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Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora

T. Groza, S. Kohler, S. Doelken, N. Collier, A. Oellrich, D. Smedley, F. M. Couto, G. Baynam, A. Zankl, P. N. Robinson
2015 Database: The Journal of Biological Databases and Curation  
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora.  ...  Here, we present a unique corpus, capturing text spans from 228 abstracts manually annotated with Human Phenotype Ontology (HPO) concepts and harmonized by three curators, which can be used as a reference  ...  Introduction The Human Phenotype Ontology (HPO) (1) is widely used for the annotation of human phenotypes and has been employed in many biomedical applications aiming to understand the phenotypic consequences  ... 
doi:10.1093/database/bav005 pmid:25725061 pmcid:PMC4343077 fatcat:6bc3qcxskfbybaevdtjc3u5nra

Chapter 16: Text Mining for Translational Bioinformatics

K. Bretonnel Cohen, Lawrence E. Hunter, Fran Lewitter, Maricel Kann
2013 PLoS Computational Biology  
Acknowledgments Anna Divoli provided helpful comments on the manuscript.  ...  , or finding mentions of phenotypes in text; and phenotype normalization, or mapping mentions of phenotypes to concepts in ontologies.  ...  The former includes a methodology for the automatic generation of test suites of arbitrary size and complexity.  ... 
doi:10.1371/journal.pcbi.1003044 pmid:23633944 pmcid:PMC3635962 fatcat:57jzfqucqzambld3tbjzjzygxa

Semantic annotation in biomedicine: the current landscape

Jelena Jovanović, Ebrahim Bagheri
2017 Journal of Biomedical Semantics  
The abundance and unstructured nature of biomedical texts, be it clinical or research content, impose significant challenges for the effective and efficient use of information and knowledge stored in such  ...  This paper focuses on annotation of biomedical entity mentions with concepts from relevant biomedical knowledge bases such as UMLS.  ...  Funding The second author graciously acknowledges funding from The Natural Sciences and Engineering Research Council of Canada (NSERC).  ... 
doi:10.1186/s13326-017-0153-x pmid:28938912 pmcid:PMC5610427 fatcat:jby2gq576vfdfmf4lsusahjrrm

Text Mining for Building Biomedical Networks Using Cancer as a Case Study

Sofia I. R. Conceição, Francisco M. Couto
2021 Biomolecules  
Many interaction databases already use text mining systems, and the development of these tools will lead to more reliable networks, as well as the possibility to personalize the networks by selecting the  ...  This has become a challenge with the notable increase in scientific literature being published, as it is hard for human curators to track all recent discoveries without using efficient tools to help them  ...  Acknowledgments: We wish to thank Francisco Pinto (BioISI, FCUL) for the helpful comments. Conflicts of Interest: The authors declare no conflict of interest.  ... 
doi:10.3390/biom11101430 pmid:34680062 pmcid:PMC8533101 fatcat:pfoi74nq5fewrgg3mchguwlbsa

PGxCorpus, a manually annotated corpus for pharmacogenomics

Joël Legrand, Romain Gogdemir, Cédric Bousquet, Kevin Dalleau, Marie-Dominique Devignes, William Digan, Chia-Ju Lee, Ndeye-Coumba Ndiaye, Nadine Petitpain, Patrice Ringot, Malika Smaïl-Tabbone, Yannick Toussaint (+1 others)
2020 Scientific Data  
This article introduces PGxCorpus, a manually annotated corpus, designed to fill this gap and to enable the automatic extraction of PGx relationships from text.  ...  A significant part of the state-of-the-art knowledge in PGx is accumulated in scientific publications, where it is hardly reusable by humans or software.  ...  Supervised learning has also been experimented [12] [13] [14] [15] [16] , but without appropriate corpora, most studies build train and test sets on the basis of PharmGKB, which is the reference database  ... 
doi:10.1038/s41597-019-0342-9 pmid:31896797 pmcid:PMC6940385 fatcat:ra3mar3jbbfubirg62t5gca6l4

Identifying Human Phenotype Terms by Combining Machine Learning and Validation Rules

