Abstract
BioASQ is a series of challenges that aims to assess the performance of information systems in supporting two tasks that are central to the biomedical question answering process: (a) the indexing of large volumes of unlabelled data, primarily scientific articles, with biomedical concepts, (b) the processing of biomedical questions and the generation of answers and supporting material. In this paper, the main results of the first two BioASQ challenges are presented.
Keywords
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Adams, J.R., Bedrick, S.: Automatic classification of pubmed abstracts with latent semantic indexing: Working notes. In: Proceedings of Question Answering Lab at CLEF (2014)
Aronson, A.R., Lang, F.-M.: An overview of metamap: historical perspective. J. Am. Med. Inf. Assoc. 17, 229–236 (2010)
Balikas, G., Partalas, I., Baskiotis, N., Artieres, T., Gaussier, E., Gallinari, P.: Evaluation infrastructure software for the challenges 2nd version. In: BioASQ Deliverable D4.7 (2014)
Balikas, G., Partalas, I., Baskiotis, N., Malakasiotis, P., Pavlopoulos, I., Androutsopoulos, I., Artieres, T., Gaussier, E., Gallinari, P.: Evaluation framework specification - 2nd version. In: BioASQ Deliverable D4.5 (2013)
Balikas, G., Partalas, I., Kosmopoulos, A., Petridis, S., Baskiotis, N., Malakasiotis, P., Pavlopoulos, I., Androutsopoulos, I., Artieres, T., Gaussier, E., Gallinari, P.: Evaluation framework specifications. In: BioASQ Deliverable D4, 1 (2013)
Balikas, G., Partalas, I., Ngonga Ngomo, A.-C., Krithara, A., Paliouras, G.: Results of the bioasq track of the question answering lab at CLEF 2014. In: Working Notes for CLEF 2014 Conference, September 15–18, 2014, Sheffield, UK, pp. 1181–1193 (2014)
Choi, S., Choi, J.: Classification and retrieval of biomedical literatures: Snumedinfo at clef qa track bioasq 2014. In: Proceedings of Question Answering Lab at CLEF (2014)
Doms, A.: GoPubMed: Ontology-based literature search for the life sciences. Ph.D. thesis, Technische Universität Dresden (2010)
Huang, M., Névéol, A., Zhiyong, L.: Recommending mesh terms for annotating biomedical articles. JAMIA 18(5), 660–667 (2011)
Mork James, G., Dina, D.-F., Schmidt Susan, C.. Aronson Alan, R.: Recent enhancements to the nlm medical text indexer. In: Proceedings of Question Answering Lab at CLEF (2014)
Jimeno-Yepes, A.J., Plaza, L., Mork, J.G., Aronson, A.R., Díaz, A.: Mesh indexing based on automatically generated summaries. BMC Bioinformatics 14, 208 (2013)
Kosmopoulos, A., Partalas, I., Gaussier, E., Paliouras, G., Androutsopoulos, I.: Evaluation measures for hierarchical classification: a unified view and novel approaches. In: Data Mining and Knowledge Discovery. Springer (2014)
Lin, C.-Y.: ROUGE: A package for automatic evaluation of summaries. In: Proceedings of the ACL Workshop ‘Text Summarization Branches Out’, Barcelona, Spain, pp. 74–81 (2004)
Liu, K., Wu, J., Peng, S., Zhai, C., Zhu, S.: The fudan-uiuc participation in the bioasq challenge task 2a: The antinomyra system. In: Proceedings of Question Answering Lab at CLEF (2014)
Liu, Y.: Bioasq system descriptions (wishart team). Technical report (2013)
Mao, Y., Lu, Z.: Ncbi at the 2013 bioasq challenge task: Learning to rank for automatic mesh indexing. Technical report (2013)
