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folterj committed Jul 3, 2024
2 parents 6a08c16 + f3b56cc commit 34437c2
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74 changes: 74 additions & 0 deletions dev3/2024-07-02/example-metadata/min-specimen-biosample.json
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{
"@context": [
"https://w3id.org/ro/crate/1.1/context",
{
"organism_classification": "https://schema.org/taxonomicRange",
"BioChemEntity": "https://schema.org/BioChemEntity",
"obo": "http://purl.obolibrary.org/obo/",
"acquisiton_method": {
"@reverse": "https://schema.org/result",
"@type": "@id"
},
"biological_entity": "https://schema.org/about",
"preparation_method": "https://www.wikidata.org/wiki/Property:P1537"
}
],
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.1"
},
"about": {
"@id": "./"
}
},
{
"@id": "./",
"@type": "Dataset",
"name": "Light microscopy photo of a fly",
"description": "Light microscopy photo of a fruit fly.",
"licence": "https://creativecommons.org/licenses/by/4.0/",
"hasPart": {
"@id": "./dros-mel-image.zarr/"
}
},
{
"@id": "./dros-mel-image.zarr/",
"@type": "Dataset",
"name": "OME-ZARR files",
"description": "the ome zarr files of the fly.",
"acquisition_method": [
"_:b0"
],
"preparation_method": [
"_b:1"
],
"biological_entity": [
"_:b2"
]
},
{
"@id": "_:b0",
"@type": [
"http://purl.obolibrary.org/obo/FBbi_00000243"
]
},
{
"@id": "_:b1",
"@type": [
"obo:OBI_0000272"
],
"description": "The fruit flies were individually encased in epoxy resin..."
},
{
"@id": "_:b2",
"@type": [
"BioChemEntity"
],
"organism_classification": "NCBI:txid7227"
}
]
}

62 changes: 62 additions & 0 deletions dev3/2024-07-02/example-metadata/minimal.json
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{
"@context": [
"https://w3id.org/ro/crate/1.1/context",
{
"organism_classification": "https://schema.org/taxonomicRange",
"BioChemEntity": "https://schema.org/BioChemEntity",
"obo": "http://purl.obolibrary.org/obo/",
"acquisiton_method": {
"@reverse": "https://schema.org/result",
"@type": "@id"
},
"biological_entity": "https://schema.org/about"
}
],
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.1"
},
"about": {
"@id": "./"
}
},
{
"@id": "./",
"@type": "Dataset",
"name": "Light microscopy photo of a fly",
"description": "Light microscopy photo of a fruit fly.",
"licence": "https://creativecommons.org/licenses/by/4.0/",
"hasPart": {
"@id": "./dros-mel-image.zarr/"
}
},
{
"@id": "./dros-mel-image.zarr/",
"@type": "Dataset",
"name": "OME-ZARR files",
"description": "the ome zarr files of the fly.",
"acquisiton_method": [
"_:b0"
],
"preparation_method": [
"_b:1"
]
},
{
"@id": "_:b0",
"@type": [
"http://purl.obolibrary.org/obo/FBbi_00000243"
]
},
{
"@id": "_:b21",
"@type": [
"BioChemEntity"
],
"organism_classification": "NCBI:txid7227"
}
]
}
1 change: 1 addition & 0 deletions dev3/2024-07-02/images/graph-min-specimen-biosample.svg
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1 change: 1 addition & 0 deletions dev3/2024-07-02/images/graph-minimal.svg
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177 changes: 177 additions & 0 deletions dev3/2024-07-02/ro-crate-metadata-proposal.md
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RO-Crate metadata minimal design
=====


RO-Crate provides a mechanism to package data together with metadata. In general this looks like a directory of files (or sub-directories) with an ro-crate-metadata.json to describe the files. We want to test mechanisms for storing extensible metadata alongside the OME-Zarr images. This document proposes a minimal schema for the ro-crate-metadata.json focused on describing what was imaged and the imaging technique.

