Reactome: a database of reactions, pathways and biological processes
Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathway...
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| Published in | Nucleic acids research Vol. 39; no. Database issue; pp. D691 - D697 |
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| Main Authors | , , , , , , , , , , , , , , , , , , , , , |
| Format | Journal Article |
| Language | English |
| Published |
England
Oxford University Press
01.01.2011
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| Subjects | |
| Online Access | Get full text |
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| Abstract | Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice. |
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| AbstractList | Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice. Reactome ( http://www.reactome.org ) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice. |
| Author | Caudy, Michael Croft, David Wu, Guanming Gopinath, Gopal Stein, Lincoln D'Eustachio, Peter Matthews, Lisa Schmidt, Esther Mahajan, Shahana Garapati, Phani Hermjakob, Henning Jassal, Bijay Birney, Ewan Gillespie, Marc May, Bruce Ndegwa, Nelson Kalatskaya, Irina Haw, Robin Shamovsky, Veronica O'Kelly, Gavin Jupe, Steven Yung, Christina |
| AuthorAffiliation | 1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, 2 Ontario Institute for Cancer Research, Informatics and Bio-Computing, Toronto, ON, M5G0A3, Canada, 3 St. John's University, College of Pharmacy and Allied Health Professions, Queens, NY 11439, 4 NYU School of Medicine, Department of Biochemistry, New York, NY 10016, 5 US Food and Drug Administration, Center for Food Safety and Applied Nutrition, Laurel, MD 20708, 6 Hunter College, School of Health Sciences, New York, NY 10010, 7 Cold Spring Harbor Laboratory, Bioinformatics and Genomics, Cold Spring Harbor, NY 11724, USA, 8 University of Toronto, Department of Molecular Genetics, Toronto, ON, M5S 1A1, Canada |
| AuthorAffiliation_xml | – name: 1 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK, 2 Ontario Institute for Cancer Research, Informatics and Bio-Computing, Toronto, ON, M5G0A3, Canada, 3 St. John's University, College of Pharmacy and Allied Health Professions, Queens, NY 11439, 4 NYU School of Medicine, Department of Biochemistry, New York, NY 10016, 5 US Food and Drug Administration, Center for Food Safety and Applied Nutrition, Laurel, MD 20708, 6 Hunter College, School of Health Sciences, New York, NY 10010, 7 Cold Spring Harbor Laboratory, Bioinformatics and Genomics, Cold Spring Harbor, NY 11724, USA, 8 University of Toronto, Department of Molecular Genetics, Toronto, ON, M5S 1A1, Canada |
| Author_xml | – sequence: 1 fullname: Croft, David – sequence: 2 fullname: O'Kelly, Gavin – sequence: 3 fullname: Wu, Guanming – sequence: 4 fullname: Haw, Robin – sequence: 5 fullname: Gillespie, Marc – sequence: 6 fullname: Matthews, Lisa – sequence: 7 fullname: Caudy, Michael – sequence: 8 fullname: Garapati, Phani – sequence: 9 fullname: Gopinath, Gopal – sequence: 10 fullname: Jassal, Bijay – sequence: 11 fullname: Jupe, Steven – sequence: 12 fullname: Kalatskaya, Irina – sequence: 13 fullname: Mahajan, Shahana – sequence: 14 fullname: May, Bruce – sequence: 15 fullname: Ndegwa, Nelson – sequence: 16 fullname: Schmidt, Esther – sequence: 17 fullname: Shamovsky, Veronica – sequence: 18 fullname: Yung, Christina – sequence: 19 fullname: Birney, Ewan – sequence: 20 fullname: Hermjakob, Henning – sequence: 21 fullname: D'Eustachio, Peter – sequence: 22 fullname: Stein, Lincoln |
| BackLink | https://www.ncbi.nlm.nih.gov/pubmed/21067998$$D View this record in MEDLINE/PubMed |
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| SubjectTerms | Biological Phenomena Computer Graphics Databases, Factual Databases, Genetic Databases, Protein Drosophila Gene Expression Regulation Humans Internet Metabolic Networks and Pathways Models, Biological Oryza sativa Signal Transduction |
| Title | Reactome: a database of reactions, pathways and biological processes |
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