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

Abstract

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.

Bio-TDS: bioscience query tool discovery system

“…Numerous bioinformatics tool repositories or retrieval systems have been developed (1,2), but do not provide natural language processing functionality allowing users to enter their queries as free text. This problem has accelerated the growth of community based discussion platforms such as SEQAnswer Wiki (http://SEQAnswers.com/wiki/SEQAnswers), Biostars (https://www.biostars.org/) and ARAPORT (https://www.araport.org/) (3–5).…”

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

“…Each way is not without difficulty, both for very young and very old tools. To the rescue come registries of software like Bio.Tools [17], and the resource identification initiative (https://scicrunch.org/resources) expands the same concept well beyond software. For sharing whole workflows, myExperiment (http://myexperiment.org/) is a well-established repository used by multiple workflow systems and research communities [10], complementing more specific workflow repositories like CWL Viewer [33] (https://view.commonwl.org/), Galaxy's ToolShed (https:// galaxyproject.org/toolshed/workflow-sharing/), and Dockstore [30].…”

“…(However, this situation is not a problem when the tool identifier (like RRID) is combined with a desired version.) The registries OMICtools [14] and Bio.Tools [17] have begun to integrate Debian's curated package descriptions into their catalogues. With Debian, all control over the packaging is with the individual package maintainers, but the scientific packages are commonly teammaintained, which facilitates mass changes like the introduction of references to catalogues from Debian in analogy to references to publications that are already offered today.…”

Enabling Precision Medicine via standard communication of HTS provenance, analysis, and results

“…At the heart of CWL workflows are WL tool descriptions. A command line, often with an accompanying Docker container, is described with parameters; and linking to and from registries like ELIXIR's (European Life-sciences Infrastructure for Biological Information) bio.tools [64]. These are then wired together in another YAML file to form a workflow template, which can be executed repeatedly on any supported platform by specifying input files and workflow parameters.…”