Journal Article10.1093/nar/gkad1025
The Reactome Pathway Knowledgebase 2024.
Marija Milacic,Deidre Beavers,P. Conley,Chuqiao Gong,Marc Gillespie,Johannes Griss,Robin Haw,Bijay Jassal,Lisa Matthews,Bruce May,Robert Petryszak,Eliot Ragueneau,Karen Rothfels,Cristoffer Sevilla,Veronica Shamovsky,Ralf Stephan,Krishna Tiwari,Thawfeek M. Varusai,Joel Weiser,Adam Wright,Guanming Wu,Lincoln Stein,H. Hermjakob,Peter D'Eustachio +23 more
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TL;DR: Progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways are reviewed.
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Abstract: The Reactome Knowledgebase (https://reactome.org), an Elixir and GCBR core biological data resource, provides manually curated molecular details of a broad range of normal and disease-related biological processes. Processes are annotated as an ordered network of molecular transformations in a single consistent data model. Reactome thus functions both as a digital archive of manually curated human biological processes and as a tool for discovering functional relationships in data such as gene expression profiles or somatic mutation catalogs from tumor cells. Here we review progress towards annotation of the entire human proteome, targeted annotation of disease-causing genetic variants of proteins and of small-molecule drugs in a pathway context, and towards supporting explicit annotation of cell- and tissue-specific pathways. Finally, we briefly discuss issues involved in making Reactome more fully interoperable with other related resources such as the Gene Ontology and maintaining the resulting community resource network.
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TL;DR: The Alliance of Genome Resources is an extensible coalition of knowledgebases focused on genetics and genomics of model organisms. The Alliance has added and enhanced tools for browsing, downloading, mining, visualizing, and searching its resources. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community.
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References
The FAIR Guiding Principles for scientific data management and stewardship
Mark Wilkinson,Michel Dumontier,IJsbrand Jan Aalbersberg,Gabrielle Appleton,Myles Axton,Arie Baak,Niklas Blomberg,Jan-Willem Boiten,Luiz Olavo Bonino da Silva Santos,Philip E. Bourne,Jildau Bouwman,Anthony J. Brookes,Timothy Clark,Mercè Crosas,Ingrid Dillo,Olivier G. Dumon,Scott C. Edmunds,Chris T. Evelo,Richard Finkers,Alejandra Gonzalez-Beltran,Alasdair J. G. Gray,Paul Groth,Carole Goble,Jeffrey S. Grethe,Jaap Heringa,Peter A C 't Hoen,Rob Hooft,Tobias Kuhn,Ruben Kok,Joost N. Kok,Scott J. Lusher,Maryann E. Martone,Albert Mons,Abel L. Packer,Bengt Persson,Philippe Rocca-Serra,Marco Roos,Rene van Schaik,Susanna-Assunta Sansone,Erik Anthony Schultes,Thierry Sengstag,Ted Slater,George Strawn,Morris A. Swertz,Mark Thompson,Johan van der Lei,Erik M. van Mulligen,Jan Velterop,Andra Waagmeester,Peter Wittenburg,Katherine Wolstencroft,Jun Zhao,Barend Mons,Barend Mons +53 more
TL;DR: The FAIR Data Principles as mentioned in this paper are a set of data reuse principles that focus on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals.
COSMIC: the Catalogue Of Somatic Mutations In Cancer
John Tate,Sally Bamford,Harry Jubb,Harry Jubb,Zbyslaw Sondka,David Beare,Nidhi Bindal,Harry Boutselakis,Charlotte G. Cole,Celestino Creatore,Elisabeth Dawson,Peter Fish,Bhavana Harsha,Charlie Hathaway,Steve C Jupe,Chai Yin Kok,Kate Noble,Laura Ponting,Christopher C Ramshaw,Claire Rye,Helen E. Speedy,Raymund Stefancsik,Sam Thompson,Shicai Wang,Sari Ward,Peter J. Campbell,Simon A. Forbes +26 more
TL;DR: Improvements to the public website and data-download systems and new functionality in COSMIC-3D allows exploration of mutations within three-dimensional protein structures, their protein structural and functional impacts, and implications for druggability.
KEGG for taxonomy-based analysis of pathways and genomes
TL;DR: An increasing number of eukaryotic genomes have been included in KEGG for better representation of organisms in the taxonomic tree, and the Brite hierarchy viewer is used for taxonomy mapping.
