Literature DB >> 20226267

Evolution of the Sequence Ontology terms and relationships.

Christopher J Mungall1, Colin Batchelor, Karen Eilbeck.   

Abstract

The Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both genomic and derived sequence. The SO is working within the guidelines of the OBO Foundry to provide interoperability between SO and the other related OBO ontologies. Here, we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence.
Copyright © 2010 Elsevier Inc. All rights reserved.

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Year:  2010        PMID: 20226267      PMCID: PMC3052763          DOI: 10.1016/j.jbi.2010.03.002

Source DB:  PubMed          Journal:  J Biomed Inform        ISSN: 1532-0464            Impact factor:   6.317


  14 in total

1.  Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.

Authors:  M Ashburner; C A Ball; J A Blake; D Botstein; H Butler; J M Cherry; A P Davis; K Dolinski; S S Dwight; J T Eppig; M A Harris; D P Hill; L Issel-Tarver; A Kasarskis; S Lewis; J C Matese; J E Richardson; M Ringwald; G M Rubin; G Sherlock
Journal:  Nat Genet       Date:  2000-05       Impact factor: 38.330

2.  Biodynamic ontology: applying BFO in the biomedical domain.

Authors:  Pierre Grenon; Barry Smith; Louis Goldberg
Journal:  Stud Health Technol Inform       Date:  2004

3.  The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration.

Authors:  Barry Smith; Michael Ashburner; Cornelius Rosse; Jonathan Bard; William Bug; Werner Ceusters; Louis J Goldberg; Karen Eilbeck; Amelia Ireland; Christopher J Mungall; Neocles Leontis; Philippe Rocca-Serra; Alan Ruttenberg; Susanna-Assunta Sansone; Richard H Scheuermann; Nigam Shah; Patricia L Whetzel; Suzanna Lewis
Journal:  Nat Biotechnol       Date:  2007-11       Impact factor: 54.908

4.  The RNA Ontology Consortium: an open invitation to the RNA community.

Authors:  Neocles B Leontis; Russ B Altman; Helen M Berman; Steven E Brenner; James W Brown; David R Engelke; Stephen C Harvey; Stephen R Holbrook; Fabrice Jossinet; Suzanna E Lewis; François Major; David H Mathews; Jane S Richardson; James R Williamson; Eric Westhof
Journal:  RNA       Date:  2006-02-16       Impact factor: 4.942

5.  PNA hybridizes to complementary oligonucleotides obeying the Watson-Crick hydrogen-bonding rules.

Authors:  M Egholm; O Buchardt; L Christensen; C Behrens; S M Freier; D A Driver; R H Berg; S K Kim; B Norden; P E Nielsen
Journal:  Nature       Date:  1993-10-07       Impact factor: 49.962

6.  A Chado case study: an ontology-based modular schema for representing genome-associated biological information.

Authors:  Christopher J Mungall; David B Emmert
Journal:  Bioinformatics       Date:  2007-07-01       Impact factor: 6.937

7.  The Sequence Ontology: a tool for the unification of genome annotations.

Authors:  Karen Eilbeck; Suzanna E Lewis; Christopher J Mungall; Mark Yandell; Lincoln Stein; Richard Durbin; Michael Ashburner
Journal:  Genome Biol       Date:  2005-04-29       Impact factor: 13.583

8.  Relations in biomedical ontologies.

Authors:  Barry Smith; Werner Ceusters; Bert Klagges; Jacob Köhler; Anand Kumar; Jane Lomax; Chris Mungall; Fabian Neuhaus; Alan L Rector; Cornelius Rosse
Journal:  Genome Biol       Date:  2005-04-28       Impact factor: 13.583

9.  The ontology of biological sequences.

Authors:  Robert Hoehndorf; Janet Kelso; Heinrich Herre
Journal:  BMC Bioinformatics       Date:  2009-11-18       Impact factor: 3.169

