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Nucleic Acids Res. 2009 January; 37(Database issue): D619–D622. Published online 2009 January. doi: 10.1093/nar/gkn863. | PMCID: PMC2686536 |
Reactome knowledgebase of human biological pathways and processes Lisa Matthews,1 Gopal Gopinath,1 Marc Gillespie,1,2 Michael Caudy,1 David Croft,3 Bernard de Bono,3 Phani Garapati,3 Jill Hemish,1 Henning Hermjakob,3 Bijay Jassal,3 Alex Kanapin,1 Suzanna Lewis,4 Shahana Mahajan,5,6 Bruce May,1 Esther Schmidt,3 Imre Vastrik,3 Guanming Wu,1 Ewan Birney,3 Lincoln Stein,1,7 and Peter D’Eustachio1,6* 1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, 2College of Pharmacy and Allied Health Professions, St. John's University, Queens, NY 11439, USA, 3European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK, 4Lawrence Berkeley National Laboratory, Berkeley, CA 94720, 5Hunter College, New York, NY 10010, 6NYU School of Medicine, New York, NY 10016, USA and 7Ontario Institute for Cancer Research, Toronto, ON, Canada M5G0A3 Received September 17, 2008; Revised October 14, 2008; Accepted October 16, 2008. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. Reactome ( http://www.reactome.org) is an expert-authored, peer-reviewed knowledgebase of human reactions and pathways that functions as a data mining resource and electronic textbook. Its current release includes 2975 human proteins, 2907 reactions and 4455 literature citations. A new entity-level pathway viewer and improved search and data mining tools facilitate searching and visualizing pathway data and the analysis of user-supplied high-throughput data sets. Reactome has increased its utility to the model organism communities with improved orthology prediction methods allowing pathway inference for 22 species and through collaborations to create manually curated Reactome pathway datasets for species including Arabidopsis, Oryza sativa (rice), Drosophila and Gallus gallus (chicken). Reactome's data content and software can all be freely used and redistributed under open source terms. EXPANDED COVERAGE OF HUMAN PATHWAYS The current release of Reactome (version 26, September 2008) covers approximately 12.5% of 20 000 curated UniProt human proteins, a 2.7-fold increase over the last three years. Forty-six major domains of human biology, such as apoptosis, the HIV and influenza life cycles, DNA replication, transcription, hemostasis and carbohydrate metabolism are annotated, as are normal functions of 1005 proteins associated with OMIM disease phenotypes ( http://www.ncbi.nlm.nih.gov/omim/). IMPROVED TOOLS, SOFTWARE AND DATA MODEL Revised orthology prediction methods The OrthoMCL clustering procedure ( 1, 2) ( http://reactome.org/electronic_inference.html) applied to data from OrthoMCL DB ( http://www.orthomcl.org/cgi-bin/OrthoMclWeb.cgi), Version 2, is used to identify orthologs of curated human proteins in each of 22 evolutionarily divergent species for which high-quality whole-genome sequence data are available ( 3). In line with changes in the OrthoMCL clustering procedure, only the longest transcript of each gene is considered, and a gene-based rather than a protein-based method is used to map the Ensembl identifiers used by OrthoMCL to the UniProt accessions used in Reactome. These changes have improved our success rate for electronic inference without measurably affecting accuracy. Improved tools for analysis of large-scale data sets, data-mining and modeling SkyPainter The current version of the SkyPainter tool allows users to more effectively visualize the functional relationships among genes identified in large-scale experiments (A and B). For a user-submitted list of genes, each reaction arrow on the reaction map is colored according to the number of user-specified genes whose products participate in the reaction. In addition, hypergeometric testing is now used to display statistically over-represented events in the event hierarchy. Statistically over-represented events may also be viewed as an ordered list and a mapping from submitted identifiers to reactions is provided. The colored reaction maps can be downloaded in publication quality PNG, SVG or PDF format.
