fix(portal): data model changes #4659
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davidruvolo51
changed the title
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davidruvolo51
approved these changes
Feb 7, 2025
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Looks great! I don't have any comments for this PR.
I have a few comments for the future discussion.
- What should we do with tissue type? Should it be merged with material type? Or is there another way to model this?
- When creating a schema using the RD3_V2 template, it takes a while to import the
MedDRA.csvfile and the ontology is not loaded in the form. It is also unclear what the difference is between this ontology and the ones we use in patient registries (e.g., OMIM, ORDO, HPO, etc.). In future versions, we might want to determine the level of catalogue integration and remove tables that aren't needed or duplicates of the patient registries.
| @@ -3,6 +3,7 @@ Biosamples,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43376,"A natural subst | |||
| Biosamples,,id,string,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C93400,A unique proper name or character sequence that identifies this particular material,"Beacon v2, FAIR Genomes, DCAT examples, RD3" | |||
| Biosamples,,alternate ids,string_array,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C90353,A backup sequence of characters used to identify an entity,RD3 | |||
| Biosamples,,material type,ontology,,,,BiospecimenType,,,,http://purl.obolibrary.org/obo/NCIT_C70713,"The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes","FAIR Genomes, RD3" | |||
| Biosamples,,tissue type,ontology,,,,TissueType,,,,,, | |||
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(Flagging this for future discussion)
Further input is needed on how to handle material type and tissue type. We might need to revisit this in the future.
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I discussed this with Joeri, he agreed on adding tissue type for now, but he stated this might need to be merged at a later point.
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Linked with issue molgenis/GCC#843 |
mswertz
approved these changes
Feb 10, 2025
| @@ -3,6 +3,7 @@ Biosamples,,,,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C43376,"A natural subst | |||
| Biosamples,,id,string,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C93400,A unique proper name or character sequence that identifies this particular material,"Beacon v2, FAIR Genomes, DCAT examples, RD3" | |||
| Biosamples,,alternate ids,string_array,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C90353,A backup sequence of characters used to identify an entity,RD3 | |||
| Biosamples,,material type,ontology,,,,BiospecimenType,,,,http://purl.obolibrary.org/obo/NCIT_C70713,"The type of material taken from a biological entity for testing, diagnostic, propagation, treatment or research purposes","FAIR Genomes, RD3" | |||
| Biosamples,,tissue type,ontology,,,,TissueType,,,,,, | |||
| @@ -2,11 +2,11 @@ tableName,tableExtends,columnName,columnType,key,required,refSchema,refTable,ref | |||
| Files,,,,,,,,,,,"http://purl.obolibrary.org/obo/STATO_0000002,http://purl.obolibrary.org/obo/NCIT_C42883","An electronic file is an information content entity which conforms to a specification or format and which is meant to hold data and information in digital form, accessible to software agents.","RD3, DCAT files add-on" | |||
| Files,,name,string,1,TRUE,,,,,,http://purl.obolibrary.org/obo/NCIT_C171191,The name of a file that identifies an electronic file,"RD3, DCAT files add-on" | |||
| Files,,alternate ids,string_array,,,,,,,,http://purl.obolibrary.org/obo/NCIT_C90353,A backup sequence of characters used to identify an entity,RD3 | |||
| Files,,path,hyperlink_array,,TRUE,,,,,,http://purl.allotrope.org/ontologies/result#AFR_0001927,"A file path is an identifier for a file in a file system or network (e.g., a scp compatible <host>:<path>)","RD3, DCAT files add-on" | |||
| Files,,path,string_array,,TRUE,,,,,,http://purl.allotrope.org/ontologies/result#AFR_0001927,"A file path is an identifier for a file in a file system or network (e.g., a scp compatible <host>:<path>)","RD3, DCAT files add-on" | |||
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so we allow for non URLs. That makes sense.
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