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Automatic Term Name Generation for Gene Ontology: Task and Dataset

Yanjian Zhang, Qin Chen, Yiteng Zhang, Zhongyu Wei, Yixu Gao, Jiajie Peng, Zengfeng Huang, Weijian Sun, Xuanjing Huang
2020 Findings of the Association for Computational Linguistics: EMNLP 2020   unpublished
To fill this gap, we propose a novel task, namely term name generation for GO, and build a large-scale benchmark dataset.  ...  Terms contained in Gene Ontology (GO) have been widely used in biology and bio-medicine.  ...  Conclusions and Future Work In this paper, we propose a novel task of automatic term name generation based on the gene text for GO.  ... 
doi:10.18653/v1/2020.findings-emnlp.422 fatcat:tkqek2tmjzaondogwkwnfjmdua

Ontologies for Bioinformatics

Nadine Schuurman, Agnieszka Leszczynski
2008 Bioinformatics and Biology Insights  
An ontology is similar to a paradigm but has very strict implications for formatting and meaning in a computational context.  ...  The use of ontologies is a means of communicating and resolving semantic and organizational differences between biological databases in order to enhance their integration.  ...  The GO is not a taxonomy or index of all known proteins and gene products, but rather provides a standardized set of names for genes and proteins and the terms for characterizing-or 'annotating'-their  ... 
doi:10.4137/bbi.s451 pmid:19812775 pmcid:PMC2735951 fatcat:h6npjmreyvd37dcgmy63tuauam

Annotating biomedical ontology terms in electronic health records using crowd-sourcing

Andre Lamurias, Vasco Pedro, Luka A. Clarke, Francisco M. Couto
2015 International Conference on Biomedical Ontology  
well as drug, gene and protein mentions.  ...  We propose a crowd-sourcing pipeline to improve the precision of extraction and normalization of biomedical terms.  ...  Likewise, a golden dataset could be generated to evaluate and tune the classifier.  ... 
dblp:conf/icbo/LamuriasPCC15 fatcat:lfw6phmyvngsjmedmqn3xocwcq

Graph-in-Graph Network for Automatic Gene Ontology Description Generation [article]

Fenglin Liu, Bang Yang, Chenyu You, Xian Wu, Shen Ge, Adelaide Woicik, Sheng Wang
2022 arXiv   pre-print
Gene Ontology (GO) is the primary gene function knowledge base that enables computational tasks in biomedicine.  ...  This task aims to automatically generate a sentence that describes the function of a GO term belonging to one of the three categories, i.e., molecular function, biological process, and cellular component  ...  ACKNOWLEDGMENTS We thank all the anonymous reviewers for their constructive comments and suggestions.  ... 
arXiv:2206.05311v2 fatcat:lfniv64k3ndjrcqbpge4pvguii

Ontologies in Bioinformatics [chapter]

Robert Stevens, Chris Wroe, Phillip Lord, Carole Goble
2004 Handbook on Ontologies  
This chapter provides a survey of the need for ontologies; the nature of the domain and the knowledge tasks involved; and then an overview of ontology work in the discipline.  ...  Ontologies also provide a means for a schema definition suitable for the complexity and precision required for biology's knowledge bases.  ...  the term name.  ... 
doi:10.1007/978-3-540-24750-0_32 fatcat:uq7ieianz5bijcvyvxyh7z2o7u

Ontologies in Biological Data Visualization

Sheelagh Carpendale, Min Chen, Daniel Evanko, Nils Gehlenborg, Carsten Gorg, Larry Hunter, Francis Rowland, Margaret-Anne Storey, Hendrik Strobelt
2014 IEEE Computer Graphics and Applications  
Concepts can encompass a variety of realworld entities and abstractions such as names, objects, events, ideas, and types.  ...  A number of specifi cation languages (for example, OWL, the Web Ontology Language) have been developed for encoding ontologies.  ...  For more information, see the "Exploring On tologies in Biological Visualization" sidebar.  ... 
doi:10.1109/mcg.2014.33 pmid:24808195 fatcat:mkgfjlp4k5hodfbffq36hwjnsi

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

David P Hill, Nico Adams, Mike Bada, Colin Batchelor, Tanya Z Berardini, Heiko Dietze, Harold J Drabkin, Marcus Ennis, Rebecca E Foulger, Midori A Harris, Janna Hastings, Namrata S Kale (+7 others)
2013 BMC Genomics  
The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes.  ...  We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally  ...  Terms in the GO chemical ontology that referred to existing terms in the ChEBI ontology, but for which the matches were not detected automatically due to naming differences.  ... 
doi:10.1186/1471-2164-14-513 pmid:23895341 pmcid:PMC3733925 fatcat:ts753ihc5fdrjjz4akrcmaejga

Deep learning meets ontologies: experiments to anchor the cardiovascular disease ontology in the biomedical literature

Mercedes Arguello Casteleiro, George Demetriou, Warren Read, Maria Jesus Fernandez Prieto, Nava Maroto, Diego Maseda Fernandez, Goran Nenadic, Julie Klein, John Keane, Robert Stevens
2018 Journal of Biomedical Semantics  
Automatic identification of term variants or acceptable alternative free-text terms for gene and protein names from the millions of biomedical publications is a challenging task.  ...  Ontologies, such as the Cardiovascular Disease Ontology (CVDO), capture domain knowledge in a computational form and can provide context for gene/protein names as written in the literature.  ...  Acknowledgements Thanks to Tim Furmston for help with software and e-infrastructure, and to the anonymous reviewers for their useful comments. Funding  ... 
doi:10.1186/s13326-018-0181-1 pmid:29650041 pmcid:PMC5896136 fatcat:rnyqpxihlralfcs7c5wxa5aaci

