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Multiple PMIDs #131

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agbarnett opened this issue Dec 17, 2018 · 1 comment
Closed

Multiple PMIDs #131

agbarnett opened this issue Dec 17, 2018 · 1 comment
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@dwinter
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@agbarnett
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I'm getting multiple PMIDs when searching for a single PMID, for example:

parse_pubmed_xml(entrez_fetch(db="pubmed", id='29743284', rettype="xml"))$pmid
[1] "29743284" "22116114" "19123933" "20091554" "27544377" "21466679" "10501796" "19657121" "12511679" "8560339"  "17043045" "25923524"
[13] "15507789" "19657122" "22773335" "8237484"  "22019853" "4139420"  "24325929"    "16923978" "19465306" "8950879"  "18165753" "20701962"
[25] "20190623"

The first PMID is the right one, the others seem unrelated. I can easily work around this by just selecting the first PMID, but is there a bigger issue with related data?
@dwinter
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dwinter commented Dec 17, 2018

Thanks for filing this issue @agbarnett , looks like this is a bug in the way parse_pubmed_xml parses the record (looking for any PMID field, not specifically the one at the top-level of the record).

Will get a fix and test in the next little while. I think you can safetly everything after the first one for now (as the citation info with the correct pmid is in the top of the file).

@dwinter dwinter added the Bug label Dec 17, 2018
@dwinter dwinter self-assigned this Dec 17, 2018
dwinter added a commit that referenced this issue May 2, 2019
@dwinter
Ensure pubmed records are assigned only one PMID
991c555 
Prior to this commit, pubmed records hat contained a lit of cited papers
could generate a "pmid" field in teh pubmed record that included all
pmids. This commit fixes bug #131 and provides a test against
regression.

Thanks @agbarnett for the bug report
@dwinter dwinter closed this as completed May 2, 2019
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