Accession types¶
Every namespace fetch_series.accession recognises, what it identifies, and which body
issues it. Validated against all 104,442 rows of the reprocessed sample table: 792,610
tokens parse, and the only unrecognised value in the whole file is the - placeholder.
| Prefix | Identifies | Issued by |
|---|---|---|
GSE |
GEO series | GEO |
GSM |
GEO sample | GEO |
GPL |
GEO platform | GEO |
PRJNA |
BioProject | NCBI |
PRJEA |
BioProject (legacy EBI, mirrored by NCBI) | NCBI |
PRJDA |
BioProject (legacy DDBJ, mirrored by NCBI) | NCBI |
PRJEB |
BioProject | EBI |
PRJDB |
BioProject | DDBJ |
SAMN |
BioSample | NCBI |
SAMEA |
BioSample | EBI |
SAMD |
BioSample | DDBJ |
[SED]RP |
INSDC study (secondary study accession) | NCBI / EBI / DDBJ |
[SED]RS |
INSDC sample (secondary sample accession) | NCBI / EBI / DDBJ |
[SED]RX |
INSDC experiment (library) | NCBI / EBI / DDBJ |
[SED]RR |
INSDC run — the unit that carries files | NCBI / EBI / DDBJ |
[SED]RA |
INSDC submission | NCBI / EBI / DDBJ |
[SED]RZ |
INSDC analysis | NCBI / EBI / DDBJ |
E-[A-Z]{4}- |
ArrayExpress experiment | ArrayExpress |
S-[A-Z]+ |
BioStudies study | BioStudies |
Two things the registry gets right that inline regexes did not¶
The INSDC prefix letter carries the issuing archive. SRR1, ERR1 and DRR1 are the
same kind of entity under three namespaces, and which archive issued one decides which API
can answer about it — see routing by archive.
- is not an accession. It appears 18,623 times in the sample table as a missing-value
placeholder. It must be reported as unparsed rather than silently dropped: as a grep -f
pattern it matches every line of a metadata table.
A pattern that could never match¶
ArrayExpress accessions are hyphenated — E-MTAB-6505. This project previously carried
E-MTAB\d+$, which cannot match a real one.