= Satellite meeting for Literature and Text mining related issues =

== Topics ==

Different web tools allow researchers to search literature databases and integrate semantic information extracted from text with external databases and ontologies. Some of them even provide accessible APIs so users can build their own text mining pipelines.

'''Enhanced literature search and retrieval engines'''

[http://www.knewco.com/]

[http://www.gopubmed.com/]

[http://www.novoseek.com/]

[http://www.ihop-net.org/UniPub/iHOP/]

[http://www.ebi.ac.uk/citexplore/]

[http://www.ebi.ac.uk/Rebholz/software.html EBI text mining tools]

'''Text mining web services'''

[http://www.adaptivedisclosure.org/aida/workflows BioAID workflows]

[http://ubio.bioinfo.cnio.es/biotools/iHOP/ iHOP webservices]

[http://www.ebi.ac.uk/whatizit Whatizit]

[http://www.biosemantics.org]

[http://nactem.ac.uk/]

TM related web services provided by [http://lifesciencedb.jp/ DBCLS]
  * [http://allie.dbcls.jp/ Allie]
  * [http://orefil.dbcls.jp/ OReFiL]


'''Assessment of text mining tools (both engines and web services)'''

[http://bcms.bioinfo.cnio.es/ BioCreative MetaServer Platform] ([http://bcms.bioinfo.cnio.es/site_media/BCMS_Talk_SMBM08.pdf talk from Florian Leitner about the system])

[http://bcms.bioinfo.cnio.es/xmlrpc/ XML-RPC interface of BCMS]


'''ieXML: how to standardize the annotation of named entities'''

[http://www.ebi.ac.uk/Rebholz-srv/IeXML/]


'''Other stuff'''

[http://www.ebi.ac.uk/Rebholz/resources.html]

[http://ex.perimental.net/scaiview/] 
(This shows the front-end of a text-mining system I (Tobias) developed previously. It has overlapped tagging as a result of multi-class NER and fulltext search)


The questions that this satellite meeting could try to answer are:

'''For developers:'''

  * What are the missing elements for better integration of the different services?

  * Which are the best formats for information extraction data exchange (ieXML, RDF)?

  * Which components of the text minig architecture can be moved from to the server to the client (AJAX, browser plugins)?

  * Is it possible to build portable text mining systems? Can systems be adapted to specific domains and specific tasks without the assistance of an experienced language processing specialist?

  * How can we cope with full text data (format / copyright)? 

'''For users:'''

 * What is the actual utility of text mining in the workflows of the various communities of potential users—model organism database curators, bedside clinicians, biologists utilizing high-throughput experimental assays, hospital billing departments?

 * How usable are biomedical text mining applications? How does the application fit into the workflow of a complex bioinformatics pipeline? What kind of training does a bioscientist require to be able to use an application?

 * How robust and reliable are biomedical text mining applications? 


== Chairperson ==

 * [http://www.linkedin.com/in/albertolabarga Alberto Labarga] ([http://www.ebi.ac.uk/webservices EBI], [http://www.ebi.ac.uk/dasty Dasty], [http://www.scientifik.info/elsevier Elsevier Grand Challenge],  Univ. of Granada, Spain)

== Targets ==

 * Developers of literature and text mining related software and services
 * End-users of these services

== Attendees ==

 * Yulia Kovarskaya
 * Hong-Woo Chun
 * Yasunori Yamamoto
 * Tobias Gattermayer
 * José María Fernández
 * Pierre Lindenbaum
 * Atsuko Yamaguchi

== Date ==

 * 2009/3/17 13:00-17:00

== Room ==

 * Seminar Room (1F)

== Presentations ==
 * Alberto Labarga 
    {{{
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}}}
 
 * Hong-Woo Chun
   * Introduction of Wired-Marker and XConc that are annotation tools and publicly available to use.
 
== Results ==

 * We did an exploration of existing services
 * We explored the use of scifoaf (Pierre Lindenbaum) -> We need unique IDs (URI) for authors in publications!
 * We implemented some clients for [http://bcms.bioinfo.cnio.es/xmlrpc/ XML-RPC interface of BCMS] and [http://ubio.bioinfo.cnio.es/biotools/iHOP/ iHOP webservices]
 * We reviewed different solutions for collaborative anotations
  * [http://a.kazusa.or.jp/]
  * [https://addons.mozilla.org/en-US/firefox/addon/6219]
  * [http://www.shiftspace.org/]
  * [http://www-tsujii.is.s.u-tokyo.ac.jp/GENIA/home/wiki.cgi?page=XConc+Suite]

== TODOs ==

 * provide [http://www.ebi.ac.uk/Rebholz-srv/IeXML/ ieXML ] support for existing services 
 * further integration of automatic annotation in the collaborative annotation tools