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Error while trying to write `ncbigene.obo` via pyobo

1

pyobo call made via code: ```python from pyobo.sources.ncbigene import get_obo def get_obo_file(output_path: str): """Get the obo file.""" obo_file = get_obo() obo_file.write_obo(output_path, use_tqdm=True) ``` This resulted in the following error: ```shell...

hrshdhgd

Compare https://www.enzyme-database.org/query.php?ec=1.1.1.1 with: ``` ✗ curl -L -s https://w3id.org/biopragmatics/resources/eccode/eccode.obo | obo-grep.pl -r 'id: eccode:1.1.1.1\n' - | grep -v ^rel [Term] id: eccode:1.1.1.1 name: alcohol dehydrogenase is_a: eccode:1.1.1 ! With NAD(+)...

cmungall

Right now, everything is assumed to be an `xsd:string`. It would be good to enable putting in the datatypes

cthoyt

Current pyobo includes annotations (in the sense of GO annotations, not OWL annotations) modeled as `relationship`s (i.e `S subClassOf R some O`). An example of this is ec.obo: ```yaml [Term]...

cmungall

I already map several FlyBase gene types to SO terms: https://github.com/pyobo/pyobo/blob/dc9ad7d2aa11d42b82bca94a2be282370d4c9fcc/src/pyobo/sources/flybase.py#L100-L119 The following haven't yet got mappings: - mt_LSU_rRNA_gene - mt_SSU_rRNA_gene - C_D_box_snoRNA_gene - H_ACA_box_snoRNA_gene - C_D_box_scaRNA_gene - hpRNA_gene -...

cthoyt

This helps with massively broken OBO files that don't use CURIEs but rather only LUIDs. Not ideal, just a demo.

cthoyt

https://www.ebi.ac.uk/interpro/entry/InterPro/IPR036069/ - [DUF34/NIF3](https://www.ebi.ac.uk/interpro/entry/InterPro/IPR002678/) (IPR002678) - [DUF34/NIF3, bacteria](https://www.ebi.ac.uk/interpro/entry/InterPro/IPR017221/) (IPR017221) - [DUF34/NIF3, animal](https://www.ebi.ac.uk/interpro/entry/InterPro/IPR017222/) (IPR017222) the .obo has no relationship between these: [Term] id: interpro:IPR036069 name: DUF34/NIF3 superfamily property_value: type "Homologous_superfamily" xsd:string I...

cmungall

Annotate genes in HGNC with SO terms

4

Either find or create terms for all HGNC gene locus types that can be used to annotate all genes in HGNC: - [x] Fragile site https://github.com/The-Sequence-Ontology/SO-Ontologies/issues/301 - [x] RNA, Y...

cthoyt

from ROR message thread https://github.com/paulmillar/PIC-to-ROR/

cthoyt

cthoyt