Biomart The newly implemented Reactome BioMart tool ( http://www.biomart.org) facilitates data mining, cross-database analysis and large-scale analysis of gene function. A user can formulate queries across selected data sets (pathways, reactions and complexes) specifying data attributes and filters to narrow searches. For example, querying the Reactome dataset, a user can identify all complexes that contain a given protein (C). Alternatively, a user can link a query of the Reactome ‘complexes’ dataset to a UniProt proteome query and retrieve sequences of all the proteins in these complexes. Popular searches, e.g. all reactions or proteins or genes in a given pathway, all pathways inferred for a given species or all reactions or pathways involving a set of specified genes can be launched with predefined ‘canned’ queries. Additional context-sensitive help documentation is under construction. Changes in the Reactome data model These have been minimized, to facilitate data curation and use of the knowledgebase. Two additions are a ‘black box’ reaction class to allow the annotation of events for which not all defining attributes can be provided and an ‘entityOnOtherCell’ attribute to allow description of individual events and complexes that span two cells. We are actively collaborating in the creation of model organism Reactome projects for Arabidopsis, rice, Drosophila and chicken. The Arabidopsis Reactome ( http://arabidopsisreactome.org/), developed with the human Reactome data model, software and curation tools, contains seven manually curated pathways and 311 pathways inferred from data in KEGG ( http://www.genome.ad.jp/kegg/pathway.html) ( 4) and MetaCyc ( http://metacyc.org/) ( 5). Arabidopsis Reactome events have been electronically projected onto five other predicted plant proteomes using the OrthoMCL prediction method described above ( 6). Curation of Drosophila and chicken reactions is underway in collaboration with FlyBase and the Gallus Knowledge Extraction and Annotation project using the Reactome infrastructure and curation protocols; the first releases of these databases are planned for late 2008. In collaboration with the BioHealthbase group at University of Texas Southwestern Medical College, the life cycle of Influenza virus has been curated and reviewed and is publicly accessible as a segment of Reactome ( 7). In collaboration with the Protein Ontology group—PRO ( 8), Reactome annotations of complexes and physiological states of proteins are being applied to build a hierarchy of proteins and their functional forms. For example, protein objects used to illustrate TGF-β signaling in PRO use corresponding protein objects in the Reactome annotated pathway. The Reactome and PRO collaboration, as a source for curated annotations of proteins, extends the application of Reactome to a larger ontology community. INCREASED DATA INTEGRATION AND USER SUPPORT We are increasing the accessibility of Reactome data through data integration and improved online documentation. Reactome pathway annotations are now included in the Pathway Interaction Database ( http://pid.nci.nih.gov/) ( 9). Reactome's online documentation is now available as WIKI pages that provide easy access to user, author and curator guides as well as glossaries and standard operating procedure (SOP) guidelines. In addition, an Editorial Calendar lists modules being prepared for the knowledgebase, their planned release dates and contact information for module curators. A long-term objective of the Reactome project is to provide users with intuitive graphical representations of pathways and reactions. Toward this goal, Reactome has developed a beta version of an entity-level pathway visualization tool: through enhanced navigation features including improved zooming, scrolling and event highlighting, this tool provides a detailed graphical representation of the relationships among the molecules participating in reactions (D). Hover-over molecule/reaction descriptions allow quick and easy scanning of the molecular details of each reaction. An improved search option with an auto-complete feature at the top of the page allows directed queries over reaction and pathway names, entity names, identifiers and GO molecular function terms. New author tool with pathway diagram editing capability We are in the process of developing a user interface that couples the powerful navigation and search features of the entity level pathway visualization tool with software that draws intuitive ‘textbook style’ illustrations of pathways. To this end, we have recently developed an SBGN ( http://www.sbgn.org) based version of the Reactome author tool that can create such diagrams (E). Currently, this has been released as a beta test version and is available as a Java Web Start application at the Reactome development site: ( http://brie8.cshl.edu:8080/ReactomeTools/AuthorTool/authorToolLaunch.html). The development of Reactome is supported by a grant from the US National Institutes of Health (P41 HG003751) and a grant from the European Union Sixth Framework Programme (LSHG-CT-2003-503269). Funding for open access charge: US National Institutes of Health P41 HG003751. Conflict of interest statement. None declared. We are grateful to many scientists who collaborated with us as authors and reviewers to build the content of the knowledgebase, and for the helpful comments of the reviewers of this manscript. 1. Li L, Stoeckert C.J., Jr., Roos DS. OrthoMCL: identification of ortholog groups for eukaryotic genomes. Genome Res. 2003;9:2178–2189. [PubMed] 2. Chen F, Mackey A, Stoeckert C.J., Jr., Roos DS. OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups. Nucleic Acids Res. 2006;34:D363–D368. [PubMed] 3. Vastrik I, D’Eustachio P, Schmidt E, Joshi-Tope G, Gopinath G, Croft D, de Bono B, Gillespie M, Jassal B, Lewis S, et al. Reactome: a knowledge base of biologic pathways and processes. Genome Biol. 2007;8:R39. [PubMed] 4. Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, et al. KEGG for linking genomes to life and the environment. Nucleic Acids Res. 2008;36:D480–D484. [PubMed] 5. Caspi R, Foerster H, Fulcher CA, Kaipa P, Krummenacker M, Latendresse M, Paley S, Rhee SY, Shearer AG, Tissier C, et al. The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res. 2008;36:D623–D631. [PubMed] 6. Tsesmetzis N, Couchman M, Higgins J, Smith A, Doonan JH, Seifert GJ, Schmidt EE, Vastrik I, Birney E, Wu G, et al. Arabidopsis Reactome: a foundation knowledgebase for plant systems biology. Plant Cell. 2008;6:1426–1436. [PubMed] 7. Squires B, Macken C, Garcia-Sastre A, Godbole S, Noronha J, Hunt V, Chang R, Larsen CN, Klem E, Biersack K, et al. BioHealthBase: informatics support in the elucidation of influenza virus host pathogen interactions and virulence. Nucleic Acids Res. 2008;36:D497–D503. [PubMed] 8. Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH. Framework for a protein ontology. BMC Bioinformatics. 2007;8(Suppl 9):S1. [PubMed] 9. Schaefer CF. An introduction to the NCI Pathway Interaction Database. NCI-Nature Pathway Interaction Database. 2006 doi:10.1038/pid.2006.001. 10. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, et al. The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics. 2003;19:524–531. [PubMed] 11. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, et al. Integration of biological networks and gene expression data using Cytoscape. Nat. Protocols. 2007;2:2366–2382.
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