TY - JOUR AU - Blank, C. E. PY - 2009 DA - 2009// TI - Not so old archaea—the antiquity of biogeochemical processes in the archaeal domain of life JO - Geobiology VL - 7 UR - https://doi.org/10.1111/j.1472-4669.2009.00219.x DO - 10.1111/j.1472-4669.2009.00219.x ID - Blank2009 ER - TY - JOUR AU - Larsson, J. AU - Nylander, J. A. A. AU - Bergman, B. PY - 2011 DA - 2011// TI - Genome fluctuations in cyanobacteria reflect evolutionary, developmental and adaptive traits JO - BMC evol biol VL - 11 UR - https://doi.org/10.1186/1471-2148-11-187 DO - 10.1186/1471-2148-11-187 ID - Larsson2011 ER - TY - JOUR AU - Sachs, J. L. AU - Skophammer, R. G. AU - Bansal, N. AU - Stajich, J. E. PY - 2014 DA - 2014// TI - Evolutionary origins and diversification of proteobacterial mutualists JO - P roy soc lond b bio VL - 281 UR - https://doi.org/10.1098/rspb.2013.2146 DO - 10.1098/rspb.2013.2146 ID - Sachs2014 ER - TY - JOUR AU - Houle, D. AU - Govindaraju, D. R. AU - Omholt, S. PY - 2010 DA - 2010// TI - Phenomics: the next challenge JO - Nat rev genet VL - 11 UR - https://doi.org/10.1038/nrg2897 DO - 10.1038/nrg2897 ID - Houle2010 ER - TY - STD TI - Maddison WP, Maddison DR. Mesquite: A modular system for evolutionary analysis. Version 3.01. 2014. http://www.mesquiteproject.org. Accessed 2 Feb 2016. UR - http://www.mesquiteproject.org/ ID - ref5 ER - TY - STD TI - Maddison DR, Maddison WP. MacClade 4: Analysis of phylogeny and character evolution. 2005.http://www.macclade.org. Accessed 2 Feb 2016. UR - http://www.macclade.org/ ID - ref6 ER - TY - JOUR AU - Tomitani, A. AU - Knoll, A. H. AU - Cavanaugh, C. M. AU - Ohno, T. PY - 2006 DA - 2006// TI - The evolutionary diversification of cyanobacteria: molecular-phylogenetic and paleontological perspectives JO - Proc natl acad sci VL - 103 UR - https://doi.org/10.1073/pnas.0600999103 DO - 10.1073/pnas.0600999103 ID - Tomitani2006 ER - TY - JOUR AU - Blank, C. E. PY - 2013 DA - 2013// TI - Origin and early evolution of photosynthetic eukaryotes in freshwater environments—reinterpreting proterozoic paleobiology and biogeochemical processes in light of trait evolution JO - J phycol VL - 49 UR - https://doi.org/10.1111/jpy.12111 DO - 10.1111/jpy.12111 ID - Blank2013 ER - TY - JOUR AU - Bressan, A. AU - Terlizzi, F. AU - Credi, R. PY - 2012 DA - 2012// TI - Independent origins of vectored plant pathogenic bacteria from arthropod-associated arsenophonus endosymbionts JO - Microb ecol VL - 63 UR - https://doi.org/10.1007/s00248-011-9933-5 DO - 10.1007/s00248-011-9933-5 ID - Bressan2012 ER - TY - STD TI - Blank CE. Low rates of lateral gene transfer among metabolic genes define the evolving biogeochemical niches of archaea through deep time. Archaea. 2012: 843539. ID - ref10 ER - TY - STD TI - Blan Uyeda JC, Harmon LJ, Blank CE. A comprehensive study of cyanobacterial morphological and ecological evolutionary dynamics through deep geologic time. PloS one. 2016;11(9):e0162539. ID - ref11 ER - TY - BOOK AU - Holzinger, A. AU - Schantl, J. AU - Schroettner, M. AU - Seifert, C. AU - Verspoor, K. PY - 2014 DA - 2014// TI - Biomedical text mining: state-of-the-art, open problems and future challenges. Interactive knowledge discovery and data mining in biomedical informatics PB - Springer Berlin Heidelberg CY - Berlin ID - Holzinger2014 ER - TY - JOUR AU - Miyao, Y. AU - Sagae, K. AU - Sætre, R. AU - Matsuzaki, T. AU - Tsujii, J. I. PY - 2009 DA - 