UniProt: the Universal Protein Knowledgebase in 2023
Alex Bateman,Maria Jesus Martin,Sandra Orchard,Michele Magrane,Shadab Ahmad,Emanuele Alpi,Emily H Bowler-Barnett,Ramona Britto,Hema Bye-a-Jee,Austra Cukura,P. Denny,Tunca Doğan,ThankGod Ebenezer,Jun Fan,Penelope Garmiri,Leonardo Jose da Costa Gonzales,Emma Hatton-Ellis,Abdulrahman Hussein,Alexandr Ignatchenko,Giuseppe Insana,Rizwan Ishtiaq,Vishal Joshi,Dushyanth Jyothi,Swaathi Kandasaamy,Antonia Lock,Aurelien Luciani,Marija Lugarić,Jie Luo,Y. Lussi,Alistair MacDougall,Fábio Madeira,Mahdi Mahmoudy,Alok Mishra,Katie Moulang,Andrew Nightingale,Sangya Pundir,Guoying Qi,Shriya Raj,Pedro Duarte da Silva Fonseca Gândara Raposo,Daniel Rice,Rabie Saidi,Rafael Santos,Elena Speretta,James Stephenson,Prabhat Totoo,Edward Turner,N. Tyagi,Preethi Vasudev,Kate Warner,Xavier Watkins,Rossana Zaru,Hermann Zellner,Alan Bridge,Lucila Aimo,Ghislaine Argoud-Puy,Andrea H. Auchincloss,Kristian B. Axelsen,Parit Bansal,Delphine Baratin,Teresa M Batista Neto,Marie-Claude Blatter,Jerven Bolleman,Emmanuel Boutet,Lionel Breuza,B. Gil,C. Casals-Casas,Kamal Chikh Echioukh,Elisabeth Coudert,Béatrice A. Cuche,Edouard de Castro,Anne Estreicher,Maria Livia Famiglietti,Marc Feuermann,Elisabeth Gasteiger,Pascale Gaudet,Sebastien Gehant,Vivienne Baillie Gerritsen,Arnaud Gos,Nadine M. Gruaz,Chantal Hulo,Nevila Hyka-Nouspikel,Florence Jungo,Arnaud Kerhornou,Philippe Le Mercier,Damien Lieberherr,Patrick Masson,Anne Morgat,Venkatesh Muthukrishnan,Salvo Paesano,Ivo Pedruzzi,Sandrine Pilbout,Lucille Pourcel,Sylvain Poux,Monica Pozzato,Manuela Pruess,Nicole Redaschi,Catherine Rivoire,Christian J. A. Sigrist,K Sonesson,Shyamala Sundaram,Cathy H. Wu,Cecilia N. Arighi,Leslie Arminski,Chuming Chen,Yongxing Chen,Hongzhan Huang,Kati Laiho,Peter B. McGarvey,Darren A. Natale,Karen F. Ross,C. R. Vinayaka,Qinghua Wang,Yuqi Wang,Jian Zhang +113 more
TL;DR:
The reactome pathway knowledgebase 2022.
Marc Gillespie,Marc Gillespie,Bijay Jassal,Ralf Stephan,Marija Milacic,Karen Rothfels,Andrea Senff-Ribeiro,Andrea Senff-Ribeiro,Johannes Griss,Johannes Griss,Cristoffer Sevilla,Lisa Matthews,Chuqiao Gong,Chuan Deng,Chuan Deng,Thawfeek M. Varusai,Eliot Ragueneau,Yusra Haider,Bruce May,Veronica Shamovsky,Joel Weiser,Timothy Brunson,Nasim Sanati,Liam Beckman,Xiang Shao,Antonio Fabregat,Konstantinos Sidiropoulos,Julieth Murillo,Guilherme Viteri,Justin Cook,Solomon Shorser,Gary D. Bader,Emek Demir,Chris Sander,Robin Haw,Guanming Wu,Lincoln Stein,Lincoln Stein,Henning Hermjakob,Henning Hermjakob,Peter D'Eustachio +40 more
TL;DR: The Reactome Knowledgebase as mentioned in this paper provides manually curated molecular details across a broad range of physiological and pathological biological processes in humans, including both hereditary and acquired disease processes, annotated as an ordered network of molecular transformations in a single consistent data model.
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