@InProceedings{ashburner_et_al:DagSemProc.08131.1,
author = {Ashburner, Michael and Leser, Ulf and Rebholz-Schuhmann, Dietrich},
title = {{08131 Executive Summary – Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--5},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.1},
URN = {urn:nbn:de:0030-drops-15234},
doi = {10.4230/DagSemProc.08131.1},
annote = {Keywords: Text Mining, natural language processing, ontologies, ontology design, machine learning, bioinformatics, medical informatics, knowledge management}
}
@InProceedings{schlicker_et_al:DagSemProc.08131.2,
author = {Schlicker, Andreas and Ram{\'\i}rez, Fidel and Rahnenf\"{u}hrer, J\"{o}rg and Huthmacher, Carola and Pironti, Alejandro and Domingues, Francisco S. and Lengauer, Thomas and Albrecht, Mario},
title = {{Applications of semantic similarity measures}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.2},
URN = {urn:nbn:de:0030-drops-15198},
doi = {10.4230/DagSemProc.08131.2},
annote = {Keywords: Semantic similarity, functional similarity, Gene Ontology, domain-domain interactions}
}
@InProceedings{briscoe_et_al:DagSemProc.08131.3,
author = {Briscoe, Ted and Gasperin, Caroline and Lewin, Ian and Vlachos, Andreas},
title = {{Bootstrapping an interactive information extraction system for FlyBase curation}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.3},
URN = {urn:nbn:de:0030-drops-15086},
doi = {10.4230/DagSemProc.08131.3},
annote = {Keywords: Biomedical Text Mining, Interactive Information Extraction, Natural Language Processing}
}
@InProceedings{su_et_al:DagSemProc.08131.4,
author = {Su, Jian and Yang, Xiaofeng and Hong, Huaqing and Tateisi, Yuka and Tsujii, Jun'ichi},
title = {{Coreference Resolution in Biomedical Texts: a Machine Learning Approach}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.4},
URN = {urn:nbn:de:0030-drops-15220},
doi = {10.4230/DagSemProc.08131.4},
annote = {Keywords: Coreference resolution, biomedical text}
}
@InProceedings{spasic_et_al:DagSemProc.08131.5,
author = {Spasic, Irena and Schober, Daniel and Sansone, Susanna-Assunta and Rebholz-Schuhmann, Dietrich and Kell, Douglas B. and Paton, Norman W.},
title = {{Facilitating the development of controlled vocabularies for metabolomics technologies with text mining}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.5},
URN = {urn:nbn:de:0030-drops-15503},
doi = {10.4230/DagSemProc.08131.5},
annote = {Keywords: Text mining, ontology, controlled vocabulary, metabolomics}
}
@InProceedings{dietze_et_al:DagSemProc.08131.6,
author = {Dietze, Heiko and Alexopoulou, Dimitra and Alvers, Michael R. and Barrio-Alvers, Bill and Doms, Andreas and Hakenberg, J\"{o}rg and M\"{o}nnich, Jan and Plake, Conrad and Reischuck, Andreas and Royer, Loic and W\"{a}chter, Thomas and Zschunke, Matthias and Schroeder, Michael},
title = {{GoPubMed: Exploring Pubmed with Ontological Background Knowledge}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.6},
URN = {urn:nbn:de:0030-drops-15204},
doi = {10.4230/DagSemProc.08131.6},
annote = {Keywords: Text mining, literature search, Gene Ontology, NLP, ontology, thesaurus, PubMed}
}
@InProceedings{nenadic:DagSemProc.08131.7,
author = {Nenadic, Goran},
title = {{Mining associations and roles: role of feature extraction}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.7},
URN = {urn:nbn:de:0030-drops-15497},
doi = {10.4230/DagSemProc.08131.7},
annote = {Keywords: Text mining, associations, roles, feature engineering, feature extraction}
}
@InProceedings{leser_et_al:DagSemProc.08131.8,
author = {Leser, Ulf and Groth, Philip and Weiss, Bertram and Pohlenz, Hans-Dieter},
title = {{Mining Phenotypes for Protein Function Prediction}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.8},
URN = {urn:nbn:de:0030-drops-15133},
doi = {10.4230/DagSemProc.08131.8},
annote = {Keywords: Data mining, funciton prediction, bioinformatics, phenotypes, text mining}
}
@InProceedings{schulz:DagSemProc.08131.9,
author = {Schulz, Stefan},
title = {{Named Entity or Entity Name?}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.9},
URN = {urn:nbn:de:0030-drops-15214},
doi = {10.4230/DagSemProc.08131.9},
annote = {Keywords: Ontology, Named Entity Recognition}
}
@InProceedings{washington_et_al:DagSemProc.08131.10,
author = {Washington, N. and Gibson, M. and Mungall, C.J. and Ashburner, Michael and Gkoutos, G. and Westerfield, M. and Haendel, M. and Lewis, S. E.},
title = {{NLP and Phenotypes: using Ontologies to link Human Diseases to Animal Models}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.10},
URN = {urn:nbn:de:0030-drops-15143},
