Suggestions: 1) Add new children of `has_participant`, 2) Create sequence of events; Question about ttl files

[nlharris]

Discussed in https://github.com/biolink/biolink-model/discussions/1045

^{Originally posted by 0m1n0 June 24, 2022} Dear Biolink team,

I have some suggestions to expand Biolink Model vocabularies.

1. Add some more children to has_participant

Today, you offer the following children, which is already very useful:

actively involves enabled by has catalyst has input has output has substrate

Since I work on enzymatic reactions, I would have liked to have had the following children:

• has_substrate_or_product:
  • has_product
  • you already have has_substrate
• has_cofactor to separate from substrates/products:
  • has_input_cofactor
  • has_output_cofactor

2. Create a new relation of event sequence

In metabolic pathway study, order of reactions and/or pathways is important. The reaction succession can be traced by linking substrates and products but this can be time consuming. And I suppose sequence relationship (in time or order) can be applied in other fields, e.g. the procedure for clinical treatment.

How about to create:

• followed_by
  • directly_followed_by
• preceded_by
  • directly_preceded_by

3. Question about ttl files

What are the differences between biolink-model.owl.ttl and biolink-model.ttl? Both files must be integrated to use Biolink Model?

[nlharris]

Tagging @ 0m1n0 Thank you for submitting these suggestions and question; they kind of got lost in Discussions because we don't remember to look at that page. We will get back to you soon!