Quality Control Rules

Version 1:

The following is a list of metrics to measure the quality level of data in FaceBase. A program is run nightly that compares existing data to these metrics and flags discrepancies (only viewable when a contributor is logged in).

1. Dataset-level Requirements

1.1 Dataset-level required fields:

  • Accession (in place)
  • Title (in place)
  • Description
  • Project (in place)
  • Requires DOI
  • DOI (generated)
  • Released (in place)

1.2 Dataset-level required high-level metadata tags:

  • Organism
  • Experiment Type
  • Stage (depending on Species and specimen)
  • Anatomy
  • Gene

1.3 Dataset-level organizational requirements:

  • At least one Experiment AND one Biosample AND one Replicate associating the Experiment and Biosample

2. Experiment-level requirements

  • At least one associated Replicate
  • Experiment Type (in place)
  • Local Identifier
  • Strandedness (depending on Experiment Type value)
  • Target of Assay (depending on Experiment Type=ChIP-seq)
  • Control Assay (depending on Target of Assay value)
  • Molecule Type (depending on Experiment Type value)
  • Histone Modification (depending on Target of Assay value)
  • Chromatin Modifier (depending on Experiment Type value)
  • Transcription Factor (depending on Experiment Type value)
  • RNA-Seq Selection (depending on Experiment Type value)

3. Biosample-level requirements:

  • At least one associated Replicate
  • Local Identifier
  • Species (in place)
  • Specimen (in place)
  • Stage (depending on Species and specimen)
  • Anatomy
  • Collection Date
  • Cell Source (depending on Specimen value)
  • Cell Characterization (depending on Specimen value)

4. Replicate-level requirements:

  • Experiment (in place)
  • Biosample (in place)
  • Bioreplicate Number (in place)
  • Technical Replicate Number (in place)
  • Sequencing files (depending on associated Experiment Type)
  • Image or Mesh file (depending on associated Experiment Type)