TY - STD TI - The BioASQ Challenge. http://www.bioasq.org/. ID - ref1 ER - TY - JOUR AU - Doms, A. AU - Schroeder, M. PY - 2005 DA - 2005// TI - GoPubMed: exploring PubMed with the Gene Ontology JO - Nucleic Acids Res. VL - 33 UR - https://doi.org/10.1093/nar/gki470 DO - 10.1093/nar/gki470 ID - Doms2005 ER - TY - JOUR AU - Freitas, A. A. PY - 2011 DA - 2011// TI - A survey of hierarchical classification across different application domains JO - Data Mining Knowledge Discovery VL - 22 UR - https://doi.org/10.1007/s10618-010-0175-9 DO - 10.1007/s10618-010-0175-9 ID - Freitas2011 ER - TY - JOUR AU - Athenikos, S. J. AU - Han, H. PY - 2010 DA - 2010// TI - Biomedical question answering: A survey JO - Computer Methods and Programs in Biomedicine VL - 99 UR - https://doi.org/10.1016/j.cmpb.2009.10.003 DO - 10.1016/j.cmpb.2009.10.003 ID - Athenikos2010 ER - TY - JOUR AU - Mangold, C. PY - 2007 DA - 2007// TI - A survey and classification of semantic search approaches JO - IJMSO VL - 2 UR - https://doi.org/10.1504/IJMSO.2007.015073 DO - 10.1504/IJMSO.2007.015073 ID - Mangold2007 ER - TY - STD TI - Abacha AB, Zweigenbaum P. Medical question answering: translating medical questions into sparql queries. In: ACM International Health Informatics Symposium, IHI ’12, Miami, FL, USA, January 28–30, 2012: 2012. p. 41–50. http://doi.acm.org/10.1145/2110363.2110372. UR - http://doi.acm.org/10.1145/2110363.2110372 ID - ref6 ER - TY - STD TI - TREC Question Answering Track. http://trec.nist.gov/data/qamain.html. UR - http://trec.nist.gov/data/qamain.html ID - ref7 ER - TY - JOUR AU - Voorhees, E. M. PY - 2001 DA - 2001// TI - The TREC question answering track JO - Natural Language Eng. VL - 7 UR - https://doi.org/10.1017/S1351324901002789 DO - 10.1017/S1351324901002789 ID - Voorhees2001 ER - TY - JOUR AU - Hersh, W. AU - Voorhees, E. PY - 2009 DA - 2009// TI - TREC genomics special issue overview JO - Inf Retrieval. VL - 12 UR - https://doi.org/10.1007/s10791-008-9076-6 DO - 10.1007/s10791-008-9076-6 ID - Hersh2009 ER - TY - STD TI - Text Analysis Conference. http://www.nist.gov/tac/. ID - ref10 ER - TY - STD TI - The NTCIR project. http://research.nii.ac.jp/ntcir/index-en.html. UR - http://research.nii.ac.jp/ntcir/index-en.html ID - ref11 ER - TY - STD TI - Forner P, Giampiccolo D, Magnini B, Penas A, Rodrigo A, Sutcliffe RFE. Evaluating multilingual question answering systems at CLEF. In: Proceedings of the International Conference on Language Resources and Evaluation: 2010. Paris, France: European Language Resources Association. ID - ref12 ER - TY - STD TI - The Cross Language Evaluation Forum. http://www.clef-campaign.org/. ID - ref13 ER - TY - JOUR AU - Kosmopoulos, A. AU - Gaussier, E. AU - Paliouras, G. AU - Aseervaatham, S. PY - 2010 DA - 2010// TI - The ECIR 2010 large scale hierarchical classification workshop JO - SIGIR Forum. VL - 44 UR - https://doi.org/10.1145/1842890.1842894 DO - 10.1145/1842890.1842894 ID - Kosmopoulos2010 ER - TY - STD TI - The Large Scale Hierarchical Text Classification Challenge. http://lshtc.iit.demokritos.gr/. UR - http://lshtc.iit.demokritos.gr/ ID - ref15 ER - TY - STD TI - The JRS 2012 Data Mining Competition. http://tunedit.org/challenge/JRS12Contest. UR - http://tunedit.org/challenge/JRS12Contest ID - ref16 ER - TY - STD TI - The BioNLP Shared Task 2011. https://sites.google.com/site/bionlpst/. UR - https://sites.google.com/site/bionlpst/ ID - ref17 ER - TY - STD TI - BioCreative. http://www.biocreative.org/. ID - ref18 ER - TY - STD TI - Huang M, Lu Z. Learning to annotate scientific publications. In: COLING 2010, 23rd International Conference on Computational Linguistics, Posters Volume, 23–27 August 2010, Beijing, China: 2010. p. 463–71. http://aclweb.org/anthology-new/C/C10/C10--2053.pdf. UR - http://aclweb.org/anthology-new/C/C10/C10--2053.pdf ID - ref19 ER - TY - JOUR AU - Huang, M. AU - Névéol, A. AU - Lu, Z. PY - 2011 DA - 2011// TI - Recommending mesh terms for annotating biomedical articles JO - JAMIA VL - 18 ID - Huang2011 ER - TY - STD TI - Wahle M, Widdows D, Herskovic JR, Bernstam EV, Cohen T. Deterministic binary vectors for efficient automated indexing of medline/pubmed abstracts. In: AMIA 2012, American Medical Informatics Association Annual Symposium, Chicago, Illinois, USA, November 3-7, 2012: 2012. http://knowledge.amia.org/amia-55142-a2012a-1.636547/t-003-1.640625/f-001-1.640626/a-107-1.640909/a-108-1.640906. UR - http://knowledge.amia.org/amia-55142-a2012a-1.636547/t-003-1.640625/f-001-1.640626/a-107-1.640909/a-108-1.640906 ID - ref21 ER - TY - JOUR AU - Jimeno-Yepes, A. J. AU - Plaza, L. AU - Mork, J. G. AU - Aronson, A. R. AU - Díaz, A. PY - 2013 DA - 2013// TI - Mesh indexing based on automatically generated summaries JO - BMC Bioinf VL - 14 UR - https://doi.org/10.1186/1471-2105-14-208 DO - 10.1186/1471-2105-14-208 ID - Jimeno-Yepes2013 ER - TY - STD TI - The JavaScript Object Notation. http://www.json.com/. ID - ref23 ER - TY - STD TI - Tsoumakas G, Katakis I, Vlahavas IP. Mining multi-label data. In: Data Mining and Knowledge Discovery Handbook: 2010. p. 667–85. ID - ref24 ER - TY - JOUR AU - Kosmopoulos, A. AU - Partalas, I. AU - Gaussier, E. AU - Paliouras, G. AU - Androutsopoulos, I. PY - 2014 DA - 2014// TI - Evaluation measures for hierarchical classification: a unified view and novel approaches JO - Data Mining and Knowledge Discovery VL - 29 ID - Kosmopoulos2014 ER - TY - STD TI - Doms A. GoPubMed: Ontology-based literature search for the life sciences: PhD thesis, Technical University of Dresden; 2008. ID - ref26 ER - TY - JOUR AU - Smith, T. F. AU - Waterman, M. S. PY - 1981 DA - 1981// TI - Comparison of biosequences JO - Adv Appl Mathematics VL - 2 UR - https://doi.org/10.1016/0196-8858(81)90046-4 DO - 10.1016/0196-8858(81)90046-4 ID - Smith1981 ER - TY - CHAP AU - Mork, J. G. AU - Jimeno-Yepes, A. AU - Aronson, A. R. PY - 2013 DA - 2013// TI - The nlm medical text indexer system for indexing biomedical literature BT - BioASQ@CLEF PB - Aachen, Germany CY - CEUR Workshop Proceedings ID - Mork2013 ER - TY - STD TI - Lin C-Y. ROUGE: A package for automatic evaluation of summaries. In: Proceedings of the ACL Workshop ‘Text Summarization Branches Out’. PA, USA: 2004. p. 