Creative Commons Zero - CC0

Since our inception, we have been an open source and open access resource,  free for use by anyone under the terms of a Creative Commons Attribution 4.0 International (CC BY 4.0) license. This license granted parties the non-exclusive right to use, distribute and create derivative works based on Reactome, provided that the works are correctly attributed to OICR, NYUMC, EBI, and OHSU.

In line with the growing movement to provide free open data in the public domain, and to better support the needs of our user community, we are updating the licensing agreement for some of our web content and data to reflect the Creative Commons Public Domain (CC0). CC0 is the "no copyright reserved" option in the Creative Commons toolkit. It effectively means relinquishing all copyright and similar rights that we hold in a work and dedicating those rights to the public domain.

A Creative Commons Public Domain (CC0 1.0 Universal) Licence will now cover all Reactome annotation files, e.g. identifier mapping, specialized data files, and interaction data derived from Reactome.

A Creative Commons Attribution 4.0 International (CC BY 4.0) Licence will continue to apply to all software and code, e.g. relating to the functionality of the reactome.org, derived websites and webservices, the Curator Tool, the Functional Interaction application, SQL and Graph Database data dumps, and Pathway Illustrations (Enhanced High-Level Diagrams), Icon Library, Art and Branding Materials.

For information about how to properly credit data use, please review the Reactome License and the Creative Commons FAQ, or contact the This email address is being protected from spambots. You need JavaScript enabled to view it..

20171115 NAR Paper 2017

A new research article titled “The Reactome Pathway Knowledgebase” has been published in the forthcoming 2018 NAR Database Issue. The paper describes the deployment of a Neo4J graph database on our production server, development of a new high-performance in-memory implementation of our overrepresentation data analysis tool, improvements to the Pathway Diagram Viewer, and implementation of the new Enhanced High Level Diagrams (EHLDs). More publications from the Reactome Team can be found here.

new logo

As part of the ongoing evolution of our website, we are proud to announce the launch of our new logo. Reactome has grown and evolved over the last 14 years, and we felt it was time for a change.

The new logo brings to the forefront the value and quality of the information and analysis tools that can be found in our curated database of pathways. The layering in our logo highlights the transparency of Reactome’s nature while the rounded typography matches our openness.

Derived from a shape that exists in nature and at the same time gives structure, the logo evokes the idea of discovering by unwrapping the layers of knowledge that surround biological events.

We have refreshed our logo to reflect who we are today and to symbolize our dynamic future. Rest assured though: our high-quality data and services, and our dedication to you will remain the same!

For more information, please go to Our Logo.

Responsive Reactome 2

We’ve launched our new website and are excited to introduce you to our new look! Reactome is inviting its users to explore its new website. The new website has been designed to provide the ultimate user-friendly experience with improved navigation and functionality throughout. Created with the user experience firmly in mind, the new web interface has been designed using the latest technology, so the site is compatible with today's browsers and mobile devices. The site includes extensive documentation to help users understand Reactome’s complete range of tools for viewing pathway diagrams, analyzing experimental data and exploring protein-protein interaction networks. For software developers, our technical documentation and use cases provide a detailed overview of our extensive web services, to access our curated pathway data (ContentService) and analytical tools (AnalysisService). Biologists and bioinformaticians can now benefit from richer online content that is easier to navigate and share with others, assisting with pathway data analysis and visualization.

New and Updated Pathways. In version V62, topics with new or revised pathways include Developmental biology (Signaling by Robo receptor), Gene expression  (Transcriptional regulation by E2F6  and Transcriptional regulation by RUNX2), and Immune System (Interleukin-7 family signaling, Interleukin-15  family signalingInterleukin-35  family signaling, and Interleukin-38  family signaling). Illustrations are now available for Aquaporin-mediated transportCellular senescenceEpigenetic regulation of gene expressionGene ExpressionNegative epigenetic regulation of rRNA expressionO2/CO2 exchange in erythrocytesPeptide hormone metabolism, Positive epigenetic regulation of rRNA expressionPost-translational protein modificationResponse to metal ionsSignal Transduction, and SLC-mediated transmembrane transport.

Thanks to our Contributors. Patricia Ducy is our external author. Patricia DucyJorg GoronzyAnna HerlihyAlexander  JaworskiUmesh  KumarJavier Francisco MoraManoj PatidarYuliya  Pylayeva-GuptaKailash Singh, and Ren Sun are our external reviewers.

