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jslu9 avatar jslu9 commented on September 2, 2024

NA are now being ignored. Still unsure how to manage the other invalid identifiers. Maybe a script to check identifiers against identifiers.org.

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zakandrewking avatar zakandrewking commented on September 2, 2024

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}$

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