This is a test version of Biostars. For the public version, visit https://www.biostars.org.
GOstats Clarification: ontology information source

Hey everybody,

I am wondering what ontology file (.obo file) GOstats uses and where I could view it. Does GOstats pull its ontologies from geneontology.org (e.g. http://purl.obolibrary.org/obo/go.obo ) or is there some other source? I started looking at the source code but I haven't been able to pinpoint where the ontology information is imported.

Thanks in advance,

UPDATE: GOstats gets its ontology information from the package GO.db. Any idea if there is an obo file associated with this package, or where GO.db pulls its information from? (see my bioconductor post)

rna-seq database ontology gostats go
• 1,602 views • link
updated by Mark Mark • written by brismiller • brismiller

1 answer

From GO.db package manual:

Mappings were based on data provided by: Gene Ontology ftp://ftp.geneontology.org/pub/go/godatabase/archive/latestlite/ With a date stamp from the source of: 2018-Mar28

and

References http://www.geneontology.org/ and https://www.ncib.nlm.nih.gov/entrez/query.fcgi?db=gene

Why do you need a .obo file? What's your objective? There might be a solution possible if you let us know.

• 1 views • link
written by Mark Mark

Log in to answer this question.

More posts like this