EUtils, Pipes, Ubiquity, preprints and semi-automatic categorisation

I’ve made a few web service-related tools recently that might be of interest to Nascent readers, so here they are collected in one place:

  • PubMed’s EUtils API is powerful and fast, but a bit awkward to use in Javascript (you have to make two requests, and deal with parsing the XML). This Yahoo! Pipe provides a JSON proxy for the major EUtils commands, making it much easier to search PubMed from a web application (like the one below…). More information.
  • Mozilla Labs has produced an excellent Firefox add-on called Ubiquity, which essentially provides bookmarklets with super-powers. People have been writing all kinds of scripts for searching and manipulating information; this one is for searching PubMed.
  • Stemming from a conversation with Hilary about publishers’ preprint policies, this tool will take some text (in theory the abstract of a paper you’re thinking of posting to Nature Precedings as a preprint), send the text to JANE which recommends journals that publish similar content, then look up each of those publishers in ROMEO to find out their preprint policies. Those publishers which are happy to accept papers already available as preprints (which includes Nature Publishing Group) will show up in green.
  • The last of these tools performs a comparison of the semi-automated, semi-manual matching of MeSH terms to papers in PubMed (I believe they’re suggested by UMLSKS then manually curated) with the similarly auto-manual detection of Wikipedia terms in abstracts by GoPubMed and the corresponding categories applied to those papers in Wikipedia. This was inspired by Rattle Research and Chris Sizemore’s work with BBC news articles.


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