Project organization

Note

TODO: make a nice object diagram for “organization” section

“organization” section

A typical organization would look like below:

in: “organization.json”

{
    "$schema":      "https://.../amorphys.json#properties/organization"
    "$description": "the project organization for foraging experiment",

    "dataset": {
        "name": "HumanForagingBehavior_PostdocRoom",
        ...
    },

    "people": {
        "Keisuke": {
            "name": "Keisuke S.K. Sehara",
            ...
        },
        "Julien": {
            "name": "Julien Colomb",
            ...
        },
        ...
    },

    "affiliations": {
        "ChaosSoftware": {
            "name": "Chaos Software",
            ...
        },
        ...
    },

    "funded-by": {
        "DFG": {
            "name": "Deutliche Forschungsgesellschaft",
            ...
        },
        ...
    },

    "data-published-by": [
        { "$ref": "../people/Keisuke" },
        { "$ref": "../people/Julien" }
    ]
}

class organization

The organization section of amorphys is a subclass of section, and describes the organization of the project group. It consists of several fields:

$description

a recommended field that is equivalent to that in section.

dataset

a Dataset object representing the metadata for this dataset itself.

people

a mapping to Contributor instances representing the people involved in this project.

affiliations

a mapping to Institution instances representing the affiliations of the people involved.

funded-by

a mapping to Funding instances representing the funding sources for this project.

data-published-by

an array of references to an item or more in people, representing the people contributed to publish this dataset.

Dataset class

The instantiation of the Dataset would look something like below:

{
    "name":        "HumanForagingBehavior_PostdocRoom",
    "description": "Tracking data of human subjects performing a foraging task inside a post-doc room",
    "keywords":    ["foraging behavior", "human", "scientists"],
    "license":     {
        "name":    "CC0",
        "uri":     "http://creativecommons.org/publicdomain/zero/1.0",
        "year":    "2019",
        "authors": { "$ref": "/organization/people" }
    },
    "references": [
        {
            "reference-type": "is-supplement-to",
            "name": "Sehara K, Colomb J, Larkum ME (2019) Dendritic mechanisms underlying foraging behavior of human subjects.",
            "uri": "doi:10.1101/000000"
        }
    ]
}

class Dataset

a class to represent the metadata for this project dataset as a whole, including a license information based on a License object.

name

a string representing the identifiable name of this dataset as a whole.

description

a string representing the description of this dataset as a whole.

keywords

an array of string objects representing the free keywords for this dataset.

license

a License object corresponding to the license clause of this dataset publication.

references

an array of Citation objects referring to the articles related to this dataset.

Contributor class

The Contributor class represents the contributor to this project.

It normally looke like below:

{
    "name":       "Keisuke S.K. Sehara",
    "lastname":   "Sehara",
    "firstnames": "Keisuke S.K.",
    "uri":        "ORCID:0000-0000-0000-0000",
    "contact":    "kkkkkeeeeiiiissssuuuukkkkeeee@mail.chaos-software.cc",
    "affiliation": [
        { "$ref": "organization/affiliations/ChaosSoftware" },
        { "$ref": "organization/affiliations/NerdUniversityTokyo" }
    ]
    "roles": [
        "https://dictionary.casrai.org/Contributor_Roles/Data_curation",
        "https://dictionary.casrai.org/Contributor_Roles/Software"
    ]
},

class Contributor

It is a subclass of Person.

All the superclass properties are necessary:

• name
• uri
• lastname
• firstnames
• contact

In addition, all of the properties described below are necessary.

affiliation

an Institution object, or a reference to one, or an array of multiple of them, corresponding to the affiliations for this contributor, in relation with this dataset publication.

roles

an array of roles, specified in terms of the contributor roles (as it is defined in the CRediT taxonomy).

Institution class

The Institution class is used to represent the affiliated institution(s).

Typically, it would look like below:

{
    "name": "Chaos Software",
    "uri":  "https://www.chaos-software.cc"
}

class Institution

This is a subclass of the Individual class, with no additional properties.

name

a required property inherited from Individual.name. It represents the human-readable expression of this institution.

uri

a required property inherited from Individual.uri. It represents the URL (i.e. starting with https://) of the institution.

Funding class

class Funding

(TODO)