Reference Lists¶

Reference lists are complete sets of identifiers for an organism. They are useful for filtering, validation, and distinguishing reviewed from unreviewed proteins.

Available lists¶

Name	Content
`swissprot`	All reviewed UniProt accessions
`trembl`	All unreviewed UniProt accessions
`uniprot`	All UniProt accessions (SwissProt + TrEMBL)

Usage¶

Check membership¶

from omnipath_utils.reflists import is_swissprot, is_trembl

is_swissprot('P04637')  # True  (TP53 is reviewed)
is_trembl('P04637')     # False

Get full lists¶

from omnipath_utils.reflists import all_swissprots, all_trembls, all_uniprots

swissprots = all_swissprots()          # ~20,000 human reviewed ACs
trembls = all_trembls()                # ~200,000 human unreviewed ACs
all_acs = all_uniprots()               # union of both

Other organisms¶

All functions accept ncbi_tax_id:

from omnipath_utils.reflists import all_swissprots

mouse_sp = all_swissprots(ncbi_tax_id=10090)

Generic access¶

from omnipath_utils.reflists import get_reflist

ids = get_reflist('swissprot', ncbi_tax_id=9606)

Data source¶

Reference lists are loaded from the UniProt REST API. When pypath is available, it uses the pypath UniProt query interface; otherwise, it falls back to direct HTTP requests to rest.uniprot.org.

Results are cached in memory after first load.