2009// TI - Evaluating contributions of natural language parsers to protein-protein interaction extraction JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btn631 DO - 10.1093/bioinformatics/btn631 ID - Miyao2009 ER - TY - BOOK AU - Sætre, R. AU - Sagae, K. AU - Tsujii, J. I. PY - 2007 DA - 2007// TI - Syntactic features for protein-protein interaction extraction. In proceedings of languages in biology and medicine 2007 PB - LBM (Short Papers) CY - Singapore ID - Sætre2007 ER - TY - JOUR AU - Kemper, B. AU - Matsuzaki, T. AU - Matsuoka, Y. AU - Tsuruoka, Y. AU - Kitano, H. AU - Ananiadou, S. AU - Tsujii, J. I. PY - 2010 DA - 2010// TI - PathText: a text mining integrator for biological pathway visualizations JO - Bioinformatics VL - 26 UR - https://doi.org/10.1093/bioinformatics/btq221 DO - 10.1093/bioinformatics/btq221 ID - Kemper2010 ER - TY - JOUR AU - Hecker, M. AU - Lambeck, S. AU - Toepfer, S. AU - Someren, E. AU - Guthke, R. PY - 2009 DA - 2009// TI - Gene regulatory network inference: data integration in dynamic models—a review JO - Biosystems VL - 96 UR - https://doi.org/10.1016/j.biosystems.2008.12.004 DO - 10.1016/j.biosystems.2008.12.004 ID - Hecker2009 ER - TY - CHAP AU - Czarnecki, J. AU - Shepherd, A. J. ED - Kumar, V. D. ED - Tipney, H. J. PY - 2014 DA - 2014// TI - Mining biological networks from full-text articles BT - Biomedical literature mining PB - Springer CY - New York UR - https://doi.org/10.1007/978-1-4939-0709-0_8 DO - 10.1007/978-1-4939-0709-0_8 ID - Czarnecki2014 ER - TY - JOUR AU - Ananiadou, S. AU - Pyysalo, S. AU - Tsujii, J. I. AU - Kell, D. B. PY - 2010 DA - 2010// TI - Event extraction for systems biology by text mining the literature JO - Trends biotechnol VL - 28 UR - https://doi.org/10.1016/j.tibtech.2010.04.005 DO - 10.1016/j.tibtech.2010.04.005 ID - Ananiadou2010 ER - TY - BOOK AU - Mitchell, T. M. PY - 1997 DA - 1997// TI - Machine learning PB - McGraw Hill CY - Burr Ridge ID - Mitchell1997 ER - TY - JOUR AU - Hearst, M. A. AU - Dumais, S. T. AU - Osman, E. AU - Platt, J. AU - Scholkopf, B. PY - 1998 DA - 1998// TI - Support vector machines JO - IEEE intell syst app VL - 13 UR - https://doi.org/10.1109/5254.708428 DO - 10.1109/5254.708428 ID - Hearst1998 ER - TY - JOUR AU - Manevitz, L. M. AU - Yousef, M. PY - 2002 DA - 2002// TI - One-class SVMs for document classification JO - J mach learn res VL - 2 ID - Manevitz2002 ER - TY - STD TI - Pang B, Lee L. A sentimental education: Sentiment analysis using subjectivity summarization based on minimum cuts. In Proceedings of the 42nd annual meeting on Association for Computational Linguistics. Stroudsburg, Philadelphia: Association for computational linguistics.2004:271. ID - ref22 ER - TY - CHAP AU - Kazama, J. I. AU - Makino, T. AU - Ohta, Y. AU - Tsujii, J. I. PY - 2002 DA - 2002// TI - Tuning support vector machines for biomedical named entity recognition BT - Proceedings of the ACL-02 workshop on natural language processing in the biomedical domain-volume 3 PB - Association for Computational Linguistics CY - Stroudsburg UR - https://doi.org/10.3115/1118149.1118150 DO - 10.3115/1118149.1118150 ID - Kazama2002 ER - TY - CHAP AU - Mayfield, J. AU - Mcnamee, P. AU - Piatko, C. PY - 2003 DA - 2003// TI - Named entity recognition using hundreds of thousands of features BT - Proceedings of the seventh conference on natural language learning at HLT-NAACL 2003-volume 4 PB - Association