Abstract
Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required.Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations.Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl.Contact: jison@ebi.ac.uk
Highlights
The number and diversity of bioinformatics tools, including data resources, grows vastly
We present EDAM, an ontology of bioinformatics operations, types of data and identifiers, data formats and topics
EDAM consists of four main sub-ontologies rooted in the top level of its hierarchy: Operation, Data, Topic and Format (Table 1 and Fig. 1)
Summary
The number and diversity of bioinformatics tools, including data resources, grows vastly. To aid users in finding, comparing, selecting and integrating tools into workflows or workbenches, it is important having the tools consistently described with respect to a number of categories. These include their application domain (e.g. protein structure, metagenomics), function (e.g. alignment construction), type of input and output data (e.g. accession, feature record) and available formats of the data (e.g. FASTQ, PDB format). In the absence of accepted standards for such tool descriptions, the categorization of tools has been left to providers of tool catalogues or workbenches In this undesired situation, tools have to be described again every time they are integrated into a new framework. This leads to fragmented descriptions and inconsistent categorization
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