BioLINK 2013

The original page for BioLINK 2013 can be found here: https://sites.google.com/site/biolinksig2013/

The PDF of the full BioLINK2013 Proceedings and individual papers are also hosted here, as well as the BioLINK2013 Proceedings BibTeX file.


@Book{biolink13,
editor = {Karin Verspoor and Christian Blaschke and Lynette Hirschman and Hagit Shatkay and Alfonso Valencia},
title = {Proceedings of the {BioLINK SIG} 2013: {R}oles for text mining in biomedical knowledge discovery and translational medicine},
month = {July},
year = {2013},
address = {Berlin, Germany},
series = {Proceedings of the {BioLINK SIG}},
publisher = {The {BioLINK} Special Interest Group},
url = {http://biolinksig.org/proceedings/2013/BioLINK2013_Proceedings.pdf}
}

% Short Papers

@inproceedings{biolink13_campos,
author={David Campos and S\'{e}rgio Matos and Jos\'{e} Lu’s Oliveira},
title={Neji: a tool for heterogeneous biomedical concept identification},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={28-31},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Campos_etal.pdf}
}

@inproceedings{biolink13_kim,
author={Jin-Dong Kim and {K. Bretonnel} Cohen},
title={Natural language query processing for SPARQL generation: A prototype system for SNOMED-CT},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={32-38},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Kim_Cohen.pdf}
}

@inproceedings{biolink13_jimeno,
author={Antonio {Jimeno Yepes} and Karin Verspoor},
title={Towards automatic large-scale curation of genomic variation: improving coverage based on supplementary material},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={39-43},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Jimeno_Verspoor.pdf}
}

@inproceedings{biolink13_kissa,
author={Maria Kissa and Michael Schroeder and George Tsatsaronis},
title={Towards an Integrated Compound to Compound Relatedness Measure},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={44-47},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Kissa_etal.pdf}
}

@inproceedings{biolink13_lependu,
author={Paea {Le Pendu} and Anna {Bauer-Mehren} and Kenneth Jung and Tyler Cole and Jonathan Mortensen and Srinivasan Iyer and Nigam Shah},
title={Case studies in making sense of clinical text},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={48-51},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_LePendu_etal.pdf}
}

@inproceedings{biolink13_thomas,
author={Philippe Thomas and Ulf Leser},
title={HistoNer: {Histone} modification extraction from text},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={52-55},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Thomas_Leser.pdf}
}

% Long Papers

@inproceedings{biolink13_leitner,
author={Florian Leitner and Martin Krallinger and Sushil Tripathi and Martin Kuiper and Astrid Laegreid and Alfonso Valencia},
title={Mining cis-Regulatory Transcription Networks from Literature},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={5-12},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Leitner_etal.pdf}
}

@inproceedings{biolink13_bada,
author={Michael Bada and Dmitry Sitnikov and Judith Blake and Lawrence Hunter},
title={Occurrence of Gene Ontology, Protein Ontology, and NCBI Taxonomy Concepts in Text toward Automatic Gene Ontology Annotation},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={13-19},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Bada_etal.pdf}
}

@inproceedings{biolink13_jacob,
author={Christoph Jacob and Philippe Thomas and Ulf Leser},
title={Comprehensive Benchmark of {G}ene {O}ntology Concept Recognition tools},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={20-26},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Jacob_etal.pdf}
}

% POSTERS
@inproceedings{biolink13_roberts,
author={Phoebe Roberts},
title={A quantitative analysis of causal and associative events involving genes and proteins},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={57},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Roberts.pdf}
}

@inproceedings{biolink13_liu,
author={Haibin Liu and William {Baumgartner Jr.} and Natalie Catlett and Andrea Matthews and Phoebe Roberts and Christophe Roeder and Aaron Hooser and Daniel Ziemek and Lawrence Hunter and {K. Bretonnel} Cohen},
title={Automatic Generation of BEL Statements from Text-mined Biological Events},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={58},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Liu_Baumgartner_etal.pdf}
}

@inproceedings{biolink13_garcia1,
author={Alexander Garcia and Casey McLaughlin and Leyla Jael {Garc\'{i}a Castro}},
title={Biotea},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={59},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Garcia_etal_01.pdf}
}

@inproceedings{biolink13_hettne,
author={Kristina M. Hettne and Harish Dharuri and Reinout {van Schouwen} and Peter {A.C.} {'T Hoen} and Barend Mons and Marco Roos},
title={Explaining genome-wide association study results using concept profile analysis and the Kyoto Encyclopedia of Genes and Genomes pathway database},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={60},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Hettne_etal.pdf}
}

@inproceedings{biolink13_garcia2,
author={Alexander Garcia and Leyla Jael {Garc\'{i}a Castro} and Olga Giraldo},
title={In the Pursuit of Open Science},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={61},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Garcia_etal_02.pdf}
}

@inproceedings{biolink13_kim_poster,
author={Jin-Dong Kim},
title={PubAnnotation - a storage system for sharing of literature annotation},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={62},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Kim.pdf}
}

@inproceedings{biolink13_garcia3,
author={Alexander Garcia and Peter {Murray-Rust} and Gully {APC} Burns and Robert Stevens and Dominika Tkaczyk and Casey McLaughlin and Amaury Belin and Angelo {Di Iorio} and Leyla Garc’a and C\'{e}lya {Gruson-Daniel} and Ross Mounce and Andrea Giovanni Nuzzolese and Silvio Peroni and Jeremy Spinks and Boris {Villazon-Terrazas} and Oscar Corcho and Olga Giraldo and Mike Wabiszewski},
title={{PDFJailbreak} - a communal architecture for making biomedical PDFs semantic},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={63},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Garcia_etal_03.pdf}
}

@inproceedings{biolink13_neves,
author={Mariana Neves and Alexander Damaschun and Nancy Mah and Fritz Lekschas and Stefanie Seltmann and Harald Stachelscheid and Jean-Fred Fontaine and Andreas Kurtz and Ulf Leser},
title={Text mining for characterizing cells and tissues},
year={2013},
booktitle={Proceedings of the {BioLINK SIG}},
pages={64},
url={http://biolinksig.org/proceedings/2013/biolinksig2013_Neves_etal.pdf}
}