

IDSMR
AccDB-0098
Homehttp://swissmodel.expasy.org/repository/
EDAM topicProtein tertiary structure
Category3D structure databases
Taxonall

Available data

Data Format Query Link
Protein structure {SMR entry} HTML UniProt accession http://swissmodel.expasy.org/repository/smr.php?sptr_ac=%s

Example queries

Data Format Query Example
Protein structure {SMR entry} HTML UniProt accession P01009
website/snap.html0000644000244100017570000000235411606605760014154 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SNAP

SNAP database of human gene variations

Human gene variations.

IDSNAP
Homehttp://platform.humgen.au.dk/
EDAM topicMutation and polymorphism
TaxonHomo sapiens
website/snappi.html0000644000244100017570000000336011606605760014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SNAPPI

SNAPPI database of structures, interfaces and alignments for protein-protein interactions

Structures, interfaces and alignments for protein-protein interactions.

IDSNAPPI
Homehttp://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp
EDAM topicProtein-protein interactions
EDAM topicProtein tertiary structure
EDAM topicProtein sequence alignment
Taxonall
website/snornabase.html0000644000244100017570000000247511606605760015352 0ustar jisonindustry Bioinformatics Data Resource Catalogue

snoRNABase

snoRNABase database of human H/ACA and C/D box snoRNAs

Human H/ACA and C/D box snoRNAs.

IDsnoRNABase
IDaltsnoRNA-LBME-db
Homehttp://www-snorna.biotoul.fr/
EDAM topicsnoRNA
TaxonHomo sapiens
website/sno_scarnabase.html0000644000244100017570000000261511606605760016174 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Sno_scaRNAbase

Small nucleolar RNA and small cajal body-specific RNA database (sno/scaRNAbase)

sno/scaRNA-associated genetic and functional data, from several database sources via web-accessible search interfaces.

IDSno_scaRNAbase
Homehttp://gene.fudan.sh.cn/snoRNAbase.nsf
EDAM topicsnRNA
TaxonEukaryota
website/snpeffect.html0000644000244100017570000000320011606605760015157 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SNPeffect

SNPeffect database of molecular phenotyping of human SNPs and disease mutations

Molecular phenotyping of human SNPs and disease mutations.

IDSNPeffect
Homehttp://snpeffect.vib.be
EDAM topicMutation and polymorphism
EDAM topicHuman disease
EDAM topicGenotype and phenotype
TaxonHomo sapiens
website/snpnexus.html0000644000244100017570000000234311606605760015074 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SNPnexus

SNPnexus database for SNP selection

SNP selection database.

IDSNPnexus
Homehttp://www.snp-nexus.org
EDAM topicMutation and polymorphism
TaxonHomo sapiens
website/snpstr.html0000644000244100017570000000340711606605760014544 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SNPSTR

SNPSTR databasee

Database of compound genetic marker called SNPSTR which combines a STR marker with one or more tightly linked SNPs. Here, the SNP(s) and the microsatellite are less than 250 base pairs apart so each SNPSTR can be considered a small haplotype with no recombination occurring between the two individual markers.

IDSNPSTR
Homehttp://www.sbg.bio.ic.ac.uk/~ino/cgi-bin/SNPSTRdatabase.html
EDAM topicGenetic mapping and linkage
EDAM topicMutation and polymorphism
TaxonHomo sapiens
website/source.html0000644000244100017570000001066211606605760014514 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SOURCE

The Stanford online universal resource for Clones and ESTs (SOURCE)

A unification tool which dynamically collects and compiles data from many scientific databases, and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Homo sapiens, Mus musculus, Rattus norvegicus into easy to navigate GeneReports.

IDSOURCE
AccDB-0099
Homehttp://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch
EDAM topicmRNA, EST or cDNA
CategoryOther
TaxonHomo sapiens, Mus, Rattus

Available data

Data Format Query Link
Gene annotation (clone or EST) HTML Clone ID (IMAGE) http://smd.stanford.edu/cgi-bin/source/sourceResult?option=CloneID&criteria=%s&choice=cDNA
Gene annotation (clone or EST) HTML GenBank accession http://smd.stanford.edu/cgi-bin/source/sourceResult?option=Number&criteria=%s&choice=cDNA

Example queries

Data Format Query Example
Gene annotation (clone or EST) HTML Clone ID (IMAGE) IMAGE:611245
Gene annotation (clone or EST) HTML GenBank accession AA603779
website/soybase.html0000644000244100017570000000273411606605760014662 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SoyBase

SoyBase soybean genome database

Database of soybean genetics and molecular biology.

IDSoyBase
Homehttp://soybase.agron.iastate.edu/
EDAM topicPlant
EDAM topicGenomes
CategoryNot available
TaxonGlycine max
website/spliceaid.html0000644000244100017570000000657011606605760015154 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SpliceAid

SpliceAid database of strictly experimentally assessed target RNA sequences in humans

Experimental RNA target motifs bound by splicing proteins in humans.

IDSpliceAid
Homehttp://www.introni.it/splicing.html
EDAM topicGene structure
EDAM topicNucleic acid functional sites
EDAM topicRNA splicing
EDAM topicProtein functional sites
EDAM topicSequence motifs
TaxonHomo sapiens

Available data

Data Format Query Link
Protein report HTML Protein name http://193.206.120.228/cgi-bin/SpliceAid.pl?Protein_name=%s

Example queries

Data Format Query Example
Protein report HTML Protein name 9G8
website/splicenest.html0000644000244100017570000000274011606605760015363 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SpliceNest

SpliceNest database

Visualizing splicing of genes from EST Data, based on mappings of the GeneNest EST Contigs to genomic sequence.

IDSpliceNest
Homehttp://splicenest.molgen.mpg.de/
EDAM topicmRNA, EST or cDNA
EDAM topicGene structure
TaxonEukaryota
website/spodobase.html0000644000244100017570000000320711606605761015171 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SpodoBase

Spodoptera frugiperda database (SpodoBase)

An integrated database for the genomics of the Lepidoptera Spodoptera frugiperda.

IDSpodoBase
Homehttp://bioweb.ensam.inra.fr/spodobase/
EDAM topicOrganism
EDAM topicInvertebrate
EDAM topicGenomes
TaxonSpodoptera frugiperda
website/stcdb.html0000644000244100017570000000245411606605761014314 0ustar jisonindustry Bioinformatics Data Resource Catalogue

STCDB

Signal transduction classification database (STCDB)

Signal transduction classification.

IDSTCDB
Homehttp://bibiserv.techfak.uni-bielefeld.de/stcdb/
EDAM topicSignalling pathways
Taxonall
website/stitch.html0000644000244100017570000000260011606605761014504 0ustar jisonindustry Bioinformatics Data Resource Catalogue

STITCH

STITCH chemical-protein interactions

A resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

IDSTITCH
Homehttp://stitch.embl.de
EDAM topicProtein-ligand interactions
Taxonall
website/straininfo.net.html0000644000244100017570000000244111606605761016152 0ustar jisonindustry Bioinformatics Data Resource Catalogue

StrainInfo.net

StrainInfo.net bioportal

Search the holdings of multiple biological resource centres (BRCs) through a single web interface.

IDStrainInfo.net
Homehttp://www.straininfo.net
EDAM topicLaboratory resources
Taxonall
website/strepto-db.html0000644000244100017570000000253511606605761015300 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Strepto-DB

Strepto-DB comparative genomics of group A and group B streptococci

Database for comparative genome analyses of group A and group B streptococci.

IDStrepto-DB
Homehttp://www.oger.tu-bs.de/strepto_db/
EDAM topicComparative genomics
TaxonStreptococcus
website/string.html0000644000244100017570000000776511606605761014535 0ustar jisonindustry Bioinformatics Data Resource Catalogue

STRING

STRING protein-protein interaction database

Known and predicted protein-protein interactions.

