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Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau (+57 others)
2015 Nucleic Acids Research  
Resource providers. A non-exhaustive list of collections that have contributed or will contribute to the registry.  ...  DRCAT resource catalogue http://drcat.sourceforge.net The data resource catalogue is a collection of metadata on bioinformatics Web-based data resources.  ...  ACKNOWLEDGEMENTS The authors would like to thank Steve Pettifer and Dave Thorne for the initial discussions and ideas founding the registry effort.  ... 
doi:10.1093/nar/gkv1116 pmid:26538599 pmcid:PMC4702812 fatcat:npzer6xh7fezlbcamfmdvv552m

D1.7 Description Of The Registry User Helpdesk & Impact On User Support Via Community Forums

Jon Ison, Hans Ienasescu, Herve Menager, ELIXIR Tools Community
2018 Zenodo  
The objective of EXCELERATE Deliverable 1.7 is to provide comprehensive support for users of the ELIXIR Tools and Data Services Registry ( https://bio.tools ).  ...  We originally anticipated to provide direct support to tool users, primarily by leveraging the existing and highly popular user bioinformatics forums (BioStars, BioPlanet etc) This remains a good objective  ...  The ELIXIR Tools and Data Services Registry is the cornerstone of the WP.  ... 
doi:10.5281/zenodo.1457219 fatcat:v3fjtkdzmnhulkyaph6okmra2u

D1.5 Incorporation Of Monitoring Statistics And Benchmarking Results In Registry Releases

Jon Ison, Hans Ienasescu, Matus Kalas, Tools Community
2018 Zenodo  
to sort and filter bio.tools search results by various criteria, and 2) to render labels on bio.tools Tool Cards, perhaps even (eventually) a formal ELIXIR quality stamp.  ...  The objective of EXCELERATE Deliverable 1.5 is to review software metrics and assess their usefulness in the context of the bio.tools (https://bio.tools) registry, with view to expose in bio.tools, metrics  ...  It will involve service monitoring, resource integration, interoperability aspects, and community centred benchmarking efforts.  ... 
doi:10.5281/zenodo.1452909 fatcat:ilpaegdjcfejjehycpuodbo5qi

Using registries to integrate bioinformatics tools and services into workbench environments

Hervé Ménager, Matúš Kalaš, Kristoffer Rapacki, Jon Ison
2015 International Journal on Software Tools for Technology Transfer (STTT)  
reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made.  ...  Acknowledgments This work was partly funded by ELIXIR, the research infrastructure for life-science data.  ...  ELIXIR [8] , a European 123 infrastructure for biological information, is constructing the Tools and Data Services Registry for bioinformatics resources from around the world.  ... 
doi:10.1007/s10009-015-0392-z fatcat:kddo46wrffb4hdlgx7cwaiiuq4

The bio.tools registry of software tools and data resources for the life sciences

Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, Matúš Kalaš, Veit Schwämmle, Björn Grüning, Niall Beard, Rodrigo Lopez, Severine Duvaud, Heinz Stockinger (+24 others)
2019 Genome Biology  
We outline a pan-European enterprise to provide a catalogue (https://bio.tools) of tools and databases that can be used in these workflows. bio.tools not only lists where to find resources, but also provides  ...  Bioinformaticians and biologists rely increasingly upon workflows for the flexible utilization of the many life science tools that are needed to optimally convert data into knowledge.  ...  A practical first step [7] towards a sustainable and unified resource registry engaged enthusiastic individuals from the spectrum of European bioinformatics, to share and maintain information about resources  ... 
doi:10.1186/s13059-019-1772-6 fatcat:lahst3kyh5dpzcw5ijdfjfyoii

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.  ...  , search and collaborative tools to manage collections of documents produced at CERN.  ... 
doi:10.5281/zenodo.4292139 fatcat:cr53m3mxofewrdphtq3hvdh674

D1.4 Registry release with comprehensive coverage of ELIXIR Node resources, including resource data format curation and analysis [article]

Jon Ison, Hans Ienasescu, Piotr Chmura, Veit Schwämmle, Hervé Ménager, Bryan Brancotte, Kenzo-Hugo Hillion, Matúš Kalaš, Ahto Salumetsm, Erik Jaaniso, Heidi Peterson, Séverine Duvaud (+12 others)
2019 Zenodo  
The core aim is to provide a practical portal that will help scientists with resource discovery and interoperability.  ...  The objective of EXCELERATE Deliverable 1.4 is the development of a discovery portal (bio.tools) built upon a federated curation of a registry of key software resources for bioinformatics worldwide.  ...  /about 10 https://github.com/bio-tools/ 11 Tools and data services registry: a community effort to document bioinformatics resources.  ... 
doi:10.5281/zenodo.3373344 fatcat:tvxhgpny25fczd4g3tcy5ehj4e

D1.3 Registry Release With Comprehensive Coverage Of Elixir Node Resources, Including Resource Data Format Curation And Analysis

Jon Ison, Hans Ienasescu, Piotr Chmura, Herve Menager, ELIXIR Tools Community
2018 Zenodo  
The objective of EXCELERATE Deliverable 1.3 is the development of a discovery portal (bio.tools ) built upon a federated curation of a registry of key software resources for 1 bioinformatics worldwide.  ...  Four reports (D1.1 - D1.4) describe the portal: ● M12: prototyping†of portal software and registry data model, addition of seed content ● M24: consolidation†of software features and content to a stable  ...  The ELIXIR Tools and Data Services Registry is the cornerstone of the WP.  ... 
doi:10.5281/zenodo.1456754 fatcat:dk6t7laeynb2jfsu26hr5q4h6y

