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Using Large Biomedical Databases as Gold Annotations for Automatic Relation Extraction

Tilia Ellendorff, Fabio Rinaldi, Simon Clematide
We show how to use large biomedical databases in order to obtain a gold standard for training a machine learning system over a corpus of biomedical text.  ...  As an example we use the Comparative Toxicogenomics Database (CTD) and describe by means of a short case study how the obtained data can be applied.  ...  One very large database which is especially useful for biomedical relation extraction is the Comparative Toxicogenomics Database (CTD) (Davis et al., 2009 ).  ... 
doi:10.5167/uzh-104487 fatcat:5iuhddwvxzd47cyicnyhlhstyq

Mining microbe–disease interactions from literature via a transfer learning model

Chengkun Wu, Xinyi Xiao, Canqun Yang, JinXiang Chen, Jiacai Yi, Yanlong Qiu
2021 BMC Bioinformatics  
The structured databases for microbe–disease interactions are in limited amounts. In this paper, we aim to construct a large-scale database for microbe–disease interactions automatically.  ...  Background Interactions of microbes and diseases are of great importance for biomedical research. However, large-scale of microbe–disease interactions are hidden in the biomedical literature.  ...  Author's contributions CW and XX developed the framework and drafted the manuscript; they developed the codes, prepared the datasets for testing, drafted the discussion and revised the whole manuscript  ... 
doi:10.1186/s12859-021-04346-7 pmid:34507528 pmcid:PMC8430297 fatcat:sfeytz2knzbadnayz7w6prdia4

Knowledge-based extraction of adverse drug events from biomedical text

Ning Kang, Bharat Singh, Chinh Bui, Zubair Afzal, Erik M van Mulligen, Jan A Kors
2014 BMC Bioinformatics  
Many biomedical relation extraction systems are machine-learning based and have to be trained on large annotated corpora that are expensive and cumbersome to construct.  ...  Whether use of a knowledge base is equally advantageous for other biomedical relation-extraction tasks remains to be investigated.  ...  In recent years, many systems have been developed for the automatic extraction of biomedical events from text, such as protein-protein interactions and gene-disease relations [2, 6] .  ... 
doi:10.1186/1471-2105-15-64 pmid:24593054 pmcid:PMC3973995 fatcat:33ubfhzeg5d3tcx5o267scjyca

hPP Corpus: A Tagged Biomedical Corpus for Automatic Extraction of Human Protein Phosphorylation for Understanding Cellular Functions

Natarajan J
2020 Journal of Embryology & Stem Cell Research  
However, to our best knowledge there is no standard annotated corpus available for evaluating approaches related to the extraction of protein phosphorylation information related to human.  ...  To our best knowledge hPP corpus is the first and foremost annotated corpus available for evaluating text mining systems on extracting human protein phosphorylation from MEDLINE abstracts.  ...  Introduction Advances in biomedical research with the use of large scale experimental techniques and bioinformatics tools have greatly accelerated the publication rate of biomedical literature.  ... 
doi:10.23880/jes-16000140 fatcat:nkz7treybnaqpmkgfqn2666nqi

Improving chemical disease relation extraction with rich features and weakly labeled data

Yifan Peng, Chih-Hsuan Wei, Zhiyong Lu
2016 Journal of Cheminformatics  
More importantly, this work exemplifies the use of (freely available) curated document-level annotations in existing biomedical databases, which are largely overlooked in text-mining system development  ...  Due to the importance of identifying relations between chemicals and diseases for new drug discovery and improving chemical safety, there has been a growing interest in developing automatic relation extraction  ...  Robert Leaman for proofreading the manuscript. Competing interests The authors declare that they have no competing interests.  ... 
doi:10.1186/s13321-016-0165-z pmid:28316651 pmcid:PMC5054544 fatcat:3peg7b5gubfbpc3ir5fe6bq3bm

Biomedical Relation Extraction Using Distant Supervision

Nada Boudjellal, Huaping Zhang, Asif Khan, Arshad Ahmad
2020 Scientific Programming  
Relation extraction is the second of the two important tasks of relation extraction.  ...  This study presents an overview of relation extraction using distant supervision, providing a generalized architecture of this task based on the state-of-the-art work that proposed this method.  ...  DS has been used for the task of relation extraction (RE) and was introduced first by Mintz et al. [24] , who used it to create a large dataset for Freebase RE.  ... 
doi:10.1155/2020/8893749 fatcat:okfqki7lazbo7ilffs2eafzoru

A multi-ontology approach to annotate scientific documents based on a modularization technique

Priscilla Corrêa e Castro Gomes, Ana Maria de Carvalho Moura, Maria Cláudia Cavalcanti
2015 Journal of Biomedical Informatics  
Text annotation may help as it relies on the use of ontologies to maintain annotations based on a uniform vocabulary.  ...  Based on these annotations a set of modules are extracted from a set of distinct ontologies, and are made available for the user, for complementary annotation.  ...  In this study, relevant requirements for biomedical text annotation, such as the support for manual and automatic annotation, and the flexibility for loading ontologies were observed.  ... 
doi:10.1016/j.jbi.2015.09.022 pmid:26483172 fatcat:gh7cq62sz5dchklao6a2j32kxu

Event-based text mining for biology and functional genomics

S. Ananiadou, P. Thompson, R. Nawaz, J. McNaught, D. B. Kell
2014 Briefings in Functional Genomics  
Automatic event extraction systems facilitate the development of sophisticated semantic search applications, allowing researchers to formulate structured queries over extracted events, so as to specify  ...  databases, e.g.  ...  Makoto Miwa (NaCTeM) for his helpful comments on the manuscript.  ... 
doi:10.1093/bfgp/elu015 pmid:24907365 pmcid:PMC4499874 fatcat:qjl6uvt3wbbuplu6hrdsloyjlu

