AceView Worm Genome http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/ AceView/WormGenes gene vha-6 http://www.ncbi.nlm.nih.gov/IEB/Research/Acembly/av.cgi?exdb=AceView&db=worm&term= Arabidopsis Genome Initiative (TAIR, TIGR, MIPS) http://www.arabidopsis.org gene protein At2g17950 http://mips.gsf.de/cgi-bin/proj/thal/search_gene?code= http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf= http://arabidopsis.org/servlets/TairObject?type=locus&name= AGRICultural OnLine Access http://agricola.nal.usda.gov/ bib=0000-05160 ID example is strange; can't find db entry point Sergei Egorov 2006-02-17 AGRICultural OnLine Access http://agricola.cos.com/ IND84014403 AGRICultural OnLine Access http://agricola.nal.usda.gov/ TP248.2 P76 v.14 ID example is strange Sergei Egorov 2006-02-17 A Systematic Annotation Package for Community Analysis of Genomes https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm 8 ID example is strange: can 8 be an ID? Server requires login... Sergei Egorov 2006-02-17 American Type Culture Collection database http://www.atcc.org/ CCL-240 HL-60 http://www.atcc.org/common/catalog/numSearch/numResults.cfm?collection=ce&ATCCNum= American Type Culture Collection database http://www.atcc.org/ ATCC(dna) DNA CCL-64D Mink genomic DNA (Mv 1 Lu) http://www.atcc.org/common/catalog/numSearch/numResults.cfm?collection=ce&ATCCNum= American Type Culture Collection database http://www.atcc.org/ ATCC(in host) 123456 ID example is fake Sergei Egorov 2006-02-17 A Xenopus laevis database http://www.dkfz-heidelberg.de/molecular_embryology/axeldb.htm gene 32B3.1 http://indigene.ibaic.u-psud.fr/cgi-bin/ace/generic/tree/default?class=Locus&name= Berkeley Drosophila Genome Project EST database http://www.fruitfly.org/EST/index.shtml 123456 ID example is fake Sergei Egorov 2006-02-17 Berkeley Drosophila Genome Project database -- Insertion http://www.fruitfly.org/ 123456 ID example is fake Sergei Egorov 2006-02-17 BioModels Database http://www.ebi.ac.uk/biomodels/ BIOMD0000000045 http://www.ebi.ac.uk/compneur-srv/biomodels-main/publ-model.do?mid= BIOSIS previews http://www.biosis.org/ 200200247281 BRENDA, The Comprehensive Enzyme Information System http://www.brenda.uni-koeln.de/ 4.2.1.3 http://www.brenda.uni-koeln.de/php/result_flat.php4?ecno= CAS Registry http://www.cas.org/ chemical substance registry number up to 9 digits, divided by hyphens into 3 parts; the right digit is a checksum 58-08-2 caffeine [0-9]+[-][0-9]+[-][0-9] http://webbook.nist.gov/cgi/cbook.cgi?ID=& http://www.chemindustry.com/apps/chemicals?m=s\&t=& CAS ID Center for Biological Sequence Analysis http://www.cbs.dtu.dk/ NetNGlyc Check http://www.cbs.dtu.dk/services/TMHMM/ ? Sergei Egorov 2006-02-17 Conserved Domain Database http://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml pfam01484 Candida Genome Database http://www.candidagenome.org/ CAL0005516 http://www.candidagenome.org/cgi-bin/locus.pl?sgdid= Candida Genome Database http://www.candidagenome.org/ orf19.2475 http://www.candidagenome.org/cgi-bin/locus.pl?locus= Another ID example is HPW1 Sergei Egorov 2006-02-17 Candida Genome Database http://www.candidagenome.org/ 1490 http://www.candidagenome.org/cgi-bin/reference/reference.pl?refNo= Compugen Gene Ontology Gene Association Data PrID131022 CGSC: E.coli Genetic Stock Center http://cgsc.biology.yale.edu/ rbsK server entry point: check http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/ Sergei Egorov 2006-02-17 Chemical Entities of Biological Interest (ChEBI) database of small molecules http://www.ebi.ac.uk/chebi/ chemical compound sequential identifier positive numeral 27732 caffeine [1-9][0-9]* http://www.ebi.ac.uk/chebi/searchId.do?chebiId= CHEBI: Cell