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indicate which ontology was used
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allyhawkins committed Feb 27, 2024
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Expand Up @@ -9,17 +9,17 @@ All samples on the Portal include a core set of metadata obtained from investiga
Some investigators submitted additional metadata, such as treatment and tumor stage, which can also be found on the Portal.
All submitted metadata was standardized to maintain consistency across projects before adding to the Portal.
In addition to providing a human-readable value for the submitted metadata, we also provide an ontology term ID, if applicable.
We mapped submitted metadata for age, sex, organism, disease, tissue, and ethnicity (if applicable), to their associated ontology term IDs using the ontology lookup service.
Submitted metadata was mapped to an associated ontology term IDs obtained from HsapDV (age), PATO (sex), NCBI taxonomy (organism), MONDO (disease), UBERON (tissue), and Hancestro (ethnicity, if applicable).
Including ontology term IDs for each sample provides users with standardized metadata terms that can be used across all projects.

The Portal contains data from 500 samples and over 50 tumor types.
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The total number of samples for each diagnosis is shown in Figure 1A, along with a breakdown of the proportion of samples from each disease stage within a diagnosis group.
Figure 1A summarizes all samples from patient tumors or patient-derived xenografts currently available on the Portal.
Most samples found on the Portal were obtained from patients with leukemia (n = TODO).
The Portal also includes samples from brain and central nervous system tumors (n = TODO), sarcoma and soft tissue tumors (n = TODO), and a variety of other solid tumors (n = TODO).
Most samples were collected at initial diagnosis (n = TODO), with a smaller number of samples collected either at recurrence (n = TODO), during progressive disease (n = TODO), or post-mortem (n = TODO).
Along with the patient tumors, the Portal contains a small number of human tumor cell line samples (n = TODO).
Most samples found on the Portal were obtained from patients with leukemia (n = 192).
The Portal also includes samples from brain and central nervous system tumors (n = 154), sarcoma and soft tissue tumors (n = 68), and a variety of other solid tumors (n = 87).
Most samples were collected at initial diagnosis (n = 424), with a smaller number of samples collected either at recurrence (n = 64), during progressive disease (n = 10), or post-mortem (n = 2).
Along with the patient tumors, the Portal contains a small number of human tumor cell line samples (n = 4).


Each of the available samples contains summarized gene expression data from either single-cell or single-nuclei RNA sequencing.
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