IDSTRING
AccDB-0141
Homehttp://string-db.org/
EDAM topicProtein-protein interactions
Taxonall

Available data

Data Format Query Link
Pathway or network (protein-protein interaction) HTML STRING ID http://string-db.org/version_8_3/newstring_cgi/show_network_section.pl?identifier=%s&all_channels_on=1&interactive=no&network_flavor=evidence&targetmode=proteins
Pathway or network (protein-protein interaction) XML STRING ID http://string-db.org/api/psi-mi/interactions?identifier=%s

Example queries

Data Format Query Example
Pathway or network (protein-protein interaction) HTML STRING ID 9606.ENSP00000359866
Pathway or network (protein-protein interaction) XML STRING ID 9606.ENSP00000359866
website/structurallyconservedinterfaces.html0000644000244100017570000000306111606605761021742 0ustar jisonindustry Bioinformatics Data Resource Catalogue

StructurallyConservedInterfaces

Structurally conserved interfaces

Structures of protein-protein interfaces from PDB.

IDStructurallyConservedInterfaces
Homehttp://home.ku.edu.tr/~okeskin/INTERFACE/INTERFACES.html
EDAM topicProtein-protein interactions
EDAM topicProtein tertiary structure
Taxonall
website/sulfolobus.html0000644000244100017570000000257511606605761015416 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Sulfolobus

Sulfolobus genome database

The three sequenced Sulfolobus genomes.

IDSulfolobus
Homehttp://www.sulfolobus.org
EDAM topicProkaryote
EDAM topicGenomes
TaxonSulfolobus
website/superdrug.html0000644000244100017570000000226511606605761015235 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SuperDrug

SuperDrug drug database

Drug compounds with conformers.

IDSuperDrug
Homehttp://bioinformatics.charite.de/superdrug
EDAM topicDrugs and targets
Taxon
website/superhapten.html0000644000244100017570000000304511606605761015550 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SuperHapten

SuperHapten immunogenic compound database

Database of haptens, related antibodies and carriers.

IDSuperHapten
Homehttp://bioinformatics.charite.de/superhapten
EDAM topicImmune-related proteins and peptides
EDAM topicSmall molecules
CategoryNoneE
Taxonall
website/supernatural.html0000644000244100017570000000233511606605761015740 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SuperNatural

SuperNatural natural compound database

A searchable database of natural compounds.

IDSuperNatural
Homehttp://bioinformatics.charite.de/supernatural
EDAM topicSmall molecules
Taxon
website/superscent.html0000644000244100017570000000226211606605761015405 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Superscent

Superscent database of scents

Database of scent molecules.

IDSuperscent
Homehttp://bioinformatics.charite.de/superscent
EDAM topicScents
Taxon
website/supersite.html0000644000244100017570000000372211606605761015237 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SuperSite

SuperSite dictionary of metabolite and drug binding sites in proteins

A ligand and binding site oriented view of the protein structural space. SuperSite integrates evolutionary information in the proteins as well as predicted binding sites from LigsiteCSC.

IDSuperSite
Homehttp://bioinf-services.charite.de/supersite/
EDAM topicDrugs and targets
EDAM topicProtein functional sites
EDAM topicProtein-ligand interactions
EDAM topicMetabolites
Taxonall
website/supertarget-matador.html0000644000244100017570000000315011606605761017201 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SuperTarget-Matador

SuperTarget and Matador database

Enzyme, drug and pathways database.

IDSuperTarget-Matador
Homehttp://insilico.charite.de/supertarget
EDAM topicPathways, networks and models
EDAM topicDrugs and targets
EDAM topicEnzymes
Taxonall
website/supertoxic.html0000644000244100017570000000231711606605761015420 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Supertoxic

Supertoxic toxic compounds database

Database of toxic compounds with synonyms.

IDSupertoxic
Homehttp://bioinformatics.charite.de/supertoxic
EDAM topicSmall molecules
Taxon
website/supfam.html0000644000244100017570000000336111606605761014506 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SUPFAM

Superfamily database of structural and functional annotation

Structural and functional protein annotations (via HMM library) for all completely sequenced organisms.

IDSUPFAM
IDaltSUPERFAMILY
AccDB-0155
Homehttp://supfam.org
EDAM topicProtein families
EDAM topicProteome
EDAM topicSequence profiles and HMMs
Taxonall
website/surface.html0000644000244100017570000000272511606605761014646 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SURFACE

SURFACE database of protein surface patches

Surface residues and functions, annotated, compared and evaluated.

IDSURFACE
Homehttp://cbm.bio.uniroma2.it/surface
EDAM topicProtein functional sites
EDAM topicProtein tertiary structure
Taxonall
website/swiss-2dpage.html0000644000244100017570000002064711606605762015532 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SWISS-2DPAGE

Two-dimensional polyacrylamide gel electrophoresis database (SWISS-2DPAGE)

Data on proteins identified on various 2-D PAGE and SDS-PAGE reference maps.

IDSWISS-2DPAGE
AccDB-0101
Homehttp://www.expasy.org/ch2d/
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
Taxonall
Linkinghttp://www.expasy.org/expasy_urls.html#ch2d

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Protein identifier http://www.expasy.org/swiss-2dpage/%s
Experiment annotation (2D PAGE) HTML UniProt accession http://www.expasy.org/swiss-2dpage/%s
Experiment annotation (2D PAGE) Text UniProt accession http://www.expasy.org/swiss-2dpage/format=raw&extract&ac=%s
2D PAGE spot annotation HTML Spot serial number http://www.expasy.org/swiss-2dpage/spot=%s
2D PAGE spot annotation {SWISS-2DPAGE protein list} HTML Reference map name (SWISS-2DPAGE) http://www.expasy.org/swiss-2dpage/map=%s
Experiment annotation (2D PAGE) {SWISS-2DPAGE reference map} HTML Reference map name (SWISS-2DPAGE) http://www.expasy.org/swiss-2dpage/viewer&ac=all&map=%s
2D PAGE spot annotation HTML Spot serial number http://www.expasy.org/swiss-2dpage/spot=%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML UniProt accession P01009
Experiment annotation (2D PAGE) Text UniProt accession P01009
2D PAGE spot annotation HTML Spot serial number 2D-0017PD
2D PAGE spot annotation HTML Spot serial number 2D-0017PD
2D PAGE spot annotation {SWISS-2DPAGE protein list} HTML Reference map name (SWISS-2DPAGE) LIVER_HUMAN
Experiment annotation (2D PAGE) {SWISS-2DPAGE reference map} HTML Reference map name (SWISS-2DPAGE) LIVER_HUMAN
website/swissregulon.html0000644000244100017570000000452211606605762015760 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SwissRegulon

SwissRegulon database of regulatory site annotations

Genome-wide annotations of regulatory sites.

IDSwissRegulon
Homehttp://www.swissregulon.unibas.ch
EDAM topicNucleic acid functional sites
EDAM topicTranscription
Taxonall

Available data

Data Format Query Link
Sequence motif (nucleic acid) {SwissRegulon feature search results} HTML Database name (SwissRegulon); Sequence feature ID (SwissRegulon) http://www.swissregulon.unibas.ch/swissregulon/cgi-bin/gbrowse/%s1/?name=%s2
website/systers.html0000644000244100017570000000264511606605762014734 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SYSTERS

SYSTERS protein family database

Large-scale protein clustering based on sequence similarity.

IDSYSTERS
Homehttp://systers.molgen.mpg.de/
EDAM topicSequence clustering
EDAM topicProtein families
Taxonall
website/systomonas.html0000644000244100017570000000247111606605762015434 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Systomonas

Systomonas database for systems biology of Pseudomonads

Molecular networks in pseudomonads with focus on Pseudomonas aeruginosa.

