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Would it be possible to convert PDF files to wiki markup?
Even though this might have a slight buddhist connotation, I think the first thing to do when you do conversion between formats is to learn to let go... I dont think it is possible to make it perfectly. A very simple example is page and page numbering, either you split your document to respect it and then lose the typical document format of a wiki, or you dont and then every time there is a page number mentioned it is meaningless, worst noise if the source PDF is not provided. Beside that warning, technically I think it is very possible. In the details of the question your mention losing formatting entirely, so I guess you refer to a simple tool like pdftotext. This work great to dump PDF text content only on a wiki, I have done it several times and it is really a matter of minutes to get it right. Now what you want is way harder. Without knowing your setup (e.g. what programming language is available, how many documents you have to convert, etc) I think the best way now would be to rely on OpenOffice/LibreOffice converters. A lot of work has been put into it. This would require some serious XSLT investment though but it can be done. Once done it easy very simple to convert batches of documents through their command line interfaces. If your main objective is to open up science journals then surely a first try could be done with the ~100Gb of arXiv. Unfortunately I am afraid the "closeness" of science publishing is not a technical issue.
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For example even some journals have multiple authors so even if you use them as your main tool (especially if you want to submit to them) it was impossible to create a clean and understandable PDF with that content only. What is required is a much better open database, and in particular there should also be a free version of OpenOffice/LibreOffice, where you can try to do this conversion and test it on thousands of PDFs at once, at some point a clean and simple converter becomes “the normal”. It won't be a “the default”, but it does have to be something, which people actually use and can be used as a first option and not a novelty. That will happen gradually as the tools get better and that is when the converter market will be fully explored. I believe that in ten years time this will actually become the new normal..
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