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Add Journal Article -> main subject -> MeSH Terms #32
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Hi @Daniel-Mietchen . Yes, this is something that fits in to our workflow, and is something that could be added to WikidataIntegrator. This would be easy to implement provided the Wikidata item corresponding to the MeSH term already existed. Ideally, at some point we would import MeSH into Wikidata (or at least some parts of it). I imagine this would require a lot of work matching up items to prevent duplication though... Looking at the API response from EuropePMC (and from Pubmed), the mesh terms don't actually include the mesh ID (of course, why would they?), but only the name. So either way, we would have to parse the MeSH dump file to get the MeSH ID from the name, unless you know of a better API? We could also look into adding the items from the "chemicalList" field. |
A few notes from me.
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You may find this service useful here. SPARQL over MeSH graph. https://id.nlm.nih.gov/mesh/ |
@andrewsu Thanks for the pointer to the XML. I'm not sure yet what the "MajorTopicNY" switch does — in the example, it seems to only be used for qualifiers, while we would likely want to go mainly for descriptors. |
@Daniel-Mietchen definitely used for descriptors too, eg https://www.ncbi.nlm.nih.gov/pubmed/26611529?report=xml&format=text |
Yes, for other PMIDs, it is used for descriptors as well, but my point from above was that if the goal is to turn MeSH IDs into P921 statements, we probably cannot solely rely on those descriptors for which "MajorTopicNY" is "Y", since that would give nothing for the PMID=16046484 example. If we were to include those descriptors for which at least one qualifier's "MajorTopicNY" is set to "Y", then we would get
For PMID=26611529, we would get
I have made those sample edits to Is there a way to know whether there are PMIDs for which no "MajorTopicNY" value would be "Y"? |
I think we might as well include the qualifiers as well, no? Maybe with the "use" qualifier? |
Yes, in principle, we'd like to make use of the information provided by the qualifiers as well, but not sure P366 is the way to go. To go back to https://www.ncbi.nlm.nih.gov/pubmed/26611529?report=xml&format=text , we have, for instance <MeshHeading>
<DescriptorName UI="D043524" MajorTopicYN="Y">Peptide-N4-(N-acetyl-beta-glucosaminyl) Asparagine Amidase</DescriptorName>
<QualifierName UI="Q000737" MajorTopicYN="N">chemistry</QualifierName>
<QualifierName UI="Q000235" MajorTopicYN="N">genetics</QualifierName>
<QualifierName UI="Q000378" MajorTopicYN="N">metabolism</QualifierName>
</MeshHeading> I understand this to mean that the paper is about
Unless we have dedicated items for such things, I could imagine translating this into statements like
I have made such a test edit to a sandbox item: https://www.wikidata.org/w/index.php?title=Q13406268&oldid=500822215#P921 Other issues:
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Yeah, have to admit I'm not a fan of that sandbox model and the use of "of". Don't have an alternate suggestion, but just sharing my gut reaction. I'd argue that you'd only want to use P921 "main subject" if MajorTopicYN="Y". That would also cut down on the number of MeSH term statements and eliminate less informative/specific ones eg "mammal"... |
Meanwhile, all MeSH IDs are in Mix'n Match, and about 14k have been matched. |
I'm looking for ways to get the following workflow going:
Would this be something that could be fit into GeneWiki workflows?
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