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