This document contains conformance details of DRAO with the Minimum Information for Reporting of an Ontology (MIRO) guidelines. Please see https://github.com/owlcs/miro for full details of the MIRO guidelines.
This is a work in progress. Incomplete sections are marked with a 🔴 red circle.
A note on terminology: We often use the term "FAIRsharing community maintainers". Our community maintainers are volunteers who have claimed one or more FAIRsharing records describing resources that they develop. Once they've claimed a record they may edit it, adding high-quality annotation, publications and general information.
| Specification | |
|---|---|
| Description: | The full name of the ontology, including the acronym and the version number referred to in the report. |
| Importance: | MUST |
| Value: | Domain Resource Application Ontology (DRAO), Version 0.2.3 |
| Specification | |
|---|---|
| Description: | The names, affiliations (where appropriate) and contact details of the person, people or consortium that manage the development of the ontology. |
| Importance: | MUST |
| Value: | The FAIRsharing Team, [email protected] |
| Specification | |
|---|---|
| Description: | The licence which governs the permissions surrounding the ontology. |
| Importance: | MUST |
| Value: | Creative Commons Attribution-ShareAlike 4.0 International (CC BY-SA 4.0) |
| Specification | |
|---|---|
| Description: | The web location where the ontology file is available. |
| Importance: | MUST |
| Value: | https://github.com/FAIRsharing/domain-ontology/raw/master/releases/DRAO.owl |
| Specification | |
|---|---|
| Description: | The web location (URL) of the version control system where current and previous versions of the ontology can be found. |
| Importance: | MUST |
| Value: | https://github.com/FAIRsharing/domain-ontology |
| Specification | |
|---|---|
| Description: | A name or description of the steps taken to develop the ontology. This should describe the overall organisation of the ontology development process. |
| Importance: | MUST |
| Value: | Development. The ontology was developed using a combination of manual and automatic steps. Crowdsourcing (via the FAIRsharing user community) was used to create the initial set of values required within the ontology, and continues to be the main method for the addition of new terms. All terms within DRAO are pulled from publicly-available external ontologies. Further development details are available at the DRAO README and DRAO Development pages. Management. Users can suggest additions by adding new Knowledge Domain tags to their records within FAIRsharing, and can suggest additions and changes via the DRAO Issue Tracker. Support. Please feel free to contact us with any comments or suggestions at [email protected] or via the DRAO Issue Tracker. |
| Specification | |
|---|---|
| Description: | Justification of why the ontology is required. |
| Importance: | MUST |
| Value: | As FAIRsharing has grown, over 1800 domain tags across all areas of research were 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 (of which DRAO is one) were created to supplement these user tags. |
| Specification | |
|---|---|
| Description: | The names and citations for other ontology or ontologies in the same general area as the one being reported upon, together with a description on why the one being reported is needed instead or in addition to the others. |
| Importance: | MUST |
| Value: | DRAO is an application ontology and, as such, does not create its own classes. Instead, it pulls all required classes from over 50 publicly-available ontologies. Currently, the following ontologies are used to build DRAO: AgroVoc, AERO, BFO, CHEBI, CHEMINF, CHMO, CL, CLO, CMO, DOID, DRON, EDAM, EFO, ENVO, EO, 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, PO, PR, PRIDE, PW, SBO, SIO, SO, STATO, SWO, UBERON, UO, VariO, VO. |
| Specification | |
|---|---|
| Description: | The community or organisation performing some task or use for which the ontology was developed. |
| Importance: | MUST |
| Value: | DRAO is used by both in-house FAIRsharing curators and community maintainers to describe the resources listed in FAIRsharing records. |
| Specification | |
|---|---|
| Description: | The domain or field of interest for the ontology and the boundaries, granularity of representation and coverage of the ontology. State the requirements of the ontology, such as the competency questions it should satisfy. A visualisation or tabular representation is optional, but often helpful to illustrate the scope. |
| Importance: | MUST |
| Value: | DRAO's scope is to describe the defining features of research databases, data standards and data policies. It covers all areas of research in the Natural, Engineering, and Social Sciences. |
| Specification | |
|---|---|
| Description: | The person, group of people or organisation that actually creates the content of the ontology. This is distinct from the Ontology Owner (above) that is concerned with the management of the ontology's development. |
| Importance: | MUST |
| Value: | DRAO is developed by the FAIRsharing Team and by the FAIRsharing community maintainers. |
| Specification | |
|---|---|
| Description: | Location, usually URL, of the email list and/or the issue tracking systems used for development and managing feature requests for the ontology. |
| Importance: | MUST |
| Value: | Please feel free to contact us with any comments or suggestions at [email protected] or via the DRAO Issue Tracker. |
| Specification | |
|---|---|
| Description: | How the knowledge in the ontology was gathered, sorted, verified, etc. |
| Importance: | MUST |
