SenNet Provenance Graph

Overview

SenNet metadata which describes tissue donors, organs, tissue samples and datasets is stored in a hierarchical graph to track the provenance of any data registered in SenNet back through any other data, tissue samples, organs and sources from which each is derived.

Description

The provenance graph, an example of which for the data derived from a single tissue donor is shown below, contains three main types of graph node or entity types: Sources, Samples and Datasets. Each of these main entity types contain sub-types:

• Source (Human or Mouse)
  • Organ Donor (findable by the existence of the field Source.metadata.organ_donor_data)
  • Living/Surgical Donor (findable by the existence of the field Source.metadata.living_donor_data)
• Sample
  • Organ (findable by matching Sample.sample_category == "Organ")
  • Tissue Block (findable by matching Sample.sample_category == "Block")
  • Tissue Section (findable by matching Sample.sample_category == "Section")
  • Tissue Suspension (findable by matching Sample.sample_category == "Suspension")
• Dataset
  • Primary Data: data registered and uploaded by SenNet data providers, this data must have a direct parent entity in the provenance graph of type Sample. (findable by matching Dataset.creation_action == "Create Dataset Activity")
  • SenNet Processed Data: Data created by one of the central processing pipelines. This data must have a direct parent entity in the provenance graph of type Dataset, i.e., data derived by processing other data. ( findable by matching Dataset.creation_action == "Central Process")
  • Component Data: Separate datasets that represent the components that make up a Multi-Assay Primary Data dataset. For example a 10X Multiome Multi-Assay primary dataset is composed of both RNAseq and ATACseq assays. (findable by matching Dataset.creation_action == "Multi-Assay Split")
  • Lab/Provider Processed Data: Data created by one of the SenNet data provider labs by processing primary data. This data must have a direct parent entity in the provenance graph of type Dataset. (findable by matching Dataset.creation_action == "Lab Processed")