if the respective gene/entity from our kidney list is in the ClinGen curated list apply this group and points after reviewing the entry
if the respective gene/entity from our kidney list is NOT in the ClinGen list
review GenCC and OMIM entries
decide to split or lump if regarding modified ClinGen criteria if applicable
decide for a MONDO term (when lumping decide for only 1 "new" MONDO term and report the former ones / when splitting decide for >1 new term per Gene as disease entities)
--> use MONDO (not OMIM or Orphanet) as primary disease ontology in the manual curation effort
--> shorten the process if actionable: Genes associated with a single published disease entity should only be curated for that condition (i.e. lumped) unless there are indications to split specific phenotypic features of a syndrome or variable phenotype into separate curation(s)
Scoring logic:
if only screening publication then the category can't be more then Limited,
if there is a clinical description then the category can be Moderate,
if there is a clinical replication then the category can be Definitive
DEFINITIVE: 12-18 points; Replication over time!?
MODERATE: 7-11.99 points
LIMITED: 0.1-6.99 points
NO KNOWN RELATION: 0 points; contradictory evidence
[ ] define the scoring logic for the final table with cutoffs for the different categories
[ ] scoring logic for publications (screening = 1 point, first clinical description = 2 points, clinical replication = 3 points)
[ ] scoring logic: we further use the category "no known relation" for genes that are not trustworthy and associated with kidney disease
[ ] Write documentation for the initial manual curation effort
[ ] Set-up and finalize the curation sheet with automated high-evidence Gene implementation
[ ] Consider an automated display of a mouse-model score (2 points for a model, up to 4 points) from MGI mouse data if the Mode of Inheritance (MOI) of MGI fits the MOI of the Gene-Disease-Entity
Workflow:
--> use MONDO (not OMIM or Orphanet) as primary disease ontology in the manual curation effort --> shorten the process if actionable: Genes associated with a single published disease entity should only be curated for that condition (i.e. lumped) unless there are indications to split specific phenotypic features of a syndrome or variable phenotype into separate curation(s)
Scoring logic:
--> access the curation strategy sheet here: https://docs.google.com/spreadsheets/d/1KS9G2YR9U6uheu0zC-7zvMaSWCZv7UeVYh69BrkQK8M/edit#gid=0
TODO: