Publications by authors named "Christopher J Mungall"

87Publications

A Logical Model of Homology for Comparative Biology.

Syst Biol 2020 03;69(2):345-362

Department of Biology and School of Information and Library Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3280, USA.

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http://dx.doi.org/10.1093/sysbio/syz067DOI Listing
March 2020

ROBOT: A Tool for Automating Ontology Workflows.

BMC Bioinformatics 2019 Jul 29;20(1):407. Epub 2019 Jul 29.

Knocean Inc., Toronto, Ontario, Canada.

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http://dx.doi.org/10.1186/s12859-019-3002-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6664714PMC
July 2019

The Plant Ontology Facilitates Comparisons of Plant Development Stages Across Species.

Front Plant Sci 2019 4;10:631. Epub 2019 Jun 4.

Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States.

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http://dx.doi.org/10.3389/fpls.2019.00631DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6558174PMC
June 2019

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability.

Database (Oxford) 2018 01;2018

La Jolla Institute for Allergy and Immunology, Division of Vaccine Discovery and Center for Emerging Diseases and Biodefense, 9420 Athena Circle, La Jolla, CA 92037, USA.

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http://dx.doi.org/10.1093/database/bax105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5819722PMC
January 2018

From SNOMED CT to Uberon: Transferability of evaluation methodology between similarly structured ontologies.

Artif Intell Med 2017 06 19;79:9-14. Epub 2017 May 19.

Computer Science Department, New Jersey Institute of Technology, Newark, NJ, USA.

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http://dx.doi.org/10.1016/j.artmed.2017.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559337PMC
June 2017

BioMake: a GNU make-compatible utility for declarative workflow management.

Bioinformatics 2017 Nov;33(21):3502-3504

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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https://academic.oup.com/bioinformatics/article/33/21/3502/3
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http://dx.doi.org/10.1093/bioinformatics/btx306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860158PMC
November 2017

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

J Biomed Semantics 2016 Sep 23;7(1):57. Epub 2016 Sep 23.

Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.

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http://dx.doi.org/10.1186/s13326-016-0097-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5035502PMC
September 2016

Modeling biochemical pathways in the gene ontology.

Database (Oxford) 2016 1;2016. Epub 2016 Sep 1.

The Jackson Laboratory, Bar Harbor, ME 04609, USA.

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http://dx.doi.org/10.1093/database/baw126DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5009323PMC
November 2017

A Whole-Genome Analysis Framework for Effective Identification of Pathogenic Regulatory Variants in Mendelian Disease.

Am J Hum Genet 2016 09 25;99(3):595-606. Epub 2016 Aug 25.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestr. 63-73, 14195 Berlin, Germany; Berlin-Brandenburg Center for Regenerative Therapies (BCRT), Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute for Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse, 14195 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2016.07.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011059PMC
September 2016

High-performance web services for querying gene and variant annotation.

Genome Biol 2016 05 6;17(1):91. Epub 2016 May 6.

Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA.

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http://dx.doi.org/10.1186/s13059-016-0953-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4858870PMC
May 2016

Capturing phenotypes for precision medicine.

Cold Spring Harb Mol Case Stud 2015 Oct;1(1):a000372

Oregon Health and Science University, Portland, Oregon 97239, USA.

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http://dx.doi.org/10.1101/mcs.a000372DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4850887PMC
October 2015

INVESTIGATING THE IMPORTANCE OF ANATOMICAL HOMOLOGY FOR CROSS-SPECIES PHENOTYPE COMPARISONS USING SEMANTIC SIMILARITY. Accepted at Pacific Symposium on Biocomputing, 2016.

Pac Symp Biocomput 2016 ;21:132-43

Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA,

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October 2016

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease.

Am J Hum Genet 2015 Jul 25;97(1):111-24. Epub 2015 Jun 25.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, 14195 Berlin, Germany; Berlin Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany; Institute of Bioinformatics, Department of Mathematics and Computer Science, Freie Universität Berlin, Takustrasse 9, 14195 Berlin, Germany. Electronic address:

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http://dx.doi.org/10.1016/j.ajhg.2015.05.020DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4572507PMC
July 2015

Disease insights through cross-species phenotype comparisons.

Mamm Genome 2015 Oct 20;26(9-10):548-55. Epub 2015 Jun 20.

Skarnes Faculty Group, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK.

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http://dx.doi.org/10.1007/s00335-015-9577-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4602072PMC
October 2015

Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells.

