Identifiers.org Central Registry
The Identifiers.org Central Registry provides the necessary information for the generation and resolution of unique and perennial identifiers for life science data. Those identifiers are both in URI and compact form, and make use of Identifiers.org to provide direct access to the identified data records on the Web. Resource maintainers request an Identifiers.org prefix for their databases or services.
Description
More detailed information about this field from each metasource.
The Identifiers.org Central Registry provides the necessary information for the generation and resolution of unique and perennial identifiers for life science data. Those identifiers are both in URI and compact form, and make use of Identifiers.org to provide direct access to the identified data records on the Web. Resource maintainers request an Identifiers.org prefix for their databases or services.
metasource: Fairsharing.orgversion: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Webpage:
https://registry.identifiers.org/Webpage
More detailed information about this field from each metasource.
https://registry.identifiers.org/
metasource: Fairsharing.orgversion: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence:
Name: Creative Commons Attribution 4.0 International (CC BY 4.0)Licence name
More detailed information about this field from each metasource.
Creative Commons Attribution 4.0 International (CC BY 4.0)
metasource: Fairsharing.orgversion: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
More detailed information about this field from each metasource.
https://creativecommons.org/licenses/by/4.0/
metasource: Fairsharing.orgversion: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
PMID: 22140103
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
PMID: 18078503
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Uniform resolution of compact identifiers for biomedical data
PMID: 29737976
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
PMID: 22140103
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
PMID: 18078503
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Uniform resolution of compact identifiers for biomedical data
PMID: 29737976
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
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Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
PubMed citations: 87.
87 articles citing: Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
ELIXIR biovalidator for semantic validation of life science metadata. PMID:35380605
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032. PMID:34867870
Specifications of standards in systems and synthetic biology: status and developments in 2021. PMID:34674411
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
An updated genome-scale metabolic network reconstruction of Pseudomonas aeruginosa PA14 to characterize mucin-driven shifts in bacterial metabolism. PMID:34625561
Integrated human/SARS-CoV-2 metabolic models present novel treatment strategies against COVID-19. PMID:34353886
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus. PMID:34188046
ELIXIR: Providing a Sustainable Infrastructure for Life Science Data at European Scale. PMID:34175941
BENZ WS: the Bologna ENZyme Web Server for four-level EC number annotation. PMID:33963861
A resource to explore the discovery of rare diseases and their causative genes. PMID:33947870
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies. PMID:33918864
Genome-scale metabolic reconstruction of the non-model yeast Issatchenkia orientalis SD108 and its application to organic acids production. PMID:33134082
Executable biochemical space for specification and analysis of biochemical systems. PMID:32915842
Publishing reproducible dynamic kinetic models. PMID:32793969
Specifications of standards in systems and synthetic biology: status and developments in 2020. PMID:32598316
A comprehensive genome-scale model for Rhodosporidium toruloides IFO0880 accounting for functional genomics and phenotypic data. PMID:31720216
Data Management in Computational Systems Biology: Exploring Standards, Tools, Databases, and Packaging Best Practices. PMID:31602618
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019. PMID:31301675
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
MINERVA API and plugins: opening molecular network analysis and visualization to the community. PMID:31074494
Metabolic Modeling of Pectobacterium parmentieri SCC3193 Provides Insights into Metabolic Pathways of Plant Pathogenic Bacteria. PMID:30959803
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. PMID:30576482
Agronomic Linked Data (AgroLD): A knowledge-based system to enable integrative biology in agronomy. PMID:30500839
Harmonizing semantic annotations for computational models in biology. PMID:30462164
A data citation roadmap for scientific publishers. PMID:30457573
Integration among databases and data sets to support productive nanotechnology: Challenges and recommendations. PMID:30246165
Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. PMID:29917015
