phenopacket-format
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phenopackets
Should the evidence in the example at https://github.com/phenopackets/phenopacket-format/wiki/Tutorial be relying on the ECO codes, such as instead of having ``` evidence: - types: id: TAS ``` this should be ```...
Although the likely schema-level specification will be JSON-Schema (#31) this will live alongside a JSON-LD context that will specify the complete semantics of the format, and will be used to...
* Patient had: Skeletal muscle biopsy (SCTID: 430213002), which led to findings such as: Ragged red fibers (HP:0003200) * Patient had: Heart muscle biopsy, which led to findings such as:...
[extract from email discussion] Unsurprisingly, as Biosample and Ga4GH capture more than PXF does, the conversion is lossy. Is there a general field one could use to keep track of...
Should be subset of RO See also #7
Sorry, this is more of a question than an issue. In commit 86978bebc54bcc201d2fff21eac651fdda268520 and https://github.com/phenopackets/phenopacket-reference-implementation/commit/fefda802cb5cf6b462ab987534966df6b3bca5a7 I see that a protobuf schema is generated reflectively from the implementation API classes. As...
[extract from email discussion] To roundtrip we'd like to be able to say that the PXF ID is the Biosample ID, whereas at the moment it is just a string....
We need to not only be able to represent the phenotypic profile of a patient or group of patients, but also their organismal history. This includes relationships to other patients...
Is there a trick to using phenopacket to model patient's information at population level? E.g. Cohort of 150 colorectal carcinoma patients with hypertension phenotype?
See for example [MIAPPE paper](http://plantmethods.biomedcentral.com/articles/10.1186/s13007-016-0144-4) In broad terms, standards such as MIAPPE record experimental details and outcomes, and pxf focuses on the phenotypic observation subset, and derived knowledge-base associations of...