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Domain Resource Application Ontology

The Domain Resource Application Ontology (DRAO) is an application ontology describing cross-discipline research domains used within FAIRsharing records by curators and the user community (see also the DRAO FAIRsharing record). It is built in conjunction with the Subject Resource Application Ontology (SRAO), which describes higher-level subject areas / disciplines.

All classes within DRAO come from publicly-available ontologies. Currently, the following ontologies are used to build DRAO: BFO, CHEBI, CHEMINF, CHMO, CL, CLO, CMO, DOID, DRON, EDAM, EFO, ENVO, ERO, FBBI, FBCV, FMA, GO, HP, IAO, IDO, IDOMAL, MAMO, MFOEM, MI, MOD, MP, MS, NCBITaxon, NCIT, OAE, OBCS, OBI, OGI, OGMS, OMIT, OMP, PATO, PECO, PO, PR, PW, SBO, SIO, SO, STATO, SWO, UBERON, UO, VARIO, VO. These ontologies were added to DRAO through semi-automated procedures (see below for details).

AgroVoc and PRIDE classes were manually added as required.

Files

To view the latest release of DRAO please visit our release directory. The release files are created by merging the development files into a single document for easier loading within the editor of your choice, such as Protege.

Within any releases/ subdirectory

  • DRAO.owl - - The automatically-generated release file. It is a single file (with no imports) for ease of use.
  • refactoredIRIs-DRAO-RELNUM.txt - This is a list of IRI refactorings performed since the last release.
  • README.md - A short description of the changes made since the last release.
  • DRAO-diff.md - the output of the Robot diff command to list the differences since the previous release.

Below are short descriptions of a selection of other files found within this repository, all within the development directory:

  • DRAO.owl - This is the main "bleeding edge" development file, which imports all required classes and annotations. The only information stored directly within this file is metadata about the ontology and the required imports.
  • DRAO-merged.owl - This is a merged version of the main development file, generated automatically as a single file to be easy to view and use. Please note that it may not always be as up to date as DRAO.owl.
  • DRAO-ontofox-annotation.txt - The configuration file required by Ontofox for automatically adding annotation from the external ontologies to DRAO. It is maintained and updated by our team.
  • DRAO-annotation.owl - the file created by Ontofox containing only automatically-generated annotation from the external ontologies (no manual modifications are made to this file).
  • DRAO-fsskeleton.owl - the skeleton OWL file used by ROBOT when generating FAIRsharing-specific annotation to add to DRAO.
  • DRAO-fsannotation.owl - the FAIRsharing-specific annotation generated by ROBOT which is then imported into DRAO (no manual modifications are made to this file).
  • DRAO-manual.owl - Additional FAIRsharing-specific annotation is added manually and stored within this file. Classes in this file are from ontologies which are not loaded within Ontobee, the ontology service used by Ontofox.

In the past, the Ontodog subdirectory was used to generate FAIRsharing-specific annotation. This directory remains in case it is required in future, but is not presently used to build releases.

Background

FAIRsharing (https://www.fairsharing.org) is a manually-curated, cross-discipline, searchable portal of three linked registries covering standards, databases and data policies. Every record is designed to be interlinked, providing a detailed description not only of the resource itself, but also its relationship to other resources.

As FAIRsharing has grown, over 1000 domain tags across all areas of research have been added by users and curators. This tagging system, essentially a flat list, has become unwieldy and limited. To provide a hierarchical structure and richer semantics, two application ontologies drawn from multiple community ontologies were created to supplement these user tags. FAIRsharing domain tags are now divided into three separate fields:

  • Subject Resource Application Ontology (SRAO) - a hierarchy of academic disciplines that formalises the re3data subject list (https://www.re3data.org/browse/by-subject/). Combined with subsets of five additional ontologies, SRAO provides over 350 classes.
  • Domain Resource Application Ontology (DRAO) - This repository. A hierarchy of specific research domains and descriptors. Over fifty external ontologies are used to provide over 1000 classes.
  • Free-text user tags. A small number of FAIRsharing domain tags were not mappable to external ontologies and are retained as user tags. Existing and new user tags may be promoted to either application ontology as required.

DRAO Curation

FAIRsharing users can add any knowledge domain tags to their records. They can select from any of the pre-existing tags or make their own. If they create a new tag, then FAIRsharing curators assess that tag and, if appropriate, place it within either SRAO or DRAO. Otherwise, it will remain in our manually-curated "User tag" vocabulary.

All classes within DRAO come from publicly-available ontologies. These terms are added to DRAO by editing the Ontofox configuration file. When Ontofox is run (see the "Build" section below), the resulting output will include the new classes. New FAIRsharing-specific annotation is then added via ROBOT using the SPARQL update query available at fsannotation.ru.

Additional FAIRsharing-specific annotation is added manually and stored within DRAO-manual.owl. Classes in this file are from ontologies which are not loaded within Ontobee, the ontology service used by Ontofox.

Build

Domains are the largest set of tags available when curating FAIRsharing records. The classes used within DRAO are imported from external ontologies using Ontofox, and then appropriate annotation is added to those classes using ROBOT. DRAO is written in OWL and serialized as RDF/XML. Release files are created using ROBOT via a controlling Makefile.

Tools Used

Ontofox has been used to build the subset ontology files and associated annotation. Protege (including versions 4.3.0 and 5.2.0) has been used to check the core OWL file and its imports. ROBOT has been used to add FAIRsharing-specific annotation and to compare, check and merge all development ontology files into a single merged release file.

Further information on the development of DRAO is available from the Development page.

Usage and licence

Within FAIRsharing, DRAO and its associated user tags are used by both curators and our user community to annotation FAIRsharing records. DRAO itself is also available for general use from this repository under a CC BY 4.0 licence.

For licence information for the external ontologies used to create DRAO, please see our Licensing Compliance page.

Contact Us

Please feel free to contact us with any comments or suggestions at contact@fairsharing.org.

About

A project supporting the DRAO application ontology, a hierarchy of specific research domains and descriptors which imports subsets of terms from over 50 publicly-available ontologies.

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