Type Ontology http://lists.sourceforge.net/lists/listinfo/obo-cell-type 0000041 NCBI COG cluster http://www.ncbi.nlm.nih.gov/COG/ COG0001 http://www.ncbi.nlm.nih.gov/COG/new/release/cow.cgi?cog= NCBI COG function http://www.ncbi.nlm.nih.gov/COG/ H http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?fun= NCBI COG pathway http://www.ncbi.nlm.nih.gov/COG/ 14 http://www.ncbi.nlm.nih.gov/COG/new/release/coglist.cgi?pathw= EST database maintained at the NCBI http://www.ncbi.nlm.nih.gov/dbEST/index.html BP535535 Variation database maintained at the NCBI http://www.ncbi.nlm.nih.gov/SNP/ rs133073 STS database maintained at the NCBI http://www.ncbi.nlm.nih.gov/dbSTS/index.html BV210161 DictyBase http://dictybase.org DDB0001836 http://dictybase.org/db/cgi-bin/gene_page.pl?dictybaseid= DictyBase http://dictybase.org mlcE http://dictybase.org/db/cgi-bin/gene_page.pl?gene_name= DictyBase literature references http://dictybase.org 10157 http://dictybase.org/db/cgi-bin/dictyBase/reference/reference.pl?refNo= INSD: Dictyostelium genome database http://dictybase.org/ DDB0191090 The IUBMB Enzyme Commission http://www.chem.qmw.ac.uk/iubmb/enzyme/ enzyme registry number N.N.N.N where N is either a number or '-' 3.4.11.4 tripeptide aminopeptidase ([0-9]+|[-])[.]([0-9]+|[-])[.]([0-9]+|[-])[.]([0-9]+|[-]) http://www.genome.ad.jp/dbget-bin/www_bget?ec: EC Number server entry point: check http://www.chem.qmw.ac.uk/iubmb/enzyme/EC1/1/1/1.html Sergei Egorov 2006-02-17 The Encylopedia of E. coli metabolism http://ecocyc.org/ P2-PWY http://malibu.ai.sri.com:1555/ECOLI/new-image?type=PATHWAY&object=? CGSC: E.coli Genetic Stock Center http://cgsc.biology.yale.edu/ EG10818 server entry point: check http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/315 Sergei Egorov 2006-02-17 CGSC: E.coli Genetic Stock Center http://cgsc.biology.yale.edu/ deoC INSD: Database of automatically annotated genomic data http://www.ensembl.org HUMAN-Gene-ENSG00000007102 http://www.ensembl.org/perl/protview?peptide= The Swiss Institute of Bioinformatics database of Enzymes http://www.expasy.ch/ 1.1.1.1 http://www.expasy.ch/cgi-bin/nicezyme.pl? redirect to EC:? Sergei Egorov 2006-02-17 EBI's EST library identifier 1200 Database of Functional Annotation of Mouse http://fantom.gsc.riken.go.jp/ 0610005A07 FlyBase http://flybase.bio.indiana.edu/ FBgn0000024 http://fly.ebi.ac.uk:7081/.bin/fbidq.html? http://flybase.bio.indiana.edu/.bin/fbidq.html? two URLs, one service? Sergei Egorov 2006-02-17 Database of Genetic and molecular data of Drosophila http://www.flybase.org/ FBgn0000024 http://flybase.bio.indiana.edu/.bin/fbidq.html? http://fly.ebi.ac.uk:7081/.bin/fbidq.html? two URLs, one service? Sergei Egorov 2006-02-17 Network of Different Plant Genomic Research Projects https://gabi.rzpd.de/ HA05J18 INSD: Human Genome Database accession numbers http://www.gdb.org/ G00-128-600 http://www.gdb.org/gdb-bin/genera/accno?accessionNum= url example suggested GDB:306600 as ID format Sergei Egorov 2006-02-17 INSD: Curated gene database for Schizosaccharomyces pombe, Leishmania major and Trypanosoma brucei http://www.genedb.org/ SPCC285.16c http://www.genedb.org/genedb/Search?organism=All%3A*&name= GeneDB_Gmorsitans http://www.genedb.org/glossina Gmm-0142 http://www.genedb.org/genedb/Search?organism=glossina&name= GeneDB_Lmajor http://www.genedb.org/leish LM5.32 http://www.genedb.org/genedb/Search?organism=leish&name= GeneDB_Pfalciparum http://www.genedb.org/malaria PFD0755c http://www.genedb.org/genedb/Search?organism=malaria&name= GeneDB_Spombe http://www.genedb.org/pombe SPAC890.04C http://www.genedb.org/genedb/Search?organism=pombe&name= GeneDB_Tbrucei http://www.genedb.org/tryp Tb927.1.5250 