Enriching a biomedical event corpus with meta-knowledge annotation

Paul Thompson, Raheel Nawaz, John McNaught, Sophia Ananiadou
2011 BMC Bioinformatics  
As such, the BioLexicon must account for real usage of words in biomedical texts.  ...  Existing databases and ontologies often have a specific focus and are oriented towards human use.  ...  DRS supervised the work undertaken at the EBI, including the extraction of terms from biomedical reference data resources and their semantic relations, and the definition of the XML interchange format  ... 
doi:10.1186/1471-2105-12-393 pmid:21992002 pmcid:PMC3228855 fatcat:k7hyeyzaijatjhkgyeouf6ufrm

The BioLexicon: a large-scale terminological resource for biomedical text mining

Paul Thompson, John McNaught, Simonetta Montemagni, Nicoletta Calzolari, Riccardo del Gratta, Vivian Lee, Simone Marchi, Monica Monachini, Piotr Pezik, Valeria Quochi, CJ Rupp, Yutaka Sasaki (+3 others)
2011 BMC Bioinformatics  
As such, the BioLexicon must account for real usage of words in biomedical texts.  ...  Existing databases and ontologies often have a specific focus and are oriented towards human use.  ...  DRS supervised the work undertaken at the EBI, including the extraction of terms from biomedical reference data resources and their semantic relations, and the definition of the XML interchange format  ... 
doi:10.1186/1471-2105-12-397 pmid:21992002 pmcid:PMC3228855 fatcat:se2hsjqylbc4rmkzhpwb4ll3su

Acquisition and evaluation of verb subcategorization resources for biomedicine

Laura Rimell, Thomas Lippincott, Karin Verspoor, Helen L. Johnson, Anna Korhonen
2013 Journal of Biomedical Informatics  
on tasks such as relation extraction and syntactic or semantic parsing.  ...  Our new gold standards reveal major differences when annotators use the different definitions.  ...  We gratefully acknowledge Yuval Krymolowski for programming the SCFspecific filtering, and Diane Nicholls for syntactic annotation.  ... 
doi:10.1016/j.jbi.2013.01.001 pmid:23347886 fatcat:agqvza5c3vh5bamhiug7hf2i2y

tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles

J. M. Cejuela, P. McQuilton, L. Ponting, S. J. Marygold, R. Stefancsik, G. H. Millburn, B. Rost
2014 Database: The Journal of Biological Databases and Curation  
As part of the BioCreative IV Interactive Annotation Task, FlyBase has used tagtog to identify and extract mentions of Drosophila melanogaster gene symbols and names in full-text biomedical articles from  ...  Toward this end, we present the 'tagtog' system, a web-based annotation framework that can be used to mark up biological entities (such as genes) and concepts (such as Gene Ontology terms) in full-text  ...  Acknowledgements The authors would like to thank the BioCreative initiative for the opportunity to participate in the interactive annotation task and our interactive annotators Mary Schaeffer and Ritu  ... 
doi:10.1093/database/bau033 pmid:24715220 pmcid:PMC3978375 fatcat:ibmnb46bofeivdeqcatwpbr7ce

BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text

Po-Ting Lai, Yu-Yan Lo, Ming-Siang Huang, Yu-Cheng Hsiao, Richard Tzong-Han Tsai
2016 Database: The Journal of Biological Databases and Curation  
Automatically extracting and representing biomedical events using BEL can help biologists quickly survey and understand relevant literature.  ...  BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text.  ...  Acknowledgement We would also like to show our gratitude to the reviewers for their comment on an earlier version of the manuscript that greatly improved this paper. Conflict of interest.  ... 
doi:10.1093/database/baw064 pmid:27173520 pmcid:PMC4865328 fatcat:wx42b3ivafau3djwpxcbkeuhyi

Validating Candidate Gene-Mutation Relations in MEDLINE Abstracts via Crowdsourcing [chapter]

John D. Burger, Emily Doughty, Sam Bayer, David Tresner-Kirsch, Ben Wellner, John Aberdeen, Kyungjoon Lee, Maricel G. Kann, Lynette Hirschman
2012 Lecture Notes in Computer Science  
The biomedical literature contains rich information on such relations, but the correct pairings are difficult to extract automatically because a single abstract may mention multiple genes and mutations  ...  We extracted candidate mutations from a corpus of 250 MEDLINE abstracts using EMU combined with curated gene lists from NCBI.  ...  We have presented a promising initial experiment using crowdsourcing to validate gene-mutation relations assembled from automatically extracted genes and mutations.  ... 
doi:10.1007/978-3-642-31040-9_8 fatcat:lq2gvcvzzzez3ot5xhgzgbliwq

Special issue on bio-ontologies and phenotypes

Larisa N. Soldatova, Nigel Collier, Anika Oellrich, Tudor Groza, Karin Verspoor, Philippe Rocca-Serra, Michel Dumontier, Nigam H. Shah
2015 Journal of Biomedical Semantics  
, driven by manual, semi-and fully automatic means.  ...  bio-ontologies and phenotypes special issue includes eight papers selected from the 11 papers presented at the Bio-Ontologies SIG (Special Interest Group) and the Phenotype Day at ISMB (Intelligent Systems for  ...  Acknowledgements As editors of this thematic issue, we thank all the authors who submitted papers, the Program Committee members and the reviewers for their excellent work.  ... 
doi:10.1186/s13326-015-0040-2 pmid:26682035 pmcid:PMC4682270 fatcat:7vupjwbtd5fzpojrh3tumhb2oq
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