Add Mammalian Phenotype Ontology

[gaurav]

This PR adds terms from the Mammalian Phenotype Ontology as requested by CAM-KP (#240). I added all the MP identifiers as well as mappings from https://github.com/mapping-commons/mh_mapping_initiative to connect it to HP and other identifiers. I added sssom as an explicit prerequisite so we can use it to read the SSSOM files in that GitHub repo, but that caused a lot of our other prerequisites to change (hence all the changes to requirements.lock).

We end up with 13,335 cliques that consist only of an MP identifier and 588 cliques that combine MP identifiers with other identifiers. We have no cases where an MP: identifier is chosen over other identifiers; the clique leaders we generate are:

  26 MESH
8498 EFO
13335 MP
16014 HP
19843 NCIT
315066 UMLS

There are a bunch of mapping issues, such as:

• MP:0001914 "hemorrhage" duplicates NCIT:C26791 "hemorrhage", which includes MESH and MEDRA identifiers.
  • We might be able to use EFO to make this connection, but UberGraph doesn't contain this edge since UberGraph doesn't have EFO.
• MP:0003342 "accessory spleen" is cliqued with HP:0001748 "Polysplenia" instead of HP:0001747 "Accessory spleen"

Ordinarily I would be nervous about including MP without more/better mappings, but since this isn't going to affect autocomplete (where we specifically filter to MONDO|HP) and that MP identifiers aren't (currently) clique leaders, I think we can merge this in now and then fix cliquing issues if anybody runs into issues with them (for now, probably only CAM-KP).

Closes #240.

WIP: see how often this new information merges cliques in ways we don't expect.

Should be merged after PR #365.

[gaurav]

• Message Nico and see if he knows of any mapping sources.
• Talk to Chris about maybe allowing the MP IDs in now and fixing them later, maybe as part of an exact-label cleanup.
• Give up and get rid of the MP-only cliques, so we only include MP identifiers if they combine with an existing clique.

[Copilot]

Pull request overview

Adds Mammalian Phenotype Ontology (MP) support to the disease/phenotype compendium build, including HP↔MP mappings sourced from SSSOM files, and updates configuration/dependencies to incorporate MP into the pipeline.

Changes:

• Add MP prefix support in UberGraph SPARQL query templates and introduce MP as a recognized prefix constant.
• Add an HP↔MP concord generation step using SSSOM mappings, and include MP/HP_MP in disease pipeline config lists.
• Add sssom as a project dependency to parse SSSOM mapping files.

Reviewed changes

Copilot reviewed 6 out of 6 changed files in this pull request and generated 6 comments.

Show a summary per file

File	Description
src/ubergraph.py	Adds MP: prefix declarations to relevant SPARQL templates so MP CURIEs can be used in queries.
src/snakefiles/diseasephenotype.snakefile	Adds a new rule to generate an HP_MP concord file from SSSOM mapping URLs.
src/prefixes.py	Introduces the MP prefix constant.
src/createcompendia/diseasephenotype.py	Adds MP ID writing, HP↔MP concord extraction from SSSOM, and integrates MP into clique/typing logic.
pyproject.toml	Adds sssom dependency for parsing SSSOM TSVs.
config.yaml	Adds MP and HP_MP to disease IDs/labels/concord configuration and enables MP in UberGraph ontologies list.

Comments suppressed due to low confidence (2)

config.yaml:212

• MP was added to disease_labelsandsynonyms, which makes the pipeline require ${download_directory}/MP/labels and /MP/synonyms (see disease_compendia inputs). Currently config.generate_dirs_for_labels_and_synonyms_prefixes does not include MP, so get_obo_labels/get_obo_synonyms won’t generate those per-prefix files and Snakemake will fail. Please either add MP to generate_dirs_for_labels_and_synonyms_prefixes (config.yaml) or refactor the disease pipeline to read labels/synonyms from the common UberGraph files instead of per-prefix files.

disease_labelsandsynonyms:
  - MONDO
  - DOID
  - Orphanet
  - HP
  - MP
  - MESH
  - NCIT
  - UMLS
  - SNOMEDCT
  - EFO

config.yaml:224

• MP was added to disease_ids, which means disease_compendia will require ${intermediate_directory}/disease/ids/MP. There is a new write_mp_ids() helper, but no Snakemake rule creates this ids file in src/snakefiles/diseasephenotype.snakefile, so the workflow will be missing an input. Add a disease_mp_ids rule (calling diseasephenotype.write_mp_ids) or remove MP from disease_ids until it’s wired up.

disease_ids:
  - MONDO
  - DOID
  - Orphanet
  - HP
  - MP
  - MESH
  - NCIT
  - UMLS
  - OMIM
  - EFO

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[gaurav]

Superceded by PR #790. Closing.