BloodPAC
Cancer Moonshot - BloodPAC

changelog

BloodPAC

Data Governance Change Log

Membership Change Log

Data Format Change Log

Ongoing

Please review the public commit log for the latest ongoing changes to the datamodel:  https://github.com/occ-data/bpadictionary/commits/develop

v13 changes

12/19/2016, 6:00pm CT

  • Added cell_count to slide count.
  • Moved experimental analysis to “Case and Sample Data” category and linked it to read group.

v12 changes

12/13/2016, 8:00pm CT

  • Added collection_temperature to sample.
  • Added mutant_copies, WT_copies, copies_unit to assay result.
  • Changed ctc_variable_name and ctc_result_value by ctc_feature_name and ctc_feature_value in assay result.
  • Added slide count node and move some properties from slide image to slide count.
  • Added expected_aa_change in sample expectation
  • Added a note to clarify the correct format for sequencing_date in read group.

v11 changes

12/09/2016, 3:30pm CT

  • Added ctc_variable_name and ctc_result_value to assay result and slide image.
  • Added clinical_time_point to sample.
  • Added link from assay result to slide.
  • Added a note with some options in assay_method from assay result.

v10.3 changes

12/06/2016, 6:40pm CT

  • Added collection_datetime and processing_datetime to sample.
  • Added cell_identifier to slide image.

v10.2 changes

12/06/2016, 5:30pm CT

  • Added storage_duration_unit to sample.

v10.1 changes

12/05/2016, 9:00pm CT

  • Added tissue_type to sample.

v10 changes

12/01/2016, 5:30pm CT

  • Added ASSAY RESULT node to contain results from different assays. This node will connect to read_group for results coming from sequencing technologies; otherwise, it will connect to aliquot.
  • Specified that type_of_sample property under experiment can get “contrived” or “clinical” values.
  • Specified that ALIQUOT can also refer to different replicate under the same sample.
  • Added experimental_intent to experiment. It will take values like "analytical validation", "clinical validation", etc.
  • Added associated_experiment to experiment; it will include the submitted_id for other related experiment (I.e. "analytical validation" points to "clinical validation" and viceversa).
  • Added aliquot_concentration and aliquot_concentration_unit to aliquot.
  • Renamed sample.concentration to sample.ctc_concentration to avoid confusion with the new values in aliquot

v9 changes

12/1/2016, 8:00am CT

  • Moved disease_type and primary_site from project to case to be compatible with GDC data model to facilitate analysis with other cancer datasets.
  • Moved expected_mutation, expected_copy_number, and allele_frequency to a new node called "Sample Expectations" that connects to sample.
  • Changed total number of files from 19 to 20 to reflect above change.
  • Added several properties to Sample. These are new properties that will be added to the GDC Dictionary once the BLGSP/CPTAC changes are approved. They clarify the data quite a bit so I've added them to be a better guide for the submitters.
  • Added year_of_birth and year_of_death to demographic; these were erroneously overlooked earlier.
  • Added additional smoking fields to exposure. These again are changes in the BLGSP/CPTAC PR that have not made it to the official dictionary but improve the data.
  • Added many properties to diagnosis; most of these are BLGSP/CPTAC changes
  • Added properties to treatment; more BLGSP/CPTAC changes
  • Added some fields to read group; mostly covering spike-in information need for BloodPAC.
  • Added several percent_x properties to slide node.

v7/8 changes

v8 11/30/2016, 11:00am CT; v7 11/29/2016, 6:15pm CT

  • Added new node SUBMITTED ALIGNED READS that connects to READ GROUP to contain information about aligned read files (i.e. BAMs).
  • Added new node SUBMITTED SOMATIC MUTATION that connects to READ GROUP to contain information about somatic variant files (i.e. VCFs).
  • Minor: Changed expected_mutation type at EXPERIMENT node to “string”
  • Minor: Changed expected_copy_number type at EXPERIMENT node to “number”