Annotation Statistics. Reactome comprises 11,302 human reactions organized into 2,176 pathways involving 10,878 proteins encoded by 10,712 different human genes, 1,768 small molecules, and 11,284 complexes. These annotations are supported by 27,526 literature references. We have projected these reactions onto 121,709 orthologous proteins, creating 20,854 orthologous pathways in 18 non-human species. Version 62 has annotations for 1,334 protein variants (mutated proteins) and their post-translationally modified forms, derived from 285 proteins. These have been used to annotate 506 disease-specific complexes and 906 disease-specific reactions organized into 453 pathways and subpathways, and tagged with 294 Disease Ontology terms.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Oregon Health and Science University, New York University Langone Medical Center, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information. Please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..

SBML

As part of our efforts to give our modeling user community better experience, we have updated the SBML export to Level 3 Version 1, which is organized in a modular manner.  Our initial export provides a richer annotation  syntax and we will explore supporting other SBML Level 3 Packages in the future. The SBML data export can be used by any tool that supports SBML L3V1.

The SBML Level 3 Version 1 export is available for download here: http://reactome.org/download/current/homo_sapiens.3.1.sbml.tgz.

We are also providing a programmatic interface to access these updated SBML files through our ContentService for all species at http://reactome.org/ContentService/#!/exporter/toSBMLUsingGET

Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Langone Medical Center, Oregon Health and Science University, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

Interaction

The Reactome team has released new versions of our protein-protein interaction files derived from reactions and complexes. These files were updated following user feedback, with the goal of providing extra annotation features through support from the PSI-MITAB 2.7 data format. Interactions are computationally generated based on the data stored on complexes and reactions. The interactions provided by Reactome are not curated and are not experimental data. In addition, the complexes and reactions in species other than human are derived by orthology inference from the corresponding human complexes and reactions. Tab-delimited formatted files are also provided for human and all species.

The four new files are:

Documentation about these files is available from the Data Download page.

The former versions of the protein-protein interaction files are still available but will be removed from service as of Version 62 in September 2017. We encourage users that programmatically access these files to update the scripts.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University Langone Medical Center, Oregon Health and Science University, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information. Please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..

R-HSA-913531

New and Updated Pathways. In version V61, topics with new or revised pathways include: Gene expression (Transcriptional regulation by RUNX1), Immune System (Interleukin-12 family signaling), Signal Transduction (PTEN Regulation), and Transport of small molecules (Intracellular oxygen transport).

Thanks to our Contributors. Arkaitz Carracedo and Leonardo Salmena were our external authors. Sabine BaillyThorsten BurmesterLinda Shyue Huey ChuangYoshiaki ItoNisha KriplaniNick Leslie, and Esther van de Vosse were our external reviewers.

Annotation Statistics. Reactome comprises 11,042 human reactions organized into 2,148 pathways involving 10,940 proteins encoded by 10,691 different human genes, 1,763 small molecules, and 11,041 complexes. These annotations are supported by 26,859 literature references. We have projected these reactions onto 120,804 orthologous proteins, creating 20,780 orthologous pathways in 18 non-human species. Version 61 has annotations for 1,334 protein variants (mutated proteins) and their post-translationally modified forms, derived from 285 proteins. These have been used to annotate 506 disease-specific complexes and 906 disease-specific reactions organized into 453 pathways and subpathways, and tagged with 294 Disease Ontology terms.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Oregon Health and Science University, New York University Langone Medical Center, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information. Please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..

New and Updated Pathways. In version V60, topics with new or revised pathways include: Cell cycle (Cyclin D associated events in G1), Cell-cell communication (SDK interactions), Cellular response to external stimuli (HSP90 chaperone cycle for steroid hormone receptors (SHR)), Disease (Diseases of Mismatch Repair), Gene Expression (TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest and Transcriptional Regulation by the CBFB:RUNX3 complex), Immune System (Butyrophilins and Regulation of complement cascade), Metabolism (Synthesis of IP2, IP, and Ins in the cytosolSynthesis of PIPs at the early endosome membraneSynthesis of PIPs at the ER membraneSynthesis of PIPs at the late endosome membrane, and Synthesis of PIPs at the plasma membrane), Metabolism of proteins (CREB3 factors activate genesNeddylationProtein ubiquitination, and SUMOylation of chromatin organizing proteins), Mitophagy (Receptor Mediated Mitophagy), Neuronal System (Receptor protein tyrosine phosphatases interactions), Organelle biogenesis and maintenance (Cristae formation), and Transport of small molecules (Mitochondrial calcium ion transport).