Authors:
Erik Arner Carsten O Daub Kristoffer Vitting-Seerup Robin Andersson Berit Lilje Finn Drabløs Andreas Lennartsson Michelle Rönnerblad Olga Hrydziuszko Morana Vitezic Tom C Freeman Ahmad M N Alhendi Peter Arner Richard Axton J Kenneth Baillie Anthony Beckhouse Beatrice Bodega James Briggs Frank Brombacher Margaret Davis Michael Detmar Anna Ehrlund Mitsuhiro Endoh Afsaneh Eslami Michela Fagiolini Lynsey Fairbairn Geoffrey J Faulkner Carmelo Ferrai Malcolm E Fisher Lesley Forrester Daniel Goldowitz Reto Guler Thomas Ha Mitsuko Hara Meenhard Herlyn Tomokatsu Ikawa Chieko Kai Hiroshi Kawamoto Levon M Khachigian S Peter Klinken Soichi Kojima Haruhiko Koseki Sarah Klein Niklas Mejhert Ken Miyaguchi Yosuke Mizuno Mitsuru Morimoto Kelly J Morris Christine Mummery Yutaka Nakachi Soichi Ogishima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry Ovchinnikov Robert Passier Margaret Patrikakis Ana Pombo Xian-Yang Qin Sugata Roy Hiroki Sato Suzana Savvi Alka Saxena Anita Schwegmann Daisuke Sugiyama Rolf Swoboda Hiroshi Tanaka Andru Tomoiu Louise N Winteringham Ernst Wolvetang Chiyo Yanagi-Mizuochi Misako Yoneda Susan Zabierowski Peter Zhang Imad Abugessaisa Nicolas Bertin Alexander D Diehl Shiro Fukuda Masaaki Furuno Jayson Harshbarger Akira Hasegawa Fumi Hori Sachi Ishikawa-Kato Yuri Ishizu Masayoshi Itoh Tsugumi Kawashima Miki Kojima Naoto Kondo Marina Lizio Terrence F Meehan Christopher J Mungall Mitsuyoshi Murata Hiromi Nishiyori-Sueki Serkan Sahin Sayaka Nagao-Sato Jessica Severin Michiel J L de Hoon Jun Kawai Takeya Kasukawa Timo Lassmann Harukazu Suzuki Hideya Kawaji Kim M Summers Christine Wells David A Hume Alistair R R Forrest Albin Sandelin Piero Carninci Yoshihide Hayashizaki

Science 2015 Feb 12;347(6225):1010-4. Epub 2015 Feb 12.

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http://dx.doi.org/10.1126/science.1259418DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4681433PMC
February 2015

Finding our way through phenotypes.

PLoS Biol 2015 Jan 6;13(1):e1002033. Epub 2015 Jan 6.

Department of Biology, University of South Dakota, Vermillion, South Dakota, United States of America.

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http://dx.doi.org/10.1371/journal.pbio.1002033DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285398PMC
January 2015

Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data.

Nucleic Acids Res 2015 Jan 27;43(Database issue):D1071-8. Epub 2014 Oct 27.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA

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http://nar.oxfordjournals.org/content/43/D1/D1071.full.pdf
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http://nar.oxfordjournals.org/lookup/doi/10.1093/nar/gku1011
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http://dx.doi.org/10.1093/nar/gku1011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383880PMC
January 2015

Clinical interpretation of CNVs with cross-species phenotype data.

J Med Genet 2014 Nov 3;51(11):766-772. Epub 2014 Oct 3.

Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin,Berlin, Germany.

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http://dx.doi.org/10.1136/jmedgenet-2014-102633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501634PMC
November 2014

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology.

J Biomed Semantics 2014 11;5:34. Epub 2014 Aug 11.

Library and Department of Medical Informatics & Epidemiology, Oregon Health & Science University, Portland, OR, USA.

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http://dx.doi.org/10.1186/2041-1480-5-34DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4137724PMC
August 2014

Standardized description of scientific evidence using the Evidence Ontology (ECO).

Database (Oxford) 2014 22;2014. Epub 2014 Jul 22.

Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USAInstitute for Genome Sciences, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD 21201, USA, Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, Saccharomyces Genome Database, Department of Genetics, Stanford University, Stanford, CA 94305, USA, Computational Biology and Bioinformatics, The Jackson Laboratory, Bar Harbor, ME 04609, USA, European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD UK, Department of Epidemiology, University of Maryland School of Medicine, Baltimore, MD 21201, USA and Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA.

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http://dx.doi.org/10.1093/database/bau075DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4105709PMC
February 2015

A promoter-level mammalian expression atlas.

