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R2.2.1: (self) request terms to be added to a public ontology


Recipe metadata

identifier: R2.2.1

version: v0.1

Difficulty level

Reading Time

15 minutes

Recipe Type

Guidance

Executable Code

No

Intended Audience

Terminology Managers

Data Managers

Data Scientists

Ontologists


Main Objective:

Terms could be missing from public ontologies of choice. Where needed, new terms can be requested for these ontologies. The objective of this recipe is to provide a general guidline on how to request new terms, as well as to give some examples for specific ontologies.

Requesting new terms in public (biomedical) ontologies might be a structured, streamlined process or completely undocumented, depending on the actual ontology. Also, the process can take somewhere between days and up to a year, depending on the implemented release cycles of the target ontology.

Some ontologies, often large projects organized by consortia, have a detailed formal request process, maybe even with a dedicated ticketing and tracking system. A big number of ontologies rely on GitHub as a publicly accessible ticketing system for reporting issues on the ontology and also for requesting new terms. They might provide explicit guidelines on how to create an issue for a new term request, or they rely on GitHub issues without guidelines. And there are also ontologies relying on email for requesting new terms. These different request processes can be summarized as follows:

  • Formal request process
  • Request via GitHub with explicit guidelines
  • Request via GitHub without guidelines
  • Request via email

In most ontologies, everybody can request new terms. However, in some ontologies only members have access to the request process. In case of a request process organized via GitHub, a free GitHub account is required.

Ingredients

  • List of new terms
  • Target ontology
    • E.g. SNOMED CT, MedDRA, OBI, EFO, BAO, CL, RxNorm, BTO - BRENDA, DCAT 2

Graphical Overview of FAIRification Recipe Objectives

graph LR A(target
ontology) --> B[identify
missing term] B --> C(description of
requested term) C --> D{identify
request
process} A --> D D -->|formal
process| E[follow
guidelines] D -->|GitHub with
explicit guidelines| F[post GitHub issue
following guidelines] D -->|GitHub without
guidelines| G[post GitHub issue] D -->|email| H[write email to
editor/owner] E --> I{decision
on request} F --> I G --> I H --> I I -->|positive| J[use new term] I -->|negative| K[find alternative]

Capability & Maturity Table

FAIRification Objectives, Inputs and Outputs

Actions.Objectives.Tasks Input Output
text annotation new term(s), ontology ontology term, annotated text

Step-by-Step process

Step 1 Identify and describe relevant terms not included in public ontology of choice.

Step 2 Identify request process of the public ontology (i.e. formal request process, GitHub request with guidelines, GitHub request without guidelines, email request).

Step 3 Prepare at least the following information for requesting a new term:

  • justification for the request
  • preferred term label: a unique, unambiguous label for the term
  • potential alternative terms: common synonyms or translations
  • textual definition: expresses the meaning of the term, add sources and fully expand abbreviations
  • logical definition: suggest parent and child terms
  • example of usage: propose a use case
  • attribution: contributor names (and ORCIDs)

Step 4 Finalize and submit term request. Depending on the ontology, it can take up to a year to have the new term incorporated in the ontology, or to have the request rejected.

Examples

Formal request process

Example ontology: SNOMED CT - Systematized Nomenclature of Medicine

Scope of the ontology: conditions, clinical findings, procedures, body structures, substances, pharmaceuticals, devices, specimen

Information about requesting changes or additions: SNOMED CT has a Content Request Service (CRS). Requests can be submitted by members of SNOMED International, Nationale Release Centers or other authorized users, and must align with the Editorial guide. When submitting a request, it is important to follow the aspects mentioned in Step 3 of the Step-by-Step process. In addition to these aspects, the following is important to provide as well:

  • Reference(s) from a scientific or professional journal, or professional society
  • Fully expanded abbreviations

When submitting to the CRS, a request can have one of the sixteen possible statuses ('New', 'Draft', 'Accepted', 'Under Authoring', 'Ready for Release', 'In Inception', 'Clarification Needed', 'Pending Internal Input', 'On Hold', 'Forwarded', 'Withdrawn', 'Rejected', 'Completed', 'Appeal','Appeal rejected', 'In Appeal Clarification'). Within CRS, submitters are notified when a status has been changed.

More information can be found here and in this guide.

Request via GitHub with explicit guidelines

Example ontology: OBI - Ontology for Biomedical Investigations

Scope of the ontology: assays, devices, objectives in scientific investigations

Information about requesting changes or additions: OBI provides a GitHub repository and a mailing list. New-term requests are handled as GitHub issues. There is an explicit guideline document on how to request new terms.

For a proposed new term, they ask for the following information:

  • editor preferred term: a unique, unambiguous label for the term in American English
  • alternative terms: common synonyms or translations
  • textual definition
  • definition source for the textual definition
  • logical definition (or parent term)
  • example of usage
  • term editor: your name, and that of any collaborators, as it should appear in OBI

Request via GitHub without guidelines

Example ontology: CL - Cell Ontology

Scope of the ontology: cell types

Information about requesting changes or additions: The Cell Ontology provides a GitHub repository, a contact email, and a mail list. New-term requests (NTR) are formulated as issues on the GitHub repository.

Request via email

Example ontology: RxNorm

Scope of the ontology: drugs

Information about requesting changes or additions: Information about requesting terms can be found in the FAQ section of the Unified Medical Language System (UMLS) where RxNorm is part of.

Changes or additions to UMLS can be requested by contacting NLM Customer Support. The NLM Customer Support can be contacted through a form. If additions are specific to the source, you should contact the terminology source provider. Contact information is available in Appendix 1 of the Licence agreement.

UMLS is updated in May and November of each year.

Table of Data Standards

Data Formats Ontologies
OWL OBI, Cell Ontology
OBO Cell Ontology
Release Format 2 SNOMED CT
Rich Release Format RxNorm

Authors

Name Affiliation ORCID CRediT role
Ulrich Goldmann CeMM - Research Center for Molecular Medicine of the Austrian Academy of Sciences 0000-0003-1120-6912 Writing - Original Draft
Emma Vos The Hyve Writing - Original Draft

License:

This page is released under the Creative Commons 4.0 BY license.