-
1
-
-
84876800956
-
BioNLP 2007 workshop at ACL2007, prague, czech republic
-
Alex, B., Grover, C., and Haddow, B. (2007). BioNLP 2007 Workshop at ACL2007, Prague, Czech Republic. In Recognising Nested Named Entities in Biomedical Text, pages 65-72.
-
(2007)
Recognising Nested Named Entities in Biomedical Text
, pp. 65-72
-
-
Alex, B.1
Grover, C.2
Haddow, B.3
-
2
-
-
1542290452
-
Ontologies in biology: Design, applications and future challenges
-
Bard, J. B. L. and Rhee, S. Y. (2004). Ontologies in biology: design, applications and future challenges. Nature Reviews Genetics, 5(3):213-222.
-
(2004)
Nature Reviews Genetics
, vol.5
, Issue.3
, pp. 213-222
-
-
Bard, J.B.L.1
Rhee, S.Y.2
-
3
-
-
85013619452
-
BioTop: An upper domain ontology for the life sciences
-
Beisswanger, E., Schulz, S., Stenzhorn, H., and Hanh, U. (2008). BioTop: An upper domain ontology for the life sciences. International Journal of Applied Ontology, 3:205-212.
-
(2008)
International Journal of Applied Ontology
, vol.3
, pp. 205-212
-
-
Beisswanger, E.1
Schulz, S.2
Stenzhorn, H.3
Hanh, U.4
-
4
-
-
84938213121
-
Nymble: A high-performance learning name-finder
-
Grishman, R. editor, Washington Marriot Hotel, Washington D.C. USA
-
Bikel, D., Miller, S., Schwartz, R., and Wesichedel, R. (1997). Nymble: A high-performance learning name-finder. In Grishman, R., editor, Proceedings of the Fifth Conference on Applied Natural Language Processing (ANLP'97), Washington Marriot Hotel, Washington D.C., USA., pages 194-201.
-
(1997)
Proceedings of the Fifth Conference on Applied Natural Language Processing (ANLP'97)
, pp. 194-201
-
-
Bikel, D.1
Miller, S.2
Schwartz, R.3
Wesichedel, R.4
-
5
-
-
0036357370
-
Evaluation of the UMLS as a terminology and knowledge resource
-
San Antonio, TX, AMIA
-
Bodenreider, O., Mitchell, J. A., and McCray, A. T. (2002). Evaluation of the UMLS as a terminology and knowledge resource. In Proc. Americal Medical Informatics Association (AMIA) Annual Symposium, San Antonio, TX, pages 61-65. AMIA.
-
(2002)
Proc. Americal Medical Informatics Association (AMIA) Annual Symposium
, pp. 61-65
-
-
Bodenreider, O.1
Mitchell, J.A.2
McCray, A.T.3
-
6
-
-
0002670150
-
Extracting the names of genes and gene products with a hidden Markov model
-
Saarbrucken, Germany
-
Collier, N., Nobata, C., and Tsujii, J. (2000). Extracting the names of genes and gene products with a hidden Markov model. In Proceedings of the 18th International Conference on Computational Linguistics (COLING'2000), Saarbrucken, Germany, pages 201-207.
-
(2000)
Proceedings of the 18th International Conference on Computational Linguistics (COLING'2000)
, pp. 201-207
-
-
Collier, N.1
Nobata, C.2
Tsujii, J.3
-
7
-
-
84908088795
-
Integrating text mining into the MGI biocuration workflow
-
bap019
-
Dowell, K., McAndrews-Hill, M., Hill, D., Drabkin, D., and Blake, J. (2009). Integrating text mining into the MGI biocuration workflow. Database, bap019.
-
(2009)
Database
-
-
Dowell, K.1
McAndrews-Hill, M.2
Hill, D.3
Drabkin, D.4
Blake, J.5
-
8
-
-
0038670579
-
The human phenome project
-
Freimer, N. and Sabatti, C. (2003). The human phenome project. Nature Genetics, 34(1):15- 21.
-
(2003)
Nature Genetics
, vol.34
, Issue.1
, pp. 15-21
-
-
Freimer, N.1
Sabatti, C.2
-
9
-
-
0031633368
-
Toward information extraction: Identifying protein names from biological papers
-
Fukuda, K., Tsunoda, T., Tamura, A., and Takagi, T. (1998). Toward information extraction: identifying protein names from biological papers. In Proceedings of the Pacific Symposium on Biocomputing'98 (PSB'98), pages 707-718.
