Looking for instructions on how to relate the implementation to the CARE-SM data models

[wna-se]

I’m trying to understand how to use the CSV template to populate the CARE-SM model with information from a typical sequencing experiment and was wondering if there is a showcase with examples of how these or similar mappings have been done somewhere? Or perhaps an example of how the different Common Elements for Rare Disease Registration can be extracted from the CSV implementation?

Example: A typical sequencing experiment submitted to the European Genome–Phenome Archive (EGA).

I have information about the entities outlined in the following diagram:

How would I for example map information associated with a Sample to the CARE-SM Biobank data model? Looking at YARRRML/CARE_Fiab_yarrrml.yaml is seems like all of the model specific information is mapped to rdfs:label and I can‘t figure out where or how to add a link to the biobank.

[wna-se]

@pabloalarconm : @markwilkinson Said that you might be able to help with this.

[pabloalarconm]

Hi @wna-se

CARE-SM is a patient-centric data model, rather than a sample-centric data model. The main assessment for Genetic data is the semantic relationship of a patient, in genetic testing process, where the output is the (normally pathogenic) genetic variant detected, defined by a URL annonation code. Other additional element can be added to this representation:

• Nature of the variant annonation (DNA, mRNA, etc)
• The Zygosity
• Specific genetic method, e.g. Microarray
• The nature of the anatomical structure where its extraction was sampled: e.g. Blood.

The documentation for populating the csv template is here: https://github.com/CARE-SM/CARE-SM-Implementation/tree/main/CSV#genetic-assessment

Exampler use case for genetic information:

model,pid,protocol_id,frequency_type,frequency_value,value_datatype,comments,startdate,enddate,age,event_id,value,valueIRI,activity,target,agent,input,unit
Genotype,50012001,,,,xsd:string,,1998-06-30,1998-06-30,,788455685,601556,https://www.omim.org/entry/601556,,http://purl.obolibrary.org/obo/NCIT_C97927,http://purl.obolibrary.org/obo/GENO_0000136,,

Could you give me an example of how this sample information is represented? Is somehow broadly related to our input column in the CSV template.

Thank you, Pablo