About

A Python library for writing SciData JSON-LD files.

SciData and JSON-LD

JSON-LD is a convenient (human-readable) encoding of Resource Desctiption Framework (RDF) triples. However, unlike traditional relational databases (e.g., MySQL), the graph has no schema. This is problematic as including data from different sources results in a system with no common way to search across the data. The SciData framework is a structure for users to add data and its metadata that are organized in the graph through the associated SciData ontology.

There are three main sections of the SciData framework:

• the methodology section (describing how the research was done)

• the system section (describing what the research studied and the conditions)

• the dataset section (the experimental data, plus any derived or supplemental data)

The methodology and system sections are generic and users can add any data they need to contextualize the dataset. However, in addition they must provide a JSON-LD context file to semantically describe the data elements included. The dataset section has predefined data structures (dataseries, datagroup, and datapoint) although other strudtures can be included if needed.

Translating the content in JSON-LD. Referencing the JSON-LD below:

• ‘@context’: provides resources that define the context (meaning) of data elements in the document (as a JSON array). It consists of three sections:

  • a list of one or more ‘context’ files

  • a JSON object containing one or more definitions of namespaces used in the document

  • a JSON object with one entry ‘@base’ that defines the base URL to be prepended to all internal references (i.e. ‘@id’ entries)

• root level ‘@id’: the ‘name’ of the file and where ingested into a graph database, the graph name

• ‘@graph’: the definition of content that will be represented as triples and identified by the graph name (this is therfore a ‘quad’)

• ‘@id’ under ‘@graph’: the identifier for the graph. The scidatalib code uses the ‘@base’ to populate this, so they are consistent. As a result, all node identifiers ‘@id’s in the document are globally unique because the ‘@base’ is unique.

Example JSON-LD:

{
  "@context": [
    "https://stuchalk.github.io/scidata/contexts/scidata.jsonld",
    {
      "sci": "https://stuchalk.github.io/scidata/ontology/scidata.owl#"
    },
    {
      "@base": "https://my.research.edu/<uniqueid>/"
    }
  ],
  "@id": "file_identifier",
  "generatedAt": "<automatically added",
  "version": "1",
  "@graph": {
    "@id": "https://my.research.edu/<uniqueid>/",
    "@type": "sdo:scidataFramework",
    "uid": "<uniqueid>",
    "scidata": {
      "@type": "sdo:scientificData",
      "methodology": {
        "@id": "methodology/",
        "@type": "sdo:methodology",
        "aspects": []
      },
      "system": {
        "@id": "system/",
        "@type": "sdo:system",
        "facets": []
      },
      "dataset": {
        "@id": "dataset/",
        "@type": "sdo:dataset",
        "dataseries": [],
        "datagroup": [],
        "datapoint": []
      }
    }
  }
}