Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
Property Standard Name
The paclet uses properties across the board, here we describe the standard names for the properties
This loads the paclet.
In[23]:=
Needs["JaneShenGunther`TCGADataTool`"]
Data hierarchy
TCGADataTool allows to easily retrieve and process data for TCGA projects from GDC and TCIA portals. Data for a TCGA project is internally organized at the patient level as a of , where each represents a patient.
Patient data follows the hierarchy: Category ▶ Subcategory ▶ Property. Each patient Association is nested and contains at the first level patient identifiers and data categories labels. Category labels point to subcategories labels which then point to the actual subcategory data in the form of a List of Association:
Example data for a single patient:
(*patientidentifiers*) "bcr_patient_uuid""00ad0ffe-2105-4829-a495-1c2aceb5bb31","bcr_patient_barcode""TCGA-EK-A2R9",(*categories*)"Clinical" (*"Clinical"subcategories*)"Patient"{"bcr_patient_uuid""00AD0FFE-2105-4829-A495-1C2ACEB5BB31","bcr_patient_barcode""TCGA-EK-A2R9","vital_status""Alive"...},"FollowUp4.0"{"bcr_patient_uuid""00AD0FFE-2105-4829-A495-1C2ACEB5BB31","bcr_patient_barcode""TCGA-EK-A2R9","bcr_followup_barcode""TCGA-EK-A2R9-F58255","bcr_followup_uuid""B7035727-5282-454B-AC18-BA317E344D00",...},"Biospecimen"(*"Biospecimen"subcategories*)"Aliquot"{"bcr_patient_uuid""00AD0FFE-2105-4829-A495-1C2ACEB5BB31","bcr_sample_barcode""TCGA-EK-A2R9-01A","bcr_aliquot_barcode""TCGA-EK-A2R9-01A-11D-A18H-01",...,"bcr_patient_uuid""00AD0FFE-2105-4829-A495-1C2ACEB5BB31","bcr_sample_barcode""TCGA-EK-A2R9-01A","bcr_aliquot_barcode""TCGA-EK-A2R9-01A-11D-A18I-02","bcr_aliquot_uuid""B282ED3B-A192-4814-BD71-2DB05E1CCE1F",...,...},...,...
Some patients might not have data for all sub/categories or not all sub/categories might have been selected for download in the "Download parameters" pane of the user interface, in those cases some sub/category will simply not appear for all patients.
Most of the TCGADataTool paclet functionalities use a standard format to reference data properties. The standard property format leverages the data hierarchy and expresses each property as a concatenation of three elements: category, subcategory and property, separated by "::". For example, the standard name of the property "vital_status" from the category Clinical and subcategory Patient is: "Clinical::Patient::vital_status".
Supported data categories:
Clinical | GDC clinical patient data |
Biospecimen | GDC biospecimen patient data |
ScrapedData | data processed from different sources |
GenomicData | GDC genomic data |
Supported data categories.
Supported data subcategories:
Patient | demographic and general patient information |
Drug | drug treatments |
Radiation | radiation treatments |
FollowUpXX | follow-up data |
NewTumorEvent | new tumor events data |
NewTumorEventFollowUpXX | new tumor events forllow-up data |
OtherMalignancyForm | other malignancy data |
Ablation | ablation data |
"Clinical" subcategories.
Aliquot | aliquot data |
Analyte | analyte data |
Auxiliary | auxiliary data |
DiagnosticSlide | metadata on diagnostic slides |
Sample | biospecimen sample data |
Portion | portion data |
Protocol | protocol data |
ShipmentPortion | shipment portion |
Slide | slide metadata |
SSFNormalControl | sample submission form normal control |
SSFTumorSample | sample submission form tumor sample data |
"Biospecimen" subcategories.
RadiologicalImages | radiological metadata from TCIA |
HistologicalImages | histological images metadata from GDC API |
FollowUp | union of different versions of Clinical FollowUp data |
NewTumorEventFollowUp | union of different versions of Clinical NewTumorEventFollowUp data |
"ScrapedData" subcategories.
SimpleNucleotideVariation_MaskedSomaticMutation | GDC data for category "simple nucleotide variation" and type "masked somatic mutation" |
"GenomicData" subcategories.
The standard name of a property can be manually assembled following the aforementioned structure or it can be directly copied from the user interface [] in the "Data filtering" and "Data inspection" panes clicking on the Label value in the table summarizing the metadata of the column.
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Properties retrieval
built-in functionality to interact with tabular data | |
custom function to extract property values |
Ways to retrieve patient property values.
In[21]:=
Query[;;3,"Clinical","Patient",All,"vital_status"]@
[{"TCGAProjectData","TCGACESCExceptGenomicDataAllPatients"}]
| exampleDataTCGA |
Out[21]=
{{Alive},{Dead},{Alive}}
In[23]:=
| pullDataSlice |
| exampleDataTCGA |
Out[23]=
{Clinical::Patient::vital_status{Alive},Clinical::Patient::vital_status{Dead},Clinical::Patient::vital_status{Alive}}
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""