search

nfdi4plants / nfdi4plants_ontology

An intermediate ontology for plants used by DataPLANT to fill the ontology gap
MIT License
7 stars 10 forks source link

[Missing ontology] Gene Ontology (go) #7

Closed Freymaurer closed 3 years ago

Freymaurer commented 3 years ago

Ontology is available at: http://www.obofoundry.org/ontology/go.html

Reasons for this addition

USed by ontologies in db.

Brilator commented 3 years ago

I'd argue that the gene ontology is"only" important for derived datasets (e.g. RNASeq / gene expression data) and not so much to annotate the pipeline towards the data. And I'd be surprised if anyone ever was to use this (manually) in an excel sheet rather than annotating with tools (interproscan) or importing from existing resources.

Freymaurer commented 3 years ago

So i checked the number of ontologies from go and quite frankly we do not loose much by adding it. To summarize, our initial ontology set had references to some "directly linked" ontologies and we thought it might be a good start to add those. Our database now contains 2 316 953 terms and 9 629 are from the go ontology. So i'd argue we just keep it. At the moment most time needed to search for terms comes from the huge ncbitaxon (2 241 111) and chebi (136 671).