EuroPhenome: A repository for high-throughput mouse phenotyping data

Hugh Morgan; Tim Beck; Andrew Blake; Hilary Gates; Niels Adams; Guillaume Debouzy; Sophie Leblanc; Christoph Lengger; Holger Maier; David Melvin; Hamid Meziane; Dave Richardson; Sara Wells; Jacqui White; Joe Wood; Martin Hrabé De Angelis; Steve D.M. Brown; John M. Hancock; Ann Marie Mallon; Fatima Bosch; Jesús Ruberte; Tura Ferre; Anna Pujol; Pedro Otaegui; Sylvie Franckhauser; Jacqueline Marvel; Veronique Queste; Romain Dacquin; Sophia Djebali; Pierre Jurdic; George Kollias; Christina Chandras; Eleni Douni; Vassilis Aidinis; Mariano Barbacid; Marta Cañamero; Pierre Dubus; Glauco Tocchini-Valentini; Silvia Mandillo; Elisabetta Golini; Daniela Marazziti; Giancarlo Deidda; Nicoletta Rossi; Rafaele Matteoni; Marcello Raspa; Ferdinando Scavizzi; Richard Hugh Butler; Gianfranco Di Segni; Paolo Fruscoloni; Patrizia Calandra; Cecilia Mannironi; Daniela Scarabino; Giuseppe D. Tocchini-Valentini; Michela Zamboni; Sabrina Putti; Chiara Di Pietro; Serena Gastaldi; Yann Herault; Bernard Ryffel; Marc Le Bert; Patricia Lopes Pereirea; Véronique Brault; Emilie Dalloneau; Stéphanie Pothion; Nadia Rosenthal; Mumna Al Banchaabouchi; Raffaele Migliozzi; Ekaterina Salimova; Rudi Balling; Hansjörg Hauser; Bastian Pasche; Werner Müller; Andreas Lengeling; Valérie Gailus-Durner; Helmut Fuchs; Thure Adler; Antonio Aguilar-Pimentel; Lore Becker; Raffi Bekeredjian; Dirk H. Busch; null Julia Calzada-Wack; Patricia Da Silva-Buttkus; Irene Esposito; Jack Favor; Wolfgang Fleischmann; Lilian Garrett; Lisa Glasl; Alexander Götz; Jochen Graw; Wolfgang Hans; Sabine M. Hölter-Koch; Boris Ivandic; Hugo A. Katus; Martin Klingenspor; Thomas Klopstock; Tonia Ludwig; Kateryna Micklich; Sun Minxuan; Beatrix Naton; Frauke Neff

doi:10.1093/nar/gkp1007

EuroPhenome: A repository for high-throughput mouse phenotyping data

Hugh Morgan, Tim Beck, Andrew Blake, Hilary Gates, Niels Adams, Guillaume Debouzy, Sophie Leblanc, Christoph Lengger, Holger Maier, David Melvin, Hamid Meziane, Dave Richardson, Sara Wells, Jacqui White, Joe Wood, Martin Hrabé De Angelis, Steve D.M. Brown, John M. Hancock, Ann Marie Mallon, Fatima BoschJesús Ruberte, Tura Ferre, Anna Pujol, Pedro Otaegui, Sylvie Franckhauser, Jacqueline Marvel, Veronique Queste, Romain Dacquin, Sophia Djebali, Pierre Jurdic, George Kollias, Christina Chandras, Eleni Douni, Vassilis Aidinis, Mariano Barbacid, Marta Cañamero, Pierre Dubus, Glauco Tocchini-Valentini, Silvia Mandillo, Elisabetta Golini, Daniela Marazziti, Giancarlo Deidda, Nicoletta Rossi, Rafaele Matteoni, Marcello Raspa, Ferdinando Scavizzi, Richard Hugh Butler, Gianfranco Di Segni, Paolo Fruscoloni, Patrizia Calandra, Cecilia Mannironi, Daniela Scarabino, Giuseppe D. Tocchini-Valentini, Michela Zamboni, Sabrina Putti, Chiara Di Pietro, Serena Gastaldi, Yann Herault, Bernard Ryffel, Marc Le Bert, Patricia Lopes Pereirea, Véronique Brault, Emilie Dalloneau, Stéphanie Pothion, Nadia Rosenthal, Mumna Al Banchaabouchi, Raffaele Migliozzi, Ekaterina Salimova, Rudi Balling, Hansjörg Hauser, Bastian Pasche, Werner Müller, Andreas Lengeling, Valérie Gailus-Durner, Helmut Fuchs, Thure Adler, Antonio Aguilar-Pimentel, Lore Becker, Raffi Bekeredjian, Dirk H. Busch, Julia Calzada-Wack, Patricia Da Silva-Buttkus, Irene Esposito, Jack Favor, Wolfgang Fleischmann, Lilian Garrett, Lisa Glasl, Alexander Götz, Jochen Graw, Wolfgang Hans, Sabine M. Hölter-Koch, Boris Ivandic, Hugo A. Katus, Martin Klingenspor, Thomas Klopstock, Tonia Ludwig, Kateryna Micklich, Sun Minxuan, Beatrix Naton, Frauke Neff

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Resumen

© The Author(s) 2009. The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated highthroughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

Idioma original	Inglés
Páginas (desde-hasta)	D577-D585
Publicación	Nucleic Acids Research
Volumen	38
DOI	https://doi.org/10.1093/nar/gkp1007
Estado	Publicada - 1 ene 2010

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Morgan, H., Beck, T., Blake, A., Gates, H., Adams, N., Debouzy, G., Leblanc, S., Lengger, C., Maier, H., Melvin, D., Meziane, H., Richardson, D., Wells, S., White, J., Wood, J., De Angelis, M. H., Brown, S. D. M., Hancock, J. M., Mallon, A. M., ... Neff, F. (2010). EuroPhenome: A repository for high-throughput mouse phenotyping data. Nucleic Acids Research, 38, D577-D585. https://doi.org/10.1093/nar/gkp1007

@article{e55f77ab95ae4c4da9944dc488570b07,

title = "EuroPhenome: A repository for high-throughput mouse phenotyping data",

abstract = "{\textcopyright} The Author(s) 2009. The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated highthroughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.",

author = "Hugh Morgan and Tim Beck and Andrew Blake and Hilary Gates and Niels Adams and Guillaume Debouzy and Sophie Leblanc and Christoph Lengger and Holger Maier and David Melvin and Hamid Meziane and Dave Richardson and Sara Wells and Jacqui White and Joe Wood and {De Angelis}, {Martin Hrab{\'e}} and Brown, {Steve D.M.} and Hancock, {John M.} and Mallon, {Ann Marie} and Fatima Bosch and Jes{\'u}s Ruberte and Tura Ferre and Anna Pujol and Pedro Otaegui and Sylvie Franckhauser and Jacqueline Marvel and Veronique Queste and Romain Dacquin and Sophia Djebali and Pierre Jurdic and George Kollias and Christina Chandras and Eleni Douni and Vassilis Aidinis and Mariano Barbacid and Marta Ca{\~n}amero and Pierre Dubus and Glauco Tocchini-Valentini and Silvia Mandillo and Elisabetta Golini and Daniela Marazziti and Giancarlo Deidda and Nicoletta Rossi and Rafaele Matteoni and Marcello Raspa and Ferdinando Scavizzi and Butler, {Richard Hugh} and {Di Segni}, Gianfranco and Paolo Fruscoloni and Patrizia Calandra and Cecilia Mannironi and Daniela Scarabino and Tocchini-Valentini, {Giuseppe D.} and Michela Zamboni and Sabrina Putti and {Di Pietro}, Chiara and Serena Gastaldi and Yann Herault and Bernard Ryffel and {Le Bert}, Marc and Pereirea, {Patricia Lopes} and V{\'e}ronique Brault and Emilie Dalloneau and St{\'e}phanie Pothion and Nadia Rosenthal and Banchaabouchi, {Mumna Al} and Raffaele Migliozzi and Ekaterina Salimova and Rudi Balling and Hansj{\"o}rg Hauser and Bastian Pasche and Werner M{\"u}ller and Andreas Lengeling and Val{\'e}rie Gailus-Durner and Helmut Fuchs and Thure Adler and Antonio Aguilar-Pimentel and Lore Becker and Raffi Bekeredjian and Busch, {Dirk H.} and {Julia Calzada-Wack} and {Da Silva-Buttkus}, Patricia and Irene Esposito and Jack Favor and Wolfgang Fleischmann and Lilian Garrett and Lisa Glasl and Alexander G{\"o}tz and Jochen Graw and Wolfgang Hans and H{\"o}lter-Koch, {Sabine M.} and Boris Ivandic and Katus, {Hugo A.} and Martin Klingenspor and Thomas Klopstock and Tonia Ludwig and Kateryna Micklich and Sun Minxuan and Beatrix Naton and Frauke Neff",

year = "2010",

month = jan,

day = "1",

doi = "10.1093/nar/gkp1007",

language = "English",

volume = "38",

pages = "D577--D585",

}

Morgan, H, Beck, T, Blake, A, Gates, H, Adams, N, Debouzy, G, Leblanc, S, Lengger, C, Maier, H, Melvin, D, Meziane, H, Richardson, D, Wells, S, White, J, Wood, J, De Angelis, MH, Brown, SDM, Hancock, JM, Mallon, AM, Bosch, F , Ruberte, J, Ferre, T, Pujol, A, Otaegui, P, Franckhauser, S, Marvel, J, Queste, V, Dacquin, R, Djebali, S, Jurdic, P, Kollias, G, Chandras, C, Douni, E, Aidinis, V, Barbacid, M, Cañamero, M, Dubus, P, Tocchini-Valentini, G, Mandillo, S, Golini, E, Marazziti, D, Deidda, G, Rossi, N, Matteoni, R, Raspa, M, Scavizzi, F, Butler, RH, Di Segni, G, Fruscoloni, P, Calandra, P, Mannironi, C, Scarabino, D, Tocchini-Valentini, GD, Zamboni, M, Putti, S, Di Pietro, C, Gastaldi, S, Herault, Y, Ryffel, B, Le Bert, M, Pereirea, PL, Brault, V, Dalloneau, E, Pothion, S, Rosenthal, N, Banchaabouchi, MA, Migliozzi, R, Salimova, E, Balling, R, Hauser, H, Pasche, B, Müller, W, Lengeling, A, Gailus-Durner, V, Fuchs, H, Adler, T, Aguilar-Pimentel, A, Becker, L, Bekeredjian, R, Busch, DH, Julia Calzada-Wack, Da Silva-Buttkus, P, Esposito, I, Favor, J, Fleischmann, W, Garrett, L, Glasl, L, Götz, A, Graw, J, Hans, W, Hölter-Koch, SM, Ivandic, B, Katus, HA, Klingenspor, M, Klopstock, T, Ludwig, T, Micklich, K, Minxuan, S, Naton, B & Neff, F 2010, 'EuroPhenome: A repository for high-throughput mouse phenotyping data', Nucleic Acids Research, vol. 38, pp. D577-D585. https://doi.org/10.1093/nar/gkp1007

TY - JOUR

T1 - EuroPhenome: A repository for high-throughput mouse phenotyping data

AU - Morgan, Hugh

AU - Beck, Tim

AU - Blake, Andrew

AU - Gates, Hilary

AU - Adams, Niels

AU - Debouzy, Guillaume

AU - Leblanc, Sophie

AU - Lengger, Christoph

AU - Maier, Holger

AU - Melvin, David

AU - Meziane, Hamid

AU - Richardson, Dave

AU - Wells, Sara

AU - White, Jacqui

AU - Wood, Joe

AU - De Angelis, Martin Hrabé

AU - Brown, Steve D.M.

AU - Hancock, John M.

AU - Mallon, Ann Marie

AU - Bosch, Fatima

AU - Ruberte, Jesús

AU - Ferre, Tura

AU - Pujol, Anna

AU - Otaegui, Pedro

AU - Franckhauser, Sylvie

AU - Marvel, Jacqueline

AU - Queste, Veronique

AU - Dacquin, Romain

AU - Djebali, Sophia

AU - Jurdic, Pierre

AU - Kollias, George

AU - Chandras, Christina

AU - Douni, Eleni

AU - Aidinis, Vassilis

AU - Barbacid, Mariano

AU - Cañamero, Marta

AU - Dubus, Pierre

AU - Tocchini-Valentini, Glauco

AU - Mandillo, Silvia

AU - Golini, Elisabetta

AU - Marazziti, Daniela

AU - Deidda, Giancarlo

AU - Rossi, Nicoletta

AU - Matteoni, Rafaele

AU - Raspa, Marcello

AU - Scavizzi, Ferdinando

AU - Butler, Richard Hugh

AU - Di Segni, Gianfranco

AU - Fruscoloni, Paolo

AU - Calandra, Patrizia

AU - Mannironi, Cecilia

AU - Scarabino, Daniela

AU - Tocchini-Valentini, Giuseppe D.

AU - Zamboni, Michela

AU - Putti, Sabrina

AU - Di Pietro, Chiara

AU - Gastaldi, Serena

AU - Herault, Yann

AU - Ryffel, Bernard

AU - Le Bert, Marc

AU - Pereirea, Patricia Lopes

AU - Brault, Véronique

AU - Dalloneau, Emilie

AU - Pothion, Stéphanie

AU - Rosenthal, Nadia

AU - Banchaabouchi, Mumna Al

AU - Migliozzi, Raffaele

AU - Salimova, Ekaterina

AU - Balling, Rudi

AU - Hauser, Hansjörg

AU - Pasche, Bastian

AU - Müller, Werner

AU - Lengeling, Andreas

AU - Gailus-Durner, Valérie

AU - Fuchs, Helmut

AU - Adler, Thure

AU - Aguilar-Pimentel, Antonio

AU - Becker, Lore

AU - Bekeredjian, Raffi

AU - Busch, Dirk H.

AU - Julia Calzada-Wack, null

AU - Da Silva-Buttkus, Patricia

AU - Esposito, Irene

AU - Favor, Jack

AU - Fleischmann, Wolfgang

AU - Garrett, Lilian

AU - Glasl, Lisa

AU - Götz, Alexander

AU - Graw, Jochen

AU - Hans, Wolfgang

AU - Hölter-Koch, Sabine M.

AU - Ivandic, Boris

AU - Katus, Hugo A.

AU - Klingenspor, Martin

AU - Klopstock, Thomas

AU - Ludwig, Tonia

AU - Micklich, Kateryna

AU - Minxuan, Sun

AU - Naton, Beatrix

AU - Neff, Frauke

PY - 2010/1/1

Y1 - 2010/1/1

N2 - © The Author(s) 2009. The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated highthroughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

AB - © The Author(s) 2009. The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated highthroughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies.

U2 - 10.1093/nar/gkp1007

DO - 10.1093/nar/gkp1007

M3 - Article

SN - 0305-1048

VL - 38

SP - D577-D585

JO - Nucleic Acids Research

JF - Nucleic Acids Research

ER -

EuroPhenome: A repository for high-throughput mouse phenotyping data

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