Literature DB >> 20427557

Phenotype ontologies for mouse and man: bridging the semantic gap.

Paul N Schofield1, Georgios V Gkoutos, Michael Gruenberger, John P Sundberg, John M Hancock.   

Abstract

A major challenge of the post-genomic era is coding phenotype data from humans and model organisms such as the mouse, to permit the meaningful translation of phenotype descriptions between species. This ability is essential if we are to facilitate phenotype-driven gene function discovery and empower comparative pathobiology. Here, we review the current state of the art for phenotype and disease description in mice and humans, and discuss ways in which the semantic gap between coding systems might be bridged to facilitate the discovery and exploitation of new mouse models of human diseases.

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Year:  2010        PMID: 20427557      PMCID: PMC2860848          DOI: 10.1242/dmm.002790

Source DB:  PubMed          Journal:  Dis Model Mech        ISSN: 1754-8403            Impact factor:   5.758


  65 in total

1.  Genomewide scan for linkage reveals evidence of several susceptibility loci for alopecia areata.

Authors:  Amalia Martinez-Mir; Abraham Zlotogorski; Derek Gordon; Lynn Petukhova; Jianhong Mo; T Conrad Gilliam; Douglas Londono; Chad Haynes; Jurg Ott; Maria Hordinsky; Krassimira Nanova; David Norris; Vera Price; Madeleine Duvic; Angela M Christiano
Journal:  Am J Hum Genet       Date:  2007-01-05       Impact factor: 11.025

2.  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

3.  The NCBI dbGaP database of genotypes and phenotypes.

Authors:  Matthew D Mailman; Michael Feolo; Yumi Jin; Masato Kimura; Kimberly Tryka; Rinat Bagoutdinov; Luning Hao; Anne Kiang; Justin Paschall; Lon Phan; Natalia Popova; Stephanie Pretel; Lora Ziyabari; Moira Lee; Yu Shao; Zhen Y Wang; Karl Sirotkin; Minghong Ward; Michael Kholodov; Kerry Zbicz; Jeffrey Beck; Michael Kimelman; Sergey Shevelev; Don Preuss; Eugene Yaschenko; Alan Graeff; James Ostell; Stephen T Sherry
Journal:  Nat Genet       Date:  2007-10       Impact factor: 38.330

4.  Mouse genome informatics (MGI) resources for pathology and toxicology.

Authors:  Janan T Eppig; Judith A Blake; Carol J Bult; Joel E Richardson; James A Kadin; Martin Ringwald
Journal:  Toxicol Pathol       Date:  2007-04       Impact factor: 1.902

5.  The mouse ascending: perspectives for human-disease models.

Authors:  Nadia Rosenthal; Steve Brown
Journal:  Nat Cell Biol       Date:  2007-09       Impact factor: 28.824

6.  A method exploiting syntactic patterns and the UMLS semantics for aligning biomedical ontologies: the case of OBO disease ontologies.

Authors:  Gwenaëlle Marquet; Jean Mosser; Anita Burgun
Journal:  Int J Med Inform       Date:  2007-05-22       Impact factor: 4.046

7.  EMPReSS: standardized phenotype screens for functional annotation of the mouse genome.

Authors:  S D M Brown; P Chambon; M Hrabé de Angelis
Journal:  Nat Genet       Date:  2005-11       Impact factor: 38.330

8.  The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes.

Authors:  Judy Sprague; Leyla Bayraktaroglu; Yvonne Bradford; Tom Conlin; Nathan Dunn; David Fashena; Ken Frazer; Melissa Haendel; Douglas G Howe; Jonathan Knight; Prita Mani; Sierra A T Moxon; Christian Pich; Sridhar Ramachandran; Kevin Schaper; Erik Segerdell; Xiang Shao; Amy Singer; Peiran Song; Brock Sprunger; Ceri E Van Slyke; Monte Westerfield
Journal:  Nucleic Acids Res       Date:  2007-11-08       Impact factor: 16.971

9.  The Mouse Genome Database (MGD): mouse biology and model systems.

Authors:  Carol J Bult; Janan T Eppig; James A Kadin; Joel E Richardson; Judith A Blake
Journal:  Nucleic Acids Res       Date:  2007-12-23       Impact factor: 16.971

10.  ChEBI: a database and ontology for chemical entities of biological interest.

Authors:  Kirill Degtyarenko; Paula de Matos; Marcus Ennis; Janna Hastings; Martin Zbinden; Alan McNaught; Rafael Alcántara; Michael Darsow; Mickaël Guedj; Michael Ashburner
Journal:  Nucleic Acids Res       Date:  2007-10-11       Impact factor: 16.971

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  26 in total

Review 1.  New approaches to the representation and analysis of phenotype knowledge in human diseases and their animal models.

