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NF Schema v1.0.0

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@allaway allaway released this 26 Aug 21:01
· 588 commits to main since this release
0d77a62

This release contains the initial NF schema with all historical changes and the following logged changes:

Version Date Author Decision Rationale
1.0.0 8/18/2021 RJA Add nii file format. Needed for new dataset, no existing sufficient term
1.0.0 8/18/2021 RJA Added image mask dataType. Needed for new dataset, no existing sufficient term
1.0.0 8/18/2021 RJA Enhanced "dataType" definition. Was not very clear definition, and was confusing (previously referred to only bioinformatics data types, which is not how this term is being used).
1.0.0 8/18/2021 RJA Added cellLine values from prototype Neurofibromatosis Tools and Resources database. Ensure parity in canonical cell line names between these two resources.
1.0.0 8/18/2021 RJA Added animal model values from prototype Neurofibromatosis Tools and Resources database. Ensure parity in canonical animal model names between these two resources.
1.0.0 8/18/2021 RJA Combined modelSystemName and modelSystemStrainNomenclature (removing the latter term) They are becoming redundant; most mouse model "names" we are using are model system strain nomenclatures.
1.0.0 8/18/2021 RJA Shortened definition for Prss56Cre;R26mT It was overly detailed, source link can be used for more information.
1.0.0 8/20/2021 RJA added definitions and sources for Male, Female, Unknown attributes To help clarify usage
1.0.0 8/20/2021 RJA added "Sporadic Schwannoma" term for diagnosis To accomodate situations in which patients have non-schwannomatosis schwannomas
1.0.0 8/20/2021 RJA Changed tumorType definition to "The type of tumor that the biospecimen used to generate the data were collected from." To clarify that this attribute refers to the biospecimen, not the patient.
1.0.0 8/20/2021 RJA added "comments" attribute and added to all manifest types To collect unstructured information that may not be captured by schema.
1.0.0 8/20/2021 RJA Added additional values to NF1/NF2 genotype To account for situations in which somatic or germline hits might not be known. Long term, this could be split into more attributes (e.g. 22q LOH, NF2 somatic mutation, LZTR1 somatic mutation, etc..) but that might be burdensome to annotate. For now, keep terms simple for exploration, and rely on additional project-specific metadata.
1.0.0 8/20/2021 RJA Changed all lowercase "unknown" values to "Unknown" There was previously a mixture, harmonizing will allow us to have one single attribute (TODO). This will require remapping some values currently on the portal.
1.0.0 8/20/2021 RJA Found and removed duplicate values for "sex" attribute Was causing validation errors ('unknown' treated as canonical value rather than 'Unknown')