Comments (2)
NA are now being ignored. Still unsure how to manage the other invalid identifiers. Maybe a script to check identifiers against identifiers.org.
from bigg_models.
Here are a list of catalog ID patterns to check against (thanks @draeger)
BiGG ref name | catalog name | Pattern |
---|---|---|
ASAP | asap | ^[A-Za-z0-9-]+$ |
BRENDA | brenda | `^((\d+.-.-.-) |
CAS | cas | ^\d{1,7}\-\d{2}\-\d$ |
CCDS | ccds | ^CCDS\d+\.\d+$ |
CHEBI | chebi | ^CHEBI:\d+$ |
EcoGene | ecogene | ^EG\d+$ |
GeneID | ncbigene | ^\d+$ |
GO | go | ^GO:\d{7}$ |
GOA | goa | `^([A-N,R-Z][0-9][A-Z][A-Z, 0-9][A-Z,0-9][0-9]) |
HGNC | hgnc | `^((HGNC |
HMDB | hmdb | ^HMDB\d{5}$ |
HPRD | hprd | ^\d+$ |
HSSP | hssp | ^\w{4}$ |
InterPro | interpro | ^IPR\d{6}$ |
KEGGID | kegg.compound | ^C\d+$ |
KEGGID | kegg.drug | ^D\d+$ |
KEGGID | kegg.genes | ^\w+:[\w\d\.-]*$ |
KEGGID | kegg.reaction | ^R\d+$ |
KEGGID | kegg.glycan | ^G\d+$ |
KEGGID | kegg.pathway | ^\w{2,4}\d{5}$ |
LIPIDMAPS | lipidmaps | `^LM(FA |
METACYC | biocyc | ^[A-Z-0-9]+(?<!CHEBI)(\:)?[A-Za-z0-9+_.%-]+$ |
MGI | mgd | ^MGI:\d+$ |
PDB | pdb | ^[0-9][A-Za-z0-9]{3}$ |
PUBCHEMID | pubchem.substance | ^\d+$ |
PUBCHEMID | pubchem.compound | ^\d{1,7}\-\d{2}\-\d$ |
REACTOME | reactome | ^REACT_\d+(\.\d+)?$ |
REBASE | rebase | ^\d+$ |
SGD | sgd | `^((S\d+$) |
TubercuList | myco.tuber | `^Rv\d{4}(A |
UniProtKB_Swiss_Prot | ipi | ^IPI\d{8}$ |
UniProtKB_Swiss_Prot | uniprot.isoform | `^([A-N,R-Z][0-9][A-Z][A-Z,0-9][A-Z, 0-9][0-9]) |
UniProtKB_Swiss_Prot | 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 | ^UPA\d{5}$ |
UniProtKB_TrEMBL | ipi | ^IPI\d{8}$ |
UniProtKB_TrEMBL | uniprot.isoform | `^([A-N,R-Z][0-9][A-Z][A-Z,0-9][A-Z, 0-9][0-9]) |
UniProtKB_TrEMBL | uniprot | `^([A-N,R-Z][0-9]([A-Z][A-Z, 0-9][A-Z,0-9][0-9]){1,2}) |
UniProtKB_TrEMBL | unipathway | ^UPA\d{5}$ |
from bigg_models.
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from bigg_models.