for Computational Linguistics CY - Edmonton UR - https://doi.org/10.3115/1119176.1119205 DO - 10.3115/1119176.1119205 ID - Mayfield2003 ER - TY - JOUR AU - Lee, K. J. AU - Hwang, Y. S. AU - Kim, S. AU - Rim, H. C. PY - 2004 DA - 2004// TI - Biomedical named entity recognition using two-phase model based on SVMs JO - J biomed inform VL - 37 UR - https://doi.org/10.1016/j.jbi.2004.08.012 DO - 10.1016/j.jbi.2004.08.012 ID - Lee2004 ER - TY - JOUR AU - Perez-Riverol, Y. AU - Audain, E. AU - Millan, A. AU - Ramos, Y. AU - Sanchez, A. AU - Vizcaíno, J. A. AU - Wang, R. AU - Müller, M. AU - Machado, Y. J. AU - Betancourt, L. H. AU - González, L. J. PY - 2012 DA - 2012// TI - Isoelectric point optimization using peptide descriptors and support vector machines JO - J proteomics VL - 75 UR - https://doi.org/10.1016/j.jprot.2012.01.029 DO - 10.1016/j.jprot.2012.01.029 ID - Perez-Riverol2012 ER - TY - JOUR AU - Orrù, G. AU - Pettersson-Yeo, W. AU - Marquand, A. F. AU - Sartori, G. AU - Mechelli, A. PY - 2012 DA - 2012// TI - Using support vector machine to identify imaging biomarkers of neurological and psychiatric disease: a critical review JO - Neurosci biobehav rev VL - 36 UR - https://doi.org/10.1016/j.neubiorev.2012.01.004 DO - 10.1016/j.neubiorev.2012.01.004 ID - Orrù2012 ER - TY - BOOK AU - Kao, A. AU - Poteet, S. R. PY - 2007 DA - 2007// TI - Natural language processing and text mining PB - Springer CY - London UR - https://doi.org/10.1007/978-1-84628-754-1 DO - 10.1007/978-1-84628-754-1 ID - Kao2007 ER - TY - JOUR AU - Cui, H. PY - 2012 DA - 2012// TI - CharaParser for fine-grained semantic annotation of organism morphological descriptions JO - J assoc inf sci technol VL - 63 UR - https://doi.org/10.1002/asi.22618 DO - 10.1002/asi.22618 ID - Cui2012 ER - TY - STD TI - Thessen AE, Cui H, Mozzherin D. Applications of natural language processing in biodiversity science. Adv bioinformatics. 2012: 391574. ID - ref30 ER - TY - JOUR AU - Dahdul, W. M. AU - Cui, H. AU - Mabee, P. M. AU - Mungall, C. J. AU - Osumi-Sutherland, D. AU - Walls, R. L. AU - Haendel, M. A. PY - 2014 DA - 2014// TI - Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the biological spatial ontology JO - J biomed semant VL - 5 UR - https://doi.org/10.1186/2041-1480-5-34 DO - 10.1186/2041-1480-5-34 ID - Dahdul2014 ER - TY - JOUR AU - Etzioni, O. AU - Banko, M. AU - Soderland, S. AU - Weld, D. S. PY - 2008 DA - 2008// TI - Open information extraction from the web JO - Commun ACM VL - 51 UR - https://doi.org/10.1145/1409360.1409378 DO - 10.1145/1409360.1409378 ID - Etzioni2008 ER - TY - JOUR AU - Niu, F. AU - Zhang, C. AU - Ré, C. AU - Shavlik, J. W. PY - 2012 DA - 2012// TI - DeepDive: Web-scale knowledge-base construction using statistical learning and inference JO - VLDS VL - 12 ID - Niu2012 ER - TY - JOUR AU - Whirl-Carrillo, M. AU - McDonagh, E. M. AU - Hebert, J. M. AU - Gong, L. AU - Sangkuhl, K. AU - Thorn, C. F. AU - Altman, R. B. AU - Klein, T. E. PY - 2012 DA - 2012// TI - Pharmacogenomics knowledge for personalized medicine JO - Clin pharmacol ther VL - 92 UR - https://doi.org/10.1038/clpt.2012.96 DO - 10.1038/clpt.2012.96 ID - Whirl-Carrillo2012 ER - TY - JOUR AU - Humphreys, K. AU - Demetriou, G. AU - Gaizauskas, R. PY - 2000 DA - 2000// TI - Two applications of information extraction to biological science journal articles: enzyme interactions and protein structures JO - Pac symp biocomput