Thanks to our Contributors.  Wei-Chih Yang and Jian Lu are our external  authors. Joseph AinscoughSanjeevani  AroraJorge E Azevedo,  Jeehyeon BaeLucia BanciGautam BhaveDavid R BrownRoberta BullaAlexandre M CarmoLinda Shyue Huey ChuangKarlene A CimprichLaura CrisponiAlain de Bruin, Luisa Di Stefano , Ilaria DragoPablo C EcheverriaDu FengEmer S FerroDianne FordFrances V Fuller-PaceCem GabayDominique GagliardiMarcia  HaigisJ Wade HarperBarry HonigYoshiaki Ito, Veerle JanssensNathalie JossoJaewon  Ko , Vera Kozjak-PavlovicAnastasia KralliPaul J LehnerDominique  LeprinceBruce D LevyWei LiFrancisco LozanoJian LuMichael J Matunis, Birgit MeldalViolaine MoreauKyungjae MyungJoseph H NealeChristian Obinger,  R Jeroen PasterkampRichard PhippsDidier PicardElah PickDavid A RhodesPier e P Roger, Mark G Rush, Joshua R SanesMartin SchröderPierre ThibaultDick J H van den Boomen , Thomas E Van DykeRoberto M VanacoreNobutaka WakamiyaQinglu Wang, Bart Westendorp, Sandra E WileyMiriam WittmannGuilherme XavierWei-Chih YangAli A Zarrin, and Bing Zhu are our external reviewers.

Annotation Statistics. Reactome comprises 10,754 human reactions organized into 2,132 pathways involving 10,907 proteins encoded by 10,658 different human genes, 1,763 small molecules, and 10,748 complexes. These annotations are supported by 26,384 literature references. We have projected these reactions onto 115,881 orthologous proteins, creating 20,701 orthologous pathways in 18 non-human species. Version 60 has annotations for 1,503 protein variants (mutated proteins) and their post-translationally modified forms, derived from 285 proteins. These have been used to annotate 506 disease-specific complexes and 906 disease-specific reactions organized into 453 pathways and subpathways, and tagged with 294 Disease Ontology terms.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, Oregon Health and Science University, New York University Langone Medical Center, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information. Please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..

A new Reactome paper titled “Reactome pathway analysis: a high-performance in-memory approach” has been published in BMC Bioinformatics. More publications from the Reactome Team can be found here.

A new Reactome paper titled “Functional Interaction Network Construction and Analysis for Disease Discovery” has been published in Methods in Molecular Biology. More publications from the Reactome Team can be found here.

New and Updated Pathways. In version V59, topics with new or revised pathways include: Disease (Listeria monocytogenes entry into host cells), Hemostasis (Cell surface interaction at the vascular wall), Immune System (ButyrophilinsInterleukin 10 signalling, and Interleukin-4 and 13 signaling), Metabolism (Nicotinate metabolismSynthesis of PIPs at the nuclear envelopeVitamin B5 (pantothenate) metabolism, and Aryl hydrocarbon receptor signalling), Metabolism of proteins (E3 ubiquitin ligases ubiquitinate target proteinsPeptide-ligand binding receptorsProtein methylationRAB geranylgeranylation), Signal transduction (Class A/1 (Rhodopsin-like receptors), and Vesicle-mediated transport (TBC RABGAPs).

Thanks to our Contributors. Our external reviewers are Jorge AzevedoEster BoixLu DengPål FalnesVardan KaramyanSamuel LeibovichWeei-Chin LinCharuta PalsuledesaiJoel PomerantzWalter ReithSylvie Ricard-BlumChristian SchwerkBruce Spiegelman, and Xiaochun Yu.

Annotation Statistics. Reactome comprises 10,391 human reactions organized into 2,080 pathways involving 10,624 proteins encoded by 10,381 different human genes, and 1,735 small molecules. These annotations are supported by 25,449 literature references. We have projected these reactions onto 115,881 orthologous proteins, creating 20,164 orthologous pathways in 18 non-human species. Version 59 has annotations for 1,496 protein variants (mutated proteins) and their post-translationally modified forms, derived from 285 proteins. These have been used to annotate 506 disease-specific complexes and 897 disease-specific reactions organized into 447 pathways and subpathways, and tagged with 294 Disease Ontology terms.

