bio.tools
bio.tools catalogs computational tools and data resources for the biosciences to enable discovery, integration, and metadata-driven registration of bioinformatics software and services.
Key Features:
- Central registry: bio.tools centralizes structured descriptions of computational tools and data resources for the biosciences.
- Workbench integration: Integration metadata and descriptors support interoperability with Galaxy, Taverna, Chipster and Common Workflow Language (CWL) frameworks.
- ToolDog description generator: ToolDog analyzes source code with language-specific plugins to produce skeleton Galaxy XML or CWL descriptions and enriches them with metadata from bio.tools.
- ReGaTE automated registration: ReGaTE uses the BioBlend API to extract service metadata from Galaxy instances, enhance it with scientific metadata, and submit entries to the registry.
- Metadata enrichment: Registry entries include detailed metadata such as tool parameters and publications to support discovery and integration.
Scientific Applications:
- Enhanced discoverability: Structured and enriched tool descriptions increase visibility of bioinformatics tools and services for researchers seeking relevant software and data resources.
- Reproducibility and automation: Integration with Galaxy, CWL and workflow environments combined with enriched metadata supports reproducible experiment design and automation of bioinformatics workflows.
Methodology:
ToolDog analyzes source code using language-specific plugins to generate skeleton Galaxy XML or CWL descriptions and enriches them with metadata from bio.tools; ReGaTE extracts service metadata from Galaxy instances via the BioBlend API, enhances it with scientific metadata, and submits entries to the registry; metadata enrichment includes parameters and publications.
Topics
Details
- License:
- GPL-3.0
- Maturity:
- Emerging
- Cost:
- Free of charge
- Tool Type:
- api, web application
- Programming Languages:
- JavaScript, Python
- Added:
- 12/12/2018
- Last Updated:
- 6/16/2020
Operations
Data Inputs & Outputs
Data retrieval
Publications
Ménager H, Kalaš M, Rapacki K, Ison J. Using registries to integrate bioinformatics tools and services into workbench environments. International Journal on Software Tools for Technology Transfer. 2015;18(6):581-586. doi:10.1007/s10009-015-0392-z.
Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li J, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S. Tools and data services registry: a community effort to document bioinformatics resources. Nucleic Acids Research. 2015;44(D1):D38-D47. doi:10.1093/nar/gkv1116. PMID:26538599. PMCID:PMC4702812.
Hillion K, Kuzmin I, Khodak A, Rasche E, Crusoe M, Peterson H, Ison J, Ménager H. Using bio.tools to generate and annotate workbench tool descriptions. F1000Research. 2017;6:2074. doi:10.12688/f1000research.12974.1. PMID:29333231. PMCID:PMC5747335.
Doppelt-Azeroual O, Mareuil F, Deveaud E, Kalaš M, Soranzo N, van den Beek M, Grüning B, Ison J, Ménager H. ReGaTE: Registration of Galaxy Tools in Elixir. GigaScience. 2017;6(6). doi:10.1093/gigascience/gix022. PMID:28402416. PMCID:PMC5530318.