Authors:
Alistair R R Forrest Hideya Kawaji Michael Rehli J Kenneth Baillie Michiel J L de Hoon Vanja Haberle Timo Lassmann Ivan V Kulakovskiy Marina Lizio Masayoshi Itoh Robin Andersson Christopher J Mungall Terrence F Meehan Sebastian Schmeier Nicolas Bertin Mette Jørgensen Emmanuel Dimont Erik Arner Christian Schmidl Ulf Schaefer Yulia A Medvedeva Charles Plessy Morana Vitezic Jessica Severin Colin A Semple Yuri Ishizu Robert S Young Margherita Francescatto Intikhab Alam Davide Albanese Gabriel M Altschuler Takahiro Arakawa John A C Archer Peter Arner Magda Babina Sarah Rennie Piotr J Balwierz Anthony G Beckhouse Swati Pradhan-Bhatt Judith A Blake Antje Blumenthal Beatrice Bodega Alessandro Bonetti James Briggs Frank Brombacher A Maxwell Burroughs Andrea Califano Carlo V Cannistraci Daniel Carbajo Yun Chen Marco Chierici Yari Ciani Hans C Clevers Emiliano Dalla Carrie A Davis Michael Detmar Alexander D Diehl Taeko Dohi Finn Drabløs Albert S B Edge Matthias Edinger Karl Ekwall Mitsuhiro Endoh Hideki Enomoto Michela Fagiolini Lynsey Fairbairn Hai Fang Mary C Farach-Carson Geoffrey J Faulkner Alexander V Favorov Malcolm E Fisher Martin C Frith Rie Fujita Shiro Fukuda Cesare Furlanello Masaaki Furino Jun-ichi Furusawa Teunis B Geijtenbeek Andrew P Gibson Thomas Gingeras Daniel Goldowitz Julian Gough Sven Guhl Reto Guler Stefano Gustincich Thomas J Ha Masahide Hamaguchi Mitsuko Hara Matthias Harbers Jayson Harshbarger Akira Hasegawa Yuki Hasegawa Takehiro Hashimoto Meenhard Herlyn Kelly J Hitchens Shannan J Ho Sui Oliver M Hofmann Ilka Hoof Furni Hori Lukasz Huminiecki Kei Iida Tomokatsu Ikawa Boris R Jankovic Hui Jia Anagha Joshi Giuseppe Jurman Bogumil Kaczkowski Chieko Kai Kaoru Kaida Ai Kaiho Kazuhiro Kajiyama Mutsumi Kanamori-Katayama Artem S Kasianov Takeya Kasukawa Shintaro Katayama Sachi Kato Shuji Kawaguchi Hiroshi Kawamoto Yuki I Kawamura Tsugumi Kawashima Judith S Kempfle Tony J Kenna Juha Kere Levon M Khachigian Toshio Kitamura S Peter Klinken Alan J Knox Miki Kojima Soichi Kojima Naoto Kondo Haruhiko Koseki Shigeo Koyasu Sarah Krampitz Atsutaka Kubosaki Andrew T Kwon Jeroen F J Laros Weonju Lee Andreas Lennartsson Kang Li Berit Lilje Leonard Lipovich Alan Mackay-Sim Ri-ichiroh Manabe Jessica C Mar Benoit Marchand Anthony Mathelier Niklas Mejhert Alison Meynert Yosuke Mizuno David A de Lima Morais Hiromasa Morikawa Mitsuru Morimoto Kazuyo Moro Efthymios Motakis Hozumi Motohashi Christine L Mummery Mitsuyoshi Murata Sayaka Nagao-Sato Yutaka Nakachi Fumio Nakahara Toshiyuki Nakamura Yukio Nakamura Kenichi Nakazato Erik van Nimwegen Noriko Ninomiya Hiromi Nishiyori Shohei Noma Shohei Noma Tadasuke Noazaki Soichi Ogishima Naganari Ohkura Hiroko Ohimiya Hiroshi Ohno Mitsuhiro Ohshima Mariko Okada-Hatakeyama Yasushi Okazaki Valerio Orlando Dmitry A Ovchinnikov Arnab Pain Robert Passier Margaret Patrikakis Helena Persson Silvano Piazza James G D Prendergast Owen J L Rackham Jordan A Ramilowski Mamoon Rashid Timothy Ravasi Patrizia Rizzu Marco Roncador Sugata Roy Morten B Rye Eri Saijyo Antti Sajantila Akiko Saka Shimon Sakaguchi Mizuho Sakai Hiroki Sato Suzana Savvi Alka Saxena Claudio Schneider Erik A Schultes Gundula G Schulze-Tanzil Anita Schwegmann Thierry Sengstag Guojun Sheng Hisashi Shimoji Yishai Shimoni Jay W Shin Christophe Simon Daisuke Sugiyama Takaai Sugiyama Masanori Suzuki Naoko Suzuki Rolf K Swoboda Peter A C 't Hoen Michihira Tagami Naoko Takahashi Jun Takai Hiroshi Tanaka Hideki Tatsukawa Zuotian Tatum Mark Thompson Hiroo Toyodo Tetsuro Toyoda Elvind Valen Marc van de Wetering Linda M van den Berg Roberto Verado Dipti Vijayan Ilya E Vorontsov Wyeth W Wasserman Shoko Watanabe Christine A Wells Louise N Winteringham Ernst Wolvetang Emily J Wood Yoko Yamaguchi Masayuki Yamamoto Misako Yoneda Yohei Yonekura Shigehiro Yoshida Susan E Zabierowski Peter G Zhang Xiaobei Zhao Silvia Zucchelli Kim M Summers Harukazu Suzuki Carsten O Daub Jun Kawai Peter Heutink Winston Hide Tom C Freeman Boris Lenhard Vladimir B Bajic Martin S Taylor Vsevolod J Makeev Albin Sandelin David A Hume Piero Carninci Yoshihide Hayashizaki

