OBA LinkML mapping

[joeflack4]

Overview

At the Aug 14 meeting w/ Nico, Shahim, Madan, and Joe (notes | recording), we decided to create some OBA LinkML classes for mapping purposes.

Sub-tasks

Involves:

• [ ] Nico: Start with the simple schema “level of chemical entity in location”.

May involve:

• [ ] Nico: Map the 13 unique combinations of LOINC analyte decompositions to OBA patterns, plus some automatic slot filling for some slots.
  • Joe: Would this entail 13 LinkML classes; 1 for each combo?

Additional info

Potentially helpful links:

• OBO semantic engineering training: Basic concepts of phenotype data and ontologies
• entity_attribute_location.yaml pattern (a Dead Simple Ontology Design Patterns (DOSDP) pattern)
• entity_attribute_location.tsv: Data matching the pattern

[joeflack4]

If we can get started with this, Peter will probably want to be involved. Nico said something about him being able to produce a structured catalog of reference ranges.

[joeflack4]

Shahim said he wanted to be involved with this too, but I assigned this just to me and Madan right now.

[joeflack4]

We may choose to start working on this sooner to when Nico comes back in about 2 mon.