***Relevant links***

RO crate: https://www.researchobject.org/ro-crate/
json-ld syntax: https://www.w3.org/TR/json-ld/
json-ld playground: https://json-ld.org/playground/

***Proposal for a minimal metadata structure***

The json payload below follows the RO-Crate guidance. It contains an object per 'thing that was imaged' (instance of schema:BioChemEntity), linked to its NCBI taxon*, an object per 'imaging technique' which has a type of the relevant FBBI imagining technique.

*note that the NCBI taxon may also be 'non organismal' for synthetic entities.

```
{
"@context": [
"https://w3id.org/ro/crate/1.1/context",
{
"organism_classification": "https://schema.org/taxonomicRange",
"BioChemEntity": "https://schema.org/BioChemEntity",
"obo": "http://purl.obolibrary.org/obo/",
"acquisiton_method": {
"@reverse": "https://schema.org/result",
"@type": "@id"
},
"biological_entity": "https://schema.org/about"
}
],
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.1"
},
"about": {
"@id": "./"
}
},
{
"@id": "./",
"@type": "Dataset",
"name": "Light microscopy photo of a fly",
"description": "Light microscopy photo of a fruit fly.",
"licence": "https://creativecommons.org/licenses/by/4.0/",
"hasPart": {
"@id": "./dros-mel-image.zarr/"
}
},
{
"@id": "./dros-mel-image.zarr/",
"@type": "Dataset",
"name": "OME-ZARR files",
"description": "the ome zarr files of the fly.",
"acquisiton_method": [
"_:b0"
],
"preparation_method": [
"_b:1"
]
},
{
"@id": "_:b0",
"@type": [
"http://purl.obolibrary.org/obo/FBbi_00000243"
]
},
{
"@id": "_:b21",
"@type": [
"BioChemEntity"
],
"organism_classification": "NCBI:txid7227"
}
]
}
```

The json-ld can be converted to a very basic RDF graph, but requires a '@base' to be added to the context to provide a root for the relative URIs for the files ( json-ld playground example: https://tinyurl.com/2jxlbtlj). The following image is a basic Entity-Relation style diagram:

<img src="./images/graph-minimal.svg">



***Suggested extensions / less than minimal***

Following REMBI guidance, one of the key objects that contains data is the 'Specimen' - this contains information about how the Biosample was prepared for imaging. We can therefore extend the metadata model to have a new object to contain information on the preparation protocol (which together with the biosample forms the Specimen that was imaged).


<img src="./images/graph-min-specimen-biosample.svg">


The metadata json file would look like:

```
{
"@context": [
"https://w3id.org/ro/crate/1.1/context",
{
"organism_classification": "https://schema.org/taxonomicRange",
"BioChemEntity": "https://schema.org/BioChemEntity",
"obo": "http://purl.obolibrary.org/obo/",
"acquisiton_method": {
"@reverse": "https://schema.org/result",
"@type": "@id"
},
"biological_entity": "https://schema.org/about",
"preparation_method": "https://www.wikidata.org/wiki/Property:P1537"
}
],
"@graph": [
{
"@type": "CreativeWork",
"@id": "ro-crate-metadata.json",
"conformsTo": {
"@id": "https://w3id.org/ro/crate/1.1"
},
"about": {
"@id": "./"
}
},
{
"@id": "./",
"@type": "Dataset",
"name": "Light microscopy photo of a fly",
"description": "Light microscopy photo of a fruit fly.",
"licence": "https://creativecommons.org/licenses/by/4.0/",
"hasPart": {
"@id": "./dros-mel-image.zarr/"
}
},
{
"@id": "./dros-mel-image.zarr/",
"@type": "Dataset",
"name": "OME-ZARR files",
"description": "the ome zarr files of the fly.",
"acquisition_method": [
"_:b0"
],
"preparation_method": [
"_b:1"
],
"biological_entity": [
"_:b2"
]
},
{
"@id": "_:b0",
"@type": [
"http://purl.obolibrary.org/obo/FBbi_00000243"
]
},
{
"@id": "_:b1",
"@type": [
"obo:OBI_0000272"
],
"description": "The fruit flies were individually encased in epoxy resin..."
},
{
"@id": "_:b2",
"@type": [
"BioChemEntity"
],
"organism_classification": "NCBI:txid7227"
}
]
}
```


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