IDSystomonas
Homehttp://www.systomonas.de/
EDAM topicPathways, networks and models
TaxonPseudomondacaeae
website/sysznfc2h2.html0000644000244100017570000000260011606605762015222 0ustar jisonindustry Bioinformatics Data Resource Catalogue

SysZNFC2H2

C2H2 zinc finger gene database (SysZNFC2H2)

An information resource for C2H2 Zinc Finger genes in human and mouse.

IDSysZNFC2H2
Homehttp://epgd.biosino.org/SysZNF
EDAM topicGene family or system
TaxonHomo sapiens, Mus
website/t1dbase.html0000644000244100017570000000251511606605762014537 0ustar jisonindustry Bioinformatics Data Resource Catalogue

T1Dbase

Type 1 diabetes database (T1Dbase)

Database for type 1 diabetes (T1D): the genetics of T1D susceptibility and beta cell biology.

IDT1Dbase
Homehttp://www.t1dbase.org/page/Welcome/display
EDAM topicDisease
TaxonHomo sapiens
website/t3db.html0000644000244100017570000000310011606605763014040 0ustar jisonindustry Bioinformatics Data Resource Catalogue

T3DB

Toxin and Toxin Target Database (T3DB)

Toxin data with comprehensive toxin target information. Toxins are described by synonyms and include pollutants, pesticides, drugs, and food toxins, which are linked to corresponding toxin target records. Each toxin record (ToxCard) contains over 50 data fields and holds information such as chemical properties and descriptors, toxicity values, molecular and cellular interactions, and medical information.

IDT3DB
Homehttp://www.t3db.org/
EDAM topicToxins and targets
Taxonall
website/taed.html0000644000244100017570000000235611606605762014134 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TAED

The adaptive evolution database (TAED)

Protein-encoding gene families.

IDTAED
Homehttp://www.bioinfo.no/tools/TAED
EDAM topicGene family or system
Taxonall
website/tair.html0000644000244100017570000001212311606605762014147 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TAIR

The Arabidopsis information resource (TAIR)

Comprehensive information resources for Arabidopsis.

IDTAIR
AccDB-0102
Homehttp://www.arabidopsis.org/
EDAM topicPlant
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonArabidopsis
Linkinghttp://arabidopsis.org/about/linktotair.jsp

Available data

Data Format Query Link
Metadata and annotation {TAIR entry} HTML TAIR accession http://arabidopsis.org/servlets/TairObject?accession=%s
Gene annotation HTML Locus ID http://arabidopsis.org/servlets/TairObject?type=locus&name=%s
Metadata and annotation {TAIR stocks} HTML Stock number (TAIR) http://arabidopsis.org/servlets/StockSearcher?action=detail&stock_number=%s

Example queries

Data Format Query Example
Metadata and annotation {TAIR entry} HTML TAIR accession Clone:1768
Gene annotation HTML Locus ID AT4G18960
Metadata and annotation {TAIR stocks} HTML Stock number (TAIR) C00006
website/tarbase.html0000644000244100017570000000233511606605762014635 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TarBase

miRNA target database (TarBase)

The database of experimentally supported targets.

IDTarBase
Homehttp://microrna.gr/tarbase
EDAM topicmiRNA
Taxonall
website/tassdb.html0000644000244100017570000000616511606605762014501 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TassDB

Tandem splice site database

TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors.

IDTassDB
Homehttp://helios.informatik.uni-freiburg.de/TassDB/
EDAM topicNucleic acid functional sites
EDAM topicRNA splicing
EDAM topicGene structure
Taxonall

Available data

Data Format Query Link
Nucleic acid features (splice sites) {Tandem splice site} HTML Gene symbol http://gen100.imb-jena.de/TassDB2/emboss_access.pl?entry=%s

Example queries

Data Format Query Example
Nucleic acid features (splice sites) {Tandem splice site} HTML Gene symbol AATF
website/taxon.html0000644000244100017570000000520111606605762014340 0ustar jisonindustry Bioinformatics Data Resource Catalogue

taxon

NCBI's taxonomic identifier

NCBI's taxonomic identifier

IDtaxon
Homehttp://www.ncbi.nlm.nih.gov/Taxonomy/
EDAM topicTaxonomy
Taxonall

Available data

Data Format Query Link
Taxonomic data {NCBI taxon} HTML NCBI taxonomy ID http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=%s

Example queries

Data Format Query Example
Taxonomic data {NCBI taxon} HTML NCBI taxonomy ID 9606
website/tbmap.html0000644000244100017570000000305011606605762014312 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TBMap

Mapping names in TreeBASE

TBMap is a project to map names in the the phylogenetic database TreeBASE to names in taxonomic databases, such as uBio, ITIS, IPNI, and the NCBI taxonomy database.

IDTBMap
Homehttp://linnaeus.zoology.gla.ac.uk/~rpage/tbmap
EDAM topicTaxonomy
EDAM topicPhylogenetics
Taxonall
website/tcacycle.html0000644000244100017570000000555711606605762015014 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TCACycle

TCA cycle gene mutation database

TCA cycle gene mutation database.

IDTCACycle
Homehttp://chromium.liacs.nl/lovd_sdh/home.php
EDAM topicGenotype and phenotype
Taxonall
RESThttp://www.gen2phen.org/post/development-lovd-restful-atom-webservice

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://chromium.liacs.nl/LOVDv.2.0-dev/api/rest.php/genes?search_symbol=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol CRYAA
website/tcdb.html0000644000244100017570000000621611606605762014132 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TCDB

Transport classification database

A comprehensive IUBMB approved classification system for membrane transport proteins known as the Transporter Classification (TC) system. The TC system is analogous to the Enzyme Commission (EC) system for classification of enzymes, but incorporates phylogenetic information additionally.

IDTCDB
AccDB-0135
Homehttp://www.tcdb.org/
EDAM topicMembrane protein
EDAM topicProtein families
CategoryProtein family/group databases
Taxonall

Available data

Data Format Query Link
Protein report (membrane protein) {TCDB entry} HTML TCID http://www.tcdb.org/tcdb/index.php?tc=%s

Example queries

Data Format Query Example
Protein report (membrane protein) {TCDB entry} HTML TCID 1.A.1.2.3
website/tdr.html0000644000244100017570000000261411606605762014005 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TDR

TDR targets database

Identification and ranking of targets against neglected tropical diseases.

IDTDR
Homehttp://tdrtargets.org/
EDAM topicPharmacoinformatics
EDAM topicDrugs and targets
Taxonall
website/tigrfams.html0000644000244100017570000000575011606605762015034 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TIGRFAMs

A protein family database

Protein families based on hidden Markov models (HMMs).

IDTIGRFAMs
AccDB-0104
Homehttp://www.tigr.org/TIGRFAMs/
EDAM topicProtein families
EDAM topicSequence profiles and HMMs
CategoryFamily and domain databases
Taxonall

Available data

Data Format Query Link
Sequence profile metadata {TIGRFAM entry} HTML TIGRFam ID http://cmr.jcvi.org/cgi-bin/CMR/HmmReport.cgi?hmm_acc=%s

Example queries

Data Format Query Example
Sequence profile metadata {TIGRFAM entry} HTML TIGRFam ID TIGR01920
website/tigr.html0000644000244100017570000000557411606605762014171 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TIGR

The bacterial database(s) of The Institute of Genome Research

The TIGR bacterial Genome Annotation Database.

IDTIGR
AccDB-0103
EDAM topicGenomes
EDAM topicPlant
CategoryGenome annotation databases
TaxonBacteria, Archaea

Available data

Data Format Query Link
Gene annotation HTML Locus ID (CMR) http://cmr.jcvi.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s

Example queries

Data Format Query Example
Gene annotation HTML Locus ID (CMR) BOV_A0688
website/tmadb.html0000644000244100017570000000275311606605763014310 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TmaDB

Tissue microarray database

Tissue microarray (TMA) database for archiving all aspects of data associated with TMAs.

