search

ELIXIR-Belgium / seek

For finding, sharing and exchanging Data, Models, Simulations and Processes in Science.
http://www.seek4science.org
BSD 3-Clause "New" or "Revised" License
2 stars 1 forks source link

SOP info in ISAjson #28

Open floradanna opened 2 years ago

floradanna commented 2 years ago

@rabuono I think we need to figure out what's best for SOP and then make specific issues about it.

        "protocols": [
            {
                "@id": "#protocol/seek id of the attribute with isaTag=protocol from template", //Probably best to have SEEK ID of the SOP assigned as Protocol for that Sample Type
                "name": "name of the attribute with isaTag=protocol from template", //Probably best is to use SOP title as discussed since it reflects User's name for protocol
                "protocolType": {
                    "annotationValue": "isa_protocol_type from template", //We have been adding these as the "Attribute name" of the attribute with isatag=protocol. For example "sample collection".
                    "termAccession": "iri of the attribute with isaTag=protocol from template",//This is about the title of the attribute, if defined by an ontology term. 
                    "termSource": "abbreviated ontology name (from the iri), as defined in ontologySourceReferences above"
                },
                "description": "description of the attribute with isaTag=protocol from template", //Originally this was supposed to be SOP description
                "uri": "iri again", //I am not sure SEEK has a IRI field for registering SOPs
                "version": "",
                "parameters": [
                    {
                        "@id": "#parameter/seek id of the attribute with isaTag=parameter_value from template", //Is associated with Sample Type, not Template.
                        "parameterName": {
                            "annotationValue": "attribute name of the attribute",
                            "termSource": "abbreviated ontology name (from the iri), as in ontologySourceReferences above",
                            "termAccession": "iri of the attribute with isaTag=parameter_value from template" //IRI of the term used as title for the attribute, if defined by an ontology term
                        }
                    }
                ],

"description": "description of the attribute with isaTag=protocol from template", //Originally this was supposed to be SOP description. Could we discuss if maybe we could pre-populate the protocol attribute with the SOP title? Or How do we use this attribute in dynamic table?

rabuono commented 2 years ago

Another point of discussion is the lack of reference to the specific SOP file in SEEK being used when exporting an ISAjson. We currently make use of its Description, and the '@id' does incorporate its SEEK ID in (example '"@id": "#protocol/7_43"' is about SEEK SOP of ID 7 being applied in SEEK Assay of ID 43). But no more info from that SOP file (or even its location) is provided.