10.  Framework for a protein ontology.

Authors:  Darren A Natale; Cecilia N Arighi; Winona C Barker; Judith Blake; Ti-Cheng Chang; Zhangzhi Hu; Hongfang Liu; Barry Smith; Cathy H Wu
Journal:  BMC Bioinformatics       Date:  2007-11-27       Impact factor: 3.169

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  47 in total

1.  Ontological realism: A methodology for coordinated evolution of scientific ontologies.

Authors:  Barry Smith; Werner Ceusters
Journal:  Appl Ontol       Date:  2010-11-15       Impact factor: 1.115

2.  GMO Genetic Elements Thesaurus (GMO-GET): a controlled vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms.

Authors:  Paulien Adamse; Emilie Dagand; Karen Bohmert-Tatarev; Daniela Wahler; Manoela Miranda; Esther J Kok; Joachim Bendiek
Journal:  BMC Bioinformatics       Date:  2021-02-05       Impact factor: 3.169

3.  GIDL: a rule based expert system for GenBank Intelligent Data Loading into the Molecular Biodiversity Database.

Authors:  Paolo Pannarale; Domenico Catalano; Giorgio De Caro; Giorgio Grillo; Pietro Leo; Graziano Pappadà; Francesco Rubino; Gaetano Scioscia; Flavio Licciulli
Journal:  BMC Bioinformatics       Date:  2012-03-28       Impact factor: 3.169

4.  A common layer of interoperability for biomedical ontologies based on OWL EL.

Authors:  Robert Hoehndorf; Michel Dumontier; Anika Oellrich; Sarala Wimalaratne; Dietrich Rebholz-Schuhmann; Paul Schofield; Georgios V Gkoutos
Journal:  Bioinformatics       Date:  2011-02-21       Impact factor: 6.937

5.  Ontologies for clinical and translational research: Introduction.

Authors:  Barry Smith; Richard H Scheuermann
Journal:  J Biomed Inform       Date:  2011-01-15       Impact factor: 6.317

6.  Principles and Recommendations for Standardizing the Use of the Next-Generation Sequencing Variant File in Clinical Settings.

Authors:  Ira M Lubin; Nazneen Aziz; Lawrence J Babb; Dennis Ballinger; Himani Bisht; Deanna M Church; Shaun Cordes; Karen Eilbeck; Fiona Hyland; Lisa Kalman; Melissa Landrum; Edward R Lockhart; Donna Maglott; Gabor Marth; John D Pfeifer; Heidi L Rehm; Somak Roy; Zivana Tezak; Rebecca Truty; Mollie Ullman-Cullere; Karl V Voelkerding; Elizabeth A Worthey; Alexander W Zaranek; Justin M Zook
Journal:  J Mol Diagn       Date:  2017-03-18       Impact factor: 5.568

7.  Tutorial on Protein Ontology Resources.

Authors:  Cecilia N Arighi; Harold Drabkin; Karen R Christie; Karen E Ross; Darren A Natale
Journal:  Methods Mol Biol       Date:  2017

8.  Preserving sequence annotations across reference sequences.

Authors:  Zuotian Tatum; Marco Roos; Andrew P Gibson; Peter Em Taschner; Mark Thompson; Erik A Schultes; Jeroen Fj Laros
Journal:  J Biomed Semantics       Date:  2014-06-03

9.  Relations as patterns: bridging the gap between OBO and OWL.

Authors:  Robert Hoehndorf; Anika Oellrich; Michel Dumontier; Janet Kelso; Dietrich Rebholz-Schuhmann; Heinrich Herre
Journal:  BMC Bioinformatics       Date:  2010-08-31       Impact factor: 3.169

Review 10.  Calling International Rescue: knowledge lost in literature and data landslide!

Authors:  Teresa K Attwood; Douglas B Kell; Philip McDermott; James Marsh; Steve R Pettifer; David Thorne
Journal:  Biochem J       Date:  2009-12-10       Impact factor: 3.857

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