IDTmaDB
Homehttp://www.bioinformatics.leeds.ac.uk/tmadb/
EDAM topicGene expression and regulation
EDAM topicMicroarrays
Taxonall
website/tomatestdb.html0000644000244100017570000000247611606605763015371 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Tomatestdb

An EST database from multiple Tomato species

A collection of tomato EST sequences downloaded from dbEST.

IDTomatestdb
Homehttp://biosrv.cab.unina.it/tomatestdb/
EDAM topicmRNA, EST or cDNA
TaxonSolanum lycopersicum
website/topdb.html0000644000244100017570000001326111606605763014325 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ToPDB

Topology of transmembrane proteins

Transmembrane protein datasets containing experimentally derived topology information.

IDToPDB
Homehttp://toPDB.enzim.hu
EDAM topicMembrane protein
Taxonall

Available data

Data Format Query Link
Protein report (membrane protein) {TOPDB entry} HTML Protein ID (TopDB) http://toPDB.enzim.hu/?m=show&tab=HTML&id=%s
Protein report (membrane protein) {TOPDB entry} HTML {graphic} Protein ID (TopDB) http://toPDB.enzim.hu/?m=show&tab=Graph&id=%s
Protein report (membrane protein) {TOPDB entry} HTML {flash} Protein ID (TopDB) http://toPDB.enzim.hu/?m=show&tab=Flash&id=%s
Protein report (membrane protein) {TOPDB entry} XML Protein ID (TopDB) http://toPDB.enzim.hu/?m=show&tab=XML&id=%s

Example queries

Data Format Query Example
Protein report (membrane protein) {TOPDB entry} HTML Protein ID (TopDB) AP00085
Protein report (membrane protein) {TOPDB entry} HTML {graphic} Protein ID (TopDB) AP00085
Protein report (membrane protein) {TOPDB entry} HTML {flash} Protein ID (TopDB) AP00085
Protein report (membrane protein) {TOPDB entry} XML Protein ID (TopDB) AP00085
website/topdom.html0000644000244100017570000000342011606605763014513 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TOPDOM

Transmembrane domains and motifs

A collection of domains and sequence motifs located conservatively in one side of transmembrane proteins.

IDTOPDOM
Homehttp://topdom.enzim.hu
EDAM topicMembrane protein
EDAM topicSequence motifs
EDAM topicNucleic acid functional sites
EDAM topicSequence motifs
Taxonall
website/transdab.html0000644000244100017570000000517111606605763015014 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Transdab

Database of transglutaminase substrate proteins

Database of transglutaminase substrate proteins.

IDTransdab
Homehttp://genomics.dote.hu/wiki
EDAM topicSpecific protein
Taxonall

Available data

Data Format Query Link
Protein report HTML Protein name http://genomics.dote.hu/wiki/index.php/%s

Example queries

Data Format Query Example
Protein report HTML Protein name Histone_H1_%28kinase%29
website/transpath.html0000644000244100017570000000372611606605763015226 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TRANSPATH

TRANSPATH database

Information on signaling molecules, metabolic enzymes, second messengers, endogenous metabolites, miRNAs and the reactions they are involved in, resulting in a complex network of interconnected chains of reactions and pathways.

IDTRANSPATH
Homehttp://www.biobase.de/index.php?id=transpathdatabases
EDAM topicSignalling pathways
EDAM topicPathways, networks and models
EDAM topicMetabolites
EDAM topicEnzymes
Taxonall
website/transpogene.html0000644000244100017570000000246411606605763015545 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TranspoGene

Transposed elements in proteins for 7 organisms

Data on the influence of Transposed Elements (TEs) on the transcriptome of 7 species.

IDTranspoGene
Homehttp://transpogene.tau.ac.il/
EDAM topicMobile genetic elements
Taxonall
website/trbase.html0000644000244100017570000000232211606605763014471 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TRBase

Tandem repeats database

Tandem repeats in the human genome.

IDTRBase
Homehttp://trbase.ex.ac.uk/
EDAM topicRepeat sequence
TaxonHomo sapiens
website/treefam.html0000644000244100017570000000304511606605763014637 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TreeFam

Phylogenetic trees of animal genes

Phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families.

IDTreeFam
Homehttp://www.treefam.org
EDAM topicPhylogenetics
EDAM topicGene family or system
TaxonMetazoa
website/trnasequences.html0000644000244100017570000000323711606605763016077 0ustar jisonindustry Bioinformatics Data Resource Catalogue

tRNASequences

tRNA sequences database

Compilation of tRNA sequences and sequence of tRNA genes.

IDtRNASequences
Homehttp://www.staff.uni-bayreuth.de/~btc914/search/index.html
EDAM topicNucleic acid sequences
EDAM topictRNA
EDAM topicGene family or system
Taxonall
website/tropgene-db.html0000644000244100017570000000237711606605763015431 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TropGENE-DB

TropGENE database

Genetic and genomic information about tropical crops studied by Cirad.

IDTropGENE-DB
Homehttp://tropgenedb.cirad.fr/
EDAM topicGenomes
TaxonSpermatophyta
website/trsdb.html0000644000244100017570000000322411606605763014331 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TrSDB

TrSDB transcription factors

Biological Proteome KnowledgeBase linking IPI and SPTR-NR based Proteome analyses with TranScout, TransMem and ProtLoc and offering crosslinks with other relevant biodatabases such as SWISS-PROT, NCBI Refseq, Ensembl, InterPro or Gene Ontology Annotation.

IDTrSDB
Homehttp://bioinf.uab.es/cgi-bin/trsdb/trsdb.pl
EDAM topicTranscription factor and binding site
EDAM topicProteome
Taxonall
website/ttd.html0000644000244100017570000000335511606605762014012 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TTD

Therapeutic Target Database (TTD)

A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information provided are fully referenced.

IDTTD
Homehttp://bidd.nus.edu.sg/group/cjttd/TTD_HOME.asp
EDAM topicDrugs and targets
Taxonall
website/tuberculist.html0000644000244100017570000000632011606605763015560 0ustar jisonindustry Bioinformatics Data Resource Catalogue

TubercuList

Mycobacterium tuberculosis strain H37Rv genome database

Mycobacterium tuberculosis strain H37Rv genome database

IDTubercuList
AccDB-0106
Homehttp://genolist.pasteur.fr/TubercuList/
EDAM topicProkaryote
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonMycobacterium tuberculosis

Available data

Data Format Query Link
Gene annotation HTML Sequence accession (nucleic acid) http://genolist.pasteur.fr/TubercuList/genome.cgi?external_query+%s

Example queries

Data Format Query Example
Gene annotation HTML Sequence accession (nucleic acid) None
website/u12db.html0000644000244100017570000000237311606605763014134 0ustar jisonindustry Bioinformatics Data Resource Catalogue

U12DB

U12-type intron database

U12-type intron database

IDU12DB
Homehttp://genome.imim.es/cgi-bin/u12db/u12db.cgi
EDAM topicGene structure
Taxonall
website/ucd-2dpage.html0000644000244100017570000000427211606605763015132 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UCD-2DPAGE

University College Dublin 2-DE Proteome Database

University College Dublin 2-DE Proteome Database

IDUCD-2DPAGE
AccDB-0047
Homehttp://proteomics-portal.ucd.ie:8082/cgi-bin/2d/2d.cgi
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
TaxonHomo sapiens

Available data

Data Format Query Link
2D PAGE spot annotation HTML UniProt accession http://proteomics-portal.ucd.ie:8082/cgi-bin/2d/2d.cgi?%s
website/ucsc.html0000644000244100017570000000531211606605763014150 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UCSC

UCSC genome browser

UCSC genome browser

IDUCSC
AccDB-0139
Homehttp://genome.ucsc.edu
EDAM topicGenomes
CategoryGenome annotation databases
Taxonall

Available data

Data Format Query Link
Gene annotation HTML Identifier {UCSC} http://genome.ucsc.edu/cgi-bin/hgGene?hgg_gene=%s1&org=%s2

Example queries

Data Format Query Example
Gene annotation HTML Identifier {UCSC} M117.2.2
website/umd-dmd.html0000644000244100017570000000265711606605763014553 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UMD-DMD

UMD-DMD France genotype-phenotype dystrophinopathy patients

Knowledgebase related to mutations of the DMD gene.

