Reading a Gene Product Association Data (GPAD) file

  1. Download a GPAD file

  2. Load the GPAD file into the GpadReader

  3. Get Annotations

Bonus: Each line in the GPAD file is stored in a namedtuple:

  • Namedtuple fields

  • Print a subset of the namedtuple fields

1) Download a GPAD file and GO Dag file

from os.path import exists
if not exists('goa_human.gpad'):
    !rm -f goa_human.gpad.gz
    !wget http://current.geneontology.org/annotations/goa_human.gpad.gz
    !gunzip goa_human.gpad.gz

if not exists('go-basic.obo'):
    !wget http://geneontology.org/ontology/go-basic.obo

2) Load the GPAD file into the GpadReader

from goatools.base import get_godag
from goatools.anno.gpad_reader import GpadReader

godag = get_godag("go-basic.obo")
anno = GpadReader("goa_human.gpad", godag=godag)

  EXISTS: go-basic.obo
go-basic.obo: fmt(1.2) rel(2022-11-03) 46,800 Terms
HMS:0:00:16.880690 635,765 annotations READ: goa_human.gpad

3) Get Annotations

The annotations will be stored in three dicts, one for each GODAG branch, where:

  • the key is the protein ID and

  • the value is a list of GO IDs associated with the protein.

ns2assc = anno.get_ns2assc()

for namespace, associations in ns2assc.items():
    for protein_id, go_ids in sorted(associations.items())[:3]:
        print("{NS} {PROT:7} : {GOs}".format(
            NS=namespace,
            PROT=protein_id,
            GOs=' '.join(sorted(go_ids))))

MF A0A024RBG1 : GO:0000298 GO:0008486 GO:0034431 GO:0034432 GO:0046872 GO:0050072
MF A0A075B6Q5 : GO:0003823 GO:0034987
MF A0A075B6R2 : GO:0003823 GO:0034987
CC A0A024RBG1 : GO:0005634 GO:0005737 GO:0005829
CC A0A075B6H5 : GO:0005886
CC A0A075B6H7 : GO:0005615 GO:0005886 GO:0019814
BP A0A024RBG1 : GO:0071543 GO:1901907 GO:1901909 GO:1901911
BP A0A075B6H5 : GO:0007166
BP A0A075B6H7 : GO:0002250 GO:0002377 GO:0006955

Bonus: The GPAD is stored as a list of named tuples

The list of namedtuples is stored in the GpadReader data member named associations.

Each namedtuple stores data for one line in the GPAD file.

# Sort the list of GPAD namedtuples by ID
nts = sorted(anno.associations, key=lambda nt:nt.DB_ID)

# Print one namedtuple
print(nts[0])

ntgpadobj(DB='UniProtKB', DB_ID='A0A024RBG1', Qualifier={'enables'}, GO_ID='GO:0046872', DB_Reference={'GO_REF:0000043'}, ECO='ECO:0000501', Evidence_Code='IEA', With_From={'UniProtKB-KW:KW-0479'}, Taxon=None, Date=datetime.date(2022, 9, 7), Assigned_By='UniProt', Extension=None, Properties={}, NS='MF')

Namedtuple fields

DB             #  0 required 1              UniProtKB
DB_ID          #  1 required 1              P12345
DB_Symbol      #  2 required 1              PHO3
Qualifier      #  3 optional 0 or greater   NOT
GO_ID          #  4 required 1              GO:0003993
DB_Reference   #  5 required 1 or greater   PMID:2676709
Evidence_Code  #  6 required 1              IMP
With_From      #  7 optional 0 or greater   GO:0000346
Aspect         #  8 required 1              F
DB_Name        #  9 optional 0 or 1         Toll-like receptor 4
DB_Synonym     # 10 optional 0 or greater   hToll|Tollbooth
DB_Type        # 11 required 1              protein
Taxon          # 12 required 1 or 2         taxon:9606
Date           # 13 required 1              20090118
Assigned_By    # 14 required 1              SGD
Annotation_Extension # 15 optional 0 or greater part_of(CL:0000576)
Gene_Product_Form_ID # 16 optional 0 or 1       UniProtKB:P12345-2