-
(1998)
Proceedings of the Pacific Symposium on Biocomputing'98 (PSB'98)
, pp. 707-718
-
-
Fukuda, K.1
Tsunoda, T.2
Tamura, A.3
Takagi, T.4
-
10
-
-
0034069495
-
Gene ontology: Tool for the unification of biology
-
Gene Ontology Consortium
-
Gene Ontology Consortium (2000). Gene ontology: Tool for the unification of biology. Nature Genetics, 25:19-29.
-
(2000)
Nature Genetics
, vol.25
, pp. 19-29
-
-
-
11
-
-
13444266370
-
Online mendelian inheritance of man (OMIM), a knowledgebase of human genes and genetic disorders
-
Hamosh, A., Scott, A. F., Amberger, J. S., and Bocchini, C. A. (2005). Online mendelian inheritance of man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Research, 33(suppl 1):D514-D517.
-
(2005)
Nucleic Acids Research
, vol.33
, Issue.SUPPL. 1
-
-
Hamosh, A.1
Scott, A.F.2
Amberger, J.S.3
Bocchini, C.A.4
-
12
-
-
84862261069
-
Text mining for the biocuration workflow
-
(bas020).doi:10.1093/database/base020
-
Hirschman, L., Burns, G., Krallinger, M., Arighi, C., Bretonnel Cohen, K., Valencia, A., Wu, C., Chatr-Aryamontri, A., Dowell, K., Huala, E., Lourenco, A., Nash, R., Veuthey, A., Wiegers, T., and Winter, A. (2012). Text mining for the biocuration workflow. Database, 2012(bas020). doi:10.1093/database/base020.
-
(2012)
Database, 2012
-
-
Hirschman, L.1
Burns, G.2
Krallinger, M.3
Arighi, C.4
Bretonnel Cohen, K.5
Valencia, A.6
Wu, C.7
Chatr-Aryamontri, A.8
Dowell, K.9
Huala, E.10
Lourenco, A.11
Nash, R.12
Veuthey, A.13
Wiegers, T.14
Winter, A.15
-
13
-
-
84863990917
-
Semantic integration of physiology phenotypes with an application to the cellular phenotype ontology
-
Hoehndorf, R., Harris, M. A., Herre, H., Rustici, G., and Gkoutos, G. V. (2012). Semantic integration of physiology phenotypes with an application to the cellular phenotype ontology. Bioinformatics, 28(13):1783-1789.
-
(2012)
Bioinformatics
, vol.28
, Issue.13
, pp. 1783-1789
-
-
Hoehndorf, R.1
Harris, M.A.2
Herre, H.3
Rustici, G.4
Gkoutos, G.V.5
-
14
-
-
79951761477
-
Interoperability between phenotype and anatomy ontologies
-
Hoehndorf, R., Oellrich, A., and Rebholz-Schuhmann, R. (2010). Interoperability between phenotype and anatomy ontologies. Bioinformatics, 24(24):3112-3118.
-
(2010)
Bioinformatics
, vol.24
, Issue.24
, pp. 3112-3118
-
-
Hoehndorf, R.1
Oellrich, A.2
Rebholz-Schuhmann, R.3
-
15
-
-
33344465511
-
Biomedical language processing: Perspective what's beyond pubmed?
-
Hunter, L. and Bretonnel Cohen, K. (2006). Biomedical language processing: Perspective what's beyond pubmed? Molecular Cell, 21(5):589-594.
-
(2006)
Molecular Cell
, vol.21
, Issue.5
, pp. 589-594
-
-
Hunter, L.1
Bretonnel Cohen, K.2
-
16
-
-
44649165797
-
Assessment of disease named entity recognition on a corpus of annotated sentences
-
Jimeno, A., Jimenez-Ruiz, E., Lee, V., Gaudan, S., Berlanga, R., and Rebholz-Schuhmann, D. (2008). Assessment of disease named entity recognition on a corpus of annotated sentences. BMC Bioinformatics, 9(Suppl 3):S3.