doi = {10.4230/DagSemProc.08131.10},
annote = {Keywords: Phenotypes, ontologies, annotation}
}
@InProceedings{buitelaar:DagSemProc.08131.11,
author = {Buitelaar, Paul},
title = {{Ontologies \& Text Mining (for Life Sciences)}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.11},
URN = {urn:nbn:de:0030-drops-15095},
doi = {10.4230/DagSemProc.08131.11},
annote = {Keywords: Ontology Search; Ontology Population; Ontology Learning; Lexical Enrichment of Ontologies}
}
@InProceedings{alexopoulou_et_al:DagSemProc.08131.12,
author = {Alexopoulou, Dimitra and W\"{a}chter, Thomas and Pickersgill, Laura and Eyre, Cecilia and Schroeder, Michael},
title = {{Ontology learning with text mining: Two use cases in lipoprotein metabolism and toxicology}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.12},
URN = {urn:nbn:de:0030-drops-15063},
doi = {10.4230/DagSemProc.08131.12},
annote = {Keywords: Automatic Term Recognition, Ontology Learning, Lipoprotein Metabolism}
}
@InProceedings{kim:DagSemProc.08131.13,
author = {Kim, Jung-Jae},
title = {{Ontology-based Extraction of Transcription Regulation Events}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.13},
URN = {urn:nbn:de:0030-drops-15112},
doi = {10.4230/DagSemProc.08131.13},
annote = {Keywords: Information extraction, ontology, transcription regulation, inference, ontology semantics}
}
@InProceedings{milward:DagSemProc.08131.14,
author = {Milward, David},
title = {{Ontology-Based Interactive Information Extraction}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.14},
URN = {urn:nbn:de:0030-drops-15150},
doi = {10.4230/DagSemProc.08131.14},
annote = {Keywords: Information extraction, ontologies, text mining}
}
@InProceedings{hakenberg:DagSemProc.08131.15,
author = {Hakenberg, J\"{o}rg},
title = {{Services for annotation of biomedical text}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.15},
URN = {urn:nbn:de:0030-drops-15101},
doi = {10.4230/DagSemProc.08131.15},
annote = {Keywords: BioCreative, NER, EMN, GN, information extraction, web-service, AliBaba}
}
@InProceedings{schuchhardt:DagSemProc.08131.16,
author = {Schuchhardt, Johannes},
title = {{Systems biology approaches for prioritizing therapeutic gene targets}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.16},
URN = {urn:nbn:de:0030-drops-15053},
doi = {10.4230/DagSemProc.08131.16},
annote = {Keywords: Rational therapy, predictive modelling, data integration, ontologies, pathway databases}
}
@InProceedings{krauthammer_et_al:DagSemProc.08131.17,
author = {Krauthammer, Michael and Luong, Thaibinh},
title = {{Term Mapping Using Matrix Operations}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.17},
URN = {urn:nbn:de:0030-drops-15126},
doi = {10.4230/DagSemProc.08131.17},
annote = {Keywords: Term Identification}
}
@InProceedings{park:DagSemProc.08131.18,
author = {Park, Jong C.},
title = {{Text Mining and Management Tools for Resource Construction and Validation in the Life Sciences}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.18},
URN = {urn:nbn:de:0030-drops-15181},
doi = {10.4230/DagSemProc.08131.18},
annote = {Keywords: Text Mining, Resource Construction, Resource Validation, Gene Ontology}
}
@InProceedings{mueller_et_al:DagSemProc.08131.19,
author = {Mueller, Hans-Michael and Rangarajan, Arun and Teal, Tracy K. and van Auken, Kimberly and Chan, Juancarlos and Sternberg, Paul W.},
title = {{Textpresso - an Information Retrieval and Extraction System for Biological Literature}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.19},
URN = {urn:nbn:de:0030-drops-15169},
doi = {10.4230/DagSemProc.08131.19},
annote = {Keywords: Information retrieval, literature search engine, information extraction, automated literature curation, semantic search, ontology,}
}
@InProceedings{beisswanger_et_al:DagSemProc.08131.20,
author = {Beisswanger, Elena and Poprat, Michael and Hahn, Udo},
title = {{WordNet-Inspired Terminological Resources for Bio-NLP}},
booktitle = {Ontologies and Text Mining for Life Sciences : Current Status and Future Perspectives},
pages = {1--1},
series = {Dagstuhl Seminar Proceedings (DagSemProc)},
ISSN = {1862-4405},
year = {2008},
volume = {8131},
editor = {Michael Ashburner and Ulf Leser and Dietrich Rebholz-Schuhmann},
publisher = {Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
address = {Dagstuhl, Germany},
URL = {https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.08131.20},
URN = {urn:nbn:de:0030-drops-15073},
doi = {10.4230/DagSemProc.08131.20},
annote = {Keywords: WordNet, Bio-Ontologies}
}
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