74–81. ID - ref29 ER - TY - CHAP AU - Galanis, D. AU - Lampouras, G. AU - Androutsopoulos, I. PY - 2012 DA - 2012// TI - Extractive multi-document summarization with integer linear programming and support vector regression BT - COLING PB - Indian Institute of Technology Bombay CY - India ID - Galanis2012 ER - TY - CHAP AU - Weissenborn, D. AU - Tsatsaronis, G. AU - Schroeder, M. PY - 2013 DA - 2013// TI - Answering factoid questions in the biomedical domain BT - BioASQ@CLEF PB - CEUR Workshop Proceedings CY - Aachen, Germany ID - Weissenborn2013 ER - TY - CHAP AU - Tsoumakas, G. AU - Laliotis, M. AU - Markontanatos, N. AU - Vlahavas, I. PY - 2013 DA - 2013// TI - Large-scale semantic indexing of biomedical publications BT - 1st BioASQ Workshop: A Challenge on Large-scale Biomedical Semantic Indexing and Question Answering PB - CEUR Workshop Proceedings CY - Aachen, Germany ID - Tsoumakas2013 ER - TY - STD TI - Mork JG, Demner-Fushman D, Schmidt S, Aronson AR. Recent enhancements to the NLM medical text indexer. In: Working Notes for CLEF 2014 Conference, Sheffield, UK, September 15–18, 2014: 2014. p. 1328–1336. http://ceur-ws.org/Vol-1180/CLEF2014wn-QA-MorkEt2014.pdf. UR - http://ceur-ws.org/Vol-1180/CLEF2014wn-QA-MorkEt2014.pdf ID - ref33 ER - TY - JOUR AU - Demsar, J. PY - 2006 DA - 2006// TI - Statistical comparisons of classifiers over multiple data sets JO - J Machine Learning Res VL - 7 ID - Demsar2006 ER - TY - STD TI - Mork J, Jimeno-Yepes A, Aronson A. September 27th, 2013. The NLM Medical text indexer system for indexing biomedical literature. Valencia, Spain. http://ceur-ws.org/Vol-1094/bioasq2013_submission_3.pdf. ID - ref35 ER - TY - STD TI - BioASQ Task 1a. http://bioasq.lip6.fr/general_information/Task1a/. UR - http://bioasq.lip6.fr/general_information/Task1a/ ID - ref36 ER - TY - CHAP AU - Ribadas, F. AU - de Campos, L. AU - Darriba, V. AU - Romero, A. PY - 2013 DA - 2013// TI - Two hierarchical text categorization approaches for bioasq semantic indexing challenge BT - 1st BioASQ Workshop: A Challenge on Large-scale Biomedical Semantic Indexing and Question Answering PB - CEUR Workshop Proceedings CY - Aachen, Germany ID - Ribadas2013 ER - TY - STD TI - Balikas G, Partalas I, Kosmopoulos A, Petridis S, Malakasiotis P, Pavlopoulos I, et al.Bioasq evaluation framework specifications. Project deliverable D4.1 (May 2013). http://bioasq.org/sites/default/files/PublicDocuments/BioASQ_D4.1-EvaluationFrameworkSpecification_final.pdf. UR - http://bioasq.org/sites/default/files/PublicDocuments/BioASQ_D4.1-EvaluationFrameworkSpecification_final.pdf ID - ref38 ER - TY - STD TI - Malakasiotis P, Androutsopoulos I, Pavlopoulos I. Challenge evaluation report. Project deliverable D5.2 (December 2013). http://www.bioasq.org/sites/default/files/PublicDocuments/BioASQ_D5.2-ChallengeEvaluation_final.pdf. ID - ref39 ER - TY - STD TI - The PONTE EU Project. http://www.ponte-project.eu/. ID - ref40 ER - TY - STD TI - The BioASQ Annotation Tool. http://at.bioasq.org. UR - http://at.bioasq.org ID - ref41 ER - TY - STD TI - The MongoDB. http://www.mongodb.org/. ID - ref42 ER - TY - STD TI - Malakasiotis P, Androutsopoulos I, Almirantis Y, Polychronopoulos D, Pavlopoulos I. Tutorials and guidelines. Project deliverable D3.4 (January 2013). http://bioasq.org/sites/default/files/PublicDocuments/2013-D3.4-TutorialsGuidelines.pdf. UR - http://bioasq.org/sites/default/files/PublicDocuments/2013-D3.4-TutorialsGuidelines.pdf ID - ref43 ER - TY - CHAP AU - Tang, L. AU - Rajan, S. AU - Narayanan, V. K. PY - 2009 DA - 2009// TI - Large scale multi-label classification via metalabeler BT - Proceedings of the 18th International Conference on World Wide Web, WWW ’09 PB - ACM CY - New York, NY, USA ID - Tang2009 ER - TY - STD TI - 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. Aachen, Germany:CEUR Workshop Proceedings; 2013. ID - ref45 ER - TY - JOUR AU - Aronson, A. R. AU - Lang, F. -. M. PY - 2010 DA - 2010// TI - An overview of metamap: historical perspective and recent advances JO - J Am Med Inf Assoc VL - 17 UR - https://doi.org/10.1136/jamia.2009.002733 DO - 10.1136/jamia.2009.002733 ID - Aronson2010 ER - TY - STD TI - The Indri Engine. http://www.lemurproject.org/indri.php. ID - ref47 ER - TY - STD TI - Liu Y. Bioasq system descriptions (wishart team). Technical report. 2013. ID - ref48 ER - TY - STD TI - Mao Y, Lu Z. Ncbi at the 2013 bioasq challenge task: Learning to rank for automatic mesh indexing. Technical report. 2013. ID - ref49 ER - TY - STD TI - The PolySearch Tool. http://wishart.biology.ualberta.ca/polysearch/. UR - http://wishart.biology.ualberta.ca/polysearch/ ID - ref50 ER - TY - CHAP AU - Robertson, S. PY - 2006 DA - 2006// TI - On gmap: and other transformations BT - CIKM PB - ACM CY - NY, USA ID - Robertson2006 ER - TY - JOUR AU - Sanderson, M. PY - 2010 DA - 2010// TI - Test collection based evaluation of information retrieval systems JO - Found Trends Inf Retrieval VL - 4 UR - https://doi.org/10.1561/1500000009 DO - 10.1561/1500000009 ID - Sanderson2010 ER - TY - STD TI - The Joint Chemical Dictionary. http://biosemantics.org/index.php/resources/jochem. UR - http://biosemantics.org/index.php/resources/jochem ID - ref53 ER - TY - JOUR AU - Hettne, K. M. AU - Stierum, R. H. AU - Schuemie, M. J. AU - Hendriksen, P. J. M. AU - Schijvenaars, B. J. A. AU - van Mulligen, E. M. PY - 2009 DA - 2009// TI - A dictionary to identify small molecules and drugs in free text JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp535 DO - 10.1093/bioinformatics/btp535 ID - Hettne2009 ER - TY - STD TI - The Gene Ontology. http://www.geneontology.org/. ID - ref55 ER - TY - STD TI - UniProt. http://www.uniprot.org/. ID - ref56 ER - TY - STD TI - The Disease Ontology Wiki. http://do-wiki.nubic.northwestern.edu/do-wiki/index.php/Main_Page. UR - http://do-wiki.nubic.northwestern.edu/do-wiki/index.php/Main_Page ID - ref57 ER - TY - STD TI - MeSH. http://www.nlm.nih.gov/mesh/. ID - ref58 ER - TY - STD TI - PubMed. http://www.ncbi.nlm.nih.gov/pubmed/. ID - ref59 ER - TY - STD TI - PMC. http://www.ncbi.nlm.nih.gov/pmc/. ID - ref60 ER - TY - STD TI - The Linked Life Data Project. http://linkedlifedata.com/. UR - http://linkedlifedata.com/ ID - ref61 ER -