Nature 2014 Mar;507(7493):462-70

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http://dx.doi.org/10.1038/nature13182DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4529748PMC
March 2014

TermGenie - a web-application for pattern-based ontology class generation.

J Biomed Semantics 2014 11;5:48. Epub 2014 Dec 11.

Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, CA 94720 USA.

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http://dx.doi.org/10.1186/2041-1480-5-48DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4417543PMC
May 2015

The environment ontology: contextualising biological and biomedical entities.

J Biomed Semantics 2013 Dec 11;4(1):43. Epub 2013 Dec 11.

HGF-MPG Research Group on Deep-Sea Ecology and Technology, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Am Handelshafen 12, Bremerhaven 27570, Germany.

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http://dx.doi.org/10.1186/2041-1480-4-43DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3904460PMC
December 2013

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D966-74. Epub 2013 Nov 11.

Institute for Medical Genetics and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Berlin-Brandenburg Center for Regenerative Therapies, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany, Lawrence Berkeley National Laboratory, Mail Stop 84R0171, Berkeley, CA 94720, USA, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SA, UK, Department of Medical Genetics, Cambridge University Addenbrooke's Hospital, Cambridge CB2 2QQ, UK, Université Paul Sabatier, Faculté de Chirurgie Dentaire, CHU Toulouse, France, Centre for Genomic Medicine, Central Manchester University Hospitals NHS Foundation Trust, Manchester Academic Health Sciences Centre (MAHSC), Manchester, UK, Centre for Genomic Medicine, Institute of Human Development, Faculty of Medical and Human Sciences, University of Manchester, MAHSC, Manchester M13 9WL, UK, Institute of Genetic Medicine. Newcastle University, Central Parkway, Newcastle upon Tyne, NE1 3BZ, UK, Department of Computer Science, University of Toronto, Ontario, Canada, Centre for Computational Medicine, Hospital for Sick Children, Toronto, Ontario, Canada, Department of Clinical Genetics, Leeds Teaching Hospitals NHS Trust, Leeds LS2 9NS, UK, MRC Human Genetics Unit, MRC Institute of Genetic and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, The Jackson Laboratory, Bar Harbor, ME 04609, USA, Center for Molecular and Vascular Biology, University of Leuven, Belgium, Department of Neuropediatrics, University Medical Center Schleswig-Holstein, Kiel Campus, 24105 Kiel, Germany, NE Thames Genetics Service, Great Ormond Street Hospital, London WC1N 3JH, UK, Drexel University College of Medicine, Philadelphia, PA 19102, USA, Department of Haematology, University of Cambridge and NHS Blood and Transplant Cambridge, CB2 0PT Cambridge, UK, Autism and Developmental Medicine Institute, Geisinger Health System

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http://dx.doi.org/10.1093/nar/gkt1026DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965098PMC
January 2014

Improved exome prioritization of disease genes through cross-species phenotype comparison.

Genome Res 2014 Feb 25;24(2):340-8. Epub 2013 Oct 25.

Institute for Medical and Human Genetics, Charité-Universitätsmedizin Berlin, Augustenburger Platz 1, 13353 Berlin, Germany;

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http://dx.doi.org/10.1101/gr.160325.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3912424PMC
February 2014

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments.

J Biomed Semantics 2013 Oct 7;4(1):20. Epub 2013 Oct 7.

European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.

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http://dx.doi.org/10.1186/2041-1480-4-20DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3852282PMC
October 2013

Ontology based molecular signatures for immune cell types via gene expression analysis.

