Abstract
Biomedical data repositories such as the Gene Expression Omnibus (GEO) enable the search and discovery of relevant biomedical digital data objects. Similarly, resources such as OMICtools, index bioinformatics tools that can extract knowledge from these digital data objects. However, systematic access to pre-generated ‘canned’ analyses applied by bioinformatics tools to biomedical digital data objects is currently not available. Datasets2Tools is a repository indexing 31,473 canned bioinformatics analyses applied to 6,431 datasets. The Datasets2Tools repository also contains the indexing of 4,901 published bioinformatics software tools, and all the analyzed datasets. Datasets2Tools enables users to rapidly find datasets, tools, and canned analyses through an intuitive web interface, a Google Chrome extension, and an API. Furthermore, Datasets2Tools provides a platform for contributing canned analyses, datasets, and tools, as well as evaluating these digital objects according to their compliance with the findable, accessible, interoperable, and reusable (FAIR) principles. By incorporating community engagement, Datasets2Tools promotes sharing of digital resources to stimulate the extraction of knowledge from biomedical research data. Datasets2Tools is freely available from: http://amp.pharm.mssm.edu/datasets2tools.
Highlights
The introduction of the web enabled several software-based extensions of traditional print publications of research output: a) Research articles can be published in soft form so they can be more copied and distributed; b) Data collected by research studies can be made more available to others for reuse and integrative retrospective analyses; and c) Methods and software tools to analyze and visualize research data are becoming more powerful and accessible
The rapid growth in data collection due to the advancement of high-content biotechnologies that extract large amounts of information from biological samples led to the development of centralized biomedical repositories to manage this wealth of data, for example, the Gene Expression Omnibus (GEO)[1] for transcriptomics and epigenomics data
Datasets2Tools is delivered as a Google Chrome browser extension and an Application Programming Interface (API)
Summary
The introduction of the web enabled several software-based extensions of traditional print publications of research output: a) Research articles can be published in soft form so they can be more copied and distributed; b) Data collected by research studies can be made more available to others for reuse and integrative retrospective analyses; and c) Methods and software tools to analyze and visualize research data are becoming more powerful and accessible While these developments, facilitated by the introduction of the web, have been critical for advancing biomedical research, much work remains to improve how research results are communicated digitally. Several efforts have been made to aggregate and index bioinformatics tools, for example, OMICtools[4]
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