Satellite meeting for Literature and Text mining related issues


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

 EBI text mining tools

Text mining web services

 BioAID workflows

 iHOP webservices


TM related web services provided by  DBCLS

Collaborative annotation tools

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

 BioCreative MetaServer Platform ( talk from Florian Leitner about the system)

 XML-RPC interface of BCMS

ieXML: how to standardize the annotation of named entities

Other stuff (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)



  • Hong-Woo Chun
    • Introduction of Wired-Marker and XConc that are annotation tools and publicly available to use.
  • We explored the use of  scifoaf (Pierre Lindenbaum) -> We need unique IDs (URI) for authors in publications!
  • We reviewed different solutions for collaborative anotations


  • provide  ieXML support for existing services
  • further integration of automatic annotation in the collaborative annotation tools