Accessing MeSH NXO

[eric-czech]

Hey @dhimmel, I was trying to pull the 2021 MeSH NXO like this:

from nxontology import NXOntology
url = "https://github.com/related-sciences/nxontology-data/raw/71cf538dc5c258ada880d58663b0205b7b7f8561/001_medical_subject_headings_mesh_desctree.json.gz"
nxo = NXOntology.read_node_link_json(url)

I was a little surprised to find that the node ids are ints and that there isn't a lot of data attached to them:

pd.Series(type(n) for n in nxo.graph.nodes).value_counts()
<class 'int'>    920388

nxo.node_info(1).data
{'name': 'Organisms Category',
 'description': None,
 'pubchem_hnid': 1269010,
 'url': 'http://www.ncbi.nlm.nih.gov/mesh/1000066'}

Is there another way to get the unique ids, class, and tree numbers (for descriptors)?

[dhimmel]

You'll want to use the MeSH in the output/mesh branch rather than the output/pubchem branch. We could consider no longer exporting MeSH from pubchem now that we have a dedicated export path for MeSH.

See the data here. Regarding the weird directory path undefined/actions_github_pages_1651177463639, looking into that in https://github.com/peaceiris/actions-gh-pages/issues/740, but data is still usable, just make sure to commit hash version.

[dhimmel]

You'll probably want the mesh_topical_descriptor_descendants.json.gz network. It only includes nodes that descend from a Topical Descriptor and so would exclude parts of MeSH such as Geographical Descriptors and disconnected Supplemental Concept Records.

[eric-czech]

You'll want to use the MeSH in the output/mesh branch rather than the output/pubchem branch.

🤦

See the data here.

Awesome, thanks! That works.

[dhimmel]

BTW if you'd like MeSH 2022, it will now be created upon the next CI mesh export following d0b3c82738c600448b026a3cd20152a5de8c4780 (which might now work due to the deploy bug)

[eric-czech]

That would be really great actually. Can I kick off these workflows myself sooner in https://github.com/related-sciences/nxontology-data/actions/workflows/create.yaml? Should I check "Overwrite output on an existing branch"?

[dhimmel]

Yes kick off yourself and select overwrite, but I'm worried there will be a deployment bug. If so, you could try deleting the output/mesh branch and then rerunning. Should work that way.

[eric-czech]

https://github.com/related-sciences/nxontology-data/actions/runs/2296536149 🎉

It did fail the first time but not the second after deleting the branch, as you suggested.

[dhimmel]

Regarding the weird directory path undefined/actions_github_pages_1651177463639

https://github.com/related-sciences/nxontology-data/pull/6 fixed the weird path issue, so now the output/mesh branch contents are proper.