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 GeneOntologyData (1.0.0) current version: 1.1.0 »

Source Notebook

Access hierarchical relation and associated gene product information for Gene Ontology concepts

Contributed by: Keiko Hirayama

ResourceFunction["GeneOntologyData"][id]

retrieves a Gene Ontology dataset for a given id.

ResourceFunction["GeneOntologyData"][{id1,id2,…}]

gives the dataset for the specified idi.

Details

The dataset is based on the Gene Ontology (GO) knowledgebase.
The id values are Gene Ontology identifiers provided as a number string with or without the prefix "GO:".
Information about a Gene Ontology concept is provided in a form of Dataset containing the following keys:
"GeneOntologyAccessionNumber"unique accession number assigned to the Gene Ontology concept
"Name"name of the concept
"Definition"detailed description of the concept
"Synonyms"synonyms of the concept
"GraphData"hierarchical relationships associated with the concept
"AssociatedGenes"information on genes associated with the concept

Examples

Basic Examples (2) 

Find information about a Gene Ontology concept:

In[1]:=
godata = ResourceFunction["GeneOntologyData"]["0031929"]
Out[1]=

Visualize the hierarchical relationships about the term. Hover over any vertex and edge to find the associated Gene Ontology terms and their relations:

In[2]:=
Graph[Normal@godata["GraphData"][All, "Edge"], VertexLabels -> Placed["Name", Tooltip], EdgeLabels -> Normal@godata["GraphData"][All, Rule[#"Edge", Placed[#"Relation", Tooltip]] &]]
Out[2]=

Scope (3) 

Retrieve data for gene ontology terms associated with the biological activities concerning the lymph node development and B cell proliferation:

In[3]:=
gobiodata = ResourceFunction["GeneOntologyData"][{"GO:0048535", "GO:0042100"}]
Out[3]=

Find a gene associated with both biological activities:

In[4]:=
gene = Intersection @@ Normal[gobiodata[All, #"AssociatedGenes"[[All, 1]] &]]
Out[4]=

Use the BioDBnetGeneData resource function to find more about the gene:

In[5]:=
ResourceFunction[ ResourceObject[<|"Name" -> "BioDBnetGeneData", "ShortName" -> "BioDBnetGeneData", "UUID" -> "73f25ec5-bf6c-435a-8087-74a79d984422", "ResourceType" -> "Function", "Version" -> "1.0.0", "Description" -> "Access information on genes available in major biological databases", "RepositoryLocation" -> URL[ "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"], "SymbolName" -> "FunctionRepository`$f4720c38dbf74195bd13e18f466ed042`BioDBnetGeneData", "FunctionLocation" -> CloudObject[ "https://www.wolframcloud.com/obj/90cea3ec-6d0a-42f7-828a-46ffd6ae44dd"]|>, ResourceSystemBase -> Automatic]][gene]
Out[5]=

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

  • 1.1.0 – 05 March 2025
  • 1.0.0 – 10 January 2025

Source Metadata

  • Citation:
    • Ashburner et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000 May;25(1):25-9. DOI: 10.1038/75556
    • The Gene Ontology Consortium. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. DOI: 10.1093/genetics/iyad031

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