A data model for describing parameters taken from literature

[MFSY]

Three specific models are needed here:

• a data model to describe scientific publication
  • valuable vocabulary sources (schema.org)
• a data model to describe parameters:
  - shape of a parameter
  - numeric parameters with units
  - others ?
• a data model to describe the provenance of a parameter
  • from which publication it comes from and where ?
    • this is related to how the parameter is linked to the paper it help annotate
  • who did the annotation, when, evidence sources,... ?

[MFSY]

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.