Biogang:Discussion/Elsevier Grand Challenge

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Elsevier Grand Challenge

Elsevier Grand Challenge is a contest created to improve scientific communication. Organisers are looking for new ways to:

  1. improve the process/methods/results of creating, reviewing and editing scientific content
  2. interpret, visualize or connect the knowledge more effectively, and/or
  3. provide tools/ideas for measuring the impact of these improvements.

Below is a summary of discussion on the challenge at FriendFeed.

The prize

  • supports the attendance of less established scientists at (potentially non-traditional) conferences


  • extraction of DOI from PDF and associated knowledge
  • mobile PubMed Reader (like Google Reader)
    • what is the difference with getting rss from pubmed ? (see below, Pubmed RSS extract option no.1)** -> the main difference is that based on the manuscripts you have on your "reader" you can get related information on that manuscript, such as references from and to, other papers by authors etc. Instead of being a static RSS reader, it would be something more interactive. (this is if I understood correctly Attila's suggestion)
  • creating semantic abstract
    • thinking about editing abstracts in RDFa in order to identify genes, proteins, etc. genomic regions, (non-)interactions, softwares, databases etc.... SKOS SKOS Needed ?.
    • giving authors a unique URI
  • filtering relation between abstract based on structured info (proteins, ligands, taxonomy, citations etc.)
  • online environment/suite for building and following peer-review/edit workflows

Pubmed RSS extract option no.1

Easily create RSS feeds based on keywords that match title and/or abstract of Pubmed articles using Yahoo Pipes!. Here's a good example (feel free to clone and play around with the source). Virtually a custom RSS feed can be created using any section of the article, and also can be combined with RSS data from other sources. I raise a hand as having the expertise to implement any ideas that might involve this tool.

"Feedflare" style enhancement of Pubmed RSS feeds

Another option for enhancing PubMed RSS feeds would be to do something a bit like Feedburners 'feedflare' ... (responsible for the little "Add to","Email this" etc links that Feedburner can add to the bottom of an item). As well as the obvious "Post to CiteULike", "Post to Connotea", "Full text link" etc links, the 'pubmed flare' could suggest related articles based on the users existing articles in CiteULike and Connotea, and could also tap into Postgenomic somehow. Since I'm FriendFeed obsessed at the moment ... we could probably also use the FriendFeed API to scan for known publisher URLs, feed these into the Connotea WebCite service or the CiteULike Plugin API to extract PMIDs and DOIs etc, then add a link "Discussions about this article on FriendFeed" to the feed item if someone is talking about it. * 07:00, 28 June 2008 (UTC):