Three specific models are needed here: a data model to describ

A data model for describing parameters taken from literature about neuroshapes HOT 1 OPEN

incf commented on June 15, 2024

A data model for describing parameters taken from literature

from neuroshapes.

Comments (1)

MFSY commented on June 15, 2024

The general goal can be to propose schemas and vocabularies to describe:

scientific publication: parameters need to refer to the paper they annotate.
- @apdavison: proposed in this PR to reuse schema.og.
annotations taken from a scientific publication: parameters being a subset of them
- the W3C Annotation data model should definitely be explored.
relation between annotations/parameters and scientific publication:
- provenance: prov shapes already exist.
- the W3C Annotation data model has some relations as well.
relation between parameters and models within which they are used

Data
Here are listed projects and initiatives that have parameters data extracted from scientific papers and from which use cases can be obtained. Other projects are welcomed and can be listed below. @apdavison may have other use cases: would be nice to add them here for comparison and discussions.

1- Neurocurator at Bue Brain Project: https://github.com/BlueBrain/corpus-thalamus

example of used literature annotation: https://github.com/BlueBrain/corpus-thalamus/blob/master/10.1371%252Fjournal.pone.0107780.pcr#L37

{
        "annotId": "5803c136-061b-11e6-89bf-c869cd917532",
        "authors": [
            "iavarone",
            "oreilly"
        ],
        "comment": "",
        "experimentProperties": [],
        "localizer": {
            "location": 60402,
            "text": "The total surface area of the model IN was 9864 mm2 ;",
            "type": "text"
        },
        "parameters": [
            {
                "description": {
                    "depVar": {
                        "typeId": "BBP-121003",
                        "values": {
                            "statistic": "raw",
                            "type": "simple",
                            "unit": "um^2",
                            "values": [
                                9864.0
                            ]
                        }
                    },
                    "type": "pointValue"
                },
                "id": "870f0288-061b-11e6-9d1c-c869cd917532",
                "isExperimentProperty": false,
                "requiredTags": [
                    {
                        "id": "NIFCELL:nifext_46",
                        "name": "Thalamus interneuron small",
                        "rootId": "sao1813327414"
                    }
                ]
            }
        ],
        "pubId": "10.1371/journal.pone.0107780",
        "tags": [
            {
                "id": "NIFGA:birnlex_1595",
                "name": "Dorsal nucleus of lateral geniculate body"
            },
            {
                "id": "NIFINV:birnlex_2300",
                "name": "Computational model"
            },
            {
                "id": "NIFORG:birnlex_167",
                "name": "Mouse"
            },
            {
                "id": "NIFCELL:nifext_46",
                "name": "Thalamus interneuron small"
            }
        ],
        "version": "1"
    }

This example is very close to the Web Annotation Data model.

from neuroshapes.

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