Biomedical Informatics on the Cloud: A Treasure Hunt for Advancing Cardiovascular Medicine. PMID:29700073
Community-driven roadmap for integrated disease maps. PMID:29688273
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017. PMID:29596055
LAILAPS-QSM: A RESTful API and JAVA library for semantic query suggestions. PMID:29529024
Biotea: semantics for Pubmed Central. PMID:29312824
From word models to executable models of signaling networks using automated assembly. PMID:29175850
Data Portal for the Library of Integrated Network-based Cellular Signatures (LINCS) program: integrated access to diverse large-scale cellular perturbation response data. PMID:29140462
Using semantics for representing experimental protocols. PMID:29132408
BioModels: expanding horizons to include more modelling approaches and formats. PMID:29106614
biochem4j: Integrated and extensible biochemical knowledge through graph databases. PMID:28708831
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PMID:28662064
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016. PMID:28187405
Publication of nuclear magnetic resonance experimental data with semantic web technology and the application thereof to biomedical research of proteins. PMID:27927232
Bio-TDS: bioscience query tool discovery system. PMID:27924016
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants. PMID:27842607
Harnessing Big Data for Systems Pharmacology. PMID:27814027
The health care and life sciences community profile for dataset descriptions. PMID:27602295
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. PMID:27374120
Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources. PMID:27336457
Generation of open biomedical datasets through ontology-driven transformation and integration processes. PMID:27255189
DisGeNET-RDF: harnessing the innovative power of the Semantic Web to explore the genetic basis of diseases. PMID:27153650
SBtab: a flexible table format for data exchange in systems biology. PMID:27153616
RegenBase: a knowledge base of spinal cord injury biology for translational research. PMID:27055827
The systems biology format converter. PMID:27044654
Challenges in horizontal model integration. PMID:26968798
Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization. PMID:26559508
BiGG Models: A platform for integrating, standardizing and sharing genome-scale models. PMID:26476456
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Data integration in biological research: an overview. PMID:26336651
BioModels: Content, Features, Functionality, and Use. PMID:26225232
Human metabolic atlas: an online resource for human metabolism. PMID:26209309
Achieving human and machine accessibility of cited data in scholarly publications. PMID:26167542
From Peer-Reviewed to Peer-Reproduced in Scholarly Publishing: The Complementary Roles of Data Models and Workflows in Bioinformatics. PMID:26154165
Visualisation of BioPAX Networks using BioLayout Express (3D). PMID:25949802
KaBOB: ontology-based semantic integration of biomedical databases. PMID:25903923
Promoting Coordinated Development of Community-Based Information Standards for Modeling in Biology: The COMBINE Initiative. PMID:25759811
Combining computational models, semantic annotations and simulation experiments in a graph database. PMID:25754863
Computationally Modeling Lipid Metabolism and Aging: A Mini-review. PMID:25750699
OpenCOR: a modular and interoperable approach to computational biology. PMID:25705192
SPARQL-enabled identifier conversion with Identifiers.org. PMID:25638809
Integration of a constraint-based metabolic model of Brassica napus developing seeds with (13)C-metabolic flux analysis. PMID:25566296
Improving collaboration by standardization efforts in systems biology. PMID:25538939
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. PMID:25494900
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. PMID:25477381
BioModels: ten-year anniversary. PMID:25414348
BioModels linked dataset. PMID:25182954
Guidelines for managing data and processes in bone and cartilage tissue engineering. PMID:24564199
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. PMID:24495517
The EBI RDF platform: linked open data for the life sciences. PMID:24413672
Path2Models: large-scale generation of computational models from biochemical pathway maps. PMID:24180668
Variation Ontology for annotation of variation effects and mechanisms. PMID:24162187
NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps. PMID:24099179
Metingear: a development environment for annotating genome-scale metabolic models. PMID:23766418
Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data. PMID:23734622
Structure, function, and behaviour of computational models in systems biology. PMID:23721297
The MetaboLights repository: curation challenges in metabolomics. PMID:23630246
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
Precise generation of systems biology models from KEGG pathways. PMID:23433509
VarioML framework for comprehensive variation data representation and exchange. PMID:23031277 -
MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
PubMed citations: 42.