IDUMD-DMD
Homehttp://www.umd.be/DMD/
EDAM topicGenotype and phenotype
EDAM topicHuman disease
TaxonHomo sapiens
website/umd.html0000644000244100017570000000232511606605764014002 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UMD

Universal mutation database

Collection of mutations in human genes associated with genetic diseases.

IDUMD
Homehttp://umd.be
EDAM topicHuman disease
TaxonHomo sapiens
website/unigene.html0000644000244100017570000000631211606605763014646 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniGene

UniGene gene-oriented nucleotide sequence clusters

Each UniGene entry is a set of transcript sequences that appear to come from the same transcription locus (gene or expressed pseudogene), together with information on protein similarities, gene expression, cDNA clone reagents, and genomic location.

IDUniGene
AccDB-0107
Homehttp://www.ncbi.nlm.nih.gov/sites/entrez?db=UniGene
EDAM topicmRNA, EST or cDNA
EDAM topicSequence clustering
EDAM topicNucleic acid classification
EDAM topicGene expression and regulation
CategorySequence databases
Taxonall

Available data

Data Format Query Link
Gene annotation (transcript) HTML UniGene taxon; Sequence cluster ID (UniGene) http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s1&CID=%s2

Example queries

Data Format Query Example
website/unihi.html0000644000244100017570000000236711606605763014336 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniHI

Unified human interactome database

Protein interaction analysis.

IDUniHI
Homehttp://www.mdc-berlin.de/unihi
EDAM topicProtein-protein interactions
TaxonHomo sapiens
website/unilib.html0000644000244100017570000000260011606605763014472 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UNILIB

Unified library database

A library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap.

IDUNILIB
Homehttp://binfo.ym.edu.tw/edu/seminars/clho/UniLib Browser_kidney.htm
EDAM topicmRNA, EST or cDNA
Taxonall
website/uniparc.html0000644000244100017570000000564611606605764014667 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniParc

UniProt Archive

Part of UniProt project - a non-redundant archive of protein sequences extracted from public databases UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, PIR-PSD, EMBL, EMBL WGS, Ensembl, IPI, PDB, PIR-PSD, RefSeq, FlyBase, WormBase, H-Invitational Database, TROME database, European Patent Office proteins, United States Patent and Trademark Office proteins (USPTO) and Japan Patent Office proteins.

IDUniParc
Homehttp://www.uniprot.org/
EDAM topicProtein sequences
Taxonall

Available data

Data Format Query Link
Sequence record {UniParc entry} HTML UniParc accession http://www.uniprot.org/uniparc/%s

Example queries

Data Format Query Example
Sequence record {UniParc entry} HTML UniParc accession UPI0000000001
website/unipathway.html0000644000244100017570000000267611606605764015417 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Unipathway

Unipathway

A manually curated database of metabolic pathways for the UniProtKB/Swiss-Prot knowledgebase. It provides a structured controlled vocabulary to describe the role of a protein in a metabolic pathway.

IDUnipathway
Homehttp://www.grenoble.prabi.fr/obiwarehouse/unipathway
EDAM topicMetabolic pathways
Taxonall
website/uniprot.html0000644000244100017570000001457311606605764014725 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniProt

Universal protein resource

A comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

IDUniProt
IDaltUniProtKB
Homehttp://www.uniprot.org/
EDAM topicProtein sequences
Taxonall

Available data

Data Format Query Link
Sequence record full HTML UniProt accession http://www.uniprot.org/uniprot/%s
Sequence record full uniprot UniProt accession http://www.uniprot.org/uniprot/%s.txt
Sequence record full XML UniProt accession http://www.uniprot.org/uniprot/%s.xml
Sequence record full RDF UniProt accession http://www.uniprot.org/uniprot/%s.rdf
Sequence record full FASTA format UniProt accession http://www.uniprot.org/uniprot/%s.fasta

Example queries

Data Format Query Example
Sequence record full HTML UniProt accession P12345
Sequence record full uniprot UniProt accession P12345
Sequence record full XML UniProt accession P12345
Sequence record full RDF UniProt accession P12345
Sequence record full FASTA format UniProt accession P12345
website/uniprotkb_swiss-prot.html0000644000244100017570000001475311606605764017454 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniProtKB_Swiss-Prot

Universal protein resource knowledge base / Swiss-Prot

Section of the UniProt knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature

IDUniProtKB_Swiss-Prot
IDaltSwissProt
Homehttp://www.uniprot.org
EDAM topicProtein sequences
Taxonall

Available data

Data Format Query Link
Sequence record full HTML UniProt accession http://www.uniprot.org/uniprot/%s
Sequence record full Text UniProt accession http://www.uniprot.org/uniprot/%s.txt
Sequence record full XML UniProt accession http://www.uniprot.org/uniprot/%s.xml
Sequence record full RDF UniProt accession http://www.uniprot.org/uniprot/%s.rdf
Sequence record full FASTA format UniProt accession http://www.uniprot.org/uniprot/%s.fasta

Example queries

Data Format Query Example
Sequence record full HTML UniProt accession P12345
Sequence record full Text UniProt accession P12345
Sequence record full XML UniProt accession P12345
Sequence record full RDF UniProt accession P12345
Sequence record full FASTA format UniProt accession P12345
website/uniprotkb_trembl.html0000644000244100017570000001464611606605764016610 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniProtKB_TrEMBL

Universal protein resource knowledge base / Swiss-Prot

Section of the UniProt knowledgebase, containing computationally analysed records waiting for full manual annotation

IDUniProtKB_TrEMBL
IDaltTrEMBL
Homehttp://www.uniprot.org/
EDAM topicProtein sequences
Taxonall

Available data

Data Format Query Link
Sequence record full HTML UniProt accession http://www.uniprot.org/uniprot/%s
Sequence record full Text UniProt accession http://www.uniprot.org/uniprot/%s.txt
Sequence record full XML UniProt accession http://www.uniprot.org/uniprot/%s.xml
Sequence record full RDF UniProt accession http://www.uniprot.org/uniprot/%s.rdf
Sequence record full FASTA format UniProt accession http://www.uniprot.org/uniprot/%s.fasta

Example queries

Data Format Query Example
Sequence record full HTML UniProt accession Q00177
Sequence record full Text UniProt accession Q00177
Sequence record full XML UniProt accession Q00177
Sequence record full RDF UniProt accession Q00177
Sequence record full FASTA format UniProt accession Q00177
website/uniref.html0000644000244100017570000003326711606605764014516 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniRef

Non-redundant reference (UniRef) databases

Clustered sets of sequences from UniProt Knowledgebase (including splice variants and isoforms) and selected UniParc records, in order to obtain complete coverage of sequence space at several resolutions while hiding redundant sequences (but not their descriptions) from view.

