Michael Baudis
Michael Baudis
This PR follows previous discussions in the Metadata Task Team (e.g. @mcourtot, @helenp ...), last on 2017-04-27; as well as general agreement about this objects with the schema integration team...
The object time"stamps" for creation and update time have gone through several permutations. While they have converged to `created` and `updated`, in`assay_metadata.proto` there is now `message_create_time`, `message_update_time`, inconsistent with all...
In "reads.proto" and "variants.proto", there are erroneous formats for the `created` and `updated` time stamps (int64, "milliseconds from the epoch"). The use of ISO8601 for time attributes had long been...
The `Disease` object references `OntologyClass` for [ICD-O values](https://github.com/phenopackets/phenopacket-schema/blob/d3c75d358d99c8d479a2d433a9ea39cf71ad592d/src/main/proto/phenopackets/schema/v2/core/disease.proto#L47) used for `primary_site` annotations. Which ICD-O ontology implementation does this refer to? While the codes themselves are well defined/known, It is no...
The v2 documentation provides different options for TNM findings: * `clinical_tnm_finding` in `Disease`, with the description "child terms of NCIT:C48232 (Cancer TNM Finding)" and examples [in the documentation](https://phenopacket-schema.readthedocs.io/en/latest/cancer-example.html#diseases) (but partially...
**What is this request referring to?** Result of genomic copy number assessment of a genomic element or region **What is the name you would like SO to give the term?**...
**SO term name and accession** copy_number_variation (SO: 00011563) **Parent term name and accession** sequence_length_alteration (SO: 0000248) **Suggested new parent term name and accession** sequence_alteration (SO:0001059) **Reason for the change** Copy...
Hi, I suggest adding an option to filter (blacklist, optional whitelist) keys: * `-exclude_keys _id` ... or such. Helpful if one wants to represent the "content related" parts of a...
I suggest specification of ISO8601 for date/time values (see GA4GH; https://github.com/ga4gh/schemas/blob/master/doc/source/api/metadata.rst). This requires conversion of the current examples: `"created": "!!date 2016 1 14"` => `"created": "2016-01-14"` ... and replacement of...
In `assay_metadata.proto`, `Experiment`does not contain an attribute to link to the respective bio_metadata objects. For `Experiment`, the object description says "An experimental preparation of a sample". This implies referencing the...