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Metadata Specification

Each data request includes a text file called SAMPLE_INFO.txt that provides a number of file level properties (sample identifiers, clinical attributes, etc).

Standard Metadata

Below are the set of tags which may exist for any given file in St. Jude Cloud. All optional metadata will have sj_ prepended to their tag name.

Property Description
file_path The path to the file in your St. Jude Cloud project.
subject_name A unique subject identifier assigned internally at St. Jude.
sample_name A unique sample identifier assigned internally at St. Jude.
sample_type One of Autopsy, Cell line, Diagnosis, Germline, Metastasis, Relapse, or Xenograft
sequencing_type Whether the file was generated from Whole Genome (WGS), Whole Exome (WES), or RNA-Seq.
file_type One of the file types available in St. Jude Cloud
description Optional field that may contain additional file information.
sj_diseases Short disease identifier assigned at the time of genomic sequencing. Note that this diagnosis may be refined after undergoing genomic testing. When including diagnosis in your analysis, we recommend you use attr_diagnosis, which is the most up to date value for diagnosis.
sj_datasets If present, the datasets in the data browser which this file is associated with.
sj_pmid_accessions If the file was associated with a paper, the related Pubmed accession number.
sj_ega_accessions If the file was associated with a paper, the related EGA accession number.
sj_dataset_accession If present, the permanent accession number assigned in St. Jude Cloud.
sj_embargo_date The embargo date, which specifies the first date which the files can be used in a publication.

Clinical and Phenotypic Information

Also included is a set of phenotypic information queried from the physician or research team's records at the time of sample submission to St. Jude Cloud. These are all considered to be optional, as the level of information gathered for each sample varies. If empty, the physician or research team did not indicate a value for the field. All basic clinical or phenotypic information will have attr_ prepended to their tag name.

Property Description
attr_age_at_diagnosis Age at first diagnosis. This field is normalized as a decimal value. If empty, the physician or research team did not indicate a value for this field.
attr_diagnosis Primary diagnosis reported by the clinic.
attr_ethnicity Self-reported ethnicity. Values are normalized according to the US Census Bureau classifications.
attr_race Self-reported race. Values are normalized according to the US Census Bureau classifications.
attr_sex Self-reported sex.
attr_oncotree_disease_code The disease code (assigned at the time of genomic sequencing) as specified by Oncotree Version 2019-03-01

Short Disease Code Mapping

Embedded in both the filename and the SAMPLE_INFO.txt file that comes with your data request will be a list of short diagnosis codes (sj_diseases). These short codes were assigned at the time that the sample was sent for sequencing, and they are not necessarily the final diagnosis (attr_diagnosis). For instance, the diagnosis is often refined as the sample undergoes genomic testing. Below, we include a table of short disease code to long disease name mappings so you can interpret what these abbreviations mean.

Short Disease Code Long Diagnosis Description
ACT Adrenocortical Carcinoma
AEL Acute erythroid leukemia (AML M6)
ALCL Anaplastic Large Cell Lymphoma
ALL Acute Lymphoblastic Leukemia
ALS Amyotrophic Lateral Sclerosis ("Lou Gehrig\'s Disease"")"
ALZ Alzheimer's Disease
AML Acute Myeloid Leukemia
AMLM Acute Megakaryoblastic Leukemia
ANEM Anemia
ASPS Alveolar Soft Part Sarcoma
AUL Acute Undifferentiated Leukemia
BALL B-cell Acute Lymphoblastic Leukemia
BCC Basal Cell Carcinoma
BLACA Bladder Cancer
BT Brain Tumor
CA Carcinoma
CBF Acute Myeloid Leukemia - Core Binding Factor subtype
CLL Chronic Lymphocytic Leukemia
CML Chronic Myelogenous Leukemia
CMML Chronic Myelomonocytic Leukemia
CMV Cytomegalovirus
CNS Central Nervous System
CPC Choroid Plexus Carcinoma
CRC Colorectal Cancer
CS Chondrosarcoma
CTP Congenital Thrombocytopenia
DIPG Diffuse Intrinsic Pontine Glioma
DLBCL Diffuse Large B-cell Lymphoma
DOWN Down Syndrome
DSRCT Desmoplastic Small Round Cell Tumor
E2A B-Lineage Acute Lymphoblastic Leukemia - E2A-PBX1 subtype
ECD Erdheim-Chester Disease
EPD Ependymoma
ERG Acute Lymphoblastic Leukemia - ERG alteration subtype
ETV Acute Lymphoblastic Leukemia - ETV6-RUNX1 fusion subtype
EWS Ewing's Sarcoma
GCT Germ Cell Tumor
GENBN General Bone
GENKY General Kidney
GENLK General Leukemia
GICT Giant Cell Tumor
GIST Gastrointestinal Stromal Tumor
HB Hepatoblastoma
HGG High Grade Glioma
HGS High Grade Sarcoma
HIST Histiocytosis
HL Hodgkin's Lymphoma
HM Hematopoietic Malignancies
HS Hidradenitis Suppurativa
HYPER Acute Lymphoblastic Leukemia - Hyperdiploid subtype
HYPO Acute Lymphoblastic Leukemia - Hypodiploid subtype
IFS Infantile Fibromyosarcoma
INF Acute Lymphoblastic Leukemia (Infant)
ITP Idiopathic Thrombocytopenia
JMML Juvenile Myelomonocytic Leukemia
LCH Langerhans Cell Histiocytocis
LGG Low Grade Glioma
LM Liver Malignancies
MB Medulloblastoma
MDS Myelodysplastic Syndrome
MEL Melanoma
MLL Mixed Lineage Leukemia
MM Multiple Myeloma
MPAL Acute Lymphoblastic Leukemia - Multi-phenotypic
MPNST Malignant Peripheral Nerve Sheath Tumor
MRT Malignant Rhabdoid Tumour
MYF Myelofibrosis
NBL Neuroblastoma
NEUTP Neutropenia
NHL Non-Hodgkin's Lymphoma
NM Non-malignancy
NORM Control Sample
NPC Nasopharyngeal Carcinoma
NPCA Nasopharyngeal Carcinoma
OS Osteosarcoma
PF Posterior Fossa
PGL Paraganglioma
PHALL Acute Lymphoblastic Leukemia - BCR-ABL1 fusion subtype
PHCML Ph+ Chronic Myeloid Leukemia
PML Promyelocitic Leukemia
PRAD Prostate Adenocarcoma
PSO Psoriasis
RB Retinoblastoma
RCC Renal cell carcinoma
RECA Renal Cancer
RHB Rhabdomyosarcoma
SBO Spina Bifida Occulta
SCD Sickle Cell Disease
SCZ Schizophrenia
SS Synovial Sarcoma
ST Solid Tumor
STS Soft Tissue Sarcoma
TALL T-cell Acute Lymphoblastic Leukemia
TCP Thrombocytopenia
TESCA Testicular Cancer
THCA Thyroid Carcinoma
WLM Wilms' tumor