Curate missing design pattern templates and deprecate unused

[balhoff]

src/design_patterns

• [ ] Add missing. We're missing a lot common patterns: Prioritize any that are also used on annotation. ~1hr, 2-3 people
  • metabolism
  • catabolism
  • biosynthesis
• [ ] Review and remove unused. ~1hr, 3-4 people
• [ ] Renaming to more meaningful follow dosdp naming best practice; see https://github.com/INCATools/dead_simple_owl_design_patterns/issues/67
  • ~1hr 1-2 people
  • don't use geeky terms like 'x_specification'; instead 'cell_fate_specification', or 'specification_by_cell_type'
• [ ] Ensure all DPs have an editor-friendly description field
  • ~2hrs 3-5 people
• [ ] Review list of terms that do not conform to a DP to determine next course of action

This is a summary of usage of the currently curated DPs: (number of lines in tsv file: 1 line means just the header)

15417	total
3501	regulation.tsv
3009	negative_regulation.tsv
2988	positive_regulation.tsv
2072	regulation_by.tsv
727	macromolecular_complex_binding.tsv
654	involved_in_x_y.tsv
467	x_development.tsv
373	chemical_transport.tsv
273	x_morphogenesis.tsv
228	cc_assembly.tsv
215	occursIn.tsv
178	part_of_cell_component.tsv
126	x_formation.tsv
103	protein_localization_to.tsv
69	import_across_membrane.tsv
67	import_across_plasma_membrane.tsv
67	transmembrane_import_into_cell.tsv
51	integral_membrane_component.tsv
51	intrinsic_membrane_component.tsv
50	cc_disassembly.tsv
47	extrinsic_membrane_component.tsv
20	anchored_membrane_component.tsv
14	multi_organism_process.tsv
13	x_maturation.tsv
11	x_structural_organization.tsv
9	establishment_of_protein_localization_to.tsv
7	chromosomal_region.tsv
5	cc_transport.tsv
4	cc_transport_from_to.tsv
2	membrane_spanning_component.tsv
2	vesicle_mediated_transport_from_to.tsv
1	activator_activity.tsv
1	bounding_membrane_of_organelle.tsv
1	cc_organization.tsv
1	envenomation.tsv
1	export_across_membrane.tsv
1	import_into_cell.tsv
1	inhibitor_activity.tsv
1	membrane_region.tsv
1	mf_binding.tsv
1	protein_complex_by_activity.tsv
1	regulator_activity.tsv
1	single_organism_process.tsv
1	vesicle_mediated_transport.tsv
1	x_specification.tsv

[balhoff]

Added metabolism, catabolism, and biosynthesis in #22516.