4 ms·

> you have formatting editors who make the PDF look good and give it a thorough last read (finding for me several errors that peer review never found - missing

by a3_nm 9y ago

> you have formatting editors who make the PDF look good and give it a thorough last read (finding for me several errors that peer review never found - missing or switched references, for example). This may depend on the field, but in CS I have never seen this. There is essentially no change made by the publisher to papers, and when they do make changes, more often than not it is to introduce errors. In any case, the huge profit margins of publishers indicate that the cost of this dubious service is much lower than the charge. But the most important point is this: doing minor copyediting shouldn't be grounds to own the journal and own copyright on the published articles. The journals should be owned by scientists, or by a nonprofit scientific society. Even assuming that research needs to pay for copyediting services, these should be contractors of the nonprofit (with competition among them), not owners of the journal and articles.

capnrefsmmat 9y ago
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
ArneBab 9y ago
In geophysics I also see lots of polishing, and that helps the quality a lot (though you have to be vigilant as author and always check the new version lest some fix to an assumed typo changes the meaning of a sentence in a subtle-but-important way).

by a3_nm 9y ago

capnrefsmmat 9y ago

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

ArneBab 9y ago

In geophysics I also see lots of polishing, and that helps the quality a lot (though you have to be vigilant as author and always check the new version lest some fix to an assumed typo changes the meaning of a sentence in a subtle-but-important way).