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Critical Assessment of Information Extraction in Biology - data sets are available from Resources/Corpora and require registration.

BC Workshop '12

Track III-Systems Descriptions [2012-01-25]

The BioCreative-2012 Workshop on Interactive Text Mining in the Biocuration Workflow aims to bring together the biocuration and text mining communities towards the development and evaluation of interactive text mining tools and systems to improve utility and usability in the biocuration workflow. This workshop offers 3 tracks, in which Track III is an interactive text mining and user evaluation task. Several groups have submitted a text mining/NLP system targeted to a specific biocuration task. These systems will be formally evaluated but not competitively.

We invite curators to participate in a user study on the system of their choice prior to the BioCreative workshop. Below we list the text mining systems that have registered to participate in the Track III. Note that only the description of each system and proposed task are described. A more detailed document for each system is available at the bottom of this page. The systems will be available for testing on March 1st, 2012, and results from the evaluation should be returned by March 25.

The testing will involve manual curation of a set of documents manually (approx. 25) and curation of a set of documents using the selected system (approx. 25). Time on task as well as feedback on the usability of the systems will be captured.

The results of this evaluation will be presented during the BioCreative workshop on April 5 in Washington DC. Attendance to the workshop is not a prerequisite to participate, but you are more welcome to do so.

Express your interest or register by sending an email to using Subject:BioCreative-2012 Track III-testing. Please indicate in decreasing order of preference the systems you would like to test (if more than 1), the database or resource that you belong to, and whether you are a junior or senior biocurator.

TextPressoCuration of subcellular localization using Gene ontology cellular componentFull-textCecilia Arighi
PCSCuration of Entity-Quality terms from phylogenetic literature using ontologiesN/ACecilia Arighi
TagtogProtein/gene mentions recognition via interactive learning and annotation frameworkAbstractJohn Wilbur
PubTatorDocument triage (relevant documents for curation) and bioconcept annotation (gene, disease, chemicals)AbstractKevin Cohen
PPIinterfinderMining of protein-protein interaction for human proteins (abstract and full legth articles):document classification and extraction of interacting proteins and keywords.AbstractMartin Krallinger
eFIPMining Protein Interactions of Phosphorylated Proteins from the Literature. Document classification and information extraction of phosphorylated protein, protein binding partners and impact keyword AbstractMartin Krallinger
AcetylationDocument retrieval and ranking based on relevance on protein acetylationAbstractCecilia Arighi
T-HODDocument triage for disease-related genes (relevant documents for curation) and bioconcept annotation (gene, disease and relation)AbstractCecilia Arighi
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