"Semantic Medline"

Interesting story in Information Today...

Cognition launches Semantic Medline
http://newsbreaks.infotoday.com/wndReader.asp?ArticleId=50075

"...enables complex health and life science material to be rapidly and efficiently discovered with greater precision and completeness using natural language processing (NLP) technology"

I tried a quick search "exercise and depression" just to see it working - results are mostly relevant on the first couple of pages - it does offer you to select the correct meaning e.g. of depression (feeling of sadness/hopelessness) but still seems to bring up records referring to other meanings (e.g. ST segmental depression) - although I guess it's impossible to avoid that - and the definitions might be more useful if sourced from a medical dictionary which they don't appear to be. It would be interesting to compare results using MeSH.

Given that my search retrieved over 7000 results, it would also be useful to have some options for narrowing the search - suggesting additional search terms (e.g. are you interested in a particular population e.g. postnatal?)

http://www.semanticmedline.com

NaCTeM developments

Really good to see the latest Mental Health demonstrator from the ASSERT project: http://nactem3.mc.man.ac.uk:8080/ASSERT_Refactored/. I really like the visualisation - I think this will really help social scientists get to grips with text mining and has the potential to facilitate and speed up the systematic review process.

And in a nice join up between two of my projects (NaCTeM and CO-ODE), NaCTeM has released its TerMine Plugin for Protégé. The plugin "uses text mining tools to extract candidate terms from a corpus of text and provides an interface for rapidly bringing these terms into an OWL ontology. It uses the TerMine term extraction tool provided by NaCTeM to extract concepts from text. The plugin accesses TerMine via a Web Service over the Internet."
The plugin can be downloaded from http://www.co-ode.org/downloads/protege-x/plugins/

Also worth mentioning the Kleio demonstrator http://nactem4.mc.man.ac.uk:8080/Kleio/ developed from Phase 1 of NaCTeM.

New JISC briefing papers

Two new briefing papers:

• Research in the social sciences: an overview of JISC activities
  http://www.jisc.ac.uk/publications/publications/socialsciencesresearchv1.aspx
• Research in the biomedical sciences: an overview of JISC activities
  http://www.jisc.ac.uk/publications/publications/bioscienceresearchv1.aspx

This adds to the collection of briefing papers aimed at researchers:

• Research in the physical sciences: an overview of JISC activities http://www.jisc.ac.uk/publications/publications/physicalsciencesresearchv1.aspx
• Research in the arts and humanities: an overview of JISC activities http://www.jisc.ac.uk/publications/publications/artshumanitiesresearchv1.aspx

Information World Review - various news

Information World Review (Dec 07):

• Good to see VizNet getting a mention, "VizNet rescues research from data overload"
• Interesting article on scientific information, "STM Mines Workflow": "Information overload is shifting the researcher's search and find paradigm away from document retrieval and towards information extraction"
• A useful article, "Back to basics: the wiki" on the advantages and strengths of wikis in a corporate environment, choosing between open source and commercial wikis and some suggestions of how wikis can be utilised and for what: "You need a wiki when...communication is a chore; important information is scattered around email inboxes" "Think wiki for bottom-up rather than top-down content control where you don't need centralised governance. think CMS for top-down content control where compliance demands such governance"

Information World Review (Jan 08):

• "Wales urges librarians to help build better Wikipedia" on Jimmy Wales' plea for librarians to get involved in the Wikipedia Academies to teach wiki editing skills.
• "The time has come for the semantic web to SPARQL" talks about SPARQL which "is designed to pick up truly relevant information from the internet in RDF format" and GRDDL (Gleaning Resource Descriptions from Dialects of Languages) which extracts RDF from XML and XHTML.

More accurate name searching

Tidying up my Bloglines, came across this story from 2006 in New Scientist:
http://technology.newscientist.com/article.ns?id=dn10588&feedId=online-news_rss20
about a search engine being developed which can distinguish between different instances of the same name, by identifying common keywords to cluster similar results together. In testing, it was between 70 and 95% accurate. Another application of text mining? Will be interesting to see how the Institute of Education project working with the ASSERT project at NaCTeM (National Centre for Text Mining) will get on.

Info World Review : interesting news items

Information World Review (Nov 07) features some interesting items...

- a news item, Search and aggregators set to dominate, on the recent Outsell Information Industry Outlook report:
"Watson Healy said 2008 would be 'year of the wiki', with Web 2.0 technology replacing complex portals and knowledge management, and that 'a critical mass of information professionals would take charge of wikis, blogs or other 2.0 technologies on behalf of their organisations".

- an item, PubMed recasts rules for open access re-use, on the new guidelines recently agreed by the UK PubMed Central Publishers Panel:
"Under the terms of the statement of principles, open access (OA) published articles can be copied and the text data mined for further research, as long as the original author is fully attributed".

Latest Ariadne : NaCTeM, repositories and KIDDM

http://www.ariadne.ac.uk/issue53/

Good to see NaCTeM :-) A good overview of the current services and a run-through their roadmap:
"NaCTeM's text mining tools and services offer numerous benefits to a wide range of users. These range from considerable reductions in time and effort for finding and linking pertinent information from large scale textual resources, to customised solutions in semantic data analysis and knowledge management. Enhancing metadata is one of the important benefits of deploying text mining services. TM is being used for subject classification, creation of taxonomies, controlled vocabularies, ontology building and Semantic Web activities. As NaCTeM enters into its second phase we are aiming for improved levels of collaboration with Semantic Grid and Digital Library initiatives and contributions to bridging the gap between the library world and the e-Science world through an improved facility for constructing metadata descriptions from textual descriptions via TM."

Other interesting snippets:

• SURFshare programme covering the research lifecycle http://www.surffoundation.nl/smartsite.dws?ch=ENG&id=5463


• a discussion on the use of Google as a repository : "Repositories, libraries and Google complement each other in helping to provide a broad range of services to information seekers. This union begins with an effective advocacy campaign to boost repository content; here it is described, stored and managed; search engines, like Google, can then locate and present items in response to a search request. Relying on Google to provide search and discovery of this hidden material misses out a valuable step, that of making it available in the first instance. That is why university libraries need Google and Google needs university libraries."


• feedback from ECDL conference, including a workshop on a european repository ecology, featuring a neat diagram showing how presentations are disseminated after a conference using a mix of web2.0, repositories and journals http://www.ariadne.ac.uk/issue53/ecdl-2007-rpt/#10