Manuel Lobo, Andre Lamurias, Francisco M. Couto
2017 BioMed Research International  
The Human Phenotype Ontology (HPO) is an ontology that provides a standardized vocabulary for phenotypic abnormalities found in human diseases.  ...  Named-Entity Recognition is commonly used to identify biological entities such as proteins, genes, and chemical compounds found in scientific articles.  ...  The Human Phenotype Ontology (HPO) [3] is an ontology that provides a standardized vocabulary for phenotypic abnormalities found in human diseases.  ... 
doi:10.1155/2017/8565739 pmid:29250549 pmcid:PMC5700471 fatcat:mrd2gcodnrakvdnkktpbuosgny

Clinical natural language processing for radiation oncology: A review and practical primer

Danielle S. Bitterman, Timothy A. Miller, Raymond H. Mak, Guergana K. Savova
2021 International Journal of Radiation Oncology, Biology, Physics  
Natural language processing (NLP), which aims to convert human language into expressions that can be analyzed by computers, is one of the most rapidly developing and widely used technologies in the field  ...  Recent major NLP algorithmic advances have significantly improved their performance, leading to a surge in academic and industry interest in developing tools to automate information extraction and phenotyping  ...  were manually labeled with the cancer outcome and used to train, validate, and test the models.  ... 
doi:10.1016/j.ijrobp.2021.01.044 pmid:33545300 fatcat:vhlkvw7kbzfw5p6dg3jigbkrse

Concept annotation in the CRAFT corpus

Michael Bada, Miriam Eckert, Donald Evans, Kristin Garcia, Krista Shipley, Dmitry Sitnikov, William A Baumgartner, K Cohen, Karin Verspoor, Judith A Blake, Lawrence E Hunter
2012 BMC Bioinformatics  
Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text.  ...  CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI  ...  Acknowledgements The authors gratefully acknowledge their support from NIH, 5R01 LM008111, 2R01 LM009254, 5 T15 LM009451, and 3 T15 LM009451.  ... 
doi:10.1186/1471-2105-13-161 pmid:22776079 pmcid:PMC3476437 fatcat:kuulhujx4ratnkoywafxggkhmi

How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience

M. Krallinger, F. Leitner, M. Vazquez, D. Salgado, C. Marcelle, M. Tyers, A. Valencia, A. Chatr-aryamontri
2012 Database: The Journal of Biological Databases and Curation  
Two ontologies that have been successfully used for this purpose are the Gene Ontology (GO) for annotating aspects of gene products and the Molecular Interaction ontology (PSI-MI) used by databases that  ...  Here, we provide a general overview of current text-mining methods to automatically extract annotations of GO and PSI-MI ontology terms in the context of the BioCreative (Critical Assessment of Information  ...  Acknowledgements We would like to thank Lynette Hirschman and Christian Blaschke for their active feedback in the BioCreative tasks described in this article.  ... 
doi:10.1093/database/bas017 pmid:22438567 pmcid:PMC3309177 fatcat:3q2zwcobxfaebl4rw4hsnddid4

Knowledge environments representing molecular entities for the virtual physiological human

M. Hofmann-Apitius, J. Fluck, L. Furlong, O. Fornes, C. Kolarik, S. Hanser, M. Boeker, S. Schulz, F. Sanz, R. Klinger, T. Mevissen, T. Gattermayer (+2 others)
2008 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
In essence, the virtual physiological human (VPH) is a multiscale representation of human physiology spanning from the molecular level via cellular processes and multicellular organization of tissues to  ...  The different scales of the VPH deal with different entities, relationships and processes, and in consequence the models used to describe and simulate biological functions vary significantly.  ...  In the course of EU project @neurIST, we therefore generated a dedicated ontology that contains all relevant concepts for the description of the clinical phenotype and in addition comprises concepts that  ... 
doi:10.1098/rsta.2008.0099 pmid:18559317 fatcat:ib6jt7mzkrg6fcq4vs5w7xwkfa

Development of Clinical Concept Extraction Applications: A Methodology Review [article]

Sunyang Fu, David Chen, Huan He, Sijia Liu, Sungrim Moon, Kevin J Peterson, Feichen Shen, Liwei Wang, Yanshan Wang, Andrew Wen, Yiqing Zhao, Sunghwan Sohn, Hongfang Liu
2020 arXiv   pre-print
After title and abstract screening, 224 publications were selected. The methods used for developing clinical concept extraction applications were discussed in this review.  ...  in English and published from January 2009 through June 2019 from Ovid MEDLINE In-Process & Other Non-Indexed Citations, Ovid MEDLINE, Ovid EMBASE, Scopus, Web of Science, and the ACM Digital Library.  ...  Acknowledgements We gratefully acknowledge Katelyn Cordie and Luke Carlson for editorial support.  ... 
arXiv:1910.11377v3 fatcat:rt3flc4kvvhqzawa5nqp6pucy4

PGxCorpus: a Manually Annotated Corpus for Pharmacogenomics: Supplement Information: Tables S1 and S2 with detailed performances of the baseline experiment [article]

Joel Legrand, Romain Gogdemir, Cedric Bousquet, Kevin Dalleau, Marie-Dominique Devignes, William Digan, Chia-Ju Lee, Ndeye-Coumba Ndiaye, Nadine Petitpain, Patrice Ringot, Malika Smail-Tabbone, Yannick Toussaint (+1 others)
2019 bioRxiv   pre-print
But, existing works are limited by the absence of high quality annotated corpora focusing on the domain. This absence restricts in particular the use of supervised machine learning approaches.  ...  We present in this article the method used to annotate consistently texts, and a baseline experiment that illustrates how this resource may be leveraged to synthesize and summarize PGx knowledge.  ...  Acknowledgements The authors acknowledge their funding institutions: the French National Research Agency (ANR) supports the PractiKPharma project (ANR-15-CE23-0028) and the University of Lorraine program  ... 
doi:10.1101/534388 fatcat:xj5lqifzy5aajle2kvovcr7yra

Auto-CORPus: Automated and Consistent Outputs from Research Publications [article]

Yan Hu, Shujian Sun, Thomas Rowlands, Tim Beck, Joram Matthias Posma
2021 biorxiv/medrxiv   pre-print
Motivation: The availability of improved natural language processing (NLP) algorithms and models enable researchers to analyse larger corpora using open source tools.  ...  The output is a single JSON file that contains the text for each section, table data in machine-readable format and lists of phenotypes and abbreviations found in the article.  ...  ) for testing the package and providing feedback.  ... 
doi:10.1101/2021.01.08.425887 fatcat:sydv35p66jfnldstnx2ujl32ti

Biomedical text mining and its applications in cancer research

Fei Zhu, Preecha Patumcharoenpol, Cheng Zhang, Yang Yang, Jonathan Chan, Asawin Meechai, Wanwipa Vongsangnak, Bairong Shen
2013 Journal of Biomedical Informatics  
In this review, we introduce the basic concepts underlying text mining and examine some frequently used algorithms, tools, and data sets, as well as assessing how much these algorithms have been utilized  ...  Biomedical text mining on cancer research is computationally automatic and high-throughput in nature. However, it is error-prone due to the complexity of natural language processing.  ...  Textpresso [66, 67] uses an ontology, returns searching goals for classes of biological concepts (e.g., gene, allele, cell, or phenotype), classes of relations of objects (e.g., association, regulation  ... 
doi:10.1016/j.jbi.2012.10.007 pmid:23159498 fatcat:xd7j77sbwfhklkat6tael64lbq

Natural language processing: State of the art and prospects for significant progress, a workshop sponsored by the National Library of Medicine

Carol Friedman, Thomas C. Rindflesch, Milton Corn
2013 Journal of Biomedical Informatics  
Specific goals of the NLMsponsored workshop were to identify the current state of the art, grand challenges and specific roadblocks, and to identify effective use and best practices.  ...  and in the general language domain.  ...  Acknowledgment We are grateful to Graciela Rosemblat and Dongwook Shin for assistance with the figures.  ... 
doi:10.1016/j.jbi.2013.06.004 pmid:23810857 fatcat:owtr62gt5jeojin5ugt6gurbg4
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