Convert TermGenie templates to DOSDPs

[dosumis]

This probably needs to be done by hand.

List of GO TG templates (review - do we really want all of them?):

(How do we generate this given that TG is down?

Location of GO TG template javascript:

https://github.com/geneontology/termgenie/tree/master/TermGenie/TermGenieRulesDynamic/src/main/resources/rules/go

[cmungall]

I think by hand. Should we just split this up amongst us? I think this would be really good pre-meeting training in DPs. Note that you don't need to be a programmer to do this, for the phenotype project a curator wrote all the YAML.

I suggest people make PRs and these are reviewed by @dosumis and myself.

[dosumis]

Munged together a table to track progress. Note - some of these rules appear to be meta-patterns: either a refinement of a more general pattern or specifying multiple patterns taking the same fillers (e.g. all reg). We should think about how to do the latter with the TG replacement.

Type	TG_pattern_file	to keep?	claimed_by	DOSDP_file	Notes
	all_regulation.js	BP_regulation, BP_negative_regulation, BP_positive_regulation	@dosumis
	all_regulation_mf.js	?	?	TODO
	cc_assembly_disassembly.js	?	?	TODO
	cc_organization.js	?	?	TODO
	cc_transport.js	?	?	TODO
	cc_transport_from_to.js	?	?	TODO
	envenomation.js	?	?	TODO
	involved_in.js	?	?	TODO
	involved_in_mf_bp.js	?	?	TODO
	involved_in_x_y.js	?	?	TODO
	macromolecular_complex_binding.js	?	?	TODO
	occurs_in.js	?	?	TODO
	part_of_cell_component.js	?	?	TODO
	protein_complex_by_activity.js	?	?	TODO
	protein_localization_to.js	?	?	TODO
	regulation_by.js	?	?	TODO
	single_multi_organism_process.js	?	?	TODO
	x_development.js	?	?	TODO
	x_formation.js	?	?	TODO
	x_maturation.js	?	?	TODO
	x_morphogenesis.js	?	?	TODO
	x_regulation_triad.js	?	?	TODO
	x_structural_organization.js	?	?	TODO
chebi	biosynthesis_from.js	@dosumis	biosynthesis_from.yaml	TODO
chebi	biosynthesis_via.js	?	?	TODO
chebi	catabolism_to.js	?	?	TODO
chebi	catabolism_via.js	?	?	TODO
chebi	chemical_binding.js	?	?	TODO
chebi	chemical_export.js	?	?	TODO
chebi	chemical_homeostasis.js	?	?	TODO
chebi	chemical_import.js	?	?	TODO
chebi	chemical_import_into.js	?	?	TODO
chebi	chemical_response_to.js	?	?	TODO
chebi	chemical_transport.js	?	?	TODO
chebi	chemical_transport_from_to.js	?	?	TODO
chebi	chemical_transporter_activity.js	?	?	TODO
chebi	metabolism_catabolism_biosynthesis.js	?	?	TODO
chebi	transmembrane_transport_bp.js	?	?	TODO
chebi	transmembrane_transport_mf.js	?	?	TODO
cl	cell_apoptosis.js	?	?	TODO
cl	cell_differentiation.js	?	?	TODO
cl	cell_migration.js	?	?	TODO
uberon	metazoan_development.js	?	?	TODO
uberon	metazoan_formation.js	?	?	TODO
uberon	metazoan_maturation.js	?	?	TODO
uberon	metazoan_morphogenesis.js	?	?	TODO
uberon	metazoan_structural_organization.js	?	?	TODO
pro	protein_binding.js	?	?	TODO
pro	structural_protein_complex.js	?	?	TODO
plant	plant_development.js	?	?	TODO
plant	plant_formation.js	?	?	TODO
plant	plant_maturation.js	?	?	TODO
plant	plant_morphogenesis.js	?	?	TODO
plant	plant_structural_organization.js	?	?	TODO

[dosumis]

This pattern outline is a good place to start.

I'll do the first few as examples to give you all something to follow. Note - I now have a way to spec synonym combinations (actually turns out to be possible with the basic DOSDP spec).

[dosumis]

Added draft regulation patterns (see above)

[pgaudet]

This is now a Project: https://github.com/geneontology/go-ontology/projects/16