Table 1.
Extraction patterns and contextual cues for databases
| Database | Patterns | Contextual cues |
|---|---|---|
| ENA | [A-Z][0–9]{5}; [A-Z]{2}[0–9]{6}; [A-Z]{3}[0–9]{5}; [A-Z]{4}[0–9]{8,10}; [A-Z]{5}[0–9]{7} | genbank, gen, ddbj, embl |
| UniProt | [A-N,R-Z][0–9][A-Z][A-Z, 0–9][A-Z, 0–9][0–9]; [O,P,Q][0–9][A-Z, 0–9][A-Z, 0–9][A-Z, 0–9][0–9] | swissprot, sprot, uniprot |
| PDBe | [0–9][A-Z, 0–9]{3} | pdb |
| InterPro | IPR[0–9]{6} | interpro |
| Pfam | PF(AM)?[0–9]{5} | hmm, family, pfam |
| ArrayExpress | E-[A-Z]{4}-[0–9]+ | arrayexpress |
| OMIM | [0–9]{6} | omim |
| Ensembl | ENS[A-Z]*G[0–9]{11}+ | ensembl |
| RefSeq | (AC|AP|NC|NG|NM|NP|NR|NT|NW|NZ|XM|XP|XR|YP|ZP|NS)_([A-Z]{4})*[0–9]{6,9}(?:[.][0–9]+)? | refseq |
| RefSNP | RS[0–9]{5,9} | snp |