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{ "count": 2, "next": null, "previous": null, "list": [ { "name": "bio.tools", "description": "The community registry of computational tools and data resources for biosciences.", "homepage": "https://bio.tools", "biotoolsID": "bio.tools", "biotoolsCURIE": "biotools:bio.tools", "version": [], "otherID": [ { "value": "RRID:SCR_014695", "type": "rrid", "version": null } ], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_2422", "term": "Data retrieval" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_0958", "term": "Tool metadata" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_3464", "term": "JSON" }, { "uri": "http://edamontology.org/format_3750", "term": "YAML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Web API", "Web application", "Database portal" ], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" }, { "uri": "http://edamontology.org/topic_0219", "term": "Data submission, annotation and curation" }, { "uri": "http://edamontology.org/topic_3307", "term": "Computational biology" } ], "operatingSystem": [], "language": [ "JavaScript", "Python" ], "license": "GPL-3.0", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": "Open access", "elixirPlatform": [ "Tools" ], "elixirNode": [ "Denmark" ], "elixirCommunity": [], "link": [ { "url": "https://biotools.readthedocs.io/en/latest/support.html?highlight=help", "type": [ "Helpdesk" ], "note": null }, { "url": "https://github.com/bio-tools/biotoolsregistry/issues", "type": [ "Issue tracker" ], "note": null }, { "url": "https://biotools.readthedocs.io/en/latest/contributors_guide.html#mailing-list", "type": [ "Mailing list" ], "note": null }, { "url": "https://github.com/bio-tools/biotoolsregistry/", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bio-tools/biotoolsRegistry", "type": "Source code", "note": null, "version": null } ], "documentation": [ { "url": "https://biotools.readthedocs.io/en/latest/api_usage_guide.html", "type": [ "API documentation" ], "note": "API usage guide" }, { "url": "https://biotools.readthedocs.io/en/latest/api_reference.html", "type": [ "API documentation" ], "note": "API Reference" }, { "url": "https://biotools.readthedocs.io/en/latest/publications.html#citation", "type": [ "Citation instructions" ], "note": null }, { "url": "https://biotools.readthedocs.io/en/latest/contributors_guide.html", "type": [ "Contributions policy" ], "note": null }, { "url": "https://biotools.readthedocs.io/en/latest/", "type": [ "General" ], "note": null }, { "url": "https://biotools.readthedocs.io/en/latest/governance.html", "type": [ "Governance" ], "note": null }, { "url": "https://biotools.readthedocs.io/en/latest/curators_guide.html", "type": [ "User manual" ], "note": "Curators Guide" } ], "publication": [ { "doi": "10.1093/nar/gkv1116", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Tools and data services registry: A community effort to document bioinformatics resources", "abstract": "© The Author(s) 2015.Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand. Here we present a community-driven curation effort, supported by ELIXIR-the European infrastructure for biological information-that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners. As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.", "date": "2016-01-04T00:00:00Z", "citationCount": 73, "authors": [ { "name": "Ison J." }, { "name": "Rapacki K." }, { "name": "Menager H." }, { "name": "Kalas M." }, { "name": "Rydza E." }, { "name": "Chmura P." }, { "name": "Anthon C." }, { "name": "Beard N." }, { "name": "Berka K." }, { "name": "Bolser D." }, { "name": "Booth T." }, { "name": "Bretaudeau A." }, { "name": "Brezovsky J." }, { "name": "Casadio R." }, { "name": "Cesareni G." }, { "name": "Coppens F." }, { "name": "Cornell M." }, { "name": "Cuccuru G." }, { "name": "Davidsen K." }, { "name": "Della Vedova G." }, { "name": "Dogan T." }, { "name": "Doppelt-Azeroual O." }, { "name": "Emery L." }, { "name": "Gasteiger E." }, { "name": "Gatter T." }, { "name": "Goldberg T." }, { "name": "Grosjean M." }, { "name": "Gruuing B." }, { "name": "Helmer-Citterich M." }, { "name": "Ienasescu H." }, { "name": "Ioannidis V." }, { "name": "Jespersen M.C." }, { "name": "Jimenez R." }, { "name": "Juty N." }, { "name": "Juvan P." }, { "name": "Koch M." }, { "name": "Laibe C." }, { "name": "Li J.