Aber-OWL: a framework for ontology-based data access in biology.
TLDR
In this paper, the ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL).Abstract:
Background
Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning.read more
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Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.
Edison Ong,Zuoshuang Xiang,Bin Zhao,Yue Liu,Yu Lin,Jie Zheng,Christopher J. Mungall,Mélanie Courtot,Alan Ruttenberg,Yongqun He +9 more
TL;DR: Ontobee is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms and is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (OBO) library.
Journal ArticleDOI
AgroPortal: A vocabulary and ontology repository for agronomy
Clement Jonquet,Anne Toulet,Elizabeth Arnaud,Sophie Aubin,Esther Dzale Yeumo,Vincent Emonet,John Graybeal,Marie-Angélique Laporte,Mark A. Musen,Valeria Pesce,Pierre Larmande +10 more
TL;DR: The AgroPortal project re-uses the biomedical domain's semantic tools and insights to serve agronomy, but also food, plant, and biodiversity sciences, and offers a portal that features ontology hosting, search, versioning, visualization, comment, and recommendation; enables semantic annotation; stores and exploits ontology alignments; and enables interoperation with the semantic web.
Journal ArticleDOI
The anatomy of phenotype ontologies: principles, properties and applications.
TL;DR: The development and products of the ontological approach to phenotype capture, the formal content of phenotype ontologies and how their content can be used computationally are described.
Journal ArticleDOI
OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.
TL;DR: In this article, a method, OPA2Vec, is proposed to generate vector representations of biological entities in ontologies by combining formal ontology axioms and annotation axiom from the ontology meta-data.
Journal ArticleDOI
NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation
Marcos Martínez-Romero,Clement Jonquet,Clement Jonquet,Martin J. O'Connor,John Graybeal,Alejandro Pazos,Mark A. Musen +6 more
TL;DR: A new version of the NCBO Ontology Recommender, which suggests relevant ontologies for annotating biomedical text data, combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability and usefulness.
References
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Gene Ontology: tool for the unification of biology
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TL;DR: This work describes the OBO Foundry initiative and provides guidelines for those who might wish to become involved and describes an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality.
Ajax: A New Approach to Web Applications
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Relations in biomedical ontologies
Barry Smith,Barry Smith,Werner Ceusters,Bert R. E. Klagges,Jacob Köhler,Anand Kumar,Jane Lomax,Christopher J. Mungall,Fabian Neuhaus,Alan L. Rector,Cornelius Rosse +10 more
TL;DR: A methodology for providing consistent and unambiguous formal definitions of the relational expressions used in biomedical ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation is advanced.
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