Add AGRO-AGROVOC mappings

[cthoyt]

This PR adds predicted mappings between AGRO labels/synonyms and the English preferred terms from AGROVOC. The SPARQL query could be extended to use other alternative labels if desired.

@KrishnaTO can you do a sanity check - I'm surprised the number of suggestions is quite low

[KrishnaTO]

A quick check shows good matches, wherever labels match or def exists.

This is a great tool! Do you know if the AGROVOC synonyms are currently checked? Not to mention, our ontology also has lots of common labels as synonyms instead of the rdfs:labels.

[cthoyt]

maybe it wasn't clear from the description but all of the labels/synonyms from AGRO are considered. Currently only the preferred labels from AGROVOC are considered. That could be updated if you think it's important.

[KrishnaTO]

Got it, compared to the previous mappings, some terms have changed between either one of the sources.

As well, AGROVOC seems to use "ENTRY TERMS" for synonyms (example), so there may be some mods there.

But so happy with this tool, thanks @cthoyt !

[KrishnaTO]

@cthoyt How did you bypass the agro parsing error?
I was attempting to run the "scripts/generate_agrovoc_mappings.py" file locally, and can't figure out how you parsed AGRO?

File "/.../.local/lib/python3.8/site-packages/pronto/parsers/rdfxml.py", line 182, in _compact_datatype
    raise ValueError(f"invalid datatype: {iri!r}")
ValueError: invalid datatype: 'http://www.w3.org/2000/01/rdf-schema#anyURI'

Note: I do have the dev versions of pyobo, pystow, and biomappings you updated. Did you mod pronto as well?

[cthoyt]

@KrishnaTO I just went through PyStow and PyOBO to make sure there's a a PyPI release that's sufficient to make this work, so you can just get the new releases from pip uninstall pystow pyobo bioregistry && pip install --upgrade pystow bioregistry pyobo. Let me know if that fixes it - otherwise the error you showed is because it's using an RDF/XML reader for AGRO, which might be because it's not finding the recently added OBO link

[KrishnaTO]

It found the right path for AgrO after the mentioned reinstallations.

[KrishnaTO]

@cthoyt Regarding the sanity check, AgrO has 1190 terms within its namespace (AGRO_), so 162 matches using label and synonyms (not sure if searches definitions?) isn't bad.
A lot terms may not have the correct synonyms in either database, so there are has to be additional manual curation work to add those.

The mentioned predictions were curated here with 142/162 positive exact matches. Let me know if want to merge and create a PR to this this branch.

[cthoyt]

@KrishnaTO I'm sorry I missed your comment - it's great you triaged these! I will definitely merge them in a separate PR :)