Authors:  Paul N Schofield; John P Sundberg; Robert Hoehndorf; Georgios V Gkoutos
Journal:  Brief Funct Genomics       Date:  2011-09       Impact factor: 4.241

Review 2.  Mouse genetic and phenotypic resources for human genetics.

Authors:  Paul N Schofield; Robert Hoehndorf; Georgios V Gkoutos
Journal:  Hum Mutat       Date:  2012-05       Impact factor: 4.878

3.  OntoVIP: an ontology for the annotation of object models used for medical image simulation.

Authors:  Bernard Gibaud; Germain Forestier; Hugues Benoit-Cattin; Frédéric Cervenansky; Patrick Clarysse; Denis Friboulet; Alban Gaignard; Patrick Hugonnard; Carole Lartizien; Hervé Liebgott; Johan Montagnat; Joachim Tabary; Tristan Glatard
Journal:  J Biomed Inform       Date:  2014-07-16       Impact factor: 6.317

4.  What color is the skin of a mouse?

Authors:  J P Sundberg; K A Silva
Journal:  Vet Pathol       Date:  2011-11-16       Impact factor: 2.221

5.  Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish.

Authors:  Sandra C Doelken; Sebastian Köhler; Christopher J Mungall; Georgios V Gkoutos; Barbara J Ruef; Cynthia Smith; Damian Smedley; Sebastian Bauer; Eva Klopocki; Paul N Schofield; Monte Westerfield; Peter N Robinson; Suzanna E Lewis
Journal:  Dis Model Mech       Date:  2012-10-25       Impact factor: 5.758

6.  MouseFinder: Candidate disease genes from mouse phenotype data.

Authors:  Chao-Kung Chen; Christopher J Mungall; Georgios V Gkoutos; Sandra C Doelken; Sebastian Köhler; Barbara J Ruef; Cynthia Smith; Monte Westerfield; Peter N Robinson; Suzanna E Lewis; Paul N Schofield; Damian Smedley
Journal:  Hum Mutat       Date:  2012-03-16       Impact factor: 4.878

7.  Genetic determinants of fibro-osseous lesions in aged inbred mice.

Authors:  Annerose Berndt; Cheryl Ackert-Bicknell; Kathleen A Silva; Victoria E Kennedy; Beth A Sundberg; Justin M Cates; Paul N Schofield; John P Sundberg
Journal:  Exp Mol Pathol       Date:  2015-11-14       Impact factor: 3.362

8.  InterMOD: integrated data and tools for the unification of model organism research.

Authors:  Julie Sullivan; Kalpana Karra; Sierra A T Moxon; Andrew Vallejos; Howie Motenko; J D Wong; Jelena Aleksic; Rama Balakrishnan; Gail Binkley; Todd Harris; Benjamin Hitz; Pushkala Jayaraman; Rachel Lyne; Steven Neuhauser; Christian Pich; Richard N Smith; Quang Trinh; J Michael Cherry; Joel Richardson; Lincoln Stein; Simon Twigger; Monte Westerfield; Elizabeth Worthey; Gos Micklem
Journal:  Sci Rep       Date:  2013       Impact factor: 4.379

9.  PosMed: Ranking genes and bioresources based on Semantic Web Association Study.

Authors:  Yuko Makita; Norio Kobayashi; Yuko Yoshida; Koji Doi; Yoshiki Mochizuki; Koro Nishikata; Akihiro Matsushima; Satoshi Takahashi; Manabu Ishii; Terue Takatsuki; Rinki Bhatia; Zolzaya Khadbaatar; Hajime Watabe; Hiroshi Masuya; Tetsuro Toyoda
Journal:  Nucleic Acids Res       Date:  2013-06-12       Impact factor: 16.971

10.  Semantically enabling a genome-wide association study database.

Authors:  Tim Beck; Robert C Free; Gudmundur A Thorisson; Anthony J Brookes
Journal:  J Biomed Semantics       Date:  2012-12-17
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