http://www.genedb.org/genedb/Search?organism=tryp&name= Entrez Gene Database (replaces NCBI Locus Link) http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene gene sequential identifier positive numeral 7157 tumor protein p53 [1-9][0-9]* http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=gene&cmd=Retrieve&dopt=full_report&list_uids= LocusLink ID GermOnline http://www.germonline.org/ 140116 http://germonline.unibas.ch/gene_page.php?orf_id= http://germonline.yeastgenome.org/gene_page.php?orf_id= http://germonline.biochem.s.u-tokyo.ac.jp/gene_page.php?orf_id= GenInfo identifier, used as a unique sequence identifier for nucleotide and proteins 1234567890 ID example is fake; cannot resolve GIs to URLs without knowing their type (protein/nucleotide) Sergei Egorov 2006-02-17 Gene Ontology Database http://www.geneontology.org/ concept sequential identifier 7-digit numeral 0006915 apoptosis [0-9]{7} http://godatabase.org/cgi-bin/go.cgi?query=GO: GO ID Gene Ontology Database references 0000001 Gene Ontology Annotation Database Identifier http://www.ebi.ac.uk/GOA/ P01100 Gramene: A Comparative Mapping Resource for Grains http://www.gramene.org/ P93436 http://www.gramene.org/perl/protein_search?acc= Gramene: A Comparative Mapping Resource for Grains http://www.gramene.org/ 659 http://www.gramene.org/db/mutant/search_mutant?id= ID example may be fake; need to try GR:0060198 Sergei Egorov 2006-02-17 Gramene: A Comparative Mapping Resource for Grains. http://www.gramene.org/ 110916 http://www.gramene.org/db/protein/protein_search?protein_id= Gramene: A Comparative Mapping Resource for Grains http://www.gramene.org/ 659 http://www.gramene.org/perl/pub_search?ref_id= H-Invitational Database http://www.h-invitational.jp HIX0000001 H-invitational Database http://www.h-invitational.jp/ AK093148 http://www.h-invdb.jbic.or.jp/soup/pub_Detail.pl?acc_id= http://www.jbirc.aist.go.jp/hinv/soup/pub_Detail.pl?acc_id= H-invitational Database http://www.h-invitational.jp/ HIX0014446 http://www.h-invdb.jbic.or.jp/soup/pub_Locus.pl?locus_id= http://www.jbirc.aist.go.jp/hinv/soup/pub_Locus.pl?locus_id= High-quality Automated and Manual Annotation of microbial Proteomes http://us.expasy.org/sprot/hamap/ MF_00031 http://us.expasy.org/unirules/ HUGO Gene Nomenclature Committee http://www.gene.ucl.ac.uk/nomenclature/ gene sequential identifier positive numeral 11998 tumor protein p53 [1-9][0-9]* http://www.gene.ucl.ac.uk/nomenclature/data/get_data.php?hgnc_id=HGNC: HGNC ID HGNC:ID as used by NCBI Sergei Egorov 2006-02-17 HUGO Gene Nomenclature Committee http://www.gene.ucl.ac.uk/nomenclature/ gene symbol a unique series of Latin (upper case in human) letters and Arabic numbers which usually is no longer than six characters in length; case-sensitive BRCA1 breast cancer, early onset 1 http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl?field=all_text&anchor=equals&symbol_search=Search&number=50&format=html&sortby=symbol&match= HUGO Symbol Database of homology-derived secondary structure of proteins http://www.sander.ebi.ac.uk/hssp/ 12GS Institute for Fermentation, Osaka http://www.ifo.or.jp/index_e.html 3189 Immunogenetics database, immunoglobulin and T-cell receptor genes http://imgt.cines.fr IMGT/GENE-DB IGKC Immunogenetics database, human MHC http://www.ebi.ac.uk/imgt/hla/ IMGT/HLA HLA00031 Immunogenetics database, immunoglobulins and T-cell receptors http://imgt.cines.fr IMGT/LIGM U03895 chemical compound self-describing identifier canonicalized formula with ordered layers separated by / 1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3 caffeine [-+/.,*;()?A-Za-z0-9]+ may need urlencoding Sergei Egorov 2006-02-17 International Nucleotide Sequence Database Collaboration (GenBank, EMBL, DDBJ) http://www.insdc.org/ nucleotide sequence accession number uppercase letters, followed by digits and optional .version suffix; e.g. LNNNNN, LLNNNNNN J01749 Cloning vector pBR322, complete genome [A-Z]+[0-9]+([.][0-9]+)? http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val= http://www.ebi.ac.uk/cgi-bin/emblfetch?style=html&Submit=Go&id= http://arsa.ddbj.nig.ac.jp/arsa/ddbjSplSearch?KeyWord= GenBank ID IntAct protein interaction database http://www.ebi.ac.uk/intact/ EBI-17086 http://www.ebi.ac.uk/intact/search/do/search?searchString= InterPro protein sequence database http://www.ebi.ac.uk/interpro/ Interpro IPR002928 http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac= International Protein Index http://www.ebi.ac.uk/IPI/IPIhelp.html IPI00000005.1 International Standard Book Number http://isbntools.com/ 0781702534 http://my.linkbaton.com/get?lbCC=q&nC=q&genre=book&item= Insertion sequence elements database ISA1083-2 International Standard Serial Number http://www.issn.org/ 1234-1231 The IUPHAR Compendium of Receptor Characterization and Classification 2.1.CBD Japan Collection of Microorganisms http://www.jcm.riken.go.jp/ 1339 ([a-z]+)[:](.*) KEGG_\1:\2 Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg/ chemical compound accession number C followed by 5 digits C00074 Phosphoenolpyruvate C[0-9]{5} http://www.genome.ad.jp/dbget-bin/www_bget?cpd: KEGG_COMPOUND: KEGG_DRUG: Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg/ drug accession number D followed by 5 digits D00245 Bisacodyl (JP14/USP) D[0-9]{5} http://www.genome.ad.jp/dbget-bin/www_bget?dr: EC: GeneID: GeneID: KEGG_PATHWAY: Kyoto Encyclopedia of Genes and Genomes http://www.genome.ad.jp/kegg/ pathway accession number lowercase letters, followed by 5 digits ot00020 Citrate cycle (TCA cycle) [a-z]+[0-9]{5} http://www.genome.ad.jp/dbget-bin/www_bget?path: http://www.genome.ad.jp/dbget-bin/www_bget?path: GeneID: KEGG LIGAND Database http://www.genome.ad.jp/kegg/docs/upd_ligand.html#COMPOUND 1.1.1.1 http://www.genome.ad.jp/dbget-bin/www_bget?ec: http://www.genome.ad.jp/dbget-bin/www_bget?cpd: needs editing or redirection Sergei Egorov 2006-02-17 GeneID: MaizeGDB http://www.maizegdb.org 881225 http://www.maizegdb.org/cgi-bin/id_search.cgi?id= MaizeGDB http://www.maizegdb.org ZmPK1 http://www.maizegdb.org/cgi-bin/displaylocusresults.cgi?term=? The Medline literature database 20572430 superseded by PubMed (see PMID:) Sergei Egorov 2006-02-17 MEROPS - the Peptidase Database http://merops.sanger.ac.uk/ A01.001 MEROPS: The Peptidase Database http://merops.sanger.ac.uk/ M18 http://merops.sanger/ac/uk/famcards/ check if .htm needs to be appended to URLs Sergei Egorov 2006-02-17 Medical Subject Headings http://www.nlm.nih.gov/mesh/2005/MBrowser.html mitosis http://www.nlm.nih.gov/cgi/mesh/2005/MB_cgi?mode=&term= need to preserve case and urlencode commas, spaces, ...? Sergei Egorov 2006-02-17 The Metabolic Encyclopedia of metabolic and other pathways http://metacyc.org/ GLUTDEG-PWY http://biocyc.org:1555/META/new-image?object= Mouse Genome Database http://www.informatics.jax.org/ Adcy9 http://www.informatics.jax.org/searches/marker.cgi? Mouse Genome Informatics http://www.informatics.jax.org/ gene sequential identifier positive numeral 98834 transformation related protein 53 [1-9][0-9]* http://www.informatics.jax.org/searches/accession_report.cgi?id= http://www.informatics.jax.org/searches/accession_report.cgi?id=MGI: MGI ID OMIM: MIM: is NCBI usage Sergei Egorov 2006-02-17 MIPS Functional Catalogue http://mips.gsf.de/proj/funcatDB/ 11.02 http://mips.gsf.de/cgi-bin/proj/funcatDB/search_advanced.pl?action=2&wert= The MGED Ontology http://mged.sourceforge.net/ontologies/MGEDontology.php