Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
Reads0
Chats0
TLDR
This work describes here the new parallel identification scheme and the updated supporting software infrastructure, and introduces the new Identifiers.org service, which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs).Abstract:
The Minimum Information Required in the Annotation of Models Registry (http://www.ebi.ac.uk/miriam) provides unique, perennial and location-independent identifiers for data used in the biomedical domain. At its core is a shared catalogue of data collections, for each of which an individual namespace is created, and extensive metadata recorded. This namespace allows the generation of Uniform Resource Identifiers (URIs) to uniquely identify any record in a collection. Moreover, various services are provided to facilitate the creation and resolution of the identifiers. Since its launch in 2005, the system has evolved in terms of the structure of the identifiers provided, the software infrastructure, the number of data collections recorded, as well as the scope of the Registry itself. We describe here the new parallel identification scheme and the updated supporting software infrastructure. We also introduce the new Identifiers.org service (http://identifiers.org) that is built upon the information stored in the Registry and which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs). The flexibility of the identification scheme and resolving system allows its use in many different fields, where unambiguous and perennial identification of data entities are necessary.read more
Citations
More filters
Journal ArticleDOI
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins.
Andrew D. Rouillard,Gregory W. Gundersen,Nicolas F. Fernandez,Zichen Wang,Caroline D. Monteiro,Michael G. McDermott,Avi Ma'ayan +6 more
TL;DR: The Harmonizome is a comprehensive resource of knowledge about genes and proteins that enables researchers to discover novel relationships between biological entities, as well as form novel data-driven hypotheses for experimental validation.
Journal ArticleDOI
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.
Zachary A. King,Justin S. Lu,Andreas Dräger,Andreas Dräger,Philip C. Miller,Stephen Federowicz,Joshua A. Lerman,Ali Ebrahim,Bernhard O. Palsson,Nathan E. Lewis +9 more
TL;DR: BiGG Models is presented, a completely redesigned Biochemical, Genetic and Genomic knowledge base that contains more than 75 high-quality, manually-curated genome-scale metabolic models that will facilitate diverse systems biology studies and support knowledge-based analysis of diverse experimental data.
Journal ArticleDOI
BioModels: ten-year anniversary
Vijayalakshmi Chelliah,Nick Juty,Ishan Ajmera,Raza Ali,Marine Dumousseau,Mihai Glont,Michael Hucka,Gaël Jalowicki,Sarah M. Keating,Vincent Knight-Schrijver,Audald Lloret-Villas,Kedar Nath Natarajan,Jean-Baptiste Pettit,Nicolas Rodriguez,Michael Schubert,Sarala M. Wimalaratne,Yangyang Zhao,Henning Hermjakob,Nicolas Le Novère,Camille Laibe +19 more
TL;DR: BioModels as discussed by the authors is a repository of mathematical models of biological processes, which is used to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication.
Journal ArticleDOI
The EBI RDF Platform: Linked Open Data for the Life Sciences
Simon Jupp,James Malone,Jerven Bolleman,Marco Brandizi,Mark Davies,Leyla Garcia,Anna Gaulton,Sebastien Gehant,Camille Laibe,Nicole Redaschi,Sarala M. Wimalaratne,Maria Jesus Martin,Nicolas Le Novère,Helen Parkinson,Ewan Birney,Andrew M. Jenkinson +15 more
TL;DR: The EBI RDF platform has been developed to meet an increasing demand to coordinate RDF activities across the institute and provides a new entry point to querying and exploring integrated resources available at the EBI.
Journal ArticleDOI
The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core.
Michael Hucka,Frank Bergmann,Claudine Chaouiya,Andreas Dräger,Stefan Hoops,Sarah M. Keating,Matthias König,Nicolas Le Novère,Chris J. Myers,Brett G. Olivier,Sven Sahle,James C. Schaff,Rahumann Sheriff,Lucian P. Smith,Dagmar Waltemath,Darren J. Wilkinson,Fengkai Zhang +16 more
TL;DR: This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core, which defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language.
References
More filters
Journal ArticleDOI
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
TL;DR: This work summarizes the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks, a software-independent language for describing models common to research in many areas of computational biology.