VL - 5 ID - Humphreys2000 ER - TY - CHAP AU - Gaizauskas, R. AU - Humphreys, K. AU - Demetriou, G. ED - Hicks, M. G. PY - 2000 DA - 2000// TI - Information extraction from biological science journal articles: enzyme interactions and protein structures BT - Proceedings of the workshop chemical data analysis in the large: the challenge of the automation age PB - Logos Verlag Berlin CY - Bozen ID - Gaizauskas2000 ER - TY - JOUR AU - Czarnecki, J. AU - Nobeli, I. AU - Smith, A. M. AU - Shepherd, A. J. PY - 2012 DA - 2012// TI - A text-mining system for extracting metabolic reactions from full-text articles JO - BMC bioinformatics VL - 13 UR - https://doi.org/10.1186/1471-2105-13-172 DO - 10.1186/1471-2105-13-172 ID - Czarnecki2012 ER - TY - CHAP AU - Corbett, P. AU - Murray-Rust, P. PY - 2006 DA - 2006// TI - High-throughput identification of chemistry in life science texts BT - Proceedings of the 2nd international symposium on computational life science PB - Springer CY - Cambridge ID - Corbett2006 ER - TY - STD TI - Leaman R, Gonzalez G. BANNER: An executable survey of advances in biomedical named entity recognition. Pac symp biocomput. 2008;13:652–63. ID - ref39 ER - TY - STD TI - Deléger L, Bossy R, Chaix E, Ba M, Ferré A, Bessières P, Nédellec C. Overview of the Bacteria Biotope Task at BioNLP Shared Task 2016. In: Proceedings of the 4th BioNLP shared task workshop. Berlin: Association for Computational Linguistic; 2016. p. 12–22. ID - ref40 ER - TY - JOUR AU - Perez-Riverol, Y. AU - Bai, M. AU - Leprevost, F. AU - Squizzato, S. AU - Park, Y. M. AU - Haug, O. K. AU - Carroll, A. J. AU - Spalding, D. AU - Paschall, J. AU - Wang, M. AU - Toro, N. PY - 2016 DA - 2016// TI - Omics discovery index-discovering and linking public omics datasets JO - bioRxiv VL - 1 ID - Perez-Riverol2016 ER - TY - STD TI - International Journal of Systematic and Evolutionary Microbiology. London: Society for General Microbiology. ID - ref42 ER - TY - STD TI - Proceedings of the National Academy of Sciences of the United States of America. Washington: United States National Academy of Sciences. ID - ref43 ER - TY - CHAP AU - Manning, C. D. AU - Surdeanu, M. AU - Bauer, J. AU - Finkel, J. R. AU - Bethard, S. AU - McClosky, D. PY - 2014 DA - 2014// TI - The Stanford CoreNLP natural language processing toolkit BT - Proceedings of 52nd annual meeting of the association for computational linguistics: system demonstrations PB - ACL CY - Baltimore UR - https://doi.org/10.3115/v1/P14-5010 DO - 10.3115/v1/P14-5010 ID - Manning2014 ER - TY - STD TI - Wild F. lsa: latent semantic analysis. R package version 0.73. https://www.cran.r-project.org/web/packages/lsa/index.html. Accessed 15 Apr 2014. UR - https://www.cran.r-project.org/web/packages/lsa/index.html ID - ref45 ER - TY - JOUR AU - Hornik, K. AU - Grün, B. PY - 2011 DA - 2011// TI - Topicmodels: an R package for fitting topic models JO - J stat softw VL - 40 ID - Hornik2011 ER - TY - CHAP AU - Franz, N. M. AU - Peet, R. K. AU - Weakley, A. S. ED - Wheeler, Q. D. PY - 2008 DA - 2008// TI - On the use of taxonomic concepts in support of biodiversity research and taxonomy BT - The new taxonomy PB - CRC Press CY - Boca Raton UR - https://doi.org/10.1201/9781420008562.ch5 DO - 10.1201/9781420008562.ch5 ID - Franz2008 ER - TY - JOUR AU - Chang, C. C. AU - Lin, C. J. PY - 2011 DA - 2011// TI - LIBSVM: a library for support vector machines JO - ACM