5 ms·

The scientific publishing workflow is insane, and this tool seems like it could help. In the biomedical sciences (or any field that ends up on PubMed), article

The scientific publishing workflow is insane, and this tool seems like it could help. In the biomedical sciences (or any field that ends up on PubMed), articles have to be converted to JATS XML (http://jats.nlm.nih.gov/ http://jats.nlm.nih.gov/), a standard XML dialect for journal articles. It builds in citation metadata, cross-referencing, figure references, etc., and is supposed to be a stable archival format for long-term storage of articles. Individual publishers (PLOS, BMC, etc.) build their entire publication workflows around JATS, so articles can be typeset into PDF or rendered to HTML, or delivered to e-reader apps or whatever. Since it's semantic XML, you can do bibliography mining, automatic reference following, extraction of figures, or whatever you might want to make reading or text-mining easier. But articles are often written in Word, so there's a tremendous amount of work going into manually or semi-manually converting every manuscript to semantic XML from the Word soup it arrives as. Same goes for LaTeX: a few journals just publish LaTeXed PDFs directly, but big publishers like Elsevier and Springer have semi-automated processes for converting LaTeX to in-house formats so they can provide HTML versions of pages. So, short version: an editor supporting JATS XML can support all the features you need in a scientific document, and can dramatically simplify the publication workflow and hopefully save a bunch of money. And hopefully open-access journals pass that savings on to users. For users, it could mean better e-reading apps (so you don't have to zoom in on tiny fonts in a PDF on your iPad), better support for cross-referencing and figures than Word has, automated formatting (journals style the XML, so you don't have to do margin and layout crap), and a simpler submission process.

hprotagonist 10y ago
Interesting. This seems like a tool for journal staff and editors, then, rather than practicing scientists.
- dflock 10y ago
  It's a tool for everyone in the writing-editing-publishing pipeline. They could all use the same tool, working on the same document & document format, throughout the process. This will remove a huge amount of reformatting/conversion work between steps in the pipeline.
  - hprotagonist 10y ago
    The rebuttal, guaranteed to come from anyone with tenure but also from distinctly untenured folks like myself is this: "I have all my manuscripts and biosketches and workflow in LaTex/Word. All my references are in mendeley/zotero/endnote/bibtex files i've hand-massaged. Until such time as my home journal requires me to use this format i've never heard about, and gives me the tools to convert everything I've built over the last 2-20 years, I am not interested in it unless you've got something more compelling than what you've shown me so far." getting traction is going to be _very hard_.
    - dflock 10y ago
      Of course - that's the most obvious thing in the world. Getting traction against an entrenched workflow component - a people problem - is, almost universally, very very hard. The technical problem - writing your new tool - is trivial by comparison. But they do seem to be coming at this from the journal/pull end of the workflow, which is a very good place to start.
jessriedel 10y ago
This is a very insightful comment.
dmd 10y ago
And yet if you try and submit to publishers in JATS, editors tell you they have no idea what it is, and can you please send a Word document like everyone else...
- hprotagonist 10y ago
  Yeah, that's kind of my point.
tnecniv 10y ago
Seems like a very domain specific thing. I've never heard of it in my discipline, and every article I've gone to upload supports a direct LaTeX upload.
- nograpes 10y ago
  It is domain-specific, but the domain is rather large. In the vast majority of life science fields, LaTeX is not accepted for journal articles, even in fields where you might expect it. In medical informatics, for example, direct LaTeX upload is uncommon, which you might not expect for an informatics journal.
  - tnecniv 10y ago
    Yeah, I realize I live in a bubble where everyone uses LaTeX, and that most of the world's papers are written in Word (the horror!).
    - nograpes 10y ago
      In some senses, I share your distaste for Word. But, honestly, after having written my dissertation in LaTeX, I must say that it was a terrible experience. I really wanted to love LaTeX. In the worst possible way. I wanted to sneer at people who used Word, looking down my nose and show them how reproducible research was really done. How much more efficient and beautiful my work would be using this software. I wanted to venerate Knuth and this beautiful example of open source software. It took me years before I had to admit to myself how terrible it was. I remember seeing a post on HN about how LaTeX was a cargo cult for philosophy majors (the analogy being that they were using the tools of a technical discipline without a clear purpose). For me at least, a better analogy would be an abusive relationship. I would tell my labmates about how great it was, while it was obvious that I was spending hours on getting the most trivial configuration correct. I am truly glad that some people have a good experience with LaTeX. I just wanted to say that I didn't.
      - Ar-Curunir 10y ago

hprotagonist 10y ago

Interesting. This seems like a tool for journal staff and editors, then, rather than practicing scientists.

dflock 10y ago
It's a tool for everyone in the writing-editing-publishing pipeline. They could all use the same tool, working on the same document & document format, throughout the process. This will remove a huge amount of reformatting/conversion work between steps in the pipeline.
- hprotagonist 10y ago
  The rebuttal, guaranteed to come from anyone with tenure but also from distinctly untenured folks like myself is this: "I have all my manuscripts and biosketches and workflow in LaTex/Word. All my references are in mendeley/zotero/endnote/bibtex files i've hand-massaged. Until such time as my home journal requires me to use this format i've never heard about, and gives me the tools to convert everything I've built over the last 2-20 years, I am not interested in it unless you've got something more compelling than what you've shown me so far." getting traction is going to be _very hard_.
  - dflock 10y ago
    Of course - that's the most obvious thing in the world. Getting traction against an entrenched workflow component - a people problem - is, almost universally, very very hard. The technical problem - writing your new tool - is trivial by comparison. But they do seem to be coming at this from the journal/pull end of the workflow, which is a very good place to start.

jessriedel 10y ago

This is a very insightful comment.

dmd 10y ago

And yet if you try and submit to publishers in JATS, editors tell you they have no idea what it is, and can you please send a Word document like everyone else...

hprotagonist 10y ago
Yeah, that's kind of my point.

tnecniv 10y ago

Seems like a very domain specific thing. I've never heard of it in my discipline, and every article I've gone to upload supports a direct LaTeX upload.

nograpes 10y ago
It is domain-specific, but the domain is rather large. In the vast majority of life science fields, LaTeX is not accepted for journal articles, even in fields where you might expect it. In medical informatics, for example, direct LaTeX upload is uncommon, which you might not expect for an informatics journal.
- tnecniv 10y ago
  Yeah, I realize I live in a bubble where everyone uses LaTeX, and that most of the world's papers are written in Word (the horror!).
  - nograpes 10y ago
    In some senses, I share your distaste for Word. But, honestly, after having written my dissertation in LaTeX, I must say that it was a terrible experience. I really wanted to love LaTeX. In the worst possible way. I wanted to sneer at people who used Word, looking down my nose and show them how reproducible research was really done. How much more efficient and beautiful my work would be using this software. I wanted to venerate Knuth and this beautiful example of open source software. It took me years before I had to admit to myself how terrible it was. I remember seeing a post on HN about how LaTeX was a cargo cult for philosophy majors (the analogy being that they were using the tools of a technical discipline without a clear purpose). For me at least, a better analogy would be an abusive relationship. I would tell my labmates about how great it was, while it was obvious that I was spending hours on getting the most trivial configuration correct. I am truly glad that some people have a good experience with LaTeX. I just wanted to say that I didn't.
    - Ar-Curunir 10y ago