Shared: Dataset and Low Level Objects

OntologyTerm

Examples:

{
  "term_id" : "ncit:C3059",
  "term_label" : "Glioma"
},

{
  "identifier" : "pubmed:18506748",
  "relation" : "denotes"
},

ExternalIdentifier

Example:

Dataset

All GA4GH data objects are part of a dataset. A dataset is a data-provider-specified collection of related data of multiple types. Logically, it’s akin to a folder, where it’s up to the provider what goes into the folder. Individual data objects are linked by datasetId fields to Dataset objects.

Since the grouping of content in a dataset is determined by the data provider, users should not make semantic assumptions about that data. Subsets of the data in a dataset can be selected for analysis using other metadata or attributes.

Dataset Use Cases

For server implementors, datasets are a useful level of granularity for implementing administrative features such as access control (e.g. Data set X is public; data set Y is only available to lab Z’s collaborators) and billing (e.g. the costs of hosting Dataset Y should be charged to lab Z).

For data curators, datasets are ‘the simplest thing that could possibly work’ for grouping data (e.g. Dataset X has all the reads, variants, and expression levels for a particular research project; Dataset Y has all the work product from a particular grant).

For data accessors, datasets are a simple way to scope exploration and analysis (e.g. “Are there any supporting examples in 1000genomes?”; “What is the distribution of that result in the data from our project?”).

GeoLocation

A GeoLocation object provides information about a geographic position related to a record. Examples could be:

• an address, e.g. of a lab performing an analysis
• provenance of an individual, obfuscated to a larger order administrative entity (Suffolk, U.K.)
• a lat/long/alt position where an environmental sample was collected

The geographic point object uses the default units from the DCMI point scheme and avoids optional representation in non-standard units.

"geo_data" : {
  "geo_json" : {
    "type" : "Point",
    "coordinates" : [
      8.55,
      47.37
    ]
  },
  "geo_label" : "Zurich, Switzerland, Europe",
  "info" : {
    "city" : "Zurich",
    "continent" : "Europe",
    "country" : "Switzerland"
  },
  "geo_precision" : "city"
},