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monarch-initiative / monarch-semantic-similarity-profiles

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Add jinja pipeline (config + Makfile.j2) #1

Closed matentzn closed 5 months ago

matentzn commented 1 year ago

profiles.yml contains:

ontologies:
   - id: upheno2-lattice
   - id: upheno1-equivalent
   - id: upheno1
semantic_similarity_profiles:
   - name: all
      method: semsimian 
      ontology: upheno2-lattice
      branches: 
         subject: UPHENO:0001001
         object: UPHENO:0001001
   - subset: hp-mp
      method: semsimian 
      ontology: upheno2-lattice
      branches: 
         subject: UPHENO:0001001
         object: UPHENO:0001001
      prefixes:
         subject: HP
         object: MP 
   - subset: hp-mp
      method: semsimian 
      ontology: upheno2-lattice
      branches: 
         subject: UPHENO:0001001
         object: UPHENO:0001001
      prefixes:
         subject: HP
         object: MP
   - subset: hp-mp
      method: cosine 
      ontology: upheno2-lattice
      branches: 
         subject: UPHENO:0001001
         object: UPHENO:0001001
      prefixes:
         subject: HP
         object: MP

Makefile.j2 includes all make goals to:

  1. generate ontologies in the ontologies section of the config.
  2. The semantic similarity profiles according to the config

Semsimian is oak semsimian and cosine is neat consine similarity - work with Justin and Harry to set this up.