Gene ontology annotations and resources
Judith A. Blake,Mary E. Dolan,H. Drabkin,David P. Hill,Li N,D. Sitnikov,Susan M. Bridges,Shane C. Burgess,Teresia Buza,Fiona M. McCarthy,Divyaswetha Peddinti,Lakshmi Pillai,Seth Carbon,Heiko Dietze,Amelia Ireland,Suzanna E. Lewis,Christopher J. Mungall,Pascale Gaudet,Chrisholm Rl,Petra Fey,Warren A. Kibbe,S. Basu,Deborah A. Siegele,B. K. McIntosh,Daniel P. Renfro,Adrienne E. Zweifel,James C. Hu,Nicholas H. Brown,Susan Tweedie,Yasmin Alam-Faruque,Rolf Apweiler,A. Auchinchloss,Kristian B. Axelsen,Benoit Bely,M. C. Blatter,Bonilla C,Bouguerleret L,Emmanuel Boutet,Lionel Breuza,Alan Bridge,W. M. Chan,Gayatri Chavali,Elisabeth Coudert,E. Dimmer,Anne Estreicher,L Famiglietti,Marc Feuermann,Arnaud Gos,Nadine Gruaz-Gumowski,Hieta R,Hinz C,Chantal Hulo,Rachael P. Huntley,J. James,Florence Jungo,Guillaume Keller,Kati Laiho,Duncan Legge,P. Lemercier,Damien Lieberherr,Michele Magrane,Maria Jesus Martin,Patrick Masson,Mutowo-Muellenet P,Claire O'Donovan,Ivo Pedruzzi,Klemens Pichler,Diego Poggioli,Porras Millán P,Sylvain Poux,Catherine Rivoire,Bernd Roechert,Tony Sawford,Michel Schneider,Andre Stutz,Shyamala Sundaram,Michael Tognolli,Ioannis Xenarios,Foulgar R,Jane Lomax,Paola Roncaglia,Varsha K. Khodiyar,Ruth C. Lovering,Philippa J. Talmud,Marcus C. Chibucos,Giglio Mg,Hsin-Yu Chang,Sarah Hunter,Craig McAnulla,Alex L. Mitchell,Sangrador A,Stephan R,Midori A. Harris,Stephen G. Oliver,Kim Rutherford,Wood,Jürg Bähler,Antonia Lock,Paul J. Kersey,McDowall Dm,Daniel M. Staines,Melinda R. Dwinell,Mary Shimoyama,Stan Laulederkind,Tom Hayman,Shur-Jen Wang,Timothy F. Lowry,P D'Eustachio,Lisa Matthews,Rama Balakrishnan,Gail Binkley,J. M. Cherry,Maria C. Costanzo,Selina S. Dwight,Engel,Dianna G. Fisk,Benjamin C. Hitz,Eurie L. Hong,Kalpana Karra,Miyasato,Robert S. Nash,Julie Park,Marek S. Skrzypek,Shuai Weng,Edith D. Wong,Tanya Z. Berardini,Eva Huala,Huaiyu Mi,Paul Thomas,Juancarlos Chan,Ranjana Kishore,Paul W. Sternberg,Van Auken K,Doug Howe,Monte Westerfield +134 more
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TLDR
The Gene Ontology (GO) Consortium is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies and has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology.Abstract:
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.read more
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Tools for exploring mouse models of human disease
Melissa A. Haendel,Irene Papatheodorou,Anika Oellrich,Christopher J. Mungall,Nicole L. Washington,Suzanna E. Lewis,Peter N. Robinson,Damian Smedley +7 more
TL;DR: These tools are reviewed and it is shown how they can be applied in the identification of candidate genes and therapeutic targets as well as mouse models for mechanistic studies and drug validation.
Journal ArticleDOI
Creating an ignorance-base: Exploring known unknowns in the scientific literature
TL;DR: In this paper , a knowledge base of unknowns can be connected to ontologically grounded biomedical knowledge to accelerate research in the field of prenatal nutrition, which can help students, researchers, funders, and publishers better understand the state of our collective scientific ignorance (known unknowns).
Journal ArticleDOI
Cell death-related biomarker SLC2A1 has a significant role in prognosis prediction and immunotherapy efficacy evaluation in pan-cancer
TL;DR: In this paper , the authors evaluated the role of SLC2A1 in pan-cancer using the GEPIA2.0, TIMER 2.0 and UALCAN databases.
Book ChapterDOI
Biological and Medical Ontologies: PRotein Ontology (PRO)
Davide Chicco,Marco Masseroli +1 more
TL;DR: The protein ontology does not only provide a classification of protein-related products, but also furnishes semantic relationships between these entities, and links every protein product with popular databases and resources such as the Gene Ontology and UniProtKB.
Journal ArticleDOI
OUP accepted manuscript
TL;DR: The most recent version of the PASS2 database (pass2.7) as mentioned in this paper provides a new feature called absolutely conserved interactions (ACI) between residue backbones and side chains which are obtained by aligning protein structure networks using structure-guided sequence alignments of superfamilies.
References
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Journal ArticleDOI
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
TL;DR: The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing.
Journal ArticleDOI
The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration
Barry Smith,Michael Ashburner,Cornelius Rosse,Jonathan Bard,William J. Bug,Werner Ceusters,Louis J. Goldberg,Karen Eilbeck,Amelia Ireland,Christopher J. Mungall,Neocles B. Leontis,Philippe Rocca-Serra,Alan Ruttenberg,Susanna-Assunta Sansone,Richard H. Scheuermann,Nigam H. Shah,Patricia L. Whetzel,Suzanna E. Lewis +17 more
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.
Conflict of interest statement. None declared.
TL;DR: It is found that women over 50 are more likely to have a family history of diabetes, especially if they are obese, than women under the age of 50.
Journal ArticleDOI
ChEBI: a database and ontology for chemical entities of biological interest
Kirill Degtyarenko,Paula de Matos,Marcus Ennis,Janna Hastings,Martin Zbinden,Alan McNaught,Rafael Alcántara,Michael Darsow,Mickaël Guedj,Michael Ashburner +9 more
TL;DR: A dictionary of molecular entities focused on ‘small’ chemical compounds and an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified.
Journal ArticleDOI
The OWL API: A Java API for OWL ontologies
Matthew Horridge,Sean Bechhofer +1 more
TL;DR: The OWL API is a high level Application Programming Interface (API) for working with OWL ontologies that supports parsing and rendering in the syntaxes defined in the W3C specification; manipulation of ontological structures; and the use of reasoning engines.
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Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more