Report: Registry Release With Comprehensive Coverage Of Elixir Node Resources, Including Resource Data Format Curation And Analysis

Jon Ison, Søren Brunak, Tools Platform Community
2018 Zenodo  
The objective of EXCELERATE Deliverable 1.1 is the development of a discovery portal (bio.tools) built upon a federated curation of a registry of key software resources for bioinformatics worldwide.  ...  The core aim is to provide a practical portal that will help scientists with resource discovery and interoperability.  ...  The ELIXIR Tools and Data Services Registry is the cornerstone of the WP.  ... 
doi:10.5281/zenodo.1321739 fatcat:o7vz33xmxrgrniimcldfz6wxvi

D2.2 A Report On The Coordination With Wp1 On The Incorporation Of Monitoring Statistics And Benchmarking Results In Registry Releases

Josep Gelpi Ll., Jose Mª. Fernández, Vicky Sundesha, Repchevsky, Juergen Haas
2018 Zenodo  
The data model supporting OpenEBench efforts was outlined in a previous deliverable (D2.1: Creation of a database warehouse infrastructure for storing and organizing data for online performance assessment  ...  OpenEBench provides a central data warehouse where such communities can expose their benchmarking activities for experts and non-experts users covering software developers, community participants, researchers  ...  knowledge domains. • It is directly linked to the information to be disseminated in the ELIXIR tools and services registry. • Provides direct access to information on methods and performance measures  ... 
doi:10.5281/zenodo.1452560 fatcat:6zkiwkxwprdvhijwywptobt5vu

Interoperability of population-based patient registries

Nicholas Nicholson, Andrea Perego
2020 Journal of Biomedical Informatics: X  
Enabling full interoperability within and between population-based patient-registry domains would open up access to a rich and unique source of health data for secondary data usage.  ...  It would thereby also lay the foundation for making registry data serviceable to artificial intelligence (AI) applications.  ...  Machine-readable metadata with their associated semantic descriptions and SKOS linkages to other resources would make the whole registry community amenable to the growing number of AI tools and applications  ... 
doi:10.1016/j.yjbinx.2020.100074 pmid:32838295 pmcid:PMC7293468 fatcat:4eii5dbpmrdflcbqyv4rzvop2e

Finding and sharing: new approaches to registries of databases and services for the biomedical sciences

D. Smedley, P. Schofield, C.-K. Chen, V. Aidinis, C. Ainali, J. Bard, R. Balling, E. Birney, A. Blake, E. Bongcam-Rudloff, A. J. Brookes, G. Cesareni (+18 others)
2010 Database: The Journal of Biological Databases and Curation  
. 5 A registry of resources needs to be more than just a list of databases and textual descriptions to be useful to the biological and bioinformatics communities.  ...  This tool is freely available and easy to install for other communities that wish to create their own registry of resources. and services, annotate any services provided and capture metadata on database  ... 
doi:10.1093/database/baq014 pmid:20627863 pmcid:PMC2911849 fatcat:cwaam2oayjftbcgepk3uedo5pe

Towards the Collaborative Curation of the Registry underlying identifiers.org

Nick Juty, Nicolas Le Novère, Henning Hermjakob, Camille Laibe
2013 Database: The Journal of Biological Databases and Curation  
We briefly describe the Registry, the current curation duties entailed, and our plans to extend and distribute this workload through collaborative and community efforts.  ...  The growing demand for these identifiers results in a significant increase in curational efforts to maintain the underlying registry.  ...  Acknowledgements The authors would like to express our gratitude to the users for submitting new collections and contributing updates, which greatly help us to provide a reliable service to the community  ... 
doi:10.1093/database/bat017 pmid:23584831 pmcid:PMC3625955 fatcat:2b2qhz3y6zbs5mfirlglf46peu

Linked Registries: Connecting Rare Diseases Patient Registries through a Semantic Web Layer

Pedro Sernadela, Lorena González-Castro, Claudio Carta, Eelke van der Horst, Pedro Lopes, Rajaram Kaliyaperumal, Mark Thompson, Rachel Thompson, Núria Queralt-Rosinach, Estrella Lopez, Libby Wood, Agata Robertson (+10 others)
2017 BioMed Research International  
Understanding these data is a vital step to improve patient treatments and to create the most adequate tools for personalized medicine.  ...  Patient registries are an essential tool to increase current knowledge regarding rare diseases.  ...  Although there is an overall desire in the community to increase harmonization, there is a lack of time and resources to change established procedures.  ... 
doi:10.1155/2017/8327980 pmid:29214177 pmcid:PMC5682045 fatcat:cg3n5w2qgfdt5c2emgt4smpnbe

hPSCreg—the human pluripotent stem cell registry

Stefanie Seltmann, Fritz Lekschas, Robert Müller, Harald Stachelscheid, Marie-Sophie Bittner, Weiping Zhang, Luam Kidane, Anna Seriola, Anna Veiga, Glyn Stacey, Andreas Kurtz
2015 Nucleic Acids Research  
The Registry provides comprehensive and standardized biological and legal information as well as tools to search and compare information from multiple hPSC sources and hence addresses a translational research  ...  The human pluripotent stem cell registry (hPSCreg), accessible at http://hpscreg.eu, is a public registry and data portal for human embryonic and induced pluripotent stem cell lines (hESC and hiPSC).  ...  ACKNOWLEDGEMENTS We thank all providers of cell line data and cell lines for their valuable input on development of the registry. We especially thank the CNR of the hPSCreg project.  ... 
doi:10.1093/nar/gkv963 pmid:26400179 pmcid:PMC4702942 fatcat:asg4kn4asje7jlrief4qhta5g4
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