[BUG] RO crate WIP

[Freymaurer]

Sources:

• https://github.com/nfdi4plants/isa-ro-crate-profile/blob/main/profile/isa_ro_crate.md
• https://www.researchobject.org/ro-crate/profiles.html

Must still be done:

Encoder

Assay

• Missing creator
• Missing identifier
• Missing measurementMethod
• Has not specified instrument

Covered by nfdi4plants/isa-ro-crate-profile#9?

• Has not specified url

Covered by nfdi4plants/isa-ro-crate-profile#5?

• Missing headline
• Missing description
• Missing dateCreated
• Missing dateModified
• Missing citation

LabProtocol

https://github.com/nfdi4plants/isa-ro-crate-profile/blob/main/profile/isa_ro_crate.md#labprotocol

• Missing reagent
• Missing computationalTool
• url has strange value "http://nfdi4plants.org/protocols/MyProtocol".
  Just a placeholder

Covered by nfdi4plants/isa-ro-crate-profile#13?

• Missing sameAs

Covered by nfdi4plants/isa-ro-crate-profile#10?

• Missing headline
• Has not specified name

Sample

• processSequence.outputs has additionalProperty mapped to "characteristics" and "factorValues", instead of or.

Person

• requires familiyName, but some cultures do not have one. PLUS if we must infer a person object from a isa-json authorList string we can only set name. I recommend setting familiyName as COULD. Therefore, we should also set givenName as SHOULD or move the inferred name from name to givenName.

ScholarlyArticle

• sameAs is used for DOI in the example, but the given example doi is just a doi "11.1111/abcdef123456789", which is not of type URL.
• url is used for PubMedID in the example, but the given example PMID is just a number "12345678", which is not of type URL.
• i recommend setting both DOI and PMID as identifier of type PropertyValue with value as the identifier and valueReference as "DOI"/"PMID"/..etc

More

• Do we really need to switch between PropertyValue and DefinedTerm for ontology annotations? Deciding for either one seems like a better idea.

Decoder

Everything

[HLWeil]

Regarding the PropertyValue vs DefinedTerm:
These are (in principle) not meant to be used interchangeably. Defined Term is used to depict a single ontology term. Property Value on the other hand is used to depict a term triplet (like parameterValue in isa). It can have an ontology header, ontology value and/or ontology unit.