trans intell syst technol VL - 2 UR - https://doi.org/10.1145/1961189.1961199 DO - 10.1145/1961189.1961199 ID - Chang2011 ER - TY - JOUR AU - He, H. AU - Garcia, E. PY - 2009 DA - 2009// TI - Learning from imbalanced data JO - IEEE trans knowl data eng VL - 21 UR - https://doi.org/10.1109/TKDE.2008.239 DO - 10.1109/TKDE.2008.239 ID - He2009 ER - TY - BOOK AU - Jijkoun, V. AU - Rijke, M. AU - Mur, J. PY - 2004 DA - 2004// TI - Information extraction for question answering: improving recall through syntactic patterns. In: proceedings of the 20th international conference on computational linguistics PB - Association for Computational Linguistics CY - Geneva ID - Jijkoun2004 ER - TY - STD TI - Plant 0.19. https://www.github.com/biosemantics/glossaries/tree/master/Plant/0.19. Accessed 15 Oct 2015. UR - https://www.github.com/biosemantics/glossaries/tree/master/Plant/0.19 ID - ref51 ER - TY - JOUR AU - Schriml, L. M. AU - Arze, C. AU - Nadendla, S. AU - Chang, Y. W. W. AU - Mazaitis, M. AU - Felix, V. AU - Feng, G. AU - Kibbe, W. A. PY - 2012 DA - 2012// TI - Disease ontology: a backbone for disease semantic integration JO - Nucleic acids res VL - 40 UR - https://doi.org/10.1093/nar/gkr972 DO - 10.1093/nar/gkr972 ID - Schriml2012 ER - TY - STD TI - Amazon Mechanical Turk. https://www.mturk.com/mturk/. Accessed 20 Dec 2015. UR - https://www.mturk.com/mturk/ ID - ref53 ER - TY - JOUR AU - Buckland, M. AU - Gey, F. PY - 1994 DA - 1994// TI - The relationship between recall and precision JO - J assoc inf sci VL - 45 ID - Buckland1994 ER - TY - STD TI - BioPortal Annotator. https://www.bioportal.bioontology.org/annotator. Accessed 30 Sept 2016. UR - https://www.bioportal.bioontology.org/annotator ID - ref55 ER - TY - STD TI - Poon H, Domingos P. Unsupervised semantic parsing. In: Proceedings of the 2009 Conference on Empirical Methods in Natural Language Processing: Volume 1-Volume 1. Association for Computational Linguistics. 2009: 1–10. ID - ref56 ER - TY - JOUR AU - Blank, C. E. AU - Cui, H. AU - Moore, L. R. AU - Walls, R. L. PY - 2016 DA - 2016// TI - MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions JO - J biomed semantics VL - 7 UR - https://doi.org/10.1186/s13326-016-0060-6 DO - 10.1186/s13326-016-0060-6 ID - Blank2016 ER - TY - JOUR AU - Meehan, T. F. AU - Masci, A. M. AU - Abdulla, A. AU - Cowell, L. G. AU - Blake, J. A. AU - Mungall, C. J. AU - Diehl, A. D. PY - 2011 DA - 2011// TI - Logical development of the cell ontology JO - BMC bioinformatics VL - 12 UR - https://doi.org/10.1186/1471-2105-12-6 DO - 10.1186/1471-2105-12-6 ID - Meehan2011 ER - TY - JOUR AU - Rijgersberg, H. AU - Assem, M. AU - Top, J. PY - 2013 DA - 2013// TI - Ontology of units of measure and related concepts JO - Semant web VL - 4 ID - Rijgersberg2013 ER - TY - JOUR AU - Oren, A. PY - 2004 DA - 2004// TI - A proposal for further integration of the cyanobacteria under the bacteriological code JO - Int j syst evol microbiol VL - 54 UR - https://doi.org/10.1099/ijs.0.03008-0 DO - 10.1099/ijs.0.03008-0 ID - Oren2004 ER - TY - JOUR AU - Vandamme, P. AU - Debruyne, L. AU - Brandt, E. AU - Falsen, E. PY - 2010 DA - 2010// TI - Reclassification of bacteroides ureolyticus as campylobacter ureolyticus comb. nov., and emended description of the genus campylobacter JO - Int j syst evol microbiol VL - 60 UR - https://doi.org/10.1099/ijs.0.017152-0 DO - 10.1099/ijs.0.017152-0 ID - Vandamme2010 ER -