pyobo

pyobo copied to clipboard

It's not so good to load entire ontologies, but other code in other packages relies on this. Add some unit test mock magic to allow the `pyobo.get_name`, `pyobo.ground` and other...

cthoyt

Will make generating Ooh-na-na much richer to know the version to which each name corresponds

cthoyt

Everything is in this pack: http://www.orphadata.org/data/RD-CODE/Packs/Orphanet_Nomenclature_Pack_EN.zip - Mapping to ICD-10 at https://github.com/orphanet-rare-diseases-issues/RD-CODE/tree/master/ORPHA_ICD10_mapping

cthoyt

Especially Entrez and PubChem

cthoyt

http://bigg.ucsd.edu/data_access ## Metabolite ([bigg.metabolite](https://registry.identifiers.org/registry/bigg.metabolite)) http://bigg.ucsd.edu/static/namespace/bigg_models_metabolites.txt ## Reaction ([bigg.reaction](https://registry.identifiers.org/registry/bigg.reaction#!)) http://bigg.ucsd.edu/static/namespace/bigg_models_reactions.txt ## Compartment ([bigg.compartment](https://registry.identifiers.org/registry/bigg.compartment#!)) ??

cthoyt

https://www.metanetx.org/mnxdoc/mnxref.html ## Compound ([metanetx.chemical](https://registry.identifiers.org/registry/metanetx.chemical#!)) - https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_xref.tsv - https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_prop.tsv ## Reaction ([metanetx.reaction](https://registry.identifiers.org/registry/metanetx.reaction#!)) - https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_prop.tsv - https://www.metanetx.org/cgi-bin/mnxget/mnxref/reac_xref.tsv ## Compartment ([metanetx.compartment](https://registry.identifiers.org/registry/metanetx.compartment#!)) - https://www.metanetx.org/cgi-bin/mnxget/mnxref/comp_prop.tsv - https://www.metanetx.org/cgi-bin/mnxget/mnxref/comp_xref.tsv

cthoyt

Some FamPlex equivalences have missing namespace

2

Some of the target name spaces in the FamPlex equivalences file are not recognized and are replaced by None when processing the xrefs df. Example: MEDSCAN urn:agi-aopfc:0000458 is picked up...

bgyori

Curate and integrate further MeSH mappings

1

There is another table in Gilda: https://github.com/indralab/gilda/blob/master/gilda/resources/mesh_ambig_mappings.tsv which contains mappings that the automated lexicalization-based mapping couldn't definitively figure out and could be manually curated. For instance between ``` MESH |...

bgyori

Get BioGRID xrefs

1

https://downloads.thebiogrid.org/File/BioGRID/Release-Archive/BIOGRID-3.5.184/BIOGRID-IDENTIFIERS-3.5.184.tab.zip ```python VERSION = '3.5.183' BASE_URL = 'https://downloads.thebiogrid.org/Download/BioGRID/Release-Archive' URL = f'{BASE_URL}/BIOGRID-{VERSION}/BIOGRID-IDENTIFIERS-{VERSION}.tab.zip' ```

cthoyt

WikiData property: https://www.wikidata.org/wiki/Property:P594 Already done in Bio2BEL.

cthoyt