PubMed ID citation support #24
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agitter
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Jan 10, 2018
| @@ -8,3 +8,5 @@ The website Sci-Hub, now in its fifth year of existence, provides gratis access | |||
| Sci-Hub brands itself as "the first pirate website in the world to provide mass and public access to tens of millions of research papers." | |||
| The website, started in 2011, is run by Alexandra Elbakyan, a graduate student and native of Kazakhstan who now resides in Russia [@doi:10.1126/science.aaf5675; @doi:10.1038/nature.2015.18876]. | |||
| Elbakyan describes herself as motivated to provide universal access to knowledge [@url:https://engineuring.wordpress.com/2016/03/11/sci-hub-is-a-goal-changing-the-system-is-a-method/; @url:https://www.courtlistener.com/docket/4355308/50/elsevier-inc-v-sci-hub/; @url:http://www.leafscience.org/alexandra-elbakyan/]. | |||
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| Cite the same paper in three ways [@pmid:25648772; @pmcid:PMC4304851; @doi:10.7717/peerj.705]. | |||
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Is the behavior that each is treated as a separate reference? We may want to note that behavior in the manubot-rootstock usage instructions.
| citeproc['abstract'] = abstract | ||
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| citeproc['URL'] = f"https://www.ncbi.nlm.nih.gov/pubmed/{citeproc['PMID']}" | ||
| citeproc['type'] = 'article-journal' |
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Is article-journal always the article type? PubMed apparently has books as well. As an example, https://www.ncbi.nlm.nih.gov/pubmed/29227604. It looks like a few other things like the title (BookTitle in the XML) will fail for books.
I'm okay leaving this as an uncovered corner case, but we may want to document that.
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Good catch. Previously this would fail. But now I made the failure better documented and have it throw a NotImplementedError. Added a test case
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| def extract_publication_date_parts(article): |
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Possibly repeat the documentation that article is a PubmedArticle xml element tree
agitter
approved these changes
Jan 10, 2018
dhimmel
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Jan 11, 2018
Upgrade Manubot to manubot/manubot@b53f487 Refs manubot/manubot#24
dhimmel
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Upgrade Manubot to manubot/manubot@b53f487 Refs manubot/manubot#24
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This build is based on b140c76. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/manubot-rootstock/builds/327801824 https://travis-ci.org/greenelab/manubot-rootstock/jobs/327801825 [ci skip] The full commit message that triggered this build is copied below: Enable PubMed ID citations (#98) Upgrade Manubot to manubot/manubot@b53f487 Refs manubot/manubot#24
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This build is based on b140c76. This commit was created by the following Travis CI build and job: https://travis-ci.org/greenelab/manubot-rootstock/builds/327801824 https://travis-ci.org/greenelab/manubot-rootstock/jobs/327801825 [ci skip] The full commit message that triggered this build is copied below: Enable PubMed ID citations (#98) Upgrade Manubot to manubot/manubot@b53f487 Refs manubot/manubot#24
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Only applies to manuscripts built on Travis.
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Upgrade Manubot to manubot/manubot@b53f487 Refs manubot/manubot#24
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This pull request migrates the previous
pmidcitations functionality (from NCBI Citation Exporter) topmcid. This is more accurate because the NCBI Citation Exporter only works for records in PubMed Central.pmidcitations are now supported that use the NCBI E-Utilities.pubmed.pyenables parsing the XML returned by from E-Utilities into JSON CSL metadata.Closes #21
Refs https://github.com/ncbi/citation-exporter/issues/3