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nfdi4plants / nfdi4plants_ontology

An intermediate ontology for plants used by DataPLANT to fill the ontology gap
MIT License
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[Missing ontology] Protocol Type #32

Closed HLWeil closed 2 years ago

HLWeil commented 2 years ago

Reasons for this addition

@Brilator , @Martin-Kuhl , @muehlhaus , @Freymaurer

The protocol type is a field supported by the ISA-Json model, and could have different practical uses.

E.g. the GEO file format requires descriptions for specific protocols like the extract protocol. There needs to be a mechanism to find the respective protocol in the assay. As users are free to choose the names of their sheets, just matching the name would not be the way to go.

Therefore I propose we make use of the protocol type field. Unfortunately this is only defined in ISA-Json, but not ISA-Tab. But we could expand the standard by adding a Protocol Type column to the assay sheet. This feature could be part of Swate too.

It is important to make finding the proper protocol type convenient for the user and to restrain the possibilities in a way that makes matching the proper protocol by its type automatically manageable. Therefore it would be good to extend our ontology by a protocol type ontology. Swate would be able to recommend these protocol type terms to the user when inserting the protocol type column. Additionally, we could define different, more fine grained kinds of protocol types that then get matched to more broader terms trough a is a relationship.

E.g. user specifies one protocol in his assay as a filter based extraction protocol by using Swate (which found him this term in the ontology). When exporting his arc to geo, the Geo-converter tries to find the extraction protocol and by again using the ontology can match it with the filter based extraction protocol. -> Profit

Freymaurer commented 2 years ago

To implement the Protocol Type column (ref), i need the Protocol Type Term's accession id. Maybe someone could add the term?

Brilator commented 2 years ago

How is this handled for the other ISA attributes Source Name, Sample Name, etc.?

Brilator commented 2 years ago

I have initiated a list of terms that would live "under" Protocol Type, but I'm a bit reserved to add it to the ontology for reasons.

Freymaurer commented 2 years ago

They are handled differently. There is no reason to search through relationship directed terms of Source Name and Sample Name, as their intended usecase differs.

I only need the accession of Protocol Type to search through related terms.

Brilator commented 2 years ago

[Term] id: NFDI4PSO:1000161 name: Protocol Type

https://github.com/nfdi4plants/nfdi4plants_ontology/commit/3a8e1865e91f0f00695e16b44bbfa57b64260de3

Freymaurer commented 2 years ago

https://github.com/nfdi4plants/Swate/issues/212

Protocol REF und Protocol Type sind implementiert.

image

Originally posted by @Freymaurer in https://github.com/nfdi4plants/ISADotNet/issues/61#issuecomment-1190186478

kdumschott commented 2 years ago

The protocol types listed in BioTermSubTree.xlsx have been added to nfdi4pso.