Action http://mged.sourceforge.net/ontologies/MGEDontology.php# Nottingham Arabidopsis Stock Centre Seeds Database http://arabidopsis.info N3371 http://seeds.nottingham.ac.uk/NASC/stockatidb.lasso?code= INSD: NCBI GenPept http://www.ncbi.nlm.nih.gov/ EAL72968 http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=protein&val= NCBI RefSeq http://www.ncbi.nlm.nih.gov/ 123456 ID example is fake Sergei Egorov 2006-02-17 NCBI RefSeq http://www.ncbi.nlm.nih.gov/ 123456 ID example is fake Sergei Egorov 2006-02-17 Nematode Expression Pattern DataBase http://nematode.lab.nig.ac.jp/ CELK01662 NIA Mouse cDNA Project http://lgsun.grc.nia.nih.gov/cDNA/cDNA.html L0304H12-3 Online Mendelian Inheritance in Man database http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM gene gene-related genetic disorders sequential identifier positive numeral 191170 TUMOR PROTEIN p53 [1-9][0-9]* http://www3.ncbi.nlm.nih.gov/htbin-post/Omim/dispmim? http://www.ncbi.nlm.nih.gov/entrez/dispomim.cgi?id= OMIM ID Protein Data Bank http://www.rcsb.org/pdb/ 1A4U http://www.rcsb.org/pdb/cgi/explore.cgi?pid=223051005992697&pdbId= Pfam: Protein families database of alignments and HMMs http://www.sanger.ac.uk/Software/Pfam/ PF00046 http://www.sanger.ac.uk/cgi-bin/Pfam/getacc? Pfam-B supplement to Pfam http://www.sanger.ac.uk/Software/Pfam/ PB014624 Plant Genome Network http://pgn.cornell.edu aam01-1ms3-a05 Protein Information Resource http://pir.georgetown.edu/ protein accession number uppercase letters, followed by digits S02192 cellular tumor antigen p53 - rat [A-Z]+[0-9]+ http://pir.georgetown.edu/cgi-bin/pirwww/nbrfget?uid= PIR ID PIR Superfamily Classification System http://pir.georgetown.edu/pirsf/ SF002327 http://pir.georgetown.edu/cgi-bin/ipcSF?id= PubMed http://pubmed.gov/ article sequential identifier positive numeral 16446403 Mol Cancer Res. 2006 Jan;4(1):15-25. [1-9][0-9]* http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids= Plant Ontology Consortium Database http://www.plantontology.org/ 0009004 http://www.plantontology.org/amigo/go.cgi?action=query&view=query&search_constraint=terms&query= template may have PO: before the ID? Sergei Egorov 2006-02-17 Schizosaccharomyces pombe protein data SPAC890.04C PRINTS compendium of protein fingerprints http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ PR00025 http://umber.sbs.man.ac.uk/cgi-bin/dbbrowser/PRINTS/DoPRINTS.pl?cmd_a=Display&qua_a=none&fun_a=Text&qst_a= ProDom protein domain families automatically generated from Swiss-Prot and TrEMBL http://prodes.toulouse.inra.fr/prodom/current/html/home.php PD000001 http://prodes.toulouse.inra.fr/prodom/current/cgi-bin/request.pl?question=DBEN&query= Prosite. Database of protein families and domains http://www.expasy.ch/prosite/ PS00365 http://www.expasy.ch/cgi-bin/prosite-search-ac? INSD: EMBL pseudo protein identifier CAC44644.1 NCBI PubChem database of chemical structures http://pubchem.ncbi.nlm.nih.gov/ chemical compound sequential identifier positive numeral 2519 Caffeine [1-9][0-9]* http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pccompound&term= http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid= NCBI PubChem database of chemical substances http://pubchem.ncbi.nlm.nih.gov/ chemical substance sequential identifier positive numeral 199601 Coffee [1-9][0-9]* http://http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?CMD=search&DB=pcsubstance&term= http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?sid= Rat Genome Database http://ratmap.gen.gu.se/ 5 fake ID? Sergei Egorov 2006-02-17 Reactome human pathway database http://www.reactome.org/ 70635 http://www.reactome.org/cgi-bin/eventbrowser?DB=gk_current&ID= REBASE, The Restriction