Literature DB >> 18950739

The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease.

Peter N Robinson1, Sebastian Köhler, Sebastian Bauer, Dominik Seelow, Denise Horn, Stefan Mundlos.   

Abstract

There are many thousands of hereditary diseases in humans, each of which has a specific combination of phenotypic features, but computational analysis of phenotypic data has been hampered by lack of adequate computational data structures. Therefore, we have developed a Human Phenotype Ontology (HPO) with over 8000 terms representing individual phenotypic anomalies and have annotated all clinical entries in Online Mendelian Inheritance in Man with the terms of the HPO. We show that the HPO is able to capture phenotypic similarities between diseases in a useful and highly significant fashion.

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Year:  2008        PMID： 18950739      PMCID： PMC2668030          DOI： 10.1016/j.ajhg.2008.09.017

Source DB:  PubMed          Journal:  Am J Hum Genet        ISSN： 0002-9297            Impact factor:   11.025


  27 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.  Specificity and stability in topology of protein networks.

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Journal:  Science       Date:  2002-05-03       Impact factor: 47.728

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Review 4.  The modular nature of genetic diseases.

Authors:  M Oti; H G Brunner
Journal:  Clin Genet       Date:  2007-01       Impact factor: 4.438

5.  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

6.  OBO-Edit--an ontology editor for biologists.

Authors:  John Day-Richter; Midori A Harris; Melissa Haendel; Suzanna Lewis
Journal:  Bioinformatics       Date:  2007-06-01       Impact factor: 6.937

7.  Network properties of genes harboring inherited disease mutations.

Authors:  Igor Feldman; Andrey Rzhetsky; Dennis Vitkup
Journal:  Proc Natl Acad Sci U S A       Date:  2008-03-07       Impact factor: 11.205

8.  The human disease network.

Authors:  Kwang-Il Goh; Michael E Cusick; David Valle; Barton Childs; Marc Vidal; Albert-László Barabási
Journal:  Proc Natl Acad Sci U S A       Date:  2007-05-14       Impact factor: 11.205

9.  Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis.

Authors:  Steffen Grossmann; Sebastian Bauer; Peter N Robinson; Martin Vingron
Journal:  Bioinformatics       Date:  2007-09-11       Impact factor: 6.937

10.  A probabilistic generative model for GO enrichment analysis.

Authors:  Yong Lu; Roni Rosenfeld; Itamar Simon; Gerard J Nau; Ziv Bar-Joseph
Journal:  Nucleic Acids Res       Date:  2008-08-01       Impact factor: 16.971
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  373 in total

1.  Call for participation in the neurogenetics consortium within the Human Variome Project.

Authors:  Andrea Haworth; Lars Bertram; Paola Carrera; Joanna L Elson; Corey D Braastad; Diane W Cox; Marc Cruts; Johann T den Dunnen; Matthew J Farrer; John K Fink; Sherifa A Hamed; Henry Houlden; Dennis R Johnson; Karen Nuytemans; Francesc Palau; Dipa L Raja Rayan; Peter N Robinson; Antonio Salas; Birgitt Schüle; Mary G Sweeney; Michael O Woods; Jorge Amigo; Richard G H Cotton; Maria-Jesus Sobrido
Journal:  Neurogenetics       Date:  2011-06-01       Impact factor: 2.660

2.  Exact score distribution computation for ontological similarity searches.

Authors:  Marcel H Schulz; Sebastian Köhler; Sebastian Bauer; Peter N Robinson
Journal:  BMC Bioinformatics       Date:  2011-11-12       Impact factor: 3.169

3.  Similarity-based disease risk assessment for personal genomes: proof of concept.

Authors:  Jung Hoon Woo; Albert M Lai; Wendy K Chung; Chunhua Weng
Journal:  AMIA Annu Symp Proc       Date:  2011-10-22

4.  Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.

Authors:  Robert Hoehndorf; Midori A Harris; Heinrich Herre; Gabriella Rustici; Georgios V Gkoutos
Journal:  Bioinformatics       Date:  2012-04-26       Impact factor: 6.937

5.  Phenotypic information in genomic variant databases enhances clinical care and research: the International Standards for Cytogenomic Arrays Consortium experience.

Authors:  Erin Rooney Riggs; Laird Jackson; David T Miller; Steven Van Vooren
Journal:  Hum Mutat       Date:  2012-03-20       Impact factor: 4.878

Review 6.  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

7.  Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.

Authors:  Robert Hoehndorf; Michel Dumontier; Georgios V Gkoutos
Journal:  Bioinformatics       Date:  2012-06-17       Impact factor: 6.937

Review 8.  Computational tools for prioritizing candidate genes: boosting disease gene discovery.

Authors:  Yves Moreau; Léon-Charles Tranchevent
Journal:  Nat Rev Genet       Date:  2012-07-03       Impact factor: 53.242

9.  Drug repurposing for glioblastoma based on molecular subtypes.

Authors:  Yang Chen; Rong Xu
Journal:  J Biomed Inform       Date:  2016-09-30       Impact factor: 6.317

10.  Homozygous and compound-heterozygous mutations in TGDS cause Catel-Manzke syndrome.

Authors:  Nadja Ehmke; Almuth Caliebe; Rainer Koenig; Sarina G Kant; Zornitza Stark; Valérie Cormier-Daire; Dagmar Wieczorek; Gabriele Gillessen-Kaesbach; Kirstin Hoff; Amit Kawalia; Holger Thiele; Janine Altmüller; Björn Fischer-Zirnsak; Alexej Knaus; Na Zhu; Verena Heinrich; Celine Huber; Izabela Harabula; Malte Spielmann; Denise Horn; Uwe Kornak; Jochen Hecht; Peter M Krawitz; Peter Nürnberg; Reiner Siebert; Hermann Manzke; Stefan Mundlos
Journal:  Am J Hum Genet       Date:  2014-12-04       Impact factor: 11.025
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