MIABIS - Githubissues

julesjacobsen commented 4 years ago

Does our Biosample map well to the MIABIS standard?

pnrobinson commented 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.

mbaudis commented 3 years ago

Pinging @mcourtot here...

mcourtot commented 3 years ago

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.

julesjacobsen commented 3 years ago

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

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

phenopackets / phenopacket-schema

MIABIS #215

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