FAIRe term review for MIxS/DwC eDNA checklist proposal

This repository contains scripts and documentation for the TDWG/GSC eDNA task group to conduct a term-by-term review of the FAIRe checklist.

Background

The TDWG/GSC eDNA Task Group is working to develop an eDNA checklist under the DwC and MIxS standards. To support this effort, a term-by-term review of the FAIRe checklist is being conducted to:

• Track the origin of each FAIRe term.
• Document how terms have been modified from their original source, e.g., MIxS, DwC, the DNA extension, and DwC-DP.
• Determine whether each term should be included in the proposed DwC/MIxS eDNA checklist. To help visualise the decision-making process, an R function was developed to generate decision trees that capture and display the review outcomes for each term.

General procedure for each FAIRe term

1. Create a GitHub issue for the term e.g., Review: RecordedBy #245. Note that in the modeling standard we are using, LinkML, 'terms' are referred to as 'slots'.. (Steve - Done)
2. Raise disucssion points for the term (e.g., Miwa to generate the decision making tree for each term)
3. Add comments and feedback (TG members)
4. Discuss and vote durign a meeting (e.g., whether to propose the term to GSC/TDWG)
5. Review SKOS mapping (Re-visit points raised in Issue #14)
6. Update issue status from "Review started" to "Review complete"

General points to condiser for each term

1. Scope and inclusion : In general, terms in the FAIRe checklist are there because they are identified as important/useful by the FAIRe WG. So all FAIRe terms should be proposed to MIxS and DwC-DP except for those that fall out of the GSC/TDWG scope. For example, a) targeted-assay detection protocols without sequencing data for GSC, b) Unit terms for numeric variables (as GSC has their conventions for represneting unites)
2. Modifications to existing MIxS/DwC terms : Consider whether modifications made in the FAIRe checklists should be proposed. Note that checklist-specific examples may be accepted, but not descriptions (for now) by GSC.
3. Controlled vocabularies and ontologies : Where possible, terms should be controlled using existing ontologies. Note that some of the current FAIRe controlled terms may not yet aligned with established ontologies, hence require review.
4. Future FAIRev2 development : (Probably once we complete above discussions and decisions for all exisitng FAIRe terms,) consider whether additional new terms should be proposed, both for FAIRe v2 and for the MIxS/DwC proposals.