Closed Freymaurer closed 10 months ago
I read the ncbitaxon ontology, filter out terms and write it again.
The source looks like this:
[Term] id: NCBITaxon:562 name: Escherichia coli namespace: ncbi_taxonomy alt_id: NCBITaxon:1637691 alt_id: NCBITaxon:1806490 alt_id: NCBITaxon:469598 alt_id: NCBITaxon:662101 alt_id: NCBITaxon:662104 synonym: "Bacillus coli" RELATED synonym [] synonym: "Bacterium coli" RELATED synonym [] synonym: "Bacterium coli commune" RELATED synonym [] synonym: "E. coli" EXACT common_name [] synonym: "Enterococcus coli" RELATED synonym [] synonym: "Escherichia/Shigella coli" EXACT equivalent_name [] xref: GC_ID:11 xref: PMID:10319482 is_a: NCBITaxon:561 ! Escherichia property_value: has_rank NCBITaxon:species
This is the output:
[Term] id: NCBITaxon:562 name: Escherichia coli alt_id: NCBITaxon:1637691 alt_id: NCBITaxon:1806490 alt_id: NCBITaxon:469598 alt_id: NCBITaxon:662101 alt_id: NCBITaxon:662104 synonym: { Text = ""Bacillus coli"" Scope = Related TypeName = "synonym" DBXrefs = [] } synonym: { Text = ""Bacterium coli"" Scope = Related TypeName = "synonym" DBXrefs = [] } synonym: { Text = ""Bacterium coli commune"" Scope = Related TypeName = "synonym" DBXrefs = [] } synonym: { Text = ""E. coli"" Scope = Exact TypeName = "common_name" DBXrefs = [] } synonym: { Text = ""Enterococcus coli"" Scope = Related TypeName = "synonym" DBXrefs = [] } synonym: { Text = ""Escherichia/Shigella coli"" Scope = Exact TypeName = "equivalent_name" DBXrefs = [] } xref: GC_ID:11 xref: PMID:10319482 property_value: has_rank NCBITaxon:species is_a: OBI:0100026 ! organism
Obviously the ToString method is not for TermSynonym is not overwritten which produces this error, here:
https://github.com/CSBiology/OBO.NET/blob/d4b6434bed77c96ad4c808effa87e20c4eabd18d/src/OBO.NET/OboTerm.fs#L499
I will try to do a PR tomorrow, is it possible to release this asap after review?
@omaus @kMutagene
I read the ncbitaxon ontology, filter out terms and write it again.
The source looks like this:
This is the output:
Obviously the ToString method is not for TermSynonym is not overwritten which produces this error, here:
https://github.com/CSBiology/OBO.NET/blob/d4b6434bed77c96ad4c808effa87e20c4eabd18d/src/OBO.NET/OboTerm.fs#L499
I will try to do a PR tomorrow, is it possible to release this asap after review?
@omaus @kMutagene