Wolfram Language Paclet Repository
Community-contributed installable additions to the Wolfram Language
Custom Entities
The paclet includes custom entity types containing information on various GDC projects and data properties.
This loads the paclet.
In[23]:=
Needs["JaneShenGunther`TCGADataTool`"]
GDCProject entity type
The GDCProject entity type gets defined at paclet loading time. It stores information about GDC projects, with each entity corresponding to a project available on the GDC data portal.
Get the full list of GDCProject entities.
In[38]:=
EntityList["GDCProject"]
Out[38]=
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
GENIE-GRCC
GENIE-DFCI
GENIE-NKI
GENIE-VICC
GENIE-UHN
GENIE-MDA
GENIE-MSK
GENIE-JHU
FM-AD
VAREPOP-APOLLO
CGCI-BLGSP
BEATAML1.0-CRENOLANIB
TRIO-CRU
REBC-THYR
TARGET-CCSK
MP2PRT-WT
NCICCR-DLBCL
OHSU-CNL
WCDT-MCRPC
ORGANOID-PANCREATIC
CTSP-DLBCL1
CMI-ASC
CPTAC-3
MMRF-COMMPASS
CMI-MBC
CPTAC-2
EXCEPTIONAL_RESPONDERS-ER
BEATAML1.0-COHORT
CGCI-HTMCP-CC
HCMI-CMDC
TARGET-ALL-P3
TARGET-ALL-P2
TARGET-ALL-P1
TARGET-AML
TARGET-WT
TCGA-CHOL
TARGET-OS
TARGET-RT
TCGA-LIHC
TCGA-DLBC
TCGA-BLCA
TCGA-ACC
TCGA-CESC
TCGA-PCPG
TCGA-PAAD
TCGA-MESO
TCGA-TGCT
TCGA-KIRP
TCGA-UVM
TCGA-UCS
MATCH-Z1D
TCGA-THYM
TCGA-COAD
TCGA-ESCA
CDDP_EAGLE-1
CMI-MPC
TCGA-GBM
TCGA-KICH
TCGA-HNSC
TCGA-PRAD
TCGA-OV
TCGA-LUSC
TCGA-LAML
TCGA-LGG
TARGET-NBL
TCGA-SARC
TCGA-BRCA
TCGA-READ
TCGA-LUAD
TCGA-STAD
TCGA-THCA
TCGA-KIRC
TCGA-SKCM
TCGA-UCEC
There are a total of 74 entities
In[24]:=
EntityList["GDCProject"]//Length
Out[24]=
74
For each project, information like number of cases, file size etc. are stored. Most of the information is derived from the GDC Projects API endpoint.
Inspect all property values available for TCGA-CESC entity.
In[25]:=
Entity["GDCProject","TCGA-CESC"]["PropertyAssociation"]
Out[25]=
GDC307,TCIA54,2023-02-27,{FileCount2384,CaseCount304,DataCategoryCopy Number Variation,FileCount1988,CaseCount307,DataCategorySequencing Reads,FileCount4262,CaseCount305,DataCategorySimple Nucleotide Variation,FileCount936,CaseCount307,DataCategoryDNA Methylation,FileCount632,CaseCount307,DataCategoryClinical,FileCount1242,CaseCount307,DataCategoryTranscriptome Profiling,FileCount1536,CaseCount307,DataCategoryBiospecimen,FileCount172,CaseCount172,DataCategoryProteome Profiling,FileCount1236,CaseCount304,DataCategoryStructural Variation},{Squamous Cell Neoplasms,Cystic, Mucinous and Serous Neoplasms,Adenomas and Adenocarcinomas,Complex Epithelial Neoplasms},14388,TotalFileSize,ImageTotalFileSize,TextTotalFileSize,{Cervix uteri},TCGA,TCGA-CESC,Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma,True,open,True
Case Count
Created Date
Data Categories
Disease Type
File Count
File Size
326.267
GB
314.511
GB
11.7565
GB
Primary Site
Program Name
Project ID
Project Name
Released Q
State
TCIAData Q
Get the number of patients available on GDC and TCIA data portals respectively for TCGA-CESC project.
In[48]:=
EntityValue
,"CaseCount"
TCGA-CESC | GDC PROJECT |
Out[48]=
GDC307,TCIA54
Get breakdown of project file size from the GDC portal.
In[48]:=
EntityValue
,"CaseCount"
TCGA-CESC | GDC PROJECT |
Out[48]=
GDC307,TCIA54
Entity classes group GDC projects by program and are named after the program ID.
There is an EntityClass for each program.