About the Reactome Project. Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, New York University Medical Center, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information. Please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..

10K Reactome

The Reactome team is pleased to announce that it met a major milestone in October 2016 with the annotation and release of its 10,000th human protein. Reactome (www.reactome.org) is an open access curated knowledgebase which relates human genes, proteins and other biomolecules to the biological pathways and processes in which they participate. It is a key resource for the biomedical research community, and is widely used by researchers around the world to interpret high-throughput experiments in genetics, genomics and proteomics. Given that the human genome contains roughly 20,000 protein-coding genes in total, the annotation of the 10,000th protein means that Reactome now covers half of the protein-coding portion of the genome. This makes Reactome the most comprehensive open access pathway knowledgebase available to the scientific community.

By relating genes and proteins to normal and abnormal biological pathways, Reactome allows researchers to identify patterns in large data sets. For example, researchers can use Reactome to reduce an experiment that identified thousands of genes whose activities are altered in a disease to a manageable number of key biological pathways that are disrupted by these changes. Researchers can then combine Reactome with other databases to find drugs and protein targets that might reverse the pathway alterations, or to devise ways of diagnosing the disease at an early stage. Via its web site, online tools, and specialized visualization and analysis applications, Reactome has been incorporated into more than 400 third-party genome analysis tools, and has been cited more than 4,000 times in the scientific literature. 

Reactome has been in continuous operation since 2004 and is an international collaboration among the Ontario Institute for Cancer Research in Canada, New York University School of Medicine in the United States, and the European Bioinformatics Institute in the United Kingdom. It is staffed by expert biological curators, bioinformaticians and computer scientists. Much of its content is provided by community authors and peer reviewers who are assisted by the curatorial staff. The Reactome content, including pathway data and the software infrastructure, are available to all comers free of charge under a Creative Commons open access license. Reactome is supported by grants from the US National Institutes of Health, the Ontario Research Fund, the University of Toronto, OpenTargets, Genome Canada, and the European Molecular Biology Laboratory.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..

illustration deregulated CDK5 triggers multiple neurodegenerative pathways 72

New and Updated Pathways. With version V58, Reactome has annotations for over 10,000 human proteins. New or revised pathways include: Cell cycle (FBXL7 down-regulates AURKA during mitotic entry and in early mitosis), Developmental biology (Keratinization), Disease (Oncogenic MAPK signaling and Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease models), Gene expression (PI5P Regulates TP53 AcetylationTranscriptional regulation by the AP-2 (TFAP2) family of transcription factors),  Immune system  (Neutrophil degranulation and Antimicrobial peptides), Metabolism of proteins (Synthesis of active ubiquitin: roles of E1 and E2 enzymes), Signal transduction (Signaling by MET and Downregulation of ERBB2 signaling), and Vesicle-mediated transport (RAB GEFs exchange GTP for GDP on RABs).

A pathway illustration is available for Deregulated CDK5 triggers multiple neurodegenerative pathways in Alzheimer’s disease .

Thanks to our Contributors. Our external author is Kavita Shah.  Emily AyoubJorge AzevedoWalter BirchmeierMiroslav BlumenbergMaria BogachekNullin DivechaRoman DziarskiRhys GrantDavid HainsNiels HeegardGuustaaf HeynenCatherine LindonAndrea MaratRobert StephensMichel Tremblay, and Ronald Weigel are our external reviewers.

Reactome comprises 10,168 human reactions organized into 2,069 pathways involving 10,461 proteins encoded by 10,221 different human genes, and 1,710 small molecules. These annotations are supported by 24,974 literature references. We have projected these reactions onto 110,710 orthologous proteins, creating 19,991 orthologous pathways in 18 non-human species.

Reactome is a collaboration between groups at the Ontario Institute for Cancer Research, New York University Medical Center, and The European Bioinformatics Institute. Reactome data and software are distributed under the terms of the Creative Commons Attribution 4.0 License. A full description of the new and updated content is available on the Reactome website.

Follow us on Twitter: @reactome to get frequent updates about new and updated pathways, feature updates, and more!

For more information please contact our This email address is being protected from spambots. You need JavaScript enabled to view it..