Gene Ontology (GO) Term Annotations
go_annotation.RdA comprehensive annotation table of Gene Ontology (GO) terms, including biological process, molecular function, and cellular component namespaces. This dataset supports the interpretation and functional enrichment of graph nodes labeled with GO identifiers within the tKOI framework.
Format
A data frame with 47,921 rows and 4 columns:
- identifier
A character string representing the GO identifier (e.g., "GO:0000001").
- name
The name of the GO term (e.g., "mitochondrion inheritance").
- namespace
The ontology category to which the term belongs, one of
"biological_process","molecular_function", or"cellular_component".- definition
A textual definition of the GO term, often including references and source attributions.
Source
Gene Ontology Consortium http://geneontology.org/
Details
The dataset enables mapping of functional annotations to nodes in a biological knowledge graph and is particularly useful
for characterizing enriched terms from network-based analyses such as those performed with run_tkoi.
GO terms marked as "obsolete" are included for completeness but may require special handling during analysis.
Examples
data(go_annotation)
table(go_annotation$namespace)
#>
#> biological_process cellular_component external molecular_function
#> 30741 4525 1 12654
head(go_annotation[go_annotation$namespace == "molecular_function", ])
#> identifier name
#> <char> <char>
#> 1: GO:0000005 obsolete ribosomal chaperone activity
#> 2: GO:0000006 high-affinity zinc transmembrane transporter activity
#> 3: GO:0000007 low-affinity zinc ion transmembrane transporter activity
#> 4: GO:0000008 obsolete thioredoxin
#> 5: GO:0000009 alpha-1,6-mannosyltransferase activity
#> 6: GO:0000010 heptaprenyl diphosphate synthase activity
#> namespace
#> <char>
#> 1: molecular_function
#> 2: molecular_function
#> 3: molecular_function
#> 4: molecular_function
#> 5: molecular_function
#> 6: molecular_function
#> definition
#> <char>
#> 1: OBSOLETE. Assists in the correct assembly of ribosomes or ribosomal subunits in vivo, but is not a component of the assembled ribosome when performing its normal biological function."" [GOC:jl, PMID:12150913]
#> 2: Enables the transfer of zinc ions (Zn2+) from one side of a membrane to the other, probably powered by proton motive force. In high-affinity transport the transporter is able to bind the solute even if it is only present at very low concentrations."" [TC:2.A.5.1.1]
#> 3: Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Zn2+ = Zn2+, probably powered by proton motive force. In low-affinity transport the transporter is able to bind the solute only if it is present at very high concentrations."" [GOC:mtg_transport, ISBN:0815340729]
#> 4: OBSOLETE. A small disulfide-containing redox protein that serves as a general protein disulfide oxidoreductase. Interacts with a broad range of proteins by a redox mechanism, based on the reversible oxidation of 2 cysteine thiol groups to a disulfide, accompanied by the transfer of 2 electrons and 2 protons. The net result is the covalent interconversion of a disulfide and a dithiol."" [GOC:kd]
#> 5: Catalysis of the transfer of a mannose residue to an oligosaccharide, forming an alpha-(1->6) linkage."" [GOC:mcc, PMID:2644248]
#> 6: Catalysis of the reaction: (2E,6E)-farnesyl diphosphate + 4 isopentenyl diphosphate = 4 diphosphate + all-trans-heptaprenyl diphosphate."" [PMID:9708911, RHEA:27794]