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assoc-path-informatics / interop

General discussion of topics related to interoperability
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define citation format #1

Closed nhoffman closed 2 years ago

nhoffman commented 2 years ago

@gershkovich - almost immediately, I can see that citations in raw markdown are suboptimal. We should decide how we want to cite literature in pubmed (other sources will probably just need to be done ad-hoc). I'd kind of like to avoid duplication of references. Here's one idea that we can try out and consider how to streamline it for other users. Given a pmid, a trivial script can create a formatted reference (given the link to the pmid, I'm leaving out volume and pages in this ad-hoc citations format): 

bin/cite.py 30137378
[^parr-2018]: Parr SK, et al. Automated mapping of laboratory tests to LOINC codes using noisy labels in a national electronic health record system database. J Am Med Inform Assoc. 2018 [PMID 30137378](https://pubmed.ncbi.nlm.nih.gov/30137378/)

This can be used to generate a citation, eg for Parr, 2020 [^parr-2018].

[^parr-2018]: Parr SK, et al. Automated mapping of laboratory tests to LOINC codes using noisy labels in a national electronic health record system database. J Am Med Inform Assoc. 2018 PMID 30137378

nhoffman commented 2 years ago

Unless I hear otherwise we'll go with this format