This year the BioASQ challenge will comprise the following tasks. Participants may choose to participate in any or all of the tasks and their subtasks.
BioASQ Task 8a: 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 8a will run for three consecutive periods (batches) of 5 weeks each. The first batch will start on February 03, 2020. Separate winners will be announced for each batch. Participation in the task can be partial, i.e. in some of the batches.
BioASQ Task 8b: Biomedical Semantic QA (involves IR, QA, summarization)
Task 8b will use benchmark datasets containing training and test biomedical questions, in English, along with gold standard (reference) answers. The participants will have to respond to each test question 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 (English paragraph-sized summaries). 3243 training questions (that were used as dry-run or test questions in previous year) are already available, along with their gold standard answers (relevant concepts, articles, snippets, exact answers, summaries). At least 500 new test questions will be used this year. All the questions are constructed by biomedical experts from around Europe.
The test dataset of Task 8b will be released in five batches, each containing approximately 100 questions. The first batch will start on March 04, 2020. 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.
BioASQ Task MESINESP8: Medical Semantic Indexing In Spanish
Task MESINESP will address the automatic indexing with structured medical vocabularies (DeCS terms) of abstracts from the IBECS and LILACS databases written in Spanish. The main aim is to promote the development of semantic indexing tools of practical relevance of non-English content, determining the current-state-of-the art, identifying challenges and comparing the strategies and results to those published for English data. The participants will be asked to classify new IBECS and LILACS documents, written in Spanish, before curators annotate (in effect, classify) them manually. The classes will come from the DeCS vocabulary; they will be the subject headings that are currently used to manually index the abstracts. 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 flat IR measures (e.g., precision, recall, accuracy). The participants will be able to train their classifiers, using the whole history of manually annotated abstracts. The BioASQ MESINESP Task will run in spring, 2020. More details about BioASQ Task MESINESP available here...