BMC Bioinformatics 2013 Aug 30;14:263. Epub 2013 Aug 30.

Department of Neurology, University at Buffalo School of Medicine and Biomedical Sciences, 100 High Street, Buffalo, NY 14203, USA.

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http://dx.doi.org/10.1186/1471-2105-14-263DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3844401PMC
August 2013

A knowledge based approach to matching human neurodegenerative disease and animal models.

Front Neuroinform 2013 14;7. Epub 2013 May 14.

Department of Neurosciences, Center for Research in Biological Systems, University of California San Diego, San Diego, CA, USA.

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http://dx.doi.org/10.3389/fninf.2013.00007DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3653101PMC
May 2013

A strategy for building neuroanatomy ontologies.

Bioinformatics 2012 May 7;28(9):1262-9. Epub 2012 Mar 7.

Department of Genetics, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/bts113DOI Listing
May 2012

On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report.

PLoS Comput Biol 2012 16;8(2):e1002386. Epub 2012 Feb 16.

Division of Bioinformatics, Department of Preventive Medicine, University of Southern California, Los Angeles, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.1002386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280971PMC
June 2012

MouseFinder: Candidate disease genes from mouse phenotype data.

Hum Mutat 2012 May 16;33(5):858-66. Epub 2012 Mar 16.

Vertebrate Genomics Team, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://doi.wiley.com/10.1002/humu.22051
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http://dx.doi.org/10.1002/humu.22051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3327758PMC
May 2012

Uberon, an integrative multi-species anatomy ontology.

Genome Biol 2012 Jan 31;13(1):R5. Epub 2012 Jan 31.

Genomics Division, Lawrence Berkeley National Laboratory, 1 Cycltotron Road MS 64-121, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2012-13-1-r5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334586PMC
January 2012

Formalization of taxon-based constraints to detect inconsistencies in annotation and ontology development.

BMC Bioinformatics 2010 Oct 25;11:530. Epub 2010 Oct 25.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://bmcbioinformatics.biomedcentral.com/articles/10.1186/
Publisher Site
http://dx.doi.org/10.1186/1471-2105-11-530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3098089PMC
October 2010

Evolution of the Sequence Ontology terms and relationships.

J Biomed Inform 2011 Feb 10;44(1):87-93. Epub 2010 Mar 10.

Lawrence Berkeley National Laboratory, Mail Stop 64R0121, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.jbi.2010.03.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3052763PMC
February 2011

Integrating phenotype ontologies across multiple species.

Genome Biol 2010 Jan 8;11(1):R2. Epub 2010 Jan 8.

Genome Dynamics Department, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1186/gb-2010-11-1-r2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847714PMC
January 2010

Linking human diseases to animal models using ontology-based phenotype annotation.

PLoS Biol 2009 Nov 24;7(11):e1000247. Epub 2009 Nov 24.

Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.

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http://dx.doi.org/10.1371/journal.pbio.1000247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2774506PMC
November 2009

JBrowse: a next-generation genome browser.

Genome Res 2009 Sep 1;19(9):1630-8. Epub 2009 Jul 1.

Department of Bioengineering, University of California at Berkeley, Berkeley, California 94720, USA.

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http://dx.doi.org/10.1101/gr.094607.109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2752129PMC
September 2009

AmiGO: online access to ontology and annotation data.

Bioinformatics 2009 Jan 25;25(2):288-9. Epub 2008 Nov 25.

Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1093/bioinformatics/btn615DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2639003PMC
January 2009

Obol: integrating language and meaning in bio-ontologies.

Comp Funct Genomics 2004 ;5(6-7):509-20

HHMI, Department of Molecular and Cellular Biology, 142 Life Sciences Addition, University of California, Berkeley, CA 94720-3200, USA.

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http://dx.doi.org/10.1002/cfg.435DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2447432PMC
June 2010

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

Bioinformatics 2007 Jul;23(13):i337-46

Lawrence Berkeley National Laboratory, Lawrence Berkeley National Lab, Mail Stop 64R0121, Berkeley, CA 94720, USA.

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https://academic.oup.com/bioinformatics/article/23/13/i337/2
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http://dx.doi.org/10.1093/bioinformatics/btm189DOI Listing
July 2007

The Release 5.1 annotation of Drosophila melanogaster heterochromatin.

Science 2007 Jun;316(5831):1586-91

Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.

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http://dx.doi.org/10.1126/science.1139815DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2819280PMC
June 2007

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

Genome Biol 2005 29;6(5):R44. Epub 2005 Apr 29.

Department of Molecular and Cellular Biology, Life Sciences Addition, University of California, Berkeley, CA 94729-3200, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1175956PMC
May 2006