-W." }, { "name": "Licata L." }, { "name": "Mareuil F." }, { "name": "Micetic I." }, { "name": "Friborg R.M." }, { "name": "Moretti S." }, { "name": "Morris C." }, { "name": "Moller S." }, { "name": "Nenadic A." }, { "name": "Peterson H." }, { "name": "Profiti G." }, { "name": "Rice P." }, { "name": "Romano P." }, { "name": "Roncaglia P." }, { "name": "Saidi R." }, { "name": "Schafferhans A." }, { "name": "Schwammle V." }, { "name": "Smith C." }, { "name": "Sperotto M.M." }, { "name": "Stockinger H." }, { "name": "Varekova R.S." }, { "name": "Tosatto S.C.E." }, { "name": "De La Torre V." }, { "name": "Uva P." }, { "name": "Via A." }, { "name": "Yachdav G." }, { "name": "Zambelli F." }, { "name": "Vriend G." }, { "name": "Rost B." }, { "name": "Parkinson H." }, { "name": "Longreen P." }, { "name": "Brunak S." } ], "journal": "Nucleic Acids Research" } }, { "doi": "10.12688/f1000research.12974.1", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Using bio.tools to generate and annotate workbench tool descriptions", "abstract": "© 2017 Hillion KH et al.Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.", "date": "2017-01-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Hillion K.-H." }, { "name": "Kuzmin I." }, { "name": "Khodak A." }, { "name": "Rasche E." }, { "name": "Crusoe M." }, { "name": "Peterson H." }, { "name": "Ison J." }, { "name": "Menager H." } ], "journal": "F1000Research" } }, { "doi": "10.1093/gigascience/gix022", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "ReGaTE: Registration of galaxy tools in Elixir", "abstract": "© The Author 2017.Background: Bioinformaticians routinely use multiple software tools and data sources in their day-to-day work and have been guided in their choices by a number of cataloguing initiatives. The ELIXIR Tools and Data Services Registry (bio.tools) aims to provide a central information point, independent of any specific scientific scope within bioinformatics or technological implementation. Meanwhile, efforts to integrate bioinformatics software in workbench and workflow environments have accelerated to enable the design, automation, and reproducibility of bioinformatics experiments. One such popular environment is the Galaxy framework, with currently more than 80 publicly available Galaxy servers around the world. In the context of a generic registry for bioinformatics software, such as bio.tools, Galaxy instances constitute a major source of valuable content. Yet there has been, to date, no convenient mechanism to register such services en masse. Findings: We present ReGaTE (Registration of Galaxy Tools in Elixir), a software utility that automates the process of registering the services available in a Galaxy instance. This utility uses the BioBlend application program interface to extract service metadata from a Galaxy server, enhance the metadata with the scientific information required by bio.tools, and push it to the registry. Conclusions: ReGaTE provides a fast and convenient way to publish Galaxy services in bio.tools. By doing so, service providers may increase the visibility of their services while enriching the software discovery function that bio.tools provides for its users.", "date": "2017-06-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Doppelt-Azeroual O." }, { "name": "Mareuil F." }, { "name": "Deveaud E." }, { "name": "Kalas M." }, { "name": "Soranzo N." }, { "name": "van den Beek M." }, { "name": "Gruning B." }, { "name": "Ison J." }, { "name": "Menager H." } ], "journal": "GigaScience" } }, { "doi": "10.1007/s10009-015-0392-z", "pmid": null, "pmcid": null, "type": [ "Other" ], "version": null, "note": null, "metadata": { "title": "Using registries to integrate bioinformatics tools and services into workbench environments", "abstract": "© 2015, The Author(s).The diversity and complexity of bioinformatics resources presents significant challenges to their localisation, deployment and use, creating a need for reliable systems that address these issues. Meanwhile, users demand increasingly usable and integrated ways to access and analyse data, especially within convenient, integrated “workbench” environments. Resource descriptions are the core element of registry and workbench systems, which are used to both help the user find and comprehend available software tools, data resources, and Web Services, and to localise, execute and combine them. The descriptions are, however, hard and expensive to create and maintain, because they are volatile and require an exhaustive knowledge of the described resource, its applicability to biological research, and the data model and syntax used to describe it. We present here the Workbench Integration Enabler, a software component that will ease the integration of bioinformatics resources in a workbench environment, using their description provided by the existing ELIXIR Tools and Data Services Registry.", "date": "2016-11-01T00:00:00Z", "citationCount": 3, "authors": [ { "name": "Menager H." }, { "name": "Kalas M." }, { "name": "Rapacki K." }, { "name": "Ison J." } ], "journal": "International Journal on Software Tools for Technology Transfer" } } ], "credit": [ { "name": "Contributors", "email": null, "url": "https://biotools.readthedocs.io/en/latest/contributors.html", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [], "note": null } ], "community": null, "owner": "jison", "additionDate": "2018-12-12T12:35:31Z", "lastUpdate": "2020-06-16T10:55:28Z", "editPermission": { "type": "group", "authors": [ "hans" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null }, { "name": "ToolDog", "description": "This tool aims to generate XML template for Galaxy or CWL from the description of tools from the bio.tools registry.", "homepage": "https://github.com/bio-tools/ToolDog", "biotoolsID": "tooldog", "biotoolsCURIE": "biotools:tooldog", "version": [ "0.3.5" ], "otherID": [], "relation": [], "function": [ { "operation": [ { "uri": "http://edamontology.org/operation_0335", "term": "Formatting" } ], "input": [], "output": [ { "data": { "uri": "http://edamontology.org/data_0006", "term": "Data" }, "format": [ { "uri": "http://edamontology.org/format_2332", "term": "XML" }, { "uri": "http://edamontology.org/format_3750", "term": "YAML" } ] } ], "note": null, "cmd": null } ], "toolType": [ "Command-line tool" ], "topic": [ { "uri": "http://edamontology.org/topic_0089", "term": "Ontology and terminology" }, { "uri": "http://edamontology.org/topic_0091", "term": "Bioinformatics" } ], "operatingSystem": [ "Linux" ], "language": [ "Python" ], "license": "MIT", "collectionID": [], "maturity": "Emerging", "cost": "Free of charge", "accessibility": null, "elixirPlatform": [], "elixirNode": [], "elixirCommunity": [], "link": [ { "url": "https://github.com/bio-tools/ToolDog", "type": [ "Repository" ], "note": null } ], "download": [ { "url": "https://github.com/bio-tools/ToolDog/archive/v0.3.5.tar.gz", "type": "Source code", "note": "Download link to v.0.3.5", "version": null } ], "documentation": [ { "url": "http://tooldog.readthedocs.io/en/latest/?badge=latest", "type": [ "General" ], "note": null } ], "publication": [ { "doi": "10.12688/f1000research.12974.1", "pmid": null, "pmcid": null, "type": [ "Primary" ], "version": null, "note": null, "metadata": { "title": "Using bio.tools to generate and annotate workbench tool descriptions", "abstract": "© 2017 Hillion KH et al.Workbench and workflow systems such as Galaxy, Taverna, Chipster, or Common Workflow Language (CWL)-based frameworks, facilitate the access to bioinformatics tools in a user-friendly, scalable and reproducible way. Still, the integration of tools in such environments remains a cumbersome, time consuming and error-prone process. A major consequence is the incomplete or outdated description of tools that are often missing important information, including parameters and metadata such as publication or links to documentation. ToolDog (Tool DescriptiOn Generator) facilitates the integration of tools - which have been registered in the ELIXIR tools registry (https://bio.tools) - into workbench environments by generating tool description templates. ToolDog includes two modules. The first module analyses the source code of the bioinformatics software with language-specific plugins, and generates a skeleton for a Galaxy XML or CWL tool description. The second module is dedicated to the enrichment of the generated tool description, using metadata provided by bio.tools. This last module can also be used on its own to complete or correct existing tool descriptions with missing metadata.", "date": "2017-01-01T00:00:00Z", "citationCount": 6, "authors": [ { "name": "Hillion K.-H." }, { "name": "Kuzmin I." }, { "name": "Khodak A." }, { "name": "Rasche E." }, { "name": "Crusoe M." }, { "name": "Peterson H." }, { "name": "Ison J." }, { "name": "Menager H." } ], "journal": "F1000Research" } } ], "credit": [ { "name": "Institut Pasteur", "email": null, "url": "https://research.pasteur.fr", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Institute", "typeRole": [ "Provider" ], "note": null }, { "name": "C3BI", "email": null, "url": "https://research.pasteur.fr/en/center/c3bi/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [], "note": null }, { "name": "Bioinformatics and Biostatistics Hub", "email": null, "url": "https://research.pasteur.fr/en/team/bioinformatics-and-biostatistics-hub/", "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Division", "typeRole": [ "Provider" ], "note": null }, { "name": "Hervé Ménager", "email": "hmenager@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null }, { "name": "Kenzo-Hugo Hillion", "email": "kehillio@pasteur.fr", "url": null, "orcidid": null, "gridid": null, "rorid": null, "fundrefid": null, "typeEntity": "Person", "typeRole": [ "Primary contact" ], "note": null } ], "community": null, "owner": "khillion", "additionDate": "2017-12-21T07:28:12Z", "lastUpdate": "2018-12-10T12:58:59Z", "editPermission": { "type": "group", "authors": [ "hmenager" ] }, "validated": 1, "homepage_status": 0, "elixir_badge": 0, "confidence_flag": null } ] }