Supplementary Information : A Neural Network MultiTask Learning Approach to Biomedical Named Entity Recognition

The extended Anatomical Entity Mention corpus (Pyysalo and Ananiadou, 2013) is the result of combining and extending the Anatomical Entity Mention (AnEM) corpus (Ohta et al., 2012) and the Multi-level Event Extraction corpus (MLEE) (Pyysalo et al., 2012a). AnEM consists of 500 randomly selected PubMed abstracts and full-text extracts annotated for anatomical entity mentions. MLEE consists of 262 PubMed abstracts on the molecular mechanisms of cancer, specifically relating to angiogenesis. MLEE is also annotated for anatomical entities specified in AnEM. AnatEM was created by combining the anatomical entity annotations of the AnEM and MLEE corpora, then manual annotation was done on an additional 100 documents following the selection criteria of AnEM and 350 documents following those of MLEE, for a selection of topics related to cancer. The resulting corpus thus consists of 1212 documents, 600 of which are drawn randomly from abstracts and full texts as in AnEM, and the remaining 612 are a targeted selection of PubMed abstracts relating to the molecular mechanisms of cancer.

[1]  Zhiyong Lu,et al.  PubTator: a web-based text mining tool for assisting biocuration , 2013, Nucleic Acids Res..

[2]  Sophia Ananiadou,et al.  How to make the most of NE dictionaries in statistical NER , 2008, BMC Bioinformatics.

[3]  Nigel Collier,et al.  Introduction to the Bio-entity Recognition Task at JNLPBA , 2004, NLPBA/BioNLP.

[4]  Richard Tzong-Han Tsai,et al.  Overview of BioCreative II gene mention recognition , 2008, Genome Biology.

[5]  José Luís Oliveira,et al.  Gimli: open source and high-performance biomedical name recognition , 2013, BMC Bioinformatics.

[6]  Sampo Pyysalo,et al.  Anatomical entity mention recognition at literature scale , 2013, Bioinform..

[7]  Yue Wang,et al.  The Genia Event Extraction Shared Task, 2013 Edition - Overview , 2013, BioNLP@ACL.

[8]  K. Bretonnel Cohen,et al.  A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools , 2012, BMC Bioinformatics.

[9]  Sampo Pyysalo,et al.  Overview of BioNLP Shared Task 2013 , 2013, BioNLP@ACL.

[10]  Sampo Pyysalo,et al.  Overview of BioNLP’09 Shared Task on Event Extraction , 2009, BioNLP@HLT-NAACL.

[11]  Karin M. Verspoor,et al.  BioC: a minimalist approach to interoperability for biomedical text processing , 2013, AMIA.

[12]  Goran Nenadic,et al.  LINNAEUS: A species name identification system for biomedical literature , 2010, BMC Bioinformatics.

[13]  Jun'ichi Tsujii,et al.  Corpus annotation for mining biomedical events from literature , 2008, BMC Bioinformatics.

[14]  Zhiyong Lu,et al.  NCBI disease corpus: A resource for disease name recognition and concept normalization , 2014, J. Biomed. Informatics.

[15]  Alfonso Valencia,et al.  CHEMDNER: The drugs and chemical names extraction challenge , 2015, Journal of Cheminformatics.

[16]  Yifan Peng,et al.  Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task , 2016, Database J. Biol. Databases Curation.

[17]  K. Bretonnel Cohen,et al.  Concept annotation in the CRAFT corpus , 2012, BMC Bioinformatics.

[18]  Burr Settles.  ABNER: an open source tool for automatically tagging genes, proteins and other entity names in text , 2005 .

[19]  Sampo Pyysalo,et al.  Event extraction across multiple levels of biological organization , 2012, Bioinform..

[20]  Sampo Pyysalo,et al.  Open-domain Anatomical Entity Mention Detection , 2012, ACL 2012.

[21]  Sampo Pyysalo,et al.  Overview of the ID, EPI and REL tasks of BioNLP Shared Task 2011 , 2012, BMC Bioinformatics.

[22]  Huaiyu Mi,et al.  PANTHER pathway: an ontology-based pathway database coupled with data analysis tools. , 2009, Methods in molecular biology.

[23]  Lorraine K. Tanabe,et al.  GENETAG: a tagged corpus for gene/protein named entity recognition , 2005, BMC Bioinformatics.

[24]  Jin-Dong Kim,et al.  The GENIA corpus: an annotated research abstract corpus in molecular biology domain , 2002 .

[25]  Sophia Ananiadou,et al.  Developing a Robust Part-of-Speech Tagger for Biomedical Text , 2005, Panhellenic Conference on Informatics.

[26]  Philip V. Ogren,et al.  Knowtator: A Protégé plug-in for annotated corpus construction , 2006, NAACL.

[27]  Graciela Gonzalez,et al.  BANNER: An Executable Survey of Advances in Biomedical Named Entity Recognition , 2007, Pacific Symposium on Biocomputing.