Journal ArticleDOI
The OBO Foundry : coordinated evolution of ontologies to support biomedical data integration
Barry Smith,Michael Ashburner,Cornelius Rosse,Jonathan Bard,William J. Bug,Werner Ceusters,Louis J. Goldberg,Karen Eilbeck,Amelia Ireland,Christopher J. Mungall,Neocles B. Leontis,Philippe Rocca-Serra,Alan Ruttenberg,Susanna-Assunta Sansone,Richard H. Scheuermann,Nigam H. Shah,Patricia L. Whetzel,Suzanna E. Lewis +17 more
TL;DR: This work describes the OBO Foundry initiative and provides guidelines for those who might wish to become involved and describes an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality.
Book
Linked Data
TL;DR: This Synthesis lecture provides readers with a detailed technical introduction to Linked Data, including coverage of relevant aspects of Web architecture, and provides guidance and best practices on architectural approaches to publishing Linked data.
Journal ArticleDOI
Bio2RDF: Towards a mashup to build bioinformatics knowledge systems
TL;DR: The present article details this new approach to build mashups of bioinformatics data and illustrates the building of a mashup used to explore the implication of four transcription factor genes in Parkinson's disease.
Journal ArticleDOI
Minimum information requested in the annotation of biochemical models (MIRIAM)
Nicolas Le Novère,Andrew Finney,Michael Hucka,Upinder S. Bhalla,Fabien Campagne,Julio Collado-Vides,Edmund J. Crampin,Matt D. B. Halstead,Edda Klipp,Pedro Mendes,Poul M. F. Nielsen,Herbert M. Sauro,Bruce E. Shapiro,Jacky L. Snoep,Hugh D. Spence,Barry L. Wanner +15 more
TL;DR: These rules define procedures for encoding and annotating models represented in machine-readable form to enable users to have confidence that curated models are an accurate reflection of their associated reference descriptions and to facilitate model reuse and composition into large subcellular models.
Related Papers (5)
The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Michael Hucka,Andrew Finney,Herbert M. Sauro,Hamid Bolouri,Hamid Bolouri,John Doyle,Hiroaki Kitano,Adam P. Arkin,Benjamin Bornstein,Dennis Bray,Athel Cornish-Bowden,Autumn A. Cuellar,S. Dronov,E. D. Gilles,Martin Ginkel,V. Gor,Igor Goryanin,W. J. Hedley,T. C. Hodgman,J.-H.S. Hofmeyr,Peter Hunter,Nick Juty,J. L. Kasberger,Andreas Kremling,Ursula Kummer,N Le Novère,Leslie M. Loew,D. Lucio,Pedro Mendes,E. Minch,Eric Mjolsness,Yoichi Nakayama,Melanie R. Nelson,Poul M. F. Nielsen,T. Sakurada,James C. Schaff,Bruce E. Shapiro,Thomas S. Shimizu,H. D. Spence,Jörg Stelling,Koichi Takahashi,Masaru Tomita,John Wagner,J. Wang +43 more
The Systems Biology Graphical Notation
Nicolas Le Novère,Michael Hucka,Huaiyu Mi,Stuart L. Moodie,Falk Schreiber,Falk Schreiber,Anatoly Sorokin,Emek Demir,Katja Wegner,Mirit I. Aladjem,Sarala M. Wimalaratne,Frank T Bergman,Ralph Gauges,Peter Ghazal,Hideya Kawaji,Lu Li,Yukiko Matsuoka,Alice Villéger,Sarah Elizabeth Boyd,Laurence Calzone,Mélanie Courtot,Ugur Dogrusoz,Tom C. Freeman,Akira Funahashi,Samik Ghosh,Akiya Jouraku,Sohoung Kim,Fedor A. Kolpakov,Augustin Luna,Sven Sahle,Esther Schmidt,Steven Watterson,Steven Watterson,Guanming Wu,Igor Goryanin,Douglas B. Kell,Chris Sander,Herbert M. Sauro,Jacky L. Snoep,Kurt W. Kohn,Hiroaki Kitano +40 more
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
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