42 articles citing: MIRIAM Resources: tools to generate and resolve robust cross-references in Systems Biology
Best Practices for Making Reproducible Biochemical Models. PMID:32853539
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. PMID:31225582
CiliateGEM: an open-project and a tool for predictions of ciliate metabolic variations and experimental condition design. PMID:30497359
Modelling pyruvate dehydrogenase under hypoxia and its role in cancer metabolism. PMID:29134060
Metabolic modeling to identify engineering targets for Komagataella phaffii: The effect of biomass composition on gene target identification. PMID:28691262
Harnessing Big Data for Systems Pharmacology. PMID:27814027
SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks. PMID:26452770
Implementation of linked data in the life sciences at BioHackathon 2011. PMID:25973165
OpenCOR: a modular and interoperable approach to computational biology. PMID:25705192
Improving collaboration by standardization efforts in systems biology. PMID:25538939
Towards the collaborative curation of the registry underlying Identifiers.org. PMID:23584831
LibKiSAO: a Java library for Querying KiSAO. PMID:23006857
AbsIDconvert: an absolute approach for converting genetic identifiers at different granularities. PMID:22967011
Reverse engineering biomolecular systems using -omic data: challenges, progress and opportunities. PMID:22833495
A tool for multi-scale modelling of the renal nephron. PMID:22670210
AlzPathway: a comprehensive map of signaling pathways of Alzheimer's disease. PMID:22647208
Reproducible computational biology experiments with SED-ML--the Simulation Experiment Description Markup Language. PMID:22172142
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. PMID:22140103
Identifying and relating biological concepts in the Catalogue of Life. PMID:22004596
Empowering industrial research with shared biomedical vocabularies. PMID:21963522
The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions. PMID:21878109
Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. PMID:21632604
Current trends and new challenges of databases and web applications for systems driven biological research. PMID:21423387
The Biomolecular Interaction Network Database in PSI-MI 2.5. PMID:21233089
Further developments towards a genome-scale metabolic model of yeast. PMID:21029416
The BioPAX community standard for pathway data sharing. PMID:20829833
Ranked retrieval of Computational Biology models. PMID:20701772
Annotation of SBML models through rule-based semantic integration. PMID:20626923
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. PMID:20587024
Semantic integration of data on transcriptional regulation. PMID:20427517
Snazer: the simulations and networks analyzer. PMID:20056001
BioModels.net Web Services, a free and integrated toolkit for computational modelling software. PMID:19939940
The challenges of informatics in synthetic biology: from biomolecular networks to artificial organisms. PMID:19906839
XML-based approaches for the integration of heterogeneous bio-molecular data. PMID:19828083
An editor for pathway drawing and data visualization in the Biopathways Workbench. PMID:19799790
BioGateway: a semantic systems biology tool for the life sciences. PMID:19796395
Saint: a lightweight integration environment for model annotation. PMID:19734151
libAnnotationSBML: a library for exploiting SBML annotations. PMID:19561017
CellML metadata standards, associated tools and repositories. PMID:19380315
Designing and encoding models for synthetic biology. PMID:19364720
How to deal with large models? PMID:19156132
Complexity and modularity of intracellular networks: a systematic approach for modelling and simulation. PMID:19045831 -
Uniform resolution of compact identifiers for biomedical data
PubMed citations: 22.
22 articles citing: Uniform resolution of compact identifiers for biomedical data
Providing Adverse Outcome Pathways from the AOP-Wiki in a Semantic Web Format to Increase Usability and Accessibility of the Content. PMID:35388368
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms. PMID:34664389
Ten simple rules for creating reusable pathway models for computational analysis and visualization. PMID:34411100
Recommendations for the FAIRification of genomic track metadata. PMID:34249331
Universal Spectrum Identifier for mass spectra. PMID:34183830
APICURON: a database to credit and acknowledge the work of biocurators. PMID:33882120
A decoupled, modular and scriptable architecture for tools to curate data platforms. PMID:33830216
A Second Look at FAIR in Proteomic Investigations. PMID:33719446
DriveWays: a method for identifying possibly overlapping driver pathways in cancer. PMID:33319839
Sharing voxelwise neuroimaging results from rhesus monkeys and other species with Neurovault. PMID:33137472
Identifiers.org: Compact Identifier services in the cloud. PMID:33031499
Wikidata as a knowledge graph for the life sciences. PMID:32180547
Reactome and ORCID-fine-grained credit attribution for community curation. PMID:31802127
Facilities that make the PDB data collection more powerful. PMID:31724231
Credit data generators for data reuse. PMID:31164773
Data citation needed. PMID:30971699
A data citation roadmap for scholarly data repositories. PMID:30971690
Harmonizing semantic annotations for computational models in biology. PMID:30462164
A data citation roadmap for scientific publishers. PMID:30457573
UniProt: a worldwide hub of protein knowledge. PMID:30395287
On the road to robust data citation. PMID:29737977
Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PMID:28662064
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centrally registered identifier
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
data identity and mapping
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
resource metadata
metasource: Fairsharing.org
version: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
Tags
More detailed information about this field from each metasource.
centrally registered identifier
metasource: Fairsharing.orgversion: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
data identity and mapping
metasource: Fairsharing.orgversion: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
resource metadata
metasource: Fairsharing.orgversion: FAIRsharing.org: Identifiers.org Central Registry; Identifiers.org Central Registry; DOI: https://doi.org/10.25504/FAIRsharing.n14rc8; Last edited: March 11, 2021, 11:34 a.m.; Last accessed: Jan 03 2022 7:07 p.m.
centrally registered identifier data identity and mapping resource metadata
Need help integrating and/or managing biomedical data?