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viralemergence / virion

The Global Virome in One Network
https://viralemergence.github.io/virion
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PMID, DOI #60

Open renatamuy opened 3 years ago

renatamuy commented 3 years ago

I know this info is sourced from Clover but I think we could think about completing this column (or ReferenceText) in Virion (or Clover -> Virion) to facilitate referencing and checking the context of data collection. That there are many NAs in PMID that are not direct submissions and are linked to a PMID described as PUBMED (or at least are linked to some published text) when assessing NCBI manually. I think entrez::entrez_summary() can do that by retrieving existing PMIDs from sequence databases using the accession numbers. As alternative, it would be very nice to have a DOI column for the reference text making it easy to find the source papers and check info by clicking on a doi link.

maxfarrell commented 3 years ago

Just noting here that I also have PMID / DOI information for the GMPD2 and HP3 subsets of CLOVER that weren't merged into the final version. These were largely attained through the Crossref DOI query which returns PMIDs if available