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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Journal ArticleDOI
Dynamic Proteomic Analysis of Pancreatic Mesenchyme Reveals Novel Factors That Enhance Human Embryonic Stem Cell to Pancreatic Cell Differentiation
Holger A. Russ,Limor Landsman,Christopher L. Moss,Roger Higdon,Renee L. Greer,Kelly A. Kaihara,Randy Salamon,Eugene Kolker,Matthias Hebrok +8 more
TL;DR: Evidence is provided that proteomic analysis of supporting tissues such as the pancreatic mesenchyme allows for the identification of potentially important factors guiding hESC to pancreas differentiation.
Book ChapterDOI
A Metagenomics Portal for a Democratized Sequencing World
Andreas Wilke,Elizabeth M. Glass,Elizabeth M. Glass,Daniela Bartels,Daniela Bartels,Jared M. Bischof,Jared M. Bischof,Daniel Braithwaite,Daniel Braithwaite,Mark D'Souza,Mark D'Souza,Wolfgang Gerlach,Wolfgang Gerlach,Travis Harrison,Travis Harrison,Kevin P. Keegan,Kevin P. Keegan,Hunter Matthews,Renzo Kottmann,Tobias Paczian,Tobias Paczian,Wei Tang,Wei Tang,William L. Trimble,William L. Trimble,Pelin Yilmaz,Jared Wilkening,Jared Wilkening,Narayan Desai,Narayan Desai,Folker Meyer,Folker Meyer +31 more
TL;DR: The changes from version 2 to version 3 include the addition of a dedicated gene calling stage using FragGenescan, clustering of predicted proteins at 90% identity, and the use of BLAT for the computation of similarities.
Journal ArticleDOI
PHI-base in 2022: a multi-species phenotype database for Pathogen-Host Interactions.
Martin Urban,Alayne Cuzick,James Seager,Valerie Wood,Kim Rutherford,Shilpa Yagwakote Venkatesh,Jashobanta Sahu,S Vijaylakshmi Iyer,Lokanath Khamari,Nishadi De Silva,Manuel Carbajo Martinez,Helder Pedro,Andrew D. Yates,Kim E. Hammond-Kosack +13 more
TL;DR: The Pathogen-Host Interactions Database (PHI-base) as discussed by the authors has manually curated experimentally verified pathogenicity, virulence and effector genes from fungal, bacterial and protist pathogens, which infect animal, plant, fish, insect and or fungal hosts.
Journal ArticleDOI
Whole-genome sequencing suggests mechanisms for 22q11.2 deletion-associated Parkinson's disease
Nancy J. Butcher,Nancy J. Butcher,Daniele Merico,Mehdi Zarrei,Lucas Ogura,Christian R. Marshall,Christian R. Marshall,Eva W.C. Chow,Eva W.C. Chow,Anthony E. Lang,Stephen W. Scherer,Stephen W. Scherer,Anne S. Bassett +12 more
TL;DR: The results of this first-ever pilot study of WGS in PD suggest that the cumulative burden of genome-wide sequence variants may contribute to expression of early-onset Parkinson’s disease in the presence of threshold-lowering dosage effects of a 22q11.2 deletion.
Journal ArticleDOI
Biophysical constraints on the evolution of tissue structure and function.
TL;DR: An extension of phylogenetic studies of protein interaction networks to take into account biophysical constraints to interaction imposed by tissues regulating these networks is outlined and defined explicitly as a means to track the evolution of tissue structure and function objectively.
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.
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