-
(2008)
BMC Bioinformatics
, vol.9
, Issue.SUPPL. 3
-
-
Jimeno, A.1
Jimenez-Ruiz, E.2
Lee, V.3
Gaudan, S.4
Berlanga, R.5
Rebholz-Schuhmann, D.6
-
17
-
-
68649115793
-
A realistic assessment of methods for extracting gene/protein interactions from free text
-
Kabiljo, R., Clegg, A., and Shepherd, A. (2009). A realistic assessment of methods for extracting gene/protein interactions from free text. BMC Bioinformatics, 10(1):233.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.1
, pp. 233
-
-
Kabiljo, R.1
Clegg, A.2
Shepherd, A.3
-
18
-
-
85145262163
-
Tuning support vector machines for biomedical named entity recognition
-
Kazama, J., Makino, T., Ohta, Y., and Tsujii, J. (2002). Tuning support vector machines for biomedical named entity recognition. In Workshop on Natural Language Processing in the Biomedical Domain at the Association for Computational Linguistics (ACL) 2002, pages 1-8.
-
(2002)
Workshop on Natural Language Processing in the Biomedical Domain at the Association for Computational Linguistics (ACL) 2002
, pp. 1-8
-
-
Kazama, J.1
Makino, T.2
Ohta, Y.3
Tsujii, J.4
-
20
-
-
79957939022
-
Improving phenotype name recognition
-
6657/2011, Lecture Notes in Computer Science
-
Khordad, M., Mercer, R. E., and Rogan, P. (2011). Improving phenotype name recognition. In Advances in Artificial Intelligence, volume 6657/2011, pages 246-257. Lecture Notes in Computer Science.
-
(2011)
Advances in Artificial Intelligence
, pp. 246-257
-
-
Khordad, M.1
Mercer, R.E.2
Rogan, P.3
-
21
-
-
16244414494
-
Introduction to the bio-entity recognition task at JNLPBA
-
Collier, N. Ruch, P. and Nazarenko, A. editors, Geneva, Switzerland, held in conjunction with COLING'2004
-
Kim, J., Ohta, T., Tsuruoka, Y., Tateisi, Y., and Collier, N. (2004). Introduction to the bio-entity recognition task at JNLPBA. In Collier, N., Ruch, P., and Nazarenko, A., editors, Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA), Geneva, Switzerland, pages 70-75. held in conjunction with COLING'2004.
-
(2004)
Proceedings of the International Joint Workshop on Natural Language Processing in Biomedicine and its Applications (JNLPBA)
, pp. 70-75
-
-
Kim, J.1
Ohta, T.2
Tsuruoka, Y.3
Tateisi, Y.4
Collier, N.5
-
22
-
-
4944229711
-
GENIA corpus - A semantically annotated corpus for bio-textmining
-
Kim, J. D., Ohta, T., Tateishi, Y., and Tsujii, J. (2003). GENIA corpus - a semantically annotated corpus for bio-textmining. Bioinformatics, 19(Suppl.1):180-182.
-
(2003)
Bioinformatics
, vol.19
, Issue.SUPPL.1
, pp. 180-182
-
-
Kim, J.D.1
Ohta, T.2
Tateishi, Y.3
Tsujii, J.4
-
23
-
-
80055034798
-
Generalized inference with multiple semantic role labeling system
-
Michigan, USA
-
Koomen, P., Punyakanok, V., Roth, D., and Yih, W. (2005). Generalized inference with multiple semantic role labeling system. In Ninth Conference on Computational Natural Language Learning (CoNLL '05), Michigan, USA, pages 181-184.
-
(2005)
Ninth Conference on Computational Natural Language Learning (CoNLL '05)
, pp. 181-184
-
-
Koomen, P.1
Punyakanok, V.2
Roth, D.3
Yih, W.4
-
24
-
-
8444226720
-
Term identification in the biomedical literature
-
Krauthammer, M. and Nenadic, G. (2004). Term identification in the biomedical literature. Journal of Biomedical Informatics, 37(6):512 - 526.
-
(2004)
Journal of Biomedical Informatics
, vol.37
, Issue.6
, pp. 512-526
-
-
Krauthammer, M.1
Nenadic, G.2
-
25
-
-
0142192295
-
Conditional random fields: Probabilistic models for segmenting and labeling sequence data
-
Massachusetts, USA
-
Lafferty, J., McCallum, A., and Pereira, F. (2001). Conditional random fields: probabilistic models for segmenting and labeling sequence data. In Proceedings of the Eighteenth International Conference on Machine Learning, Massachusetts, USA, pages 282-289.
