Level 1 Asset Manifest Specification

Proposed Technical Specification

Level 1

The specifications for this level are for informational use only and are still under internal development and are not yet finalized. Do not use this version for creating CFDE manifests.

...introduces models for core experimental resources like

  • samples and subjects
  • search targets in the form of annotations like the anatomical source for a given tissue sample
  • host species taxonomy for samples and subjects
  • basic support for arranging experimental resources into sub-collections based on a hierarchy of projects or studies

...also introduces two containers for aggregating experimental resources & metadata:

  • project describes administrative/funding/contract/etc. hierarchy governing ownership/management/purview/responsibility of/for subcollections of experimental resources and metadata
  • collection allows any (non-cyclic) groupings to be assigned to subcollections of experimental resources and metadata (independently of contract or funding or ownership or accountability/reporting structures encoded by project): similar in concept to "dataset" but without implying the existence of a formally-prepared publication-level data package -- any coherent and meaningful grouping can be encoded here
Level 1 model diagram
Level 1 model diagram

Level 1 technical specification: the file entity, revisited

added properties

Level 1 technical specification: introducing the bio_sample entity

added entity: list and define properties

Level 1 technical specification: introducing the subject entity

added entity: list and define properties

Level 1 technical specification: using the project table

describe the project table

Level 1 technical specification: using the collection table

describe the collection table

Level 1 technical specification: using association tables to encode inter-entity relationships

describe TSV encoding of bio_sample<->subject<->file<->bio_sample association pairs

Level 1 technical specification: using terms from controlled vocabularies: usage tables

enumerate CVs; describe usage tables and outline plan for addressing versioning; discuss parser script, to be executed somewhere in bdbag-preparation stage, which will inflate bare CV terms cited in entity fields into corresponding CV usage tables, loading term-decorator data from relevant CV OBO reference files

Level 1 metadata submission examples: schema and example TSVs

A JSON Schema document specifying the Level 1 TSV collection is here; an example Level-1-compliant TSV submission can be found here (as a collection of TSV files) and here (as a packaged BDBag archive).