IDUniRef
Homehttp://www.uniprot.org/help/uniref
EDAM topicSequence clustering
CategoryOther
Taxonall

Available data

Data Format Query Link
Sequence cluster (protein) HTML Sequence cluster ID (UniRef100) http://www.uniprot.org/uniref/UniRef100_%s
Sequence cluster (protein) XML Sequence cluster ID (UniRef100) http://www.uniprot.org/uniref/UniRef100_%s.xml
Sequence cluster (protein) RDF Sequence cluster ID (UniRef100) http://www.uniprot.org/uniref/UniRef100_%s.rdf
Sequence cluster (protein) FASTA format Sequence cluster ID (UniRef100) http://www.uniprot.org/uniref/UniRef100_%s.fasta
Sequence cluster (protein) HTML Sequence cluster ID (UniRef90) http://www.uniprot.org/uniref/UniRef90_%s
Sequence cluster (protein) XML Sequence cluster ID (UniRef90) http://www.uniprot.org/uniref/UniRef90_%s.xml
Sequence cluster (protein) RDF Sequence cluster ID (UniRef90) http://www.uniprot.org/uniref/UniRef90_%s.rdf
Sequence cluster (protein) FASTA format Sequence cluster ID (UniRef90) http://www.uniprot.org/uniref/UniRef90_%s.fasta
Sequence cluster (protein) HTML Sequence cluster ID (UniRef50) http://www.uniprot.org/uniref/UniRef50_%s
Sequence cluster (protein) XML Sequence cluster ID (UniRef50) http://www.uniprot.org/uniref/UniRef50_%s.xml
Sequence cluster (protein) RDF Sequence cluster ID (UniRef50) http://www.uniprot.org/uniref/UniRef50_%s.rdf
Sequence cluster (protein) FASTA format Sequence cluster ID (UniRef50) http://www.uniprot.org/uniref/UniRef50_%s.fasta

Example queries

Data Format Query Example
Sequence cluster (protein) HTML Sequence cluster ID (UniRef100) P02930
Sequence cluster (protein) XML Sequence cluster ID (UniRef100) P02930
Sequence cluster (protein) RDF Sequence cluster ID (UniRef100) P02930
Sequence cluster (protein) FASTA format Sequence cluster ID (UniRef100) P02930
Sequence cluster (protein) HTML Sequence cluster ID (UniRef90) P02930
Sequence cluster (protein) XML Sequence cluster ID (UniRef90) P02930
Sequence cluster (protein) RDF Sequence cluster ID (UniRef90) P02930
Sequence cluster (protein) FASTA format Sequence cluster ID (UniRef90) P02930
Sequence cluster (protein) HTML Sequence cluster ID (UniRef50) P02930
Sequence cluster (protein) XML Sequence cluster ID (UniRef50) P02930
Sequence cluster (protein) RDF Sequence cluster ID (UniRef50) P02930
Sequence cluster (protein) FASTA format Sequence cluster ID (UniRef50) P02930
website/unisave.html0000644000244100017570000000243211606605764014666 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniSave

Uniprot version archive

A repository of UniProtKB/Swiss-Prot and UniProtKB/TrEMBL entry versions.

IDUniSave
Homehttp://www.ebi.ac.uk/uniprot/unisave/
EDAM topicProtein sequences
Taxonall
website/unists.html0000644000244100017570000000554211606605764014546 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniSTS

NCBI database of sequence tagged sites

A comprehensive database of sequence tagged sites (STSs) derived from STS-based maps and other experiments. STSs are defined by PCR primer pairs and are associated with additional information such as genomic position, genes, and sequences.

IDUniSTS
Homehttp://www.ncbi.nlm.nih.gov/unists
EDAM topicGenetic mapping and linkage
Taxonall

Available data

Data Format Query Link
Gene annotation {UniSTS entry} HTML UniSTS accession http://www.ncbi.nlm.nih.gov/genome/sts/sts.cgi?uid=%s

Example queries

Data Format Query Example
Gene annotation {UniSTS entry} HTML UniSTS accession 2019
website/unite.html0000644000244100017570000000522011606605764014336 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UNITE

UNITE rDNA sequences from ectomycorrhizal asco- and basidiomycetes

UNITE is a rDNA sequence database focused on ectomycorrhizal asco- and basidiomycetes.

IDUNITE
Homehttp://unite.ut.ee/
EDAM topicrDNA
TaxonFungi

Available data

Data Format Query Link
Sequence metadata {UNITE entry} HTML UNITE accession http://unite.ut.ee/bl_forw.php?nimi=%s

Example queries

Data Format Query Example
Sequence metadata {UNITE entry} HTML UNITE accession UDB000215
website/unitrap.html0000644000244100017570000000536311606605764014704 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UniTrap

UniTrap gene trap clones

Tools for the biologist enabling optimized use of gene trap clones.

IDUniTrap
Homehttp://unitrap.cbm.fvg.it/
EDAM topicGene structure
Taxonall

Available data

Data Format Query Link
Gene annotation {UniTrap entry} HTML Gene ID (Ensembl) http://unitrap.cbm.fvg.it/gene.php?show_unitraps=1&show_domains=1&show_genes=1&ensembl_id=%s

Example queries

Data Format Query Example
Gene annotation {UniTrap entry} HTML Gene ID (Ensembl) ENSMUSG00000025903
website/utilldb.html0000644000244100017570000000261111606605764014652 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UTILLdb

URGV TILLING platform databases

Lines, phenotype categories, sequences and mutations for pea and tomatoe.

IDUTILLdb
Homehttp://urgv.evry.inra.fr/UTILLdb
EDAM topicGenotype and phenotype
TaxonPisum sativum, Solanum lycopersicum
website/utrdb.html0000644000244100017570000002242011606605764014333 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UTRdb

Regulatory motifs in eukaryotic UTRs

UTResource collect data and analysis tool for the functional classification of 5' and 3'UTRs of eukaryotic mRNAs.

IDUTRdb
Homehttp://www.ba.itb.cnr.it/UTR/
EDAM topicTranscription
EDAM topicNucleic acid functional sites
EDAM topicSequence motifs
EDAM topicmRNA, EST or cDNA
Taxonall

Available data

Data Format Query Link
Gene annotation {UTR report} HTML Locus ID (UTR) http://utrdb.ba.itb.cnr.it/getutr/%s
Gene annotation {UTR report} HTML UTR accession http://utrdb.ba.itb.cnr.it/getutra/%s
Gene annotation {UTR gene report} HTML UTRdb taxon; Gene symbol http://utrdb.ba.itb.cnr.it/getgene/%s1/%s2
Gene annotation {UTR full report} HTML Locus ID (UTR) http://utrdb.ba.itb.cnr.it/getutr/%s/1
Gene annotation {UTR full report} HTML UTR accession http://utrdb.ba.itb.cnr.it/getutra/%s/1
Gene annotation {UTR full report} HTML UTR accession http://utrdb.ba.itb.cnr.it/getutra/BA064434/1
Gene annotation {UTR full gene report} HTML UTRdb taxon; Gene symbol http://utrdb.ba.itb.cnr.it/getgene/%s1/%s2/1

Example queries

Data Format Query Example
Gene annotation {UTR report} HTML UTR accession CR478594
Gene annotation {UTR full report} HTML UTR accession CR478594
Gene annotation {UTR full report} HTML UTR accession CR478594
Gene annotation {UTR report} HTML Locus ID (UTR) 3HSAR031240
Gene annotation {UTR full report} HTML Locus ID (UTR) 3HSAR031240
Gene annotation {UTR gene report} HTML UTRdb taxon; Gene symbol hs;MDM2
Gene annotation {UTR full gene report} HTML UTRdb taxon; Gene symbol hs;MDM2
website/utrsite.html0000644000244100017570000000606011606605764014714 0ustar jisonindustry Bioinformatics Data Resource Catalogue

UTRsite

Regulatory motifs in eukaryotic UTRs

UTRSite is a collection of functional sequence patterns located in 5' or 3' UTR sequences.

IDUTRsite
Homehttp://www.ba.itb.cnr.it/UTR/
EDAM topicTranscription
EDAM topicNucleic acid functional sites
EDAM topicSequence motifs
Taxonall

Available data

Data Format Query Link
Sequence motif metadata {UTR site} HTML UTRSite ID URL: http://utrsite.ba.itb.cnr.it/index.php/UTRSite signal/Signal/frmID/%s

Example queries

Data Format Query Example
Sequence motif metadata {UTR site} HTML UTRSite ID U0001
website/vbase2.html0000644000244100017570000000553611606605764014406 0ustar jisonindustry Bioinformatics Data Resource Catalogue

VBASE2

Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse

An integrative database of germ-line variable genes from the immunoglobulin loci of human and mouse. All variable gene sequences are extracted from the EMBL-Bank.