-
(2001)
Proceedings of the Eighteenth International Conference on Machine Learning
, pp. 282-289
-
-
Lafferty, J.1
McCallum, A.2
Pereira, F.3
-
26
-
-
33947095027
-
A human phenome-interactome network of protein complexes implicated in genetic disorders
-
Lage, K., Karlberg, E. O., Storling, Z. M., Olason, P. I., Pederson, A. G., Rigina, O., Hinsby, A. M., Tumer, Z., Pociot, F., Tommerup, N., Moreau, Y., and Brunak, S. (2007). A human phenome-interactome network of protein complexes implicated in genetic disorders. Nature Biotechnology, 25:309-316.
-
(2007)
Nature Biotechnology
, vol.25
, pp. 309-316
-
-
Lage, K.1
Karlberg, E.O.2
Storling, Z.M.3
Olason, P.I.4
Pederson, A.G.5
Rigina, O.6
Hinsby, A.M.7
Tumer, Z.8
Pociot, F.9
Tommerup, N.10
Moreau, Y.11
Brunak, S.12
-
27
-
-
40549140499
-
BANNER: An executable survey of advances in biomedical named entity recognition
-
Hawai'i, USA
-
Leaman, R. and Gonzalez, G. (2008). BANNER: An executable survey of advances in biomedical named entity recognition. In Proceedings of the Pacific Symposium on Biocomputing, Hawai'i, USA, pages 652-663.
-
(2008)
Proceedings of the Pacific Symposium on Biocomputing
, pp. 652-663
-
-
Leaman, R.1
Gonzalez, G.2
-
28
-
-
84893721899
-
Ontology population from textual mentions: Task definition and benchmark
-
Sidney, Australia
-
Magnini, B., Pianta, E., Popescu, O., and Speranza, M. (2006). Ontology population from textual mentions: Task definition and benchmark. In Proc. ACL/COLINGWorkshop on Ontology Population and Learning (OLP2), Sidney, Australia, pages 26-32.
-
(2006)
Proc. ACL/COLINGWorkshop on Ontology Population and Learning (OLP2)
, pp. 26-32
-
-
Magnini, B.1
Pianta, E.2
Popescu, O.3
Speranza, M.4
-
29
-
-
33947305118
-
Identifying gene and protein mentions in text using conditional random fields
-
McDonald, R. and Pereira, F. (2005). Identifying gene and protein mentions in text using conditional random fields. BMC Bioinformatics, 6(Suppl 1:S6).
-
(2005)
BMC Bioinformatics
, vol.6
, Issue.SUPPL. 1
-
-
McDonald, R.1
Pereira, F.2
-
30
-
-
0022594196
-
An introduction to hidden Markov models
-
Rabiner, L. and Juang, B. (1986). An introduction to hidden Markov models. IEEE ASSP Magazine, pages 4-16.
-
(1986)
IEEE ASSP Magazine
, pp. 4-16
-
-
Rabiner, L.1
Juang, B.2
-
31
-
-
77951575659
-
CALBC silver standard corpus
-
Rebholz-Schuhmann, D., Jimeno-Yepes, A. J., van Mulligen, E. M., Kang, N., Kors, J., Milward, D., Corbett, P., Bukyo, E., Beisswanger, E., and Hanh, U. (2010). CALBC silver standard corpus. Journal of Bioinformatics and Computational Biology, 8(1):163-179.
-
(2010)
Journal of Bioinformatics and Computational Biology
, vol.8
, Issue.1
, pp. 163-179
-
-
Rebholz-Schuhmann, D.1
Jimeno-Yepes, A.J.2
Van Mulligen, E.M.3
Kang, N.4
Kors, J.5
Milward, D.6
Corbett, P.7
Bukyo, E.8
Beisswanger, E.9
Hanh, U.10
-
32
-
-
0033257971
-
Mining molecular binding terminology from biomedical text
-
Washington DC, USA
-
Rindflesch, T. C., Hunter, L., and Aronson, A. R. (1999). Mining molecular binding terminology from biomedical text. In American Medical Informatics Association (AMIA)'99 annual symposium, Washington DC, USA, pages 127-131.
-
(1999)
American Medical Informatics Association (AMIA)'99 Annual Symposium
, pp. 127-131
-
-
Rindflesch, T.C.1
Hunter, L.2
Aronson, A.R.3
-
33
-
-
77953936166
-
The human phenotype ontology
-
Robinson, P. N. and Mundlos, S. (2010). The human phenotype ontology. Clinical Genetics, 77(6):525-534.
-
(2010)
Clinical Genetics
, vol.77
, Issue.6
, pp. 525-534
-
-
Robinson, P.N.1
Mundlos, S.2
-
34
-
-
72249108348
-
Toward an ontological treatment of disease and diagnosis
-
San Francisco, CA
-
Scheuermann, R., Ceusters, W., and Smith, B. (2009). Toward an ontological treatment of disease and diagnosis. In AMIA Summit on Translational Bioinformatics, San Francisco, CA, pages 116-120.