Enzyme Database http://rebase.neb.com/rebase/rebase.html EcoRI http://rebase.neb.com/rebase/enz/ template may need to add .html after the ID: use ere? Sergei Egorov 2006-02-17 RESID Database of Protein Modifications AA0062 Rat Genome Database http://rgd.mcw.edu/ gene sequential identifier positive numeral 3889 tumor protein p53 [1-9][0-9]* http://rgd.mcw.edu/tools/genes/genes_view.cgi?id= RGD ID RGD: Rice database accession numbers http://www.gramene.org/ AA231856 The RNA Modification Database http://medlib.med.utah.edu/RNAmods/ 037 http://medlib.med.utah.edu/cgi-bin/rnashow.cgi? Resource Centre Primary Database Clone Identifiers http://www.rzpd.de/ IMAGp998I142450Q6 Saccharomyces Genome Database http://www.yeastgenome.org/ S000006169 http://db.yeastgenome.org/cgi-bin/locus.pl?dbid= Saccharomyces Genome Database http://www.yeastgenome.org/ GAL4 http://db.yeastgenome.org/cgi-bin/locus.pl?locus= another ID example: YEL001C Sergei Egorov 2006-02-17 Saccharomyces Genome Database http://www.yeastgenome.org/ S000049602 http://db.yeastgenome.org/cgi-bin/reference/reference.pl?dbid= Simple Modular Architecture Research Tool http://smart.embl-heidelberg.de/ SM00005 http://smart.embl-heidelberg.de/smart/do_annotation.pl?BLAST=DUMMY&DOMAIN= Glycine max Genome Database http://soybase.agron.iastate.edu/ Satt005 stkecm_([A-Z]+)_([0-9]+) STKECM_\1:\2 Science's STKE Connections Map http://stke.sciencemag.org/ chemical substance sequential identifier positive numeral 15493 Acetylcholinesterase (AChE) [1-9][0-9]* http://stke.sciencemag.org/cgi/cm/stkecm;CMC_ Science's STKE Connections Map http://stke.sciencemag.org/ pathway sequential identifier positive numeral 10827 JNK MAPK Pathway [1-9][0-9]* http://stke.sciencemag.org/cgi/cm/stkecm;CMP_ Bacillus subtilis genome sequencing project http://genolist.pasteur.fr/SubtiList/ BG10001 Bacillus subtilis Genome Sequence Project http://genolist.pasteur.fr/SubtiList/ accC The Arabidopsis Information Resource http://www.arabidopsis.org/ gene:2062713 http://www.arabidopsis.org/servlets/TairObject?accession= should gene: in the ID be part of the template? Sergei Egorov 2006-02-17 NCBI's taxonomic identifier http://www.ncbi.nlm.nih.gov/Taxonomy/tax.html 4932 this needs to be linked ASAP Sergei Egorov 2006-02-17 The Transport Protein Database http://tcdb.ucsd.edu/tcdb/ 9.A.4.1.1 http://tcdb.ucsd.edu/tcdb/tcprotein.php?substrate= Tetrahymena Genome Database http://www.ciliate.org/ PDD1 http://db.ciliate.org/cgi-bin/locus.pl?locus= another ID example: U66363 Sergei Egorov 2006-02-17 Tetrahymena Genome Database http://www.ciliate.org/ T000005818 http://db.ciliate.org/cgi-bin/reference/reference.pl?dbid= The Institute for Genomic Research, Arabidopsis thaliana database http://www.tigr.org/tdb/e2k1/ath1/ath1.shtml At3g01440 http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=ath1&orf= The Institute for Genomic Research, Comprehensive Microbial Resource http://www.tigr.org/ VCA0557 http://www.tigr.org/tigr-scripts/CMR2/GenePage.spl?locus= The Institute for Genomic Research, EGAD database http://www.tigr.org/ 74462 http://www.tigr.org/tigr-scripts/CMR2/ht_report.spl?prot_id= The Institute for Genomic Research, Genome Properties http://www.tigr.org/ GenProp0120 http://www.tigr.org/tigr-scripts/CMR2/genome_property_def.spl?prop_acc= The Institute for Genomic Research, Plasmodium falciparum database http://www.tigr.org/tdb/e2k1/pfa1/pfa1.shtml PFB0010w http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=pfa1&orf= http://www.tigr.org/tdb/GO_REF/GO_REF.shtml GO_ref is this ID real? Sergei Egorov 2006-02-17 The Institute for Genomic Research, Trypanosoma brucei database http://www.tigr.org/tdb/e2k1/tba1/ 25N14.10 