getGeneAssociation
This function collects GO annotation from http://geneontology.org/page/download-annotations.
getGeneAssociation(URL_or_file)
-
URL_or_fileeither a link to a file on geneontology.org eg. http://geneontology.org/gene-associations/gene_association.fb.gz or the path for the respective downloded .gz file. -
returnsa Pandas dataframe with the parsed table.
>>> import pandas as pd
>>> gA=age.getGeneAssociation("http://geneontology.org/gene-associations/gene_association.wb.gz")
>>> print gA.head()
DB DB_Object_ID DB_Object_Symbol Qualifier GO ID \
0 WB WBGene00000001 aap-1 GO:0005942
1 WB WBGene00000001 aap-1 GO:0005942
2 WB WBGene00000001 aap-1 GO:0008286
3 WB WBGene00000001 aap-1 GO:0008286
4 WB WBGene00000001 aap-1 GO:0008286
DB:Reference Evidence With (or) From Aspect \
0 GO_REF:0000002 IEA InterPro:IPR001720 C
1 WB_REF:WBPaper00005614|PMID:12393910 IDA C
2 WB_REF:WBPaper00005614|PMID:12393910 IGI WB:WBGene00000090 P
3 WB_REF:WBPaper00005614|PMID:12393910 IGI WB:WBGene00000898 P
4 WB_REF:WBPaper00005614|PMID:12393910 IMP P
DB_Object_Name DB_Object_Synonym DB_Object_Type Taxon Date \
0 Y110A7A.10 gene taxon:6239 20170321
1 Y110A7A.10 gene taxon:6239 20151214
2 Y110A7A.10 gene taxon:6239 20151214
3 Y110A7A.10 gene taxon:6239 20151214
4 Y110A7A.10 gene taxon:6239 20060302
Assigned_by Annotation Extension Gene Product Form ID
0 WB
1 WB
2 WB
3 WB
4 WB