Standard API protocol for ontology/terminology lookup

Date Submitted: August 24, 2023

Person Creating Document: Simon Jupp & Jane Lomax, Scibite

Idea Originator: SciBite


Problem Statement

Organisations are increasingly working to standardised ontologies and terminologies to increase the interoperability of data as part of their FAIR data strategy.  To ensure data is “Born FAIR” there is a need for the systems (ELNs, LIMS etc) that capture the data to surface these ontologies to users at authoring time. Whilst these systems may support controlled terminologies, they are often closed systems and integrate poorly with ontology or terminology management systems (OMS). This leads to a complex set of dependencies and middleware that must sync ontologies and data across systems.


Idea Proposal and Value Proposition

Data capture systems, such as ELNs and LIMS, provided by external vendors have limited API support for integrating with external Ontology Management Systems (OMS). By developing a common API interface for ontology term lookup vendors could avoid any particular lock-in when integrating an API of another system. We are proposing a standard API interface for a set of common operations relating to ontology/terminology lookup.  This standard would provide a conventional API based on the RESTful style architecture and would abstract away from any specific semantic web standard such as OWL or SKOS to cater for a wider diversity of terminology types and use-cases.


Organisations that have invested in external systems for capturing data and ontology management. At present these systems don’t talk to each other. By easing the integration of these systems via a common API protocol, organisations can benefit from each system without having to develop and maintain complicated middleware.

Managing ontologies in a central OMS that can be served to multiple applications helps organisation realise FAIR data. If external systems can readily communicate and consume ontologies from an OMS, then there is no need for costly middleware and infrastructure for connecting these different systems.


Critical Success Factors

Requires vendors of data capture systems to recognise the value of outsourcing ontology management to an external centralised system and be willing to adopt an API standard for looking up terminology with that system. Likewise requires OMS vendors to support the implementation of a common API protocol.


Other Relevant Information

A counter argument to this proposal is that W3C standards such as OWL and SKOS already exists for representing ontologies and terminologies and standard query languages, such as SPARQL, provide a common standard for different systems to communicate. Despite the availability of these technologies, the adoption and use of RDF in data management systems has been low, thus hampering the uptake of terminology standards across organisation.