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Identifiers.org - Compact Identifier Services in the Cloud

Manuel Bernal Llinares, Javier Ferrer Gomez, Nick Juty, Carole Goble, Sarala M Wimalaratne, Henning Hermjakob, Zhiyong Lu
2020 Bioinformatics  
We have also deployed the new Identifiers.org infrastructure in a commercial cloud environment, bringing our services closer to the data.  ...  In 2016, we established the Compact Identifier (CID) scheme (prefix: accession) to generate globally unique identifiers for data resources using their locally assigned accession identifiers.  ...  Acknowledgements The authors thank John Kunze, Timothy W. Clark, Rafael C. Jimenez and Greg Jenee for ongoing discussions on identifier harmonisation. Funding  ... 
doi:10.1093/bioinformatics/btaa864 pmid:33031499 pmcid:PMC8289372 fatcat:5swpz4co4bh7plvcwnclpuk3ly

Compact Identifiers Service in the Cloud

Bernal Llinares, Ferrer Gómez, Wimalaratne, Juty, Hermjakob
2020 Zenodo  
services in sync with our registry, on premises, hybrid cloud and multi-cloud environments.  ...  We have released a brand new cloud native modern identifiers.org platform, focused on its main mission, resolution of compact identifiers.  ...  Identify " … the protein we used (pdb:4y2g) in our tests … " Cite Annotate Identify, cite and annotate your data using Compact Identifiers.  ... 
doi:10.5281/zenodo.3876248 fatcat:tnc4yvfpbzab3i65uzwxkkqr3e

Identifiers.org Connecting Life Sciences Data

Manuel Bernal Llinares
2020 Zenodo  
This presentation on identifiers.org key role in connecting life sciences data, was given at "Realising the European Open Science Cloud" conference, 16 - 19 November 2020, within the context of "Devloping  ...  the PID Graph".  ...  CIs in-line Data Citation … the protein we used (pdb:2gc4) in our tests … A persistent identifier that provides access and metadata.  ... 
doi:10.5281/zenodo.4280783 fatcat:gqcccic74rffvfqvcce4tw4d7y

Our Journey to the Clouds

Manuel Bernal-Llinares
2020 Zenodo  
services in sync with our registry, on premises, hybrid cloud and multi-cloud environments.  ...  We have recently released a brand new cloud native modern identifiers.org platform, focused on its main mission, resolution of compact identifiers.  ...  Compact Identifiers for in-line data citation … the protein we used (pdb:2gc4) in our tests … A persistent identifier that provides access and metadata. stable, resolvable and location-independent URIs  ... 
doi:10.5281/zenodo.3643337 fatcat:gubqreodzzgatdo4vkwgeinlei

Uniform resolution of compact identifiers for biomedical data

Sarala M. Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A. McMurry, Niall Beard, Rafael Jimenez, Jeffrey S. Grethe, Henning Hermjakob, Maryann E. Martone, Tim Clark
2018 Scientific Data  
Author Contributions S.W. and N.J. were responsible for all software development and alignment work undertaken on the Identifiers.org system in this project.  ...  J.M. contributed architectural guidance on identifier design incorporating perspectives of the Prefix Commons project.  ...  Advice on growing and sustaining the service will be sought from additional experts in the field, and participation in key development projects, such as the European Open Science Cloud and the NIH Data  ... 
doi:10.1038/sdata.2018.29 pmid:29737976 pmcid:PMC5944906 fatcat:ig5sqxrr5ra6lhlz73crdrdaha

Uniform Resolution of Compact Identifiers for Biomedical Data [article]

Sarala Wimalaratne, Nick Juty, John Kunze, Greg Janée, Julie A McMurry, Niall Beard, Rafael Jimenez, Jeffrey Grethe, Henning Hermjakob, Tim Clark
2017 bioRxiv   pre-print
Compact identifiers have been widely used in biomedical informatics both formally and informally.  ...  , or is referenced in the web at large.  ...  He had full access to all the data in this study and takes responsibility for the integrity of the work.  ... 
doi:10.1101/101279 fatcat:4ui54who3vfjjeqlzeo6op4zmi

Unique, Persistent, Resolvable: Identifiers as the Foundation of FAIR

Nick Juty, Sarala M. Wimalaratne, Stian Soiland-Reyes, John Kunze, Carole A. Goble, Tim Clark
2019 Data Intelligence  
The FAIR principles describe characteristics intended to support access to and reuse of digital artifacts in the scientific research ecosystem.  ...  Persistent, globally unique identifiers, resolvable on the Web, and associated with a set of additional descriptive metadata, are foundational to FAIR data.  ...  service started in 1995.  ... 
doi:10.1162/dint_a_00025 fatcat:vbr5g2ovxvexppympqoo7u3zb4

Unique, Persistent, Resolvable: Identifiers as the foundation of FAIR

Nick Juty, Sarala M. Wimalaratne, Stian Soiland-Reyes, John Kunze, Carole Anne Goble, Tim Clark
2019 Zenodo  
The FAIR Principles describe characteristics intended to support access to and reuse of digital artifacts in the scientific research ecosystem.  ...  Persistent, globally unique identifiers, resolvable on the Web, and associated with a set of additional descriptive metadata, are foundational to FAIR data.  ...  service started in 1995.  ... 
doi:10.5281/zenodo.3267433 fatcat:x4yt77yggjbrjj6ado5obkncki