Mork, J., Jimeno-Yepes, A., Aronson, A.: The nlm medical text indexer system for indexing biomedical literature. In: 1st BioASQ Workshop: A Challenge on Large-scale Biomedical Semantic Indexing And Question Answering (2013)
Neves, M.: Hpi in-memory-based database system in task 2b of bioasq. In: Proceedings of Question Answering Lab at CLEF (2014)
Ngonga Ngomo, A.-C., Heino, N., Speck, R., Malakasiotis, P.: A tool suite for creating question answering benchmarks. In: Proceedings of LREC (2014)
Papanikolaou, Y., Dimitriadis, D., Tsoumakas, G., Laliotis, M., Markantonatos, N., Vlahavas, I.: Ensemble approaches for large-scale multi-label classification and question answering in biomedicine. In: Proceedings of Question Answering Lab at CLEF (2014)
Partalas, I., Gaussier, É., Ngonga Ngomo, A.-C.: Results of the first bioasq workshop. In: BioASQ@CLEF (2013)
Ribadas, F., de Campos, L., Darriba, V., Romero, A.: Two hierarchical text categorization approaches for bioasq semantic indexing challenge. In: 1st BioASQ Workshop: A Challenge on Large-scale Biomedical Semantic Indexing and Question Answering (2013)
Ribadas-Pena, F.J., de Campos Ibanez, L.M., Darriba-Bilbao, V.M., Romero, A.E.: Cole and utai participation at the 2014 bioasq semantic indexing challenge. In: Proceedings of Question Answering Lab at CLEF (2014)
Smith, T.F., Waterman, M.S.: Comparison of biosequences. Adv. Appl. Math. 2(4), 482–489 (1981)
Tang, L., Rajan, S., Narayanan, V.K.: Large scale multi-label classification via metalabeler. In: Proceedings of the 18th International Conference on World Wide Web, WWW 2009, pp. 211–220. ACM, New York (2009)
Tsoumakas, G., Laliotis, M., Markontanatos, N., Vlahavas, I.: Large-scale semantic indexing of biomedical publications. In: 1st BioASQ Workshop: A Challenge on Large-scale Biomedical Semantic Indexing and Question Answering (2013)
Wahle, M., Widdows, D., Herskovic, J.R., Bernstam, E.V., Cohen, T.: Deterministic binary vectors for efficient automated indexing of medline/pubmed abstracts. In: AMIA 2012, American Medical Informatics Association Annual Symposium, 3–7 November, 2012, Chicago, Illinois, USA (2012)
Weissenborn, D., Tsatsaronis, G., Schroeder, M.: Answering factoid questions in the biomedical domain. In: 1st BioASQ Workshop: A Challenge on Large-scale Biomedical Semantic Indexing And Question Answering (2013)
Lu, Z., Mao, Y., Wei, C.-H.: Ncbi at the 2014 bioasq challenge task: large-scale biomedical semantic indexing and question answering. In: Proceedings of Question Answering Lab at CLEF (2014)
Zhu, D., Li, D., Carterette, B., Liu, H.: An incemental approach for medline mesh indexing. In: 1st BioASQ Workshop: A Challenge on Large-scale Biomedical Semantic Indexing and Question Answering (2013)
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer International Publishing Switzerland
About this paper
Cite this paper
Balikas, G., Krithara, A., Partalas, I., Paliouras, G. (2015). BioASQ: A Challenge on Large-Scale Biomedical Semantic Indexing and Question Answering. In: Müller, H., Jimenez del Toro, O., Hanbury, A., Langs, G., Foncubierta Rodriguez, A. (eds) Multimodal Retrieval in the Medical Domain. MRDM 2015. Lecture Notes in Computer Science(), vol 9059. Springer, Cham. https://doi.org/10.1007/978-3-319-24471-6_3
Download citation
DOI: https://doi.org/10.1007/978-3-319-24471-6_3
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-24470-9
Online ISBN: 978-3-319-24471-6
eBook Packages: Computer ScienceComputer Science (R0)