• BioNLP Shared Tasks

    To share the tasks and solutions for bio-textmining

    • GE 2013

      The 2013 version of the Genia event extraction task integrates the coreference resolution task in it, while refining previous subtasks.

    • GE 2016

      Genia event extraction (GE) task, 2016

      [ Overview | Details ]

      "From text to Knowledge base: an application case to the domain of NFkB"


      Jin-Dong Kim, Database Center for Life Science (DBCLS)
      Yue Wang, Database Center for Life Science (DBCLS)...

  • BioQA

    natural language query processing for SPARQL generation.

  • Named Entity Recognition (NER)

    A survey of public gene/protein name recognizers

  • OntoFinder/OntoFactory

    To support ontology production based on existing resources, we are developing the OntoFinder/OntoFactory system, aiming at providing non-computer experts with an easy interface to assist ontology selection and term selection from BioPortal, until a user produces his/her seed ontology....

    • OntoFinder Scoring Function

      The purpose of the project is to improve the scoring function in the sorting algorithm of OntoFinder/OntoFactory.

    • Ontology Visualization

      Visualizing BioPortal ontology mappings


      Ontologies in biomedicine are used for several tasks including the standardization of terminology, the verification of data consistency, and the integration of heterogeneous biomedical databases. One can picture a set of biomedical ontologies as a web of biomedical concepts (an analogy to the World Wide Web, where we talk about a web of documents). A single ontology can be described as a group of closely related biomedical concepts....

  • PubAnnotation

    PubAnnotation aims to be "a scalable and sharable storage of text annotations."

    • The scalability is achieved by using a production level database, e.g., PostgreSQL, in the back-end.
    • The sharability is achieved by automatic alignment of text and related annotations....
  • Test


  • TextAE

    TextAE (Text Annotation Editor)

    • is a web-based annotation editor to texts,
    • works as the default editor of PubAnnotation, a sharable storage of annotation.

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