Deliverable 2.3 PID Services Registry

Martin Fenner
2020 Zenodo  
This report describes the online registry of PID-related services that has been developed by the FREYA project.  ...  It discusses the context, presents the technical decisions and bases for the work, and lists the initial content of the registry.  ...  This information is used by the Identifiers.org Resolution Service, which provides consistent access to life science data using Compact Identifiers.  ... 
doi:10.5281/zenodo.4292139 fatcat:cr53m3mxofewrdphtq3hvdh674

Deliverable 3.3 Prototypes of New PID Resources

Robin Dasler, Christine Ferguson, Tina Dohna, Uwe Schindler, Frances Madden, Manuel Bernal Llinares, Vasily Bunakov, Simon Lambert
2020 Zenodo  
This work follows the previous two deliverables in this work package, which identified gaps in the PID landscape and determined feasibility of prototype implementation, respectively.  ...  This report describes the results of the prototyping implementations of new PID types and new PID services conducted by the FREYA partners.  ...  The Identifiers.org resolver provides a stable resolution service for these Compact Identifiers, taking into consideration information such as the uptime and reliability of all available hosting resources  ... 
doi:10.5281/zenodo.4302331 fatcat:e5wgpce435fyxbi2s7nzvl3x3u

D2.1 Pid Resolution Services Best Practices

Sara Wimalaratne, Martin Fenner
2018 Zenodo  
This report describes approaches to PID resolution, and sets out best practices to be followed as well as future work in the area and a survey of the practices of different disciplines.  ...  Table 3 Examples for provider codes Provider The Identifiers.org resolver provides a stable resolution service for these Compact Identifiers with provider codes (see Table 2 ).  ...  the European Open Science Cloud, and beyond.  ... 
doi:10.5281/zenodo.1324299 fatcat:t2juizluzbe6bcg47pzgawc3de

D5.1 Interoperability Implementation Regulations

Carol Goble, Chris Evelo, Helen Parkinson, ELIXIR Interoperability Community
2018 Zenodo  
This deliverable originally aimed to present "Interoperability Implementation Regulations" as "a set of standards, rules, controlled vocabularies, authorized unique identifiers and interoperable service  ...  Rather, it addresses the necessary interoperabilityinfrastructure to support the use cases through standards, services and know-how.  ...  Identifiers.org has recently been extended to support giving credit to individual data providers/databases through the compact identifier system.  ... 
doi:10.5281/zenodo.1452414 fatcat:j6bod5nlinadhl623uez7x46m4

D2.2 PID Metadata Provenance

Martin Fenner, Joe Wass, Tom Demeranville, Sarala Wimalaratne, Richard Hallett
2019 Zenodo  
The main focus of this document is describing the implementations of provenance tracking by the persistent identifier (PID) providers Crossref, ORCID, Identifiers.org (EMBL-EBI), and DataCite in the FREYA  ...  We describe the implementations by Crossref and ORCID done previously, the DataCite implementation done as main output for this deliverable, and the conceptual work by identifiers.org.  ...  This allows identifiers.org to uniquely identify pdb datasets in the form of compact identifiers, pdb:{local identifier or accession number} eg: pdb:4hhb.  ... 
doi:10.5281/zenodo.3248652 fatcat:acc72dhkojgojivrdxrwguit4a

Assessment report on 'FAIRness of services'

Hylke Koers, Morane Gruenpeter, Patricia Herterich, Rob Hooft, Sarah Jones, Jessica Parland-von Essen, Christine Staiger
2020 Zenodo  
To realise the full potential of a FAIR ecosystem in which research can be easily shared and optimally reused, as put forward in the Turning FAIR into reality report, we must look beyond 'just' research  ...  is still lacking — a fact that was recently underlined again in the interim recommendations from the EOSC FAIR Working Group.  ...  Documentation Case Study 2: Identifiers.org Service Summary Identifiers.org is a resolution service and registry for identifiers in the life sciences, including identifiers from different domains.  ... 
doi:10.5281/zenodo.3688762 fatcat:jivqcksyt5d55me7vp6a6bzfkm

Assessment report on 'FAIRness of services'

Hylke Koers, Morane Gruenpeter, Patricia Herterich, Rob Hooft, Sarah Jones, Jessica Parland-von Essen, Christine Staiger
2020 Zenodo  
To realise the full potential of a FAIR ecosystem in which research can be easily shared and optimally reused, as put forward in the Turning FAIR into reality report, we must look beyond 'just' research  ...  is still lacking — a fact that was recently underlined again in the interim recommendations from the EOSC FAIR Working Group.  ...  Documentation Case Study 2: Identifiers.org Service Summary Identifiers.org is a resolution service and registry for identifiers in the life sciences, including identifiers from different domains.  ... 
doi:10.5281/zenodo.5470375 fatcat:267mrrcg3je25ivnk7f3xolafi
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