“There’s a vast trove of science out there locked inside the PDF format. From preprints to peer-reviewed literature and historical research, millions of scientific manuscripts today can only be found in a print-era format that is effectively inaccessible to the web of interconnected online services and APIs that are increasingly becoming the digital scaffold of today’s research infrastructure….Extracting key information from PDF files isn’t trivial. …It would therefore certainly be useful to be able to extract all key data from manuscript PDFs and store it in a more accessible, more reusable format such as XML (of the publishing industry standard JATS variety or otherwise). This would allow for the flexible conversion of the original manuscript into different forms, from mobile-friendly layouts to enhanced views like eLife’s side-by-side view (through eLife Lens). It will also make the research mineable and API-accessible to any number of tools, services and applications. From advanced search tools to the contextual presentation of semantic tags based on users’ interests, and from cross-domain mash-ups showing correlations between different papers to novel applications like ScienceFair, a move away from PDF and toward a more open and flexible format like XML would unlock a multitude of use cases for the discovery and reuse of existing research….We are embarking on a project to build on these existing open-source tools, and to improve the accuracy of the XML output. One aim of the project is to combine some of the existing tools in a modular PDF-to-XML conversion pipeline that achieves a better overall conversion result compared to using individual tools on their own. In addition, we are experimenting with a different approach to the problem: using computer vision to identify key components of the scientific manuscript in PDF format….To this end, we will be collaborating with other publishers to collate a broad corpus of valid PDF/XML pairs to help train and test our neural networks….”
“JATS4R (JATS for Reuse) is an inclusive group of publishers, vendors, and other interested organisations who use the NISO Journal Article Tag Suite (JATS) XML standard. On Monday 13th March, 2017, OASPA hosted a webinar on the history, goals and recent work of JATS4R, the importance of participation and outreach around JATS4R, and to provide a platform for discussions on how the initiative can be advanced in the future.”
“NIH-supported scientists have made over 300,000 author manuscripts available on PubMedCentral (PMC) since 2008. Now, NIH is making these papers accessible to the public in a format that will allow robust text analyses.
You can download the entire PMC collection of NIH-supported author manuscripts as a package in either XML or plain text formats….”
Abstract: In this paper, we will describe the current state of some of the tagging of articles within the PMC Open Access subset. As a case study, we will use our experiences developing the Open Access Media Importer, a tool to harvest content from the OA subset for automated upload to Wikimedia Commons.
“JATS4R aims to help standardisation of xml used in scientific publishing workflows. We take specific areas of interest (such as licenses or author contributions) and work to define best practice tagging guidelines, along with tools that can help publishers identify whether their content is compliant with those best practices.
Abstract: In our paper, we described the current state of some of the tagging of articles within the PMC Open Access subset. As a case study, we used our experiences developing the Open Access Media Importer, a tool to harvest content from the OA subset and automatically upload it to Wikimedia Commons.