| Value: | DRAO is an application ontology and, as such, does not create its own classes. Instead, it pulls all required classes from over 50 publicly-available ontologies. Currently, the following ontologies are used to build DRAO: AgroVoc, AERO, BFO, CHEBI, CHEMINF, CHMO, CL, CLO, CMO, DOID, DRON, EDAM, EFO, ENVO, EO, 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, PO, PR, PRIDE, PW, SBO, SIO, SO, STATO, SWO, UBERON, UO, VariO, VO. Issues with the hierarchy (e.g. duplicate labels from different ontologies, and mistakes due to different versions of the same ontology being imported) were manually resolved. Full details of the knowledge acquisition methodology, and issues arising from it, are available at the DRAO Development page. |
| Specification | |
|---|---|
| Description: | The location of the source whence the knowledge was gathered. |
| Importance: | SHOULD |
| Value: | As FAIRsharing has grown, over 1800 domain tags across all areas of research were added by community maintainers and curators. This tagging system was used as the basis for DRAO and its associated resource, SRAO. Additions to DRAO occur when the FAIRsharing community adds tags to their records in the "Scope and Data Types" section of a FAIRsharing entry. If they create a new tag, 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. |
| Specification | |
|---|---|
| Description: | The prioritisation of entities to be represented in the ontology and how that prioritisation was achieved. Some knowledge is more important or of greater priority to be in the ontology to support the requirements of that ontology. |
| Importance: | SHOULD |
| Value: | Priority was given to those domain tags already created by the FAIRsharing community maintainers and curators. New tags added to FAIRsharing are given top priority with DRAO as this is main use case for this application ontology. |
| Specification | |
|---|---|
| Description: | the knowledge representation language used and why it was used. For a language like OWL, indicate the OWL profile and expressivity. |
| Importance: | MUST |
| Value: | OWL version 2, AL profile. |
| Specification | |
|---|---|
| Description: | The tool(s) used in developing the ontology. |
| Importance: | OPTIONAL |
| Value: | Ontofox (Xiang Z, Courtot M, Brinkman RR, Ruttenberg A, He Y. OntoFox: web-based support for ontology reuse. BMC Research Notes. 2010, 3:175. PMID: 20569493) has been used to build the subset ontology files and associated annotation. Ontodog (Zheng J, Xiang Z, Stoeckert Jr. CJ, He Y. Ontodog: a web-based ontology community view generation tool. Bioinformatics. 2014; doi: 10.1093/bioinformatics/btu008) was used for the 0.1.0 release. Protege (including versions 4.3.0 and 5.2.0; Musen, M.A. The Protégé project: A look back and a look forward. AI Matters. Association of Computing Machinery Specific Interest Group in Artificial Intelligence, 1(4), June 2015. DOI: 10.1145/2557001.25757003) has been used to create the core OWL file and to view the ontology. ROBOT (publication) was used to add FAIRsharing-specific annotation, to merge all development ontology files and to build the releases. |
| Specification | |
|---|---|
| Description: | Number of classes, properties, axioms and types of axioms, rules and individuals in the ontology. |
| Importance: | SHOULD |
| Value: | DRAO includes 978 classes, 1 object properties, 11 annotation properties, 7489 axioms (1168 SubClassOf axioms), 0 rules, 0 individuals. |
| Specification | |
|---|---|
| Description: | The names, versions and citations of external ontologies imported into the ontology and where they are placed in the host ontology. |
| Importance: | MUST |
| Value: | DRAO is an application ontology and, as such, does not create its own classes. Instead, it pulls all required classes from over 50 publicly-available ontologies. Currently, the following ontologies are used to build DRAO: AgroVoc, AERO, BFO, CHEBI, CHEMINF, CHMO, CL, CLO, CMO, DOID, DRON, EDAM, EFO, ENVO, EO, 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, PO, PR, PRIDE, PW, SBO, SIO, SO, STATO, SWO, UBERON, UO, VariO, VO. (This was already listed in B2 and D1, for slightly different reasons.) All versions were as listed in Ontobee on the days they were retrieved (see last modification dates in the GitHub repository). Placement within DRAO will primarily follow the external ontologies' own hierarchy, except where that causes direct issues with other classes within DRAO. In such cases, the default hierarchy is manually overriden within the Ontofox configuration file. More information is available in the DRAO Development page. A full list of citations are available in the Licensing Compliance document. 🔴 Versions not added. |
| Specification | |
|---|---|
| Description: | The naming scheme for the entities in the ontology, capturing orthography, organisation rules, acronyms, and so on. |
| Importance: | MUST |
| Value: | DRAO labels are, in the first instance, taken from the tags created by the FAIRsharing community maintainers. These tags are then matched against external ontologies and the appropriate external class is assigned to the tag. If the external label matches the internal label, no further work is required. If the labels are different, in a majority of cases the FAIRsharing label is retained via the 'FAIRsharing alternative term' annotation property. In a small number of cases, we will change the FAIRsharing tag to align with the label from the external ontology. Within the FAIRsharing UI, any class with the 'FAIRsharing alternative term' annotation property will preferentially display the FAIRsharing label, while all other labels and alternative terms are displayed as synonyms. |
| Specification | |
|---|---|
| Description: | What is the scheme used for creating identifiers for entities in the ontology. State whether identifiers are semantic-free or meaningful. |
