7. Dataset About

Describing what the dataset is about (i.e what was the scope, objective, materials) and providing information about the type of data associated with the given dataset:

  • Document the nature of information available in a dataset through the Biocaddie ‘data type’ object.
A conceptual map detailing Biocaddie DATS data-type qualifiers and data distribution descriptors .

In this context, the ‘data type’ required to annotate a DataSet should be viewed as a content type [terminology needs to be specified]). This encompasses the nature of the signal recorded in a dataset or information content of interest. For instance: gene expression data or phenotypic data, electronic health records But mime-type may be used. * chemical * sequence * spectrum * audio * image * video * …

but other descriptors may be used such as Biosharing, Scicrunch or re3data category/data domain descriptors.

  • Data aggregation type:

    In the context of DataMed indexing, the information obtained from repositories may correspond to datasets served individually or may correspond to collections or records. As these 2 situations represent a very different metadata context, the Biocaddie DATS model allows to distinguish between the two cases.

  • collection (as in ‘collection of instances’)

  • singleton (as in ‘individual instance’)

  • Data refinement type:

To describe the level of data processing associated with the data available from the dataset and its distributions….[terminology needs to be specified])

  • raw data
  • preprocessed data
  • analyzed data
  • summarized data
  • curated data
  • reannotated data
  • …

  • data privacy protection type: (applicable only to human/clinical data)

    • fully identifiable none
    • pseudo-anonymized data
    • fully anonymized data
    • not information available
    • …

  • Document the Material, object, scope and Biological Entities the dataset is about and their characteristics or properties.

  • Document the nature of intervention and Treatment applied to the Material, if any or if applicable.

  • Data Types and specific Platform

Currently, in DataMed, datasets can be search according to Data Type (.e.g Proteomics data) and/or by Platform (e.g. Illumina) DATS provides a mechanism via DataType object to qualify the nature of the data collected in a Dataset. The 4 facets/attributes allow to incrementally specify the type of information contained by the data and how it has been produced

  • data acquisition / method type:
    This attribute allows to indicate the technique or technology , also known sometimes as data modality used to acquire the signal. For instance:
    • ‘crystallography’,
    • ‘mass spectrometry’
    • ‘nucleic acid sequencing’,
    • ‘computational simulation’
    • ‘questionaire based survey’
    • ‘nuclear magnetic resonance spectroscropy’
    • ‘nuclear magnetic resonance imaging’
    • ‘questionnaire’
    • …
  • platform/instrument type
    • Agilent, Bruker,Affymetrix,Illumina,SeaHorse
    • HumanHap550v3.0
    • HumanExome-12 v1.1 BeadChip
    • Sentrix Human-6 Expression BeadChip
    • SureSelect Human All Exon v2 - 44Mb
    • HiSeq 2000
    • …