Meetings & Conferences

TT:23 Utopia Documents: The Digital Meta-Library (ISMB 2009)

Steve Pettifer

“most computer science papers are rubbish” in that in CS, the thing itself is the result, which makes it a different form of literature to life scientists, where papers are about finding out things that already exist. Came to this conclusion at the 2007 Yeast Jamboree where the big model was starting to be annotated. The jamborre concluded that merging models is hard but important, and so we need support for this, but also need support in terms of dealing with papers. It is the latter he is talking about today. They talked to Portland Press, which publish a biochemical journal. Highly curated, stuff is online in html etc, but still there is room for improvement in terms of effort.

People still like to have their own pdf. Further, as we all know, there is lots of knowledge trapped in paper. Once you find papers, you often want to find the references and citations present within them. This is, increasingly, an issue of finding all sorts of auxillary data. And even if you have paper + auxillary, what comes next? What does the community think of the paper? What do my friends think? pubmed grows at about 2 papers per minute. and that’s not all of them! “Studies” show that peer-review is only slightly better than random chance: they estimate that 5% are rubbish, and 60% have errors. About 400 papers out of 1000000 in 1982 – 2002 were retracted, and only about 4000 published errata.

Next came a live demo. When looking at a paper, it will highlight things/sections it recognizes, such as the title, figures and the references (highlighted in purple). Utopia knows what it means, and if you click on references it brings up google scholar page or whatever you want.

You can also invoke “workflows” as context-specific menus. Will replace a figure with a PDB id with the actual embedded pdb structural display. If errata/comments have been added to the original paper, utopia will update your pdf with them too. If they’re scanned and there is no real text in them, utopia can’t read them, though you could probably still mark them up. Would be nice to merge yours against someone else’s out there that is in pdf, for instance. (pre-alpha release)

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Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

By Allyson Lister

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