http://www.tigr.org/tigr-scripts/euk_manatee/shared/ORF_infopage.cgi?db=tba1&orf= The Institute for Genomic Research, TIGR Gene Index http://www.tigr.org/ Cattle_TC123931 http://www.tigr.org/tigr-scripts/nhgi_scripts/tc_report.pl?tc=? The Institute for Genomic Research, TIGRFAMs HMM collection http://www.tigr.org/ TIGR00254 http://www.tigr.org/tigr-scripts/CMR2/hmm_report.spl?acc= UniProtKB-TrEMBL, a computer-annotated protein sequence database supplementing UniProtKB and containing the translations of all coding sequences (CDS) present in the EMBL Nucleotide Sequence Database but not yet integrated in UniProtKB/Swiss-Prot http://www.uniprot.org O31124 http://www.ebi.uniprot.org/entry/ The University of Minnesota Biocatalysis/Biodegradation Database http://umbbd.ahc.umn.edu/index.html e0413 http://umbbd.ahc.umn.edu:8007/umbbd/servlet/pageservlet?ptype=ep&enzymeID= The University of Minnesota Biocatalysis/Biodegradation Database http://umbbd.ahc.umn.edu/index.html acr http://umbbd.ahc.umn.edu/ may need to turn acr into acr/acr_map.html -- use ere? Sergei Egorov 2006-02-17 NCBI's UniGene database http://www.ncbi.nih.gov/UniGene cluster of nucleotide sequences sequential identifier (organism-specific) 2/3-letter organism abbreviation followed by dot and positive numeral Hs.408312 p53 cluster ([A-Z][a-z][a-z]?)[.]([1-9][0-9]*) http://www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=\1\&CID=\2 http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=unigene&cmd=search&term= Unigene ID Unified Library Database, a library-level view of the EST and SAGE libraries present in dbEST, UniGene and SAGEmap 1002 UniProt Archive; a non-redundant archive of protein sequences extracted from Swiss-Prot, TrEMBL, PIR-PSD, EMBL, Ensembl, IPI, PDB, RefSeq, FlyBase, WormBase, European Patent Office, United States Patent and Trademark Office, and Japanese Patent Office http://www.ebi.ac.uk/uniparc/ UPI000000000A http://www.ebi.ac.uk/cgi-bin/dbfetch?db=uniparc&id= The Universal Protein Knowledgebase, a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR http://www.uniprot.org/ UniProtKB/Swiss-Prot protein accession number 6 alphanumerical characters P08251 Sodium/potassium-transporting ATPase beta-1 chain [OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9] http://www.ebi.uniprot.org/entry/ Swiss-Prot Accession section of the UniProt Knowledgebase, containing annotated records, which include curator-evaluated computational analysis, as well as, information extracted from the literature http://www.uniprot.org UniProtKB/Swiss-Prot P12345 redirect to UniProt? Sergei Egorov 2006-02-17 section of the UniProt Knowledgebase, containing computationally analysed records waiting for full manual annotation http://www.uniprot.org UniProtKB/TrEMBL Q00177 Integrative database of germ-line V genes from the immunoglobulin loci of human and mouse http://www.dnaplot.de/vbase2/vbase2.php humIGKV165 WormBase, database of nematode biology http://www.wormbase.org/ lin-12 http://www.wormbase.org/db/get?class=Locus;name= WormBase, database of nematode biology http://www.wormbase.org/ cgc467 http://www.wormbase.org/db/misc/paper?name= may need to put %5Bcgc467%5D;class=Paper after the template -- use ere? Sergei Egorov 2006-02-17 C. elegans ORFeome cloning project http://worfdb.dfci.harvard.edu/ pos-1 Caenorhabditis elegans Genome Database http://www.wormbase.org/ R13H7 Wormpep, database of proteins of C. elegans http://www.wormbase.org/ CE25104 http://www.wormbase.org/db/get?class=Protein;name= may need to put WP%3A between the template and the ID -- add to template? Sergei Egorov 2006-02-17 The Zebrafish Information Network http://zfin.org/ ZDB-GENE-990415-103 http://zfin.org/cgi-bin/ZFIN_jump?record=