| Importance: | MUST |
| Value: | Semantic-free identifiers. Incremental class number, using 7 digit number with ontology name as the prefix. |
| Specification | |
|---|---|
| Description: | What metadata for each entity is to be present. This could include, but not be limited to: A natural language definition, editor, edit history, examples, entity label and synonyms, etc. |
| Importance: | MUST |
| Value: | Each class minimally requires a label and an 'imported from' annotation property stating where the class originated. Further information including textual definition, synonyms, and availability to the FAIRsharing community is optionally available. As this is an application ontology, editor and edit history are beyond its scope. |
| Specification | |
|---|---|
| Description: | If an upper ontology is used, which one is used and why is it used? If not used, then why. |
| Importance: | MUST |
| Value: | To align with the many ontologies we used from the OBO Foundry, we chose BFO as the upper-level ontology. |
| Specification | |
|---|---|
| Description: | The relationships or properties used in the ontology, which were used and why? Were new relationships required? Why? |
| Importance: | MUST |
| Value: | DRAO requires only simple subclass relationships in order to provide hierarchical tagging for FAIRsharing records. Therefore currently no other relationships are used. |
| Specification | |
|---|---|
| Description: | An axiom pattern is a regular design of axioms or a template for axioms used to represent a category of entities or common aspects of a variety of types of entities. An axiom pattern may comprise both asserted and inferred axioms. The aim of a pattern is to achieve a consistent style of representation. An important family of axiom patterns are Ontology Design pattern (ODP) which are commonly used solutions for issues in representation. |
| Importance: | MUST |
| Value: | As an application ontology, DRAO does not create its own classes. As such it does not have a defined axiom pattern. |
| Specification | |
|---|---|
| Description: | State whether or not the IRI used are dereferencable to a Web resource. Provide any standard prefix (CURIE). |
| Importance: | SHOULD |
| Value: | The majority of classes in DRAO are from external ontologies and will have their own dereferencing policy. The few DRAO IRIs (e.g. http://www.fairsharing.org/ontology/DRAO_0000001 are currently redirected to the DRAO GitHub repository. |
| Specification | |
|---|---|
| Description: | State whether the ontology will be actively maintained and developed. Describe a plan for how the ontology will be kept up to date. |
| Importance: | MUST |
| Value: | DRAO is maintained by the FAIRsharing Team, and will be actively maintained and developed for the lifetime of this project. Additions to DRAO occur when the FAIRsharing community adds tags to their records in the "Knowledge Domains" of a FAIRsharing entry. If they create a new tag, FAIRsharing curators assess that tag and, if appropriate, place it within either SRAO or DRAO. Otherwise, it will remain in our manually-curated "User-defined tag" vocabulary. |
| Specification | |
|---|---|
| Description: | Describe the procedures for managing entities that become removed, split or redefined. |
| Importance: | MUST |
| Value: | DRAO is an application ontology, and therefore as external ontologies deprecate classes, we will have to find alternatives. We may also choose to delete an term which is no longer appropriate for FAIRsharing. However, this will just be dropping an external class from an application ontology - the originating ontology will still retain that class. |
| Specification | |
|---|---|
| Description: | State or make reference to the policy that governs when new versions of the ontology are created and released. |
| Importance: | MUST |
| Value: | GitHub retains all releases of DRAO, which are produced on an as-needed basis. |
| Specification | |
|---|---|
| Description: | Description of the procedure used to judge whether the ontology achieves the claims made for the ontology. State, for example, whether the ontology is logically consistent, answers the queries it claims to answer, and whether it can answer them in a time that is reasonable for the projected use case scenario (benchmarking). |
| Importance: | MUST |
| Value: | The ontology was successfully classified by HermiT 1.3.8 in less than 1 second. |
| Specification | |
|---|---|
| Description: | A determination of whether the ontology is of value and significance. An evaluation should show that the motivation is justified and that the objectives of the ontology's development are met effectively and satisfactorily. Describe whether or not the ontology meets its stated requirements, competency questions and goals. |
| Importance: | MUST |
| Value: | DRAO is an application ontology and is therefore built specifically for record curation within FAIRsharing. It is one of three vocabularies used to describe all resources listed in FAIRsharing records. |
| Specification | |
|---|---|
| Description: | An illustration of the ontology in use in its an application setting or use case. |
| Importance: | MUST |
| Value: | Please view any record in FAIRsharing. |
| Specification | |
|---|---|
| Description: | State whether the ontology is endorsed by the W3C, the OBO foundry or some organisation representing a community. |
| Importance: | OPTIONAL |
| Value: | 🔴 This section has not been completed. |
| Specification | |
|---|---|
| Description: | An illustration of active projects and applications that use the ontology. |
| Importance: | MUST |
| Value: | DRAO is used to tag and link FAIRsharing records. |