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UPheno Use Cases

MGI and Alliance

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Cross species displays

  • Tables
  • Ribbons
  • Grids

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MGI - HMDC

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Common high level terms

Highlight indicates column contains a term that matches the search

total of annotations going down the DAG

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Maintain annotations in original ontology context

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HMDC

  • Currently the shared high level terms are created by manually mapping HP terms to MP headers
    • Requires periodic review to update for changes in HP or MP
    • Some HP terms do not readily map to any MP header and thus are missing from the grid
      • Abnormality of connective tissue (HP:0003549)
  • UPheno would replace
    • Manual high level term mapping - maybe with a slim set?

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Expand suggested terms in the MP-HP term match tool

  • Currently this uses SSSOM mappings and lexical mappings made by MGI
  • UPheno could be used to expand the suggested set of terms provided when a user enters an ID from one ontology

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Cross links between ontology browsers at MGI or outside

Insert HP cross link here

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Alliance

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Use Cases

  • Gene and Allele detail page summary ribbons
  • Shared phenotype summary pages

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Gene and Allele detail page Ribbons/Grids

  • Want to have summary ribbons similar to those for GO, Disease, and Expression
  • Need to have a set of high level terms to cover span of phenotypes from yeast to humans
    • Need to expand the set of cellular high level terms
    • Probably want to be able to tag specific terms in UPheno as being part of the ‘Alliance Slim’ similar to what we have done in DO

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All annotations

Organ system headers for annotations

Cellular annotations

Behavior/Other annotations

System doesn’t exist in species

Connected table would maintain the original context for the annotation, eg mouse data would show MP terms, Human HP terms

https://www.alliancegenome.org/gene/MGI:88059#phenotypes

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Ontology Browser/Annotation Pages

  • Want to aggregate all related phenotypes on a page and allow the user to move up and down in the ontology as desired
    • For example start from all abnormal heart phenotypes then drill down to all abnormal cardiac valve phenotypes and see all the annotations for all descendants across species
  • Example DO page in the Alliance

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abnormal heart morphology

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Definition: Any unspecified morphological anomaly of part of the heart, such as, for example, abnormal shape or colour.

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Parent terms: (from UPheno)

Child terms: (from UPheno)

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Related terms from species specific ontologies: abnormal heart morphology (MP:0000266)

Abnormal heart morphology (HP:0001627)

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Tables of annotations…

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