Closed julesjacobsen closed 3 years ago
@mbaudis I wonder if you have advice about the extent to which phenopackets should support this? We would like to keep phenopackets small-ish so that it can be combined modularly with other GA4GH standards, but at the same time the Biosample is a key component that should have interoperability with MIABIS. We should also ask Ian Fore about this.
Pinging @mcourtot here...
From the Phenopacket point of view I think you'd want interoperability but not full coverage? The relevant portion of MIABIS is probably the sample related attributes - I don't think there is interest in phenopacket in representing biobanks admin data for example.
On a side note we could do a cute analysis here, using the MIABBIS checklist against our BioSamples Phenopackets export and see what is compliant or not.
Well, we have a partial mapping. In fact we can map to the minimal, minimal information.
https://github.com/BBMRI-ERIC/miabis/blob/master/Data-describing-Sample.md - maps to a Biosample
Introduced in 2020 (Eklund et al., 2020), the component Sample is a portion or quantity of biological material that is collected from a sample donor, or which is a digital representation of a biological entity of the sample donor, such as an image.
Attribute Code Attribute Name Allowed Values Description Constraints Cardinality MIABIS-SAMPLE-01 Sample ID Coded string Unique ID of the sample within a sample collection, often represented by the sample barcode; text identifier. Sample ID meant for sharing. Pseudonymized, alphanumeric. It is recommended that sample IDs will be persistent within a given biobank. 1 MIABIS-SAMPLE-02 Detailed sample type Text list The sample type saved from a biological entity for testing diagnostic, propagation, treatment or research purposes 1 MIABIS-SAMPLE-03 Sample storage temperature List: RT, 2oC to 10oC, -18oC to -35oC, -60oC to -85oC, <-135oC, Liquid nitrogen vapor phase, Liquid nitrogen liquid phase, Other The long term storage temperature at which the sample is stored after preparation, based on SPREC v3 and MIABIS-2.0-15 0 MIABIS-SAMPLE-04 Sample creation date and time yyyy-mm-ddThh:mm:ss The date and time the sample was created in the form currently described in MIABIS-SAMPLE-02 Detailed material type. Format according to ISO8601. Could also be partial, for example, YYYY 0 MIABIS-SAMPLE-05 Anatomical site ontology String Name of ontology used for describing the anatomical source of the sample material, for example, ICD-O-3 topography code MIABIS-SAMPLE-05 and MIABIS-SAMPLE-06 are required if any ontology information is provided 0/1 MIABIS-SAMPLE-06 Anatomical site ontology version Coded string Version of selected ontology for anatomical site MIABIS-SAMPLE-05 and MIABIS-SAMPLE-06 are required if any ontology information is provided 0/1 MIABIS-SAMPLE-07 Anatomical site ontology code Coded string Anatomical site code from the selected anatomical site ontology version MIABIS-SAMPLE-05 and MIABIS-SAMPLE-06 are required if any ontology information is provided 0 MIABIS-SAMPLE-08 Anatomical site ontology description String Description from the selected anatomical site ontology code MIABIS-SAMPLE-05 and MIABIS-SAMPLE-06 are required if any ontology information is provided 0 MIABIS-SAMPLE-09 Anatomical site free text String Explanation about Anatomical site in case of unknown Anatomical site or insufficient information MIABIS-SAMPLE-05 and MIABIS-SAMPLE-06 are required if any ontology information is provided 0 MIABIS-SAMPLE-10 Sample content diagnosis Text list The ICD-10 diagnosis code describing content of the sample, such as whether the sample contains cancerous material 0...n MIABIS-SAMPLE-11 Use restrictions Text list The restrictions that may change the availability of the samples donated by the sample donor 0...n
https://github.com/BBMRI-ERIC/miabis/blob/master/Data-describing-Sample-Donor.md - maps to an Individual
Attribute Code Attribute Name Allowed Values Description Constraints Cardinality MIABIS-SAMPLEDONOR-01 Sample donor ID Coded String Sample donor ID. Unique ID code of the sample donor within the sample collection/biobank Pseudonymized, alphanumeric 1 MIABIS-SAMPLEDONOR-02 Sex Text list Biological sex of the sample donor. MIABIS-2.0-9 1 MIABIS-SAMPLEDONOR-03 Data categories Structured data The data categories from which data are available or can be linked to the sample donor. Can be several values (list modified after MIABIS-2.0-13). 0...n MIABIS-SAMPLEDONOR-04 Birth date yyyy-mm-ddThh:mm:ss Birth date of the sample donor. Coding ISO8601. Can also be partial, for example, YYYY. Date of birth is required when Event date (MIABIS-EVENT-02) is used, otherwise partial date, as in birth year, can be used 0
Does our Biosample map well to the MIABIS standard?
https://github.com/MIABIS/miabis/wiki