In[41]:=
EntityValue["GDCProject","EntityClasses"]
Out[41]=
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
,
 | GENIE |
| FM |
| VAREPOP |
| CGCI |
| BEATAML1.0 |
| TRIO |
| REBC |
| TARGET |
| MP2PRT |
| NCICCR |
| OHSU |
| WCDT |
| ORGANOID |
| CTSP |
| CMI |
| CPTAC |
| MMRF |
| EXCEPTIONAL_RESPONDERS |
| HCMI |
| TCGA |
| MATCH |
| CDDP_EAGLE |
Inspect entities included in the TCGA entity class.
In[42]:=
EntityClass["GDCProject","TCGA"]
Out[42]=
| TCGA |
In[44]:=
EntityList@EntityClass["GDCProject","TCGA"]Length[%]
Out[44]=
,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
TCGA-CHOL
TCGA-LIHC
TCGA-DLBC
TCGA-BLCA
TCGA-ACC
TCGA-CESC
TCGA-PCPG
TCGA-PAAD
TCGA-MESO
TCGA-TGCT
TCGA-KIRP
TCGA-UVM
TCGA-UCS
TCGA-THYM
TCGA-COAD
TCGA-ESCA
TCGA-GBM
TCGA-KICH
TCGA-HNSC
TCGA-PRAD
TCGA-OV
TCGA-LUSC
TCGA-LAML
TCGA-LGG
TCGA-SARC
TCGA-BRCA
TCGA-READ
TCGA-LUAD
TCGA-STAD
TCGA-THCA
TCGA-KIRC
TCGA-SKCM
TCGA-UCEC
Out[45]=
33
CDE entity type
The CDE entity type gets defined at paclet loading time. It stores information about Common Data Elements (CDE) derived from the such as data element description etc.
There are thousands of CDE entities.
In[3]:=
EntityList["CDE"]//Length
Out[3]=
71886
CDE entities are identified using their CDE ID.
In[6]:=
Entity["CDE","2001822"]
Out[6]=
2001822
CDE entities only store a subset of information available from the CDE browser.
In[7]:=
Entity["CDE","2001822"]["PropertyAssociation"]
Out[7]=
Patient Hospitalization Ind-2,the yes/no indicator that asks whether the patient was hospitalized.,2001822,xml_cde_20227105054,CHARACTER,Missing[],3
Data Element Long Name
Preferred Definition
Data Element Public ID
Documentation Version
Value Domain Datatype
Value Domain Unit Of Measure
Version
In[8]:=
Entity["CDE","649"]["PropertyAssociation"]
Out[8]=
Patient Height Measurement,the height of the patient in centimeters.,649,xml_cde_20227105054,NUMBER,Centimeters,4.1
Data Element Long Name
Preferred Definition
Data Element Public ID
Documentation Version
Value Domain Datatype
Value Domain Unit Of Measure
Version
Version refers to the CDE definition version from the CDE browser. Only the most recent version is stored for each CDE ID.
In[26]:=
RandomSeeding[123];EntityValue[RandomEntity["CDE",100],"Version"]
Out[27]=
{1,2,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,2,1,1,1,1,1,1,1,1,1,3,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1}
Documentation version refers to the file used to scrape data from the CDE browser. The file name records the file type and the file date. All CDE entities use CDE data from July 2022.
In[30]:=
RandomSeeding[123];Union@EntityValue[RandomEntity["CDE",100],"DocumentationVersion"]
Out[31]=
{xml_cde_20227105054}
ColumnHeader entity type
The ColumnHeader entity type gets loaded by the TCGA Data Tool User Interface every time data is loaded/download. It stores information about properties available in the data currently used by the user interface. For example, if only clinical patient data is in scope, then only ColumnHeader entities for clinical patient properties will be defined.
ColumnHeader entities are defined using EntityStore. Every time data is downloaded using the TCGA Data Tool User Interface it gets exported together with its corresponding for ColumnHeader entities.
Get example data EntityStore.
In[32]:=
 | exampleDataTCGA |
Out[32]=
EntityStore
 |
|
Define ColumnHeader entities from example EntityStore.
ColumnHeader entity type is now defined in the current session and can be accessed directly using built-in Entity functionalities.
ColumnHeader entities store information about properties that appear in their associated data structure and they are identified by the property standard name. Various properties that appear in GDC data files are associated with a specific CDE through a CDE ID, in those cases it is possible to retrieve additional information about the property through the associated CDE entity.
Property standard names are used as canonical names for ColumnHeader entities.
Get all property values for a ColumnHeader entity.
Get the preferred definition for property "Clinical::Patient::vital_status" from the associated CDE entity.
Not all properties have an associated CDE entity. Generally, properties under the ScrapedData category don't have an associated CDE entity but they're not the only example.