Data Governance Change Log
- BloodPAC Data Use/Services Agreement (2-5-18)
- BloodPAC Data Contributor Agreement (5-18-17)
- BloodPAC Data Contributor Agreement (4-25-17)
- BloodPAC Data Contributor Agreement (3-22-17)
- OCC Data Contributor Agreement v7 (12-9-16)
- OCC Data Contributor Agreement v7 marked (12-9-16)
- OCC Data Contributor Agreement v6 (11-15-16)
- OCC Data Contributor Agreement v5 (10-25-16)
- OCC Privacy and Security Agreement v3
Membership Change Log
Data Format Change Log
Please review the public commit log for the latest ongoing changes to the datamodel: https://github.com/occ-data/bpadictionary/commits/develop
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.
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.
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.
12/06/2016, 6:40pm CT
- Added collection_datetime and processing_datetime to sample.
- Added cell_identifier to slide image.
12/06/2016, 5:30pm CT
- Added storage_duration_unit to sample.
12/05/2016, 9:00pm CT
- Added tissue_type to sample.
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
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.
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”