Challenges - Tasks 2a & 2b - Year 2

The 2nd year round of the BioASQ challenge will comprise two tasks. Participants may choose to participate in any or all of the tasks and their subtasks.

BioASQ Task 2a: Large-scale online biomedical semantic indexing

This task will be based on the standard process followed by PubMed to index journal abstracts. The participants will be asked to classify new PubMed documents, written in English, as they become available online, before PubMed curators annotate (in effect, classify) them manually. The classes will come from the MeSH hierarchy; they will be the subject headings that are currently used to manually index the abstracts, excluding those that are already provided by the authors of each article. As new manual annotations become available, they will be used to evaluate the classification performance of participating systems (that classify articles before they are manually annotated), using standard IR measures (e.g., precision, recall, accuracy), as well as hierarchical variants of them. The participants will be able to train their classifiers, using the whole history of manually annotated abstracts.

Task 2a will run for three consecutive periods (batches) of 5 weeks each. The first batch will start on February 3, 2014. Separate winners will be announced for each batch. Participation in the task can be partial, i.e. in some of the batches.

BioASQ Task 2b: Biomedical Semantic QA (involves IR, QA, summarization)

Task 2b will use benchmark datasets containing development and test questions, in English, along with gold standard (reference) answers. The benchmark datasets will contain at least 500 questions and will be constructed by a team of biomedical experts from around Europe. The participants will have to respond with relevant concepts (from designated terminologies and ontologies), relevant articles (in English, from designated article repositories), relevant snippets (from the relevant articles), relevant RDF triples (from designated ontologies), exact answers (e.g., named entities in the case of factoid questions) and 'ideal' answers (paragraph-sized summaries), both in English.

The test dataset of Task 2b will be released in five batches, each containing approximately 100 questions. The first batch will start on March 5, 2014. Separate winners will be announced for each batch. Participation in the task can be partial; for example, it is acceptable to participate in only some of the batches, to return only relevant articles (and no concepts, triples, article snippets), or to return only exact answers (or only `ideal' answers). System responses will be evaluated both automatically and manually.