OntoVoc Report - Sprint 04/2021#


The objectives of this third sprint in April 2021 were to:

  • Revisit General Policies

  • CURIE for PIDs

  • Assess whether the use of multiple ontologies for single fields should be allowed

  • Use of IDs and labels

  • Provide guidance on cell_population annotation

General Policies#

The OntoVoc team revisited the criteria for ontologies used in the AIRR schema that it defined in the 11/2018 sprint and that were expanded in the 04/2020 sprint to include the OBO Foundry Principles.

CURIEs for PIDs#

This is not directly related to ontologies, but as it does touch upon the use of CURIEs in the AIRR Schema, it does fall into the scope of OntoVoc. Main question is whether and how we can use, e.g., ORCIDs in Repos (see #476). The top-level conclusion on this topic is that CURIE can be used by repositories for non-ontology PIDs, but that the exact specification should be addresses by ComRepo WG. However, it should be noted that there are two functions a CURIE can serve:

  • A CURIE can be used to create a unique ID. In this case the prefix serves as/provides a namespace.

  • An expanded CURIE (i.e. URI) can be used to retrieve data, i.e., using it as a PID in the strict sense.

As there is no standard what type of information is provided by an URI (in the second case) there should be hints in the schema, e.g., on human vs. machine-readable data.

Use of multiple ontologies for a single field#

While it sometime would be preferable to have multiple ontologies available for a given field, the group came to the conclusing that this is would more likely than not reduce the interoperability of the data:

  • Overlaps between two accepted ontologies would be problematic as this creates an ambiguity about which term to use. This ambiguity jeopardizes the linkage possibilities that ontologies should provide.

  • Although OLS has a term-mapping service, this does not ensure that the same term in two different ontologies represents the same concept. Also the logical structure between ontologies might differ, complicating things even further.

  • There might however be very special and restricted use cases in which ontologies are orthogonal to each other and therefore the union of both could be used. This would in addition require a common structure that should exists for OBO ontologies. However, until there is a clear use case for this that cannot be solved in any other way, we will not allow multiple ontologies per term.

Use of IDs and labels#

It should be reiterated that:

  • The id is the authorative and required part of the information, the label is at the discretion of the repository and is provided to the user as complementrary information (so that the user does not need to resolve the id).

  • Repositories MUST support searches for the official label term, they SHOULD support ontology synonyms and they MAY support their own synonyms (termed “alias”).

  • Data returned by a repository MUST provide the official term as label and MAY provide or not provide a set of synonyms/aliases in the novel synonyms array.

  • The behavior of a synonyms field can be altered by the user query.

  • Some PID types might not have a meaningful label. Therefore label MAY be NULL.

Provide guidance on cell_population annotation#

Added to documentation