Closed zakandrewking closed 9 years ago
jslu9
commented
9 years ago metabolites map to incorrect old id link outs. http://yersinia.ucsd.edu:8888/models/iAT_PLT_636/metabolites/3mob_c old_id: 3mob[c], 3mob_c, 3mob_h, 3mob_m, _3mob_c
draeger
commented
9 years ago Here are all identifiers.org addresses and id patterns for the catalogs that are currently in use in ModelPolisher:
| Name | Catalog | URL | Pattern |
|---|---|---|---|
| ASAP | asap | http://identifiers.org/asap/ | ^[A-Za-z0-9-]+$ |
| BRENDA | brenda | http://identifiers.org/brenda/ | ^((\d+.-.-.-) |
| CAS | cas | http://identifiers.org/cas/ | ^\d{1,7}-\d{2}-\d$ |
| CCDS | ccds | http://identifiers.org/ccds/ | ^CCDS\d+.\d+$ |
| CHEBI | chebi | http://identifiers.org/chebi/ | ^CHEBI:\d+$ |
| EcoGene | ecogene | http://identifiers.org/ecogene/ | ^EG\d+$ |
| GeneID | ncbigene | http://identifiers.org/ncbigene/ | ^\d+$ |
| GI | ncbigi | http://identifiers.org/ncbigi/ | ^(GI |
| GO | go | http://identifiers.org/go/ | ^GO:\d{7}$ |
| GOA | goa | http://identifiers.org/goa/ | ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9]) |
| HGNC | hgnc | http://identifiers.org/hgnc/ | ^((HGNC |
| HMDB | hmdb | http://identifiers.org/hmdb/ | ^HMDB\d{5}$ |
| HPRD | hprd | http://identifiers.org/hprd/ | ^\d+$ |
| HSSP | hssp | http://identifiers.org/hssp/ | ^\w{4}$ |
| InterPro | interpro | http://identifiers.org/interpro/ | ^IPR\d{6}$ |
| KEGGID | kegg.compound | http://identifiers.org/kegg.compound/ | ^C\d+$ |
| KEGGID | kegg.drug | http://identifiers.org/kegg.drug/ | ^D\d+$ |
| KEGGID | kegg.genes | http://identifiers.org/kegg.genes/ | ^\w+:[\w\d.-]*$ |
| KEGGID | kegg.reaction | http://identifiers.org/kegg.reaction/ | ^R\d+$ |
| KEGGID | kegg.glycan | http://identifiers.org/kegg.glycan/ | ^G\d+$ |
| KEGGID | kegg.pathway | http://identifiers.org/kegg.pathway/ | ^\w{2,4}\d{5}$ |
| LIPIDMAPS | lipidmaps | http://identifiers.org/lipidmaps/ | ^LM(FA |
| METACYC | biocyc | http://identifiers.org/biocyc/ | ^[A-Z-0-9]+(?<!CHEBI)(:)?[A-Za-z0-9+_.%-]+$ |
| MGI | mgd | http://identifiers.org/mgd/ | ^MGI:\d+$ |
| PDB | pdb | http://identifiers.org/pdb/ | ^[0-9][A-Za-z0-9]{3}$ |
| PUBCHEMID | pubchem.substance | http://identifiers.org/pubchem.substance/ | ^\d+$ |
| PUBCHEMID | pubchem.compound | http://identifiers.org/pubchem.compound/ | ^\d{1,7}-\d{2}-\d$ |
| REACTOME | reactome | http://identifiers.org/reactome/ | ^REACT_\d+(.\d+)?$ |
| REBASE | rebase | http://identifiers.org/rebase/ | ^\d+$ |
| SEED | seed | http://identifiers.org/seed/ | ^\d+.\d+$ |
| SEED | seed.compound | http://identifiers.org/seed.compound/ | ^cpd\d+$ |
| SGD | sgd | http://identifiers.org/sgd/ | ^((S\d+$) |
| TubercuList | myco.tuber | http://identifiers.org/myco.tuber/ | ^Rv\d{4}(A |
| UniProtKB_Swiss_Prot | ipi | http://identifiers.org/ipi/ | ^IPI\d{8}$ |
| UniProtKB_Swiss_Prot | uniprot.isoform | http://identifiers.org/uniprot.isoform/ | ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9]) |
| UniProtKB_Swiss_Prot | uniprot | http://identifiers.org/uniprot/ | ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2}) |
| UniProtKB_Swiss_Prot | unipathway | http://identifiers.org/unipathway/ | ^UPA\d{5}$ |
| UniProtKB_TrEMBL | ipi | http://identifiers.org/ipi/ | ^IPI\d{8}$ |
| UniProtKB_TrEMBL | uniprot.isoform | http://identifiers.org/uniprot.isoform/ | ^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z, 0-9][0-9]) |
| UniProtKB_TrEMBL | uniprot | http://identifiers.org/uniprot/ | ^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z, 0-9][0-9]){1,2}) |
| UniProtKB_TrEMBL | unipathway | http://identifiers.org/unipathway/ | ^UPA\d{5}$ |
| UPA | unipathway.compound | http://identifiers.org/unipathway.compound/ | ^UPC\d{5}$ |
| UPA | unipathway | http://identifiers.org/unipathway/ | ^UPA\d{5}$ |
These are separate concepts in the database right now (they were defined at different times), but they should really be merged.
http://identifiers.org/kegg.compound/KEGGID\thttp://identifiers.org/kegg.compound/