Model Revisions for Initial Release (v1.0)

[davidruvolo51]

Discussion Points

• Name change: what should the new name be? And the appropriate short name? All entity IDs should be adjusted accordingly
• naming for samples: is it materials, samples, or biospecimen?
• further discussion needed for resolved (in clinical table; consult experts)
• Discuss pathologicalState lookup
• Is the term sequencing too specific?
• Should we split the sequencing table into sequencing + analysis? (follow FG approach)
• Discuss how to categorize subsets in studies? Maybe belongsToCohorts?
• In the files table, we may need to revisit the status variables. Should these be a lookup?
• Add analyses table and split sequencing table (use Fair Genomes as a guide) WAIT FOR FAIR GENOMES

Changes

This is a sticky for all changes that are needed for v1.0

• organization entity: move out of lookups
• releases: move out of lookups
• in subjects, change inclusionStatus to subjectStatus (update tag)
• add yearOfDeath and tag
• record metadata: consider adding who imported/updated the record
• change labIndication to samplingReason
• add samplingDate or change sampleTimestamp
• change samplingProtocol to type reference (value, description, codesystem, code, iri)
• change samplingProtocolDeviation to type text
• change biospecimenUsability to type xref or mref and create lookup SEE COMMENT BELOW
• change pcrFree to type bool
• change to targetEnrichmentKit to ref
• change umIsPresent to type bool and rename to umisPresent
• move labProcedure lookup out of lookups folder
• in files, change belongsToSequencing to type xref and change name to producedBy*
• in files, also add ref to cohort and study
• create cohorts lookup table and reference in files, subjects, study, consent

Features

• Move all tags to a csv file and create method for refreshing the tags dataset
• Create reference entity for file status. Use https://www.ebi.ac.uk/ols/ontologies/ncit/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FNCIT_C171193
• add reference entity for solved status which has been renamed to statusOfDiagnosis

[davidruvolo51]

I have moved the following item to ticket #11: reference entity for biospecimenUsability

[davidruvolo51]

The EMX tags object is now built by pull attribute level tags and transforming them into EMX format. This eliminates the need to define tags in the YAML. The process is slightly manual in that you have to update the known tags or add additional search patterns. Errors are thrown if a tag is not recognized.

[davidruvolo51]

Regarding the user who changed a record, we need to make the distinction between the change requester and the person who made the change (i.e., data manager, coordinator, etc.).