Ontology Knowledge Mining for Ontology Alignment

Rihab Idoudi, Karim Saheb Ettabaa, Basel Solaiman, Kamel Hamrouni
2016 International Journal of Computational Intelligence Systems  
The proposed approach has been tested over the OAEI benchmark dataset and some real mammographic ontologies since this work is a part of CMCU project for Mammographic images analysis for Assistance Diagnostic  ...  The system performs good results in the terms of precision and recall with respect to other alignment system.  ...  Where Sc(c 1 , 1 )denotes the descendants and generalizing of the concept c in the ontology , and Sc(c , ) refers to the descendants and generalizing of the concept c in the ontology .  ... 
doi:10.1080/18756891.2016.1237187 fatcat:3n7usmjidzdjzesxw6xx37cj34

Chapter 9: Analyses Using Disease Ontologies

Nigam H. Shah, Tyler Cole, Mark A. Musen, Fran Lewitter, Maricel Kann
2012 PLoS Computational Biology  
We also thank Paea LePendu for assistance in creating solutions to the exercises.  ...  Acknowledgments We acknowledge use of the publicly available GO Term Finder server at http://go.princeton. edu/cgi-bin/GOTermFinder.  ...  The textual descriptions included the protein name, gene name, general descriptions of the function and catalytic activity as well as keywords and GO terms.  ... 
doi:10.1371/journal.pcbi.1002827 pmid:23300417 pmcid:PMC3531278 fatcat:c5bgcwhcmbffzcqsox4el6wkaa

THEA: ontology-driven analysis of microarray data

C. Pasquier, F. Girardot, K. Jevardat de Fombelle, R. Christen
2004 Bioinformatics  
or automatically generate meaningful generalizations according to statistical criteria (data mining).  ...  Once microarray data are quantified, normalized and classified, the analysis phase is essentially a manual and subjective task based on visual inspection of classes in the light of the vast amount of information  ...  This method has a tendency to name clusters with very generic terms.  ... 
doi:10.1093/bioinformatics/bth295 pmid:15130932 fatcat:ld26jmjo3zakrmi2q2hiw3orte

The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia

Satoshi Mizuno, Soichi Ogishima, Hidekazu Nishigori, Daniel G. Jamieson, Karin Verspoor, Hiroshi Tanaka, Nobuo Yaegashi, Jun Nakaya, Anne Croy
2016 PLoS ONE  
The PEO incorporates a wide range of key concepts and terms of PE from clinical and biomedical research in structuring the knowledge base that is specific to PE; therefore, PEO is expected to enhance PE-specific  ...  We call this pre-eclampsia ontology "PEO". To achieve interoperability with other ontologies, the core structure of PEO was compliant with the hierarchy of the Basic Formal Ontology (BFO).  ...  This work was supported by a Grant-in-Aid for Scientific Research from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) of Japan.  ... 
doi:10.1371/journal.pone.0162828 pmid:27788142 pmcid:PMC5082890 fatcat:fktpk77t2fdmxni5w2absceacu

The Renal Gene Ontology Annotation Initiative

Yasmin Alam-Faruque, Emily C. Dimmer, Rachael P. Huntley, Claire O'Donovan, Peter Scambler, Rolf Apweiler
2010 Organogenesis  
T he Gene Ontology (GO) resource provides dynamic controlled vocabularies to aid in the description of the functional attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology  ...  This report outlines the aims of this initiative and explains how the renal community can become involved to help improve the availability, quality and quantity of GO terms and their association to specific  ...  We would like to thank the GO editorial team, Bijay Jassal from Reactome and the members of the Edinburgh team of the GUDMAP Consortium.  ... 
doi:10.4161/org.6.2.11294 pmid:20885853 pmcid:PMC2901810 fatcat:svavfpz4yzbixk4jbhu4oatsum

Ontology learning from text

Wilson Wong, Wei Liu, Mohammed Bennamoun
2012 ACM Computing Surveys  
The explosion of textual information on the Read/Write Web coupled with the increasing demand for ontologies to power the Semantic Web have made (semi-)automatic ontology learning from text a very promising  ...  Ontologies are often viewed as the answer to the need for interoperable semantics in modern information systems.  ...  Outputs and Tasks in Ontology Learning There are five types of output in ontology learning, namely, terms, concepts, taxonomic relations, non-taxonomic relations, and axioms.  ... 
doi:10.1145/2333112.2333115 fatcat:4uo5bazvivh3fpbxj7yf4yoe2u

Toxicology ontology perspectives

Barry Hardy
2012 ALTEX: Alternatives to Animal Experimentation  
OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources.  ...  Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated  ...  implementation of QSARs (Quantitative Structure-Activity Relationships) for toxicology, Project Reference Number Health- F5-2008-200787 (2008-2011). the research leading to these results has received  ... 
doi:10.14573/altex.2012.2.139 pmid:22562487 fatcat:ixzxgpvnbvd2peamgwe2loy5ge
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