IDVBASE2
Homehttp://www.vbase2.org/
EDAM topicImmunoinformatics
TaxonHomo sapiens, Mus

Available data

Data Format Query Link
Gene annotation {VBASE2 entry} HTML Gene ID (VBASE2) http://vbase2.org/vgene.php?id=%s

Example queries

Data Format Query Example
Gene annotation {VBASE2 entry} HTML Gene ID (VBASE2) musIGHV028
website/vectorbase.html0000644000244100017570000001175011606605764015354 0ustar jisonindustry Bioinformatics Data Resource Catalogue

VectorBase

Invertebrate vectors of human pathogens

Invertebrate vectors of human pathogens.

IDVectorBase
AccDB-0120
Homehttp://www.vectorbase.org/
EDAM topicPathogen
CategoryGenome annotation databases
Taxonall
Linkinghttp://neuron.cse.nd.edu/vectorbase/index.php/Website_redirects

Available data

Data Format Query Link
Gene annotation {VectorBase entry} HTML Gene ID (VectorBase) http://www.vectorbase.org/Genome/BRCGene/?feature=%s
Peptide annotation {VectorBase peptide page} HTML Gene ID (VectorBase) http://www.vectorbase.org/Genome/BRCGene/?feature=%s-PA
Gene annotation (transcript) HTML Gene ID (VectorBase) http://www.vectorbase.org/Genome/BRCGene/?feature=%s-RA

Example queries

Data Format Query Example
Gene annotation {VectorBase entry} HTML Gene ID (VectorBase) AGAP005025
Peptide annotation {VectorBase peptide page} HTML Gene ID (VectorBase) AGAP005025
Gene annotation (transcript) HTML Gene ID (VectorBase) AGAP005025
website/vega.html0000644000244100017570000000245611606605764014144 0ustar jisonindustry Bioinformatics Data Resource Catalogue

VEGA

Vertebrate Genome Annotation (VEGA) database

A central repository for high quality, frequently updated, manual annotation of vertebrate finished genome sequence.

IDVEGA
Homehttp://vega.sanger.ac.uk/
EDAM topicGenomes
TaxonChordata
website/vida.html0000644000244100017570000000362611606605764014145 0ustar jisonindustry Bioinformatics Data Resource Catalogue

VIDA

Virus Database at University College London

VIDA contains a collection of homologous protein families derived from open reading frames from complete and partial virus genomes. For each family, you can get an alignment of the conserved regions, functional and taxonomy information, and links to DNA sequences and structures.

IDVIDA
Homehttp://www.biochem.ucl.ac.uk/bsm/virus_database/VIDA3/VIDA.html
EDAM topicVirus
EDAM topicProtein sequence alignment
EDAM topicProtein families
TaxonViruses
website/virusmint.html0000644000244100017570000000311411606605764015252 0ustar jisonindustry Bioinformatics Data Resource Catalogue

VirusMINT

Viral protein interaction

VirusMINT aims at collecting and annotating in a structured format all the interactions between human and viral proteins and to integrate this information in the human protein interaction network.

IDVirusMINT
Homehttp://mint.bio.uniroma2.it/virusmint/
EDAM topicVirus
EDAM topicProtein-protein interactions
TaxonViruses
website/vsgdb.html0000644000244100017570000000257611606605764014332 0ustar jisonindustry Bioinformatics Data Resource Catalogue

VSGdb

A database of trypanosomal variant surface glycoproteins

A database of trypanosomal variant surface glycoproteins.

IDVSGdb
Homehttp://leishman.cent.gla.ac.uk/pward001/vsgdb/kook_index.html
EDAM topicSpecific protein
TaxonTrypanosomatidae
website/worfdb.html0000644000244100017570000000537011606605764014503 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WorfDB

The C.elegans ORFeome cloning project

The Caenorhabditis elegans ORFeome cloning project

IDWorfDB
Homehttp://worfdb.dfci.harvard.edu/
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonCaenorhabditis elegans

Available data

Data Format Query Link
Gene annotation {WorfDB entry} HTML ORF name http://worfdb.dfci.harvard.edu/searchallwormorfs.pl?by=name&sid=%s

Example queries

Data Format Query Example
Gene annotation {WorfDB entry} HTML ORF name pos-1
website/world-2dpage_0003.html0000644000244100017570000000605411606605761016146 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WORLD-2DPAGE_0003

World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome

World-wide gel-based proteomics database (0003) for Arabidopsis thaliana leaf proteome.

IDWORLD-2DPAGE_0003
IDalt0003
Homehttp://www.expasy.org/world-2dpage/
EDAM topicTwo-dimensional gel electrophoresis
EDAM topicPlant
TaxonArabidopsis thaliana

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Sequence accession (protein) http://world-2dpage.expasy.org/repository/ac=%s&database=0003

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML Sequence accession (protein) O65719
website/world-2dpage_0004.html0000644000244100017570000000556211606605761016152 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WORLD-2DPAGE_0004

World-wide gel-based proteomics database (0004) for mature rat olfactory bulb

World-wide gel-based proteomics database (0004) for mature rat olfactory bulb.

IDWORLD-2DPAGE_0004
IDalt0004
Homehttp://www.expasy.org/world-2dpage/
EDAM topicTwo-dimensional gel electrophoresis
TaxonRattus

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Sequence accession (protein) http://world-2dpage.expasy.org/repository/ac=%s&database=0004

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML Sequence accession (protein) A7VJC3
website/world-2dpage_0005.html0000644000244100017570000000567411606605762016160 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WORLD-2DPAGE_0005

World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose

World-wide gel-based proteomics database (0005) for Botrytis cinerea mycelium cultured in carboxymethyl cellulose.

IDWORLD-2DPAGE_0005
IDalt0005
Homehttp://www.expasy.org/world-2dpage/
EDAM topicTwo-dimensional gel electrophoresis
TaxonBotrytis

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Sequence accession (protein) http://world-2dpage.expasy.org/repository/ac=%s&database=0005

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML Sequence accession (protein) A6RHV6
website/world-2dpage_0006.html0000644000244100017570000000562311606605762016153 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WORLD-2DPAGE_0006

World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee

World-wide gel-based proteomics database (0006) for hemolymph proteome of the honeybee.

IDWORLD-2DPAGE_0006
IDalt0006
Homehttp://www.expasy.org/world-2dpage/
EDAM topicTwo-dimensional gel electrophoresis
TaxonApis mellifera

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Sequence accession (protein) http://world-2dpage.expasy.org/repository/ac=%s&database=0006

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML Sequence accession (protein) AAP49283.1
website/world-2dpage_cgl14067-2dpage.html0000644000244100017570000000557311606605761020100 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WORLD-2DPAGE_CGL14067-2DPAGE

World-wide gel-based proteomics database (CGL14067-2DPAGE)

World-wide gel-based proteomics database (CGL14067-2DPAGE)

IDWORLD-2DPAGE_CGL14067-2DPAGE
IDaltCGL14067-2DPAGE
Homehttp://www.expasy.org/world-2dpage/
EDAM topicTwo-dimensional gel electrophoresis
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Sequence accession (protein) http://world-2dpage.expasy.org/repository/ac=%s&database=cgl14067-2dpage

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML Sequence accession (protein) O31139
website/world-2dpage.html0000644000244100017570000000566311606605765015515 0ustar jisonindustry Bioinformatics Data Resource Catalogue

World-2DPAGE

The world-2DPAGE database

A public repository, standards compliant, for proteomics image data published in the literature.