-
(2009)
AMIA Summit on Translational Bioinformatics
, pp. 116-120
-
-
Scheuermann, R.1
Ceusters, W.2
Smith, B.3
-
35
-
-
0041627757
-
A simple algorithm for identifying abbreviations in biomedical text
-
Hawai'i, USA
-
Schwartz, A. and Hearst, M. (2003). A simple algorithm for identifying abbreviations in biomedical text. In Pacific Symposium on BioComputing, Hawai'i, USA, pages 451-462.
-
(2003)
Pacific Symposium on BioComputing
, pp. 451-462
-
-
Schwartz, A.1
Hearst, M.2
-
37
-
-
78249235739
-
The mammalian phenotype ontology: Enabling robust annotation and comparative analysis
-
Smith, C. L. and Eppig, J. T. (2009). The mammalian phenotype ontology: enabling robust annotation and comparative analysis. Wiley Interdisciplinary Reviews: Systems Biology and Medicine, 1(3):390-399.
-
(2009)
Wiley Interdisciplinary Reviews: Systems Biology and Medicine
, vol.1
, Issue.3
, pp. 390-399
-
-
Smith, C.L.1
Eppig, J.T.2
-
38
-
-
79952371294
-
Disease named entity recognition using semisupervised learning and conditional random fields
-
Suakkaphon, N., Zhang, Z., and Chen, H. (2011). Disease named entity recognition using semisupervised learning and conditional random fields. Journal of the American Society for Information Science and Technology, 62(4):727-737.
-
(2011)
Journal of the American Society for Information Science and Technology
, vol.62
, Issue.4
, pp. 727-737
-
-
Suakkaphon, N.1
Zhang, Z.2
Chen, H.3
-
39
-
-
0003136866
-
Building an annotated corpus from biology research papers
-
Saarbrucken, Germany
-
Tateisi, Y., Ohta, T., Collier, N. H., Nobata, C., and Tsujii, J. (2000). Building an annotated corpus from biology research papers. In Proc. COLING 2000 Workshop on Semantically Annotated Corpora and Intelligent Content, Saarbrucken, Germany, pages 28-34.
-
(2000)
Proc. COLING 2000 Workshop on Semantically Annotated Corpora and Intelligent Content
, pp. 28-34
-
-
Tateisi, Y.1
Ohta, T.2
Collier, N.H.3
Nobata, C.4
Tsujii, J.5
-
40
-
-
33646502601
-
Developing a robust part-of-speech tagger for biomedical texts
-
Bozanis, P. and Houstis, E. editors, LNCS, Springer
-
Tsuruoka, Y., Tateisi, Y., Kim, J. D., Ohta, T., McNaught, J., Ananiadou, S., and Tsujii, J. (2005). Developing a robust part-of-speech tagger for biomedical texts. In Bozanis, P. and Houstis, E., editors, Advances in Informatics: 10th Panhellenic Conference on Informatics, Volos, Greece, Proceedings. LNCS, pages 382-392. Springer.
-
(2005)
Advances in Informatics: 10th Panhellenic Conference on Informatics, Volos, Greece, Proceedings
, pp. 382-392
-
-
Tsuruoka, Y.1
Tateisi, Y.2
Kim, J.D.3
Ohta, T.4
McNaught, J.5
Ananiadou, S.6
Tsujii, J.7
-
41
-
-
43249114206
-
Network-based global inference of human disease genes
-
Wu, X., Jiang, R., Zhang, M. Q., and Li, S. (2008). Network-based global inference of human disease genes. Systems Biology, 4(189).
-
(2008)
Systems Biology
, vol.4
, Issue.189
-
-
Wu, X.1
Jiang, R.2
Zhang, M.Q.3
Li, S.4
-
42
-
-
2442702846
-
Recognizing names in biomedical texts: A machine learning approach
-
Zhou, G., Zhang, J., Su, J., Shen, D., and Tan, C. (2003). Recognizing names in biomedical texts: A machine learning approach. Bioinformatics, 20(7):1178-1190.
-
(2003)
Bioinformatics
, vol.20
, Issue.7
, pp. 1178-1190
-
-
Zhou, G.1
Zhang, J.2
Su, J.3
Shen, D.4
Tan, C.5
|