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In the biomedical fields, many articles have to be deposited on PubMed Central, which requires them to be reformatted in their archival JATS XML format. Since a

In the biomedical fields, many articles have to be deposited on PubMed Central, which requires them to be reformatted in their archival JATS XML format. Since articles are typically written in Word in those fields, this process involves a lot of manual tagging of references and figures and such, only partially aided by scripts. The process must incur a fairly hefty cost in maintaining warehouses full of people to do the tagging. In principle it's great that articles are uniformly in XML -- you could easily write reader software for tablets or phones, data-mine the text, extract references, whatever -- but I haven't seen much software taking advantage of it.

lsh 9y ago
Typically there is a "script", not the code kind, that is followed for every dodgy Word document received, and following the script is outsourced. The production team is in charge of coordination with the outsourced team and final proofing of the XML and all the vagaries of pre publication that comes from 90s era processes and software and interactions with other ancient systems. However! Once published and out the door, the shiny XML is available for scraping and transformation, and, if OA, there is no reason the XML can't be made public: https://github.com/elifesciences/elife-article-xml https://github.com/elifesciences/elife-article-xml An excellent bit of software that takes advantage of it is Lens: https://github.com/elifesciences/lens https://github.com/elifesciences/lens
Nullabillity 9y ago
So... require that the scientists submit the articles in JATS instead of Word files or PDFs? LaTeX already knows about the stuff you mentioned, so it shouldn't be too hard to make it output JATS directly. In fact, that already seems to exist[1]. [1]: https://github.com/mfenner/pandoc-jats https://github.com/mfenner/pandoc-jats

lsh 9y ago

Typically there is a "script", not the code kind, that is followed for every dodgy Word document received, and following the script is outsourced. The production team is in charge of coordination with the outsourced team and final proofing of the XML and all the vagaries of pre publication that comes from 90s era processes and software and interactions with other ancient systems. However! Once published and out the door, the shiny XML is available for scraping and transformation, and, if OA, there is no reason the XML can't be made public: https://github.com/elifesciences/elife-article-xml https://github.com/elifesciences/elife-article-xml An excellent bit of software that takes advantage of it is Lens: https://github.com/elifesciences/lens https://github.com/elifesciences/lens

Nullabillity 9y ago

So... require that the scientists submit the articles in JATS instead of Word files or PDFs? LaTeX already knows about the stuff you mentioned, so it shouldn't be too hard to make it output JATS directly. In fact, that already seems to exist[1]. [1]: https://github.com/mfenner/pandoc-jats https://github.com/mfenner/pandoc-jats