Protocol: Planned Obsolescence

Author: Rhiannon Cameron [0000-0002-9578-0788]

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AKA Temporary Mints / ID Reservations Protocol

GENEPIO is an application ontology, and consequently curators often have to request new terms in other domain ontologies which then get imported to address application needs. This can add on a lot of time for a term request, because not only do GENEPIO curators need to take the time to curate the terms to determine an appropriate home, they also have to request said term, wait for curation/review, and wait for the eventual publication in the target ontology. This can take days, months, or in many cases years due to a lack of resources and personnel to manage the curator workload at said ontologies.

Rule-of-Thumb

Don't mint / reserve GENEPIO IDs for terms being requested in other ontologies unless absolutely necessary.

When is it necessary?

SCENARIO 1) Sometimes, to meet publication deadlines (e.g. of a data specification) we need an identifier that people can look-up and find a term (which is the promise we sold them in the benefit of using ontologies), which is a problem for terms taking years to get incorporated into a domain ontology. In this case we reserve and use GENEPIO IDs in the specification because (a) it is the only identifier we have at the time, (b) the target ontology may not accept the term and we need to request elsewhere, and (c) it may still end up as a non-temporary GENEPIO term if another home cannot be found for it at this time (i.e. there isn't yet an appropriate domain ontology to house it).

SCENARIO 2) In some cases IDs are assigned by the target ontology, published within the specification, but while still "in-progress" limbo of a target ontology when it comes to publication. In this scenario, those target ontology IDs have already been released in the form of a template or other application and so datasets are already associated with them. We don't want to confuse the situation, especially if there is no convenient means of normalization to a new identifier.

• In this scenario we can still mint new temporary GENEPIO terms, but we will not replace the IDs in the specification applications, instead we'll include them in the GENEPIO version as an alternative label annotation. We use alternative label because this will result in search "hits" on ontology look-up services like OLS and Ontobee.
• Also, all other annotations will ideally be exactly as requested in the target ontology submission, even if it isn't exactly how we normally ontologize GENEPIO terms as the temporary GENEPIO version should be in alignment with the target ontologies submission preferences.

Protocol

Ideally, you have already begun drafting term requests for the target ontologies where you're hoping these terms will reside. If not, you may need to revisit this protocol part-way through once you have begin that process.

1. Go to the current <Year> tab in the GENEPIO_Term ID Reservations gSheet workbook.
2. Fill in a row with an open ID (i.e. no other cells in the row have been occupied).
3. Fill in the required and other relevant columns (see the LEGEND tab for information on how to do this).
   • When known, in the OTHER Submission Request (URL) column include a link to the term submission request in the target ontology.
4. List your reference IDs in the appropriate rows of the Target Ontology Submissions Tracker - make sure these GENEPIO IDs remain associated with the requested terms as they move through the draft, submission, and published stages.
5. While awaiting publication, copy your term request information over to the appropriate tab of the GENEPIO_ROBOT Temporary Tables workbook.
   • Be sure to review the README and LEGEND guidance on using this worksheet and only include information matching the columns present in the relevant tab(s).
   • In these tables, the active ID will the GENEPIO ID and the target ontology ID should be present as an alternative label - this to ensure if users search for the target ontology ID, before it has been released by said ontology they will at least find our initial draft version of the term.
   • Also make an editor note indicating something along the lines of Planned Obsolescence: this term is a placeholder for a term requested in another ontology. Once the appropriate ontology term is available, this term’s identifier will be obsoleted with a “term replaced by” ID of the other term.
6. Update the associated Temporary Term Tables (more info below) in GENEPIO and either update the ontology using ODK and ROBOT or notify another GENEPIO curator so that they can do so for you.

Submission Requests Published

7. Now that the term requests are live in the target ontology, you can proceed with following the Obsolescence and Deprecation Protocol for terms within ROBOT tables.

Note: Don't forget to complete the appropriate Submission Tracker process by copying your submitted terms to the published tab.