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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
Example:
Methontology, On-To-Knowledge, Neon methodology. If no bespoke methodological framework was used, describe how the core activities of the ontology engineering lifecycle (such as ontology management, development and support) were addressed (http://onlinelibrary.wiley.com/doi/10.1002/047003033X.ch9/pdf).
B. Motivation
B.1 Need
Specification
Description:
Justification of why the ontology is required.
Importance:
MUST
Example:
For example, the 2015 JBMS article "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon" has the following: "Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups." http://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-21
B.2 Competition
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
Example:
The background section of the paper "The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation" in JBMS 2014 describes other attempts to describe software in ontologies or vocabularies. See http://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-25
B.3 Target audience
Specification
Description:
The community or organisation performing some task or use for which the ontology was developed.
Importance:
MUST
Example:
The Gene Ontology is used by curators of gene products to describe the major functional attributes of those gene products to provide a common language across species for describing the molecular function, biological process and cellular location of gene products.
C. Scope, requirements, development community
C.1 Scope and coverage
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.
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
Example:
The Gene Ontology is developed by the Gene Ontology Consortium.
C.3 Communication
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.
How the knowledge in the ontology was gathered, sorted, verified, etc.
Importance:
MUST
Example:
Description of the source knowledge in the materials and method section of the article for The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation in JBMS 2014 https://jbiomedsem.biomedcentral.com/articles/10.1186/2041-1480-5-25
D.2 Source knowledge location
Specification
Description:
The location of the source whence the knowledge was gathered.
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.
the knowledge representation language used and why it was used. For a language like OWL, indicate the OWL profile and expressivity.
Importance:
MUST
Example:
OWL version 2, EL profile.
E.2 Development environment
Specification
Description:
The tool(s) used in developing the ontology.
Importance:
OPTIONAL
Example:
Protégé, WebProtégé, TawnyOWL, TopBraid Composer, Swoop, etc.
E.3 Ontology metrics
Specification
Description:
Number of classes, properties, axioms and types of axioms, rules and individuals in the ontology.
Importance:
SHOULD
Example:
From the Human Phenotype Ontology NAR 2013 article "Human Phenotype Ontology provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes." https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkt1026
E.4 Incorporation of other ontologies
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
Example:
Import of Uberon core – extended version, 2016-05-11 release under the 'anatomical entity' class.
E.5 Entity naming convention
Specification
Description:
The naming scheme for the entities in the ontology, capturing orthography, organisation rules, acronyms, and so on.
What is the scheme used for creating identifiers for entities in the ontology. State whether identifiers are semantic-free or meaningful.
Importance:
MUST
Example:
Incremental class number, using 10 digit number with ontology name as the prefix.
E.7 Entity metadata policy
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
Example:
Each class minimally requires a textual definition, a label, a creator and an edit date. The Ontology for Biomedical Investigations (OBI) paper https://www.ncbi.nlm.nih.gov/pubmed/27128319 has a section entitled "Choice of metadata conventions".
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E.8 Upper ontology
Specification
Description:
If an upper ontology is used, which one is used and why is it used? If not used, then why.
The relationships or properties used in the ontology, which were used and why? Were new relationships required? Why?
Importance:
MUST
Example:
The schema.org relationships were imported and used. We used the OBO Relations Ontology.
E.10 Axiom patterns
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.
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
Example:
Outline of sustainability plan, including method to sustain and who will be responsible.
F.2 Entity deprecation strategy
Specification
Description:
Describe the procedures for managing entities that become removed, split or redefined.
Importance:
MUST
Example:
The owl:DeprecatedClass; no class is deleted from the ontology, but deprecated classes are labelled as obsolete with an annotation property.
F.3 Versioning policy
Specification
Description:
State or make reference to the policy that governs when new versions of the ontology are created and released.
Importance:
MUST
Example:
The Open Biomedical Ontologies Consortium has a versioning policy, see http://www.obofoundry.org/id-policy.html. This page states "Versions are named by a date in the following format: YYYY-MM-DD. For a given version of an ontology, the ontology should be accessible at the following URL, where is replaced by the IDSPACE in lower case." and gives further elaboration.
G. Quality Assurance
G.1 Testing
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
Example:
Examples of competency questions that can be asked. Examples of inferences that can be made. Classification time using an appropriate reasoner: "The ontology was successfully classified by both Pellet 2.3.1 and HermiT 1.3.8 (i.e., is logically consistent) in less than 1 second. All classes in the ontology are satisfiable."
G.2 Evaluation
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.
State whether the ontology is endorsed by the W3C, the OBO foundry or some organisation representing a community.
Importance:
OPTIONAL
Example:
SNOMED is mandated for use by many national health organisations. The Chemicals of Biological Interest Ontology is a member of the OBO Foundry.
G.5 Evidence of use
Specification
Description:
An illustration of active projects and applications that use the ontology.
Importance:
MUST
Example:
The Gene Ontology is used to annotate the gene products for their molecular function, biological process and cellular component in many species specific and cross-species databases.