Data modelers - Requested modifications
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Data model v2.0 - Requested modifications
39/40 completed
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RequestDescriptionPropertiesNodeReleaseRequested by
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#3In the 2.0 version, we can’t find a place to capture the total number of nucleated cells detected per slide.  Add "Nucleated Cell" to analyte.cell_typecell_typeanalyte0.2.4USC
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#4Update the descriptions for days_to_collection and days_to_procurement for clarity about how to caluclate the days and what to do in the case of a "null"days_to_collection days_to_procurementbiospecimen0.2.5UAMS
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#5Require index_date. We already require the days_to_collection and days_to_procurment and without an index_date those are meaningless. For cases without an index_date (like one time non-logitudinal data) we can add a "Not Applicable" option.index_datecase0.2.5UAMS
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#6In quantification assays for cell counting experiments specifically CTCs, we want to be able to report the concentration of the cells (aka CTCs/mL) in the test sample. Rather than having this property be calculatable using the raw cell count and aliquot volume, we think that simply reporting a locally caluclated cellular concentration would provide more value. As such we recommend the addition of a cell_concentration property to quantification_assay. cell_concentrationquantification_assay0.2.4USC & Epic
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#7Provide an explicit property on read group to provide the name of the read groupread_group_nameread_group0.2.4UAMS
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#8Only one read group can be submittered per analyte. Should users be able to submit multiple read groups per analyte/aliquot?analytesread_group0.2.4UChicago
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#10Need enumeration options for USC's CTC quantification assay. Add "HD-SCA Platform" to quantification_assay.assay_instrument and "HDSCA Enumeration" and "Fluidgm Hyperion" to quantification_assay.assay_instrument_modelassay_instrument assay_instrument_modelquantification_assay0.2.4USC
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#11Add "Cytokeratin Positive CTC", "Cytokeratin Positive CTC Cluster", "Biomarker Positive All Populations", "All Populations", and "Biomarker Positive Traditional CTC" to analyte.cell_typecell_typeanalyte0.2.4Epic
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#12Add "ESRUO-01" to quantification_assay.assay_instrument_modelassay_instrument_modelquantification_assay0.2.4Epic
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#13Add "Epic Sciences CTC Platform" to quantification_assay.assay_instrumentassay_instrumentquantification_assay0.2.4Epic
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#14Add "Immunohistochemistry" to quantification_assay.assay_methodassay_methodquantification_assay0.2.4Epic & USC
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#15We should allow users to link a contrived expectation to many aliquots. In the case of replicates we would currently be repeating the identical expectations for each replicate. Would like to ease the burden of submittersaliquotscontrived_expectations0.2.4Novartis
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X#16Add analyte_quantity and analyte_volume to capture total quantity and volume of the particular analyte being used in assayanalyte_quantity analyte_volumeanalyteXGenomicHealth
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#17Update the descriptions for aliquot_quantity and aliquot_volume to no longer reference being derived from the aliquot. It is confusing.aliquot_volume
aliquot_quantity
aliquot0.2.5GenomicHealth
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#18for assay_instrument_model add “BD Accur C6 Flow Cytometer”
for assay_instrument remove "BEAMing"
for assay_instrument add "BD Flow Cytometer"
for assay_method add “BEAMing Digital”
assay_instrument_model
assay_instrument
assay_method
pcr_assay0.2.7Novartis
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#19add "Fluidigm Hyperion"assay_instrument_modelquantification_assay0.2.7USC
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#20add "HD-SCA platform"assay_instrumentimmunoassay0.2.7USC
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#21add "CytoTrapNano CTC Platform"assay_instrumentquantification_assay
immunoassay
0.2.7CytoLumina
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#22add "C88801-RU"assay_instrument_modelquantification_assay
immunoassay
0.2.7CytoLumina
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#23add restriction to md5sum to only allow properly formatted entriesmd5sum_definitionsUChicago
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#24add "Clinical Detection"study_objectivestudy0.2.7Guardant
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#25create a new property for specific cancer morphologytumor_morphologybiospecimen0.2.7Guardant
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#26connect analytes to their corresponding study even when coming from the same case/samplestudies.submitter_idanalyte0.2.9USC
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#27add TIF to data_format for mass cytometry imagesdata_formatmass_cytometry_image0.2.9USC
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#28add "assay_target_secondary", "target_chromosome_secondary", and "target_position_secondary" to sequencing_assayassay_target_secondary
target_chromosome_secondary
target_position_secondary
sequencing_assay0.2.10Foundation
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#29rename "Insertion" to "Nonframeshift Insertion" for mutation_resultmutation_resultsequencing_assay0.2.10Foundation
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#30rename "Deletion" to "Nonframeshift Deletion" for mutation_resultmutation_resultsequencing_assay0.2.10Foundation
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#31remove "Duplication" from mutation_resultmutation_resultsequencing_assay0.2.10Foundation
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#32add "Copy Number Deletion", "Copy Number Amplification", "Nonstop", "Nonstart", and "Splice Site" to mutation_resultmutation_resultsequencing_assay0.2.10Foundation
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#33add "Serum Card" to aliquot_containeraliquot_containeraliquot0.2.10Biodesix
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#34add "Bruker Mass Spectrometer" to assay_instrumentassay_instrumentimmunoassay0.2.10Biodesix
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#35add "MALDI-ToF Mass Spectrometry" to assay_methodassay_methodimmunoassay0.2.10Biodesix
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#36Edit range field descriptions to include instructions on how to fill outhours_to_fractionation
time_to_freezer
sample
analyte
0.2.11UChicago
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X#37Extend assay_method enumeration for assay_method to faciliate group submission. Currently only "Immunohistochemistry" and "DNA Electrophoresis" assay_methodquantification_assayXUChicago
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X#38Modify analyte isolation method to make it enumeration. Determine choices to keep the isolation method concrete and preciseanalyte_isolation_methodanalyteXUChicago
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X#39add "Whole Genome Copy Number Variation" to assay_methodassay_methodsequencing_assay?XUSC
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#40add "Qubit" and "Qubit 3.0" to quantification_assay assay_instrument and assay_instrument_modelassay_instrumentquantification_assay0.2.11USC
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#41add "BioTek" and "BioTek Synergy 4" to quantificaiton_assay assay_instrumenta and assay_insturment_modelassay_instrument
assay_instrument_model
quantification_assay0.2.11Novartis
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#42add "Fluorometer" to quantification_assay.assay_methodassay_methodquantification_assay0.2.11USC & Novartis
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#43add "Molecular Devices SpectraMax" and "Molecular Devices SpectraMax M2" to quantification assayassay_instrument
assay_instrument_model
quantification_assay0.2.12GenomicHealth
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