IDWorld-2DPAGE
AccDB-0121
Homehttp://world-2dpage.expasy.org/repository/
EDAM topicTwo-dimensional gel electrophoresis
Category2D gel databases
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Sequence accession (protein) {World-2DPAGE} http://world-2dpage.expasy.org/repository/%s

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML Sequence accession (protein) {World-2DPAGE} 0020:Q20655
website/world-2dpage_nibr_2d-page.html0000644000244100017570000000554611606605761020022 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WORLD-2DPAGE_NIBR_2D-PAGE

World-wide gel-based proteomics database (NIBR 2D-PAGE)

World-wide gel-based proteomics database (NIBR 2D-PAGE)

IDWORLD-2DPAGE_NIBR_2D-PAGE
IDaltNIBR 2D-PAGE
Homehttp://www.expasy.org/world-2dpage/
EDAM topicTwo-dimensional gel electrophoresis
Taxonall

Available data

Data Format Query Link
Experiment annotation (2D PAGE) HTML Sequence accession (protein) http://world-2dpage.expasy.org/repository/ac=%s&database=nibr_2d-page

Example queries

Data Format Query Example
Experiment annotation (2D PAGE) HTML Sequence accession (protein) O54520
website/wormbase.html0000644000244100017570000001157111606605765015040 0ustar jisonindustry Bioinformatics Data Resource Catalogue

WormBase

Caenorhabditis elegans genome database

Caenorhabditis elegans genome database

IDWormBase
AccDB-0110
Homehttp://www.wormbase.org/
EDAM topicInvertebrate
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonCaenorhabditis elegans

Available data

Data Format Query Link
Gene annotation HTML Gene symbol http://www.wormbase.org/db/gene/gene?name=%s
Gene annotation HTML Gene ID http://www.wormbase.org/db/gene/gene?name=%s
Gene annotation HTML Protein identifier http://www.wormbase.org/db/gene/gene?name=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene symbol unc-26
Gene annotation HTML Gene ID R13A5.9
Gene annotation HTML Protein identifier CE02711
website/xenbase.html0000644000244100017570000000647011606605765014650 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Xenbase

Xenopus laevis and tropicalis biology and genomics resource

Xenopus laevis and tropicalis biology and genomics resource

IDXenbase
AccDB-0129
Homehttp://www.xenbase.org/
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonXenopus

Available data

Data Format Query Link
Gene annotation HTML Gene ID (Xenbase) http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=%s
Gene annotation HTML Gene ID http://www.xenbase.org/gene/showgene.do?method=displayGeneSummary&geneId=%s

Example queries

Data Format Query Example
Gene annotation HTML Gene ID (Xenbase) XB-GENE-1006026
website/yeast_complexes.html0000644000244100017570000000273211606605765016424 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Yeast_complexes

Yeast complexes database

Information on protein-protein interactions and protein complexes in yeast.

IDYeast_complexes
Homehttp://yeast-complexes.embl.de/
EDAM topicProtein-protein interactions
EDAM topicFungal
TaxonSaccharomyces cerevisiae
website/yeast-gfp.html0000644000244100017570000000445611606605765015124 0ustar jisonindustry Bioinformatics Data Resource Catalogue

Yeast-GFP

Yeast GFP fusion localization database

Yeast GFP fusion localization database

IDYeast-GFP
Homehttp://yeastgfp.ucsf.edu
EDAM topicOrganism
EDAM topicGene structure
EDAM topicFungal
CategoryOrganism-specific databases
TaxonSaccharomyces cerevisiae

Available data

Data Format Query Link
Gene annotation {Yeast-GFP entry} HTML ORF name http://yeastgfp.ucsf.edu/getOrf.php?orf=%s
website/yeastract.html0000644000244100017570000002451211606605765015217 0ustar jisonindustry Bioinformatics Data Resource Catalogue

YEASTRACT

Transcriptional regulators database

A curated repository of more than 34469 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1000 bibliographic references. It also includes the description of 291 specific DNA binding sites for more than a hundred characterized TFs.

IDYEASTRACT
Homehttp://www.yeastract.com
EDAM topicGene regulatory networks
EDAM topicNucleic acid functional sites
EDAM topicTranscription
EDAM topicTranscription factor and binding site
EDAM topicFungal
TaxonSaccharomyces cerevisiae

Available data

Data Format Query Link
Gene annotation HTML ORF name http://www.yeastract.com/view.php?existing=locus&orfname=%s
Protein report HTML ORF name http://www.yeastract.com/view.php?existing=locus&orfname=%s
Ontology metadata {GO information} HTML ORF name http://www.yeastract.com/view.php?existing=go&orfname=%s
Gene annotation HTML Gene name http://www.yeastract.com/view.php?existing=locus&orfname=%s
Protein report HTML Gene name http://www.yeastract.com/view.php?existing=locus&orfname=%s
Ontology metadata {GO information} HTML Gene name http://www.yeastract.com/view.php?existing=go&orfname=%s
Gene annotation HTML Protein name http://www.yeastract.com/view.php?existing=locus&orfname=%s
Protein report HTML Protein name http://www.yeastract.com/view.php?existing=locus&orfname=%s
Ontology metadata {GO information} HTML Protein name http://www.yeastract.com/view.php?existing=go&orfname=%s
Gene annotation (expression) {Regulation reference} HTML Transcription factor name; Gene name {target gene} http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Gene annotation (expression) {Regulation reference} HTML Transcription factor name; ORF name {target ORF} http://www.yeastract.com/view.php?existing=regulation&proteinname=%s1&orfname=%s2
Protein report (transcription factor) {TF binding site reference} HTML Transcription factor name; Identifier {Consensus sequence} http://www.yeastract.com/view.php?existing=consensus&proteinname=%s1&consensus=%s2
Protein report (transcription factor) {Documented regulators of a given set of genes} HTML Gene name http://www.yeastract.com/findregulators.php?type=doc&genes=%s
Gene annotation {Documented target genes of a given set of TFs} HTML Transcription factor name http://www.yeastract.com/findregulated.php?type=doc&tfs=%s

Example queries

Data Format Query Example
Gene annotation {Documented target genes of a given set of TFs} HTML Transcription factor name Nrg1p
website/ygob.html0000644000244100017570000000551011606605765014155 0ustar jisonindustry Bioinformatics Data Resource Catalogue

YGOB

Yeast gene order browser

Tool for visualising the syntenic context of any gene from several yeast genomes.

IDYGOB
Homehttp://wolfe.gen.tcd.ie/ygob
EDAM topicGenetic mapping and linkage
EDAM topicFungal
TaxonSaccharomyces cerevisiae

Available data

Data Format Query Link
Gene annotation {YGOB entry} HTML Gene symbol http://wolfe.gen.tcd.ie/cgi/browser/ygob.pl?gene=%s

Example queries

Data Format Query Example
Gene annotation {YGOB entry} HTML Gene symbol YAL068C
website/ymgv.html0000644000244100017570000000347211606605765014204 0ustar jisonindustry Bioinformatics Data Resource Catalogue

yMGV

Yeast microarray global viewer

Transcriptional expression profiles of yeast genes among most of the published expression datasets.

IDyMGV
Homehttp://transcriptome.ens.fr/ymgv/
EDAM topicGene expression and regulation
EDAM topicGene expression profiling
EDAM topicMicroarrays
EDAM topicFungal
TaxonSaccharomyces cerevisiae
website/zfin.html0000644000244100017570000000614411606605765014167 0ustar jisonindustry Bioinformatics Data Resource Catalogue

ZFIN

Zebrafish information network genome database

Zebrafish information network genome database

IDZFIN
AccDB-0113
Homehttp://zfin.org/
EDAM topicVertebrate
EDAM topicGenomes
EDAM topicOrganism
CategoryOrganism-specific databases
TaxonDanio rerio

Available data

Data Format Query Link
Gene annotation {ZFIN entry} HTML Gene ID (ZFIN) http://zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=%s

Example queries

Data Format Query Example
Gene annotation {ZFIN entry} HTML Gene ID (ZFIN) ZDB-GENE-011205-17