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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Big-data-based edge biomarkers: study on dynamical drug sensitivity and resistance in individuals
TL;DR: A comprehensive review on big-data-based edge biomarkers for complex diseases in an individual patient, which are defined as biomarkers based on network information and high-dimensional data, and a case study on analyzing the temporal expression data from a malaria vaccine trial by big- data-basededge biomarkers from module network rewiring-analysis.
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Association of a Reproducible Epigenetic Risk Profile for Schizophrenia With Brain Methylation and Function
Junfang Chen,Zhenxiang Zang,Urs Braun,Kristina Schwarz,Anais Harneit,Thomas Kremer,Ren Ma,Janina I. Schweiger,Carolin Moessnang,Lena S. Geiger,Han Cao,Franziska Degenhardt,Markus M. Nöthen,Markus M. Nöthen,Heike Tost,Andreas Meyer-Lindenberg,Emanuel Schwarz +16 more
TL;DR: A reproducible blood DNA-methylation signature specific for schizophrenia was identified that was correlated with altered functional DLPFC-HC coupling during working memory and mapped to methylation differences found in DLP FC postmortem samples.
Journal ArticleDOI
Identification of minimal eukaryotic introns through GeneBase, a user-friendly tool for parsing the NCBI Gene databank
Allison Piovesan,Maria Caracausi,Marco Ricci,Pierluigi Strippoli,Lorenza Vitale,Maria Chiara Pelleri +5 more
TL;DR: GeneBase, a full parser of the National Center for Biotechnology Information (NCBI) Gene database, is developed, which generates a fully structured local database with an intuitive user-friendly graphic interface for personal computers.
Journal ArticleDOI
Activation of Nrf2 by Phloretin Attenuates Palmitic Acid-Induced Endothelial Cell Oxidative Stress via AMPK-Dependent Signaling.
Qing Yang,Lin Han,Jie Li,Han Xu,Xinfeng Liu,Xinyu Wang,Chuanying Pan,Chuzhao Lei,Hong Chen,Xianyong Lan +9 more
TL;DR: The findings reveal that phloretin attenuates PA-induced oxidative stress in HUVECs via the AMPK/Nrf2 antioxidative pathway and restored the loss of mitochondrial membrane potential (MMP).
Journal ArticleDOI
Identification of key genes and pathways in renal cell carcinoma through expression profiling data.
TL;DR: This study suggests that several crucial genes including CAV1,CAV2, GNAI1, GPSM2, and GNAO1 and pathways may play key roles in RCC progression.
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.
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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.
Related Papers (5)
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