| attribute | type | cardinality | unique | required | doc |
|---|
| U-L | float | one | | | Use this attribute if the measurement represents a concentration expressed as units (U) /L |
| a-allele-cn | float | one | | | Use this attribute if the measurement represents the copy number of the A allele |
| absolute-cn | long | one | | | Use this attribute if the measurement represents the absolute copy number of a segment |
| array-log-intensity | float | one | | | Use this attribute if the measurement represents a log intensity equivalent to a one channel gene expression array
(ie Affymetrix) -- log2 scaled intensity values. |
| array-log-ratio | float | one | | | Use this attribute if the measurement represents the log ratio of a two channel gene expression array
usually expressed as log2(sample/reference) with sample as the Cy5 (red) channel and reference as the Cy3 (green) channel) |
| atac-peak | atac-peak | one | | | The target ATAC peak for this measurement |
| average-depth | float | one | | | Use this attribute if the measurement represents the average sequencing depth of a sample.
Note that in this case the measurement will not have any target |
| b-allele-cn | float | one | | | Use this attribute if the measurement represents the copy number of the B allele |
| baf | float | one | | | Use this attribute if the measurement represents the allelic fraction of the B allele in tumor tissue, for a copy number variation segment |
| baf-n | float | one | | | Use this attribute if the measurement represents the allelic fraction of the B allele in normal tissue, for a copy number variation segment |
| cell-count | long | one | | | Use this attribute if the measurement represents the number of cells in a specific cell-population |
| cell-population | cell-population | one | | | The target cell population for this measurement |
| cells-per-mm2 | float | one | | | Use this attribute if the measurement represents the number of cells per mm2 of tissue, as measured by
an imaging assay (ie IHC, Vectra, CODEX, etc.). This measurement type can be paired with a cell-population
target (:measurement/cell-population) or used alone to denote the total cell density. Note that this attribute
should only be used if a whole-cell segmentation method was used to segment the image. |
| cfdna-ng-mL | float | one | | | Use this attribute if the measurement represents a concentration of cell-free DNA (cfDNA) in blood, expressed as ng/mL |
| chromvar-tf-binding-score | float | one | | | Use this attribute if the measurement represents a transcription factor binding score
as calculated by chromVAR |
| cnv | cnv | one | | | The target cnv for this measurement |
| cnv-call | measurement.cnv-call | one | | | Use this attribute if the measurement represents the CNV overall gain (gain, loss, or neutral)
for a genetic region (cnv). This attribute refers to enums in the :measurement.cnv-call namespace. |
| contamination | float | one | | | Use this attribute if the measurement represents the fraction of reads that do not come from this sample
(expressed as a number in [0, 1]). Note that in this case the measurement will not have any target |
| epitope | epitope | one | | | The target protein epitope for this measurement |
| fpkm | float | one | | | Use this attribute if the measurement represents a FPKM value (Fragments Per Kilobase Million, a measure
of gene expression in RNAseq experiments) |
| fraction-aligned-reads | float | one | | | Use this attribute if the measurement represents the fraction of aligned reads in a sample
(expressed as a number in [0, 1]). Note that in this case the measurement will not have any target |
| fraction-reads-in-peaks | float | one | | | Use this attribute if the measurement represents the fraction of reads that are assigned to a peak in a sample
(relevant for ATACesq data and expressed as a number in [0, 1]). Note that in this case the measurement will not have any target |
| gene-product | gene-product | one | | | The target gene product for this measurement |
| id | string | one | | | The id of the measurement. Must be unique within this dataset (but not within the entire database) |
| image-intensity-mean | float | one | | | Per-segment intensity (mean) for a given epitope (marker channel) |
| image-intensity-median | float | one | | | Per-segment intensity (median) for a given epitope (marker channel) |
| image-intensity-sum | float | one | | | Per-segment intensity (sum) for a given epitope (marker channel) |
| leukocyte-count | long | one | | | Use this attribute if the measurement represents the number of leukocytes in a sample (mostly useful for
flow cytometry assays. Note that in this case the measurement will not target any specific cell-population |
| live-count | long | one | | | Use this attribute if the measurement represents the number of live cells in a sample (mostly useful for
flow cytometry assays. Note that in this case the measurement will not target any specific cell-population |
| live-percent | float | one | | | Use this attribute if the measurement represents the percentage of live cells in a sample.
Note that in tihs case the measurement will not have a target cell population |
| loh | boolean | one | | | Use this attribute if the measurement demonstrates a loss of heterozygosity (LOH) for a copy number variation segment |
| luminex-mfi | float | one | | | Use this attribute if the measurement represents MFI (Mean Fluorescence Intensity) for a Luminex Multiplex Immunoassay. |
| lymphocyte-count | long | one | | | Use this attribute if the measurement represents the number of lymphocytes in a sample (mostly useful for
flow cytometry assays. Note that in this case the measurement will not target any specific cell-population |
| median-channel-value | float | one | | | Use this attribute if the measurement represents a median channel (protein) value of a cytometry population or cluster |
| msi-status | measurement.msi-status | one | | | Use this attribute if the measurement represents the MSI (Microsatellite Instability) status of
the tumor as determined by either IHC or sequencing. This attribute refers to enums in the
:measurement.msi-status namespace. |
| n-alt-count | long | one | | | Use this attribute if the measurement represents the read depth supporting the variant allele in the normal sequencing output |
| n-depth | long | one | | | Use this attribute if the measurement represents the read depth across this locus in the normal sequencing output |
| n-ref-count | long | one | | | Use this attribute if the measurement represents the read depth supporting the reference allele in the normal sequencing output |
| nanostring-count | float | one | | | Use this attribute if the measurement represents a gene expression count from Nanostring |
| nanostring-signature | nanostring-signature | one | | | The target nanostring signature for this measurement |
| nanostring-signature-score | float | one | | | Use this attribute if the measurement represents the score for a nanostring signature |
| ng-mL | float | one | | | Use this attribute if the measurement represents a concentration expressed as ng/mL |
| nuclei-count | long | one | | | Use this attribute if the measurement represents the number of nuclei in a sample (mostly useful for
imaging assays. Note that in this case the measurement will not target any specific cell-population |
| nuclei-per-mm2 | float | one | | | Use this attribute if the measurement represents the number of nuclei per mm2 of tissue, as measured by
an imaging assay (ie IHC, Vectra, CODEX, etc.). This measurement type can be paired with a cell-population
target (:measurement/cell-population) or used alone to denote the total cell density. Note that this attribute
should only be used if a nuclei-only segmentation method was used to segment the image. |
| olink-npx | float | one | | | Use this attribute if the measurement represents npx units (i.e. Normalized protein expression
from an Olink assay, https://www.olink.com/question/what-is-npx/) |
| otu | otu | one | | | The target OTU for this measurement |
| percent-of-leukocytes | float | one | | | Use this attribute if the measurement represents the abundance of a specific cell-populations, expressed
as the percentage of the total number of leukocytes in the sample (mostly useful for flow cytometry assays |
| percent-of-live | float | one | | | Use this attribute if the measurement represents the abundance of a specific cell-populations, expressed
as the percentage of the total number of live cells in the sample (mostly useful for flow cytometry assays |
| percent-of-lymphocytes | float | one | | | Use this attribute if the measurement represents the abundance of a specific cell-populations, expressed
as the percentage of the total number of lymphocytes in the sample (mostly useful for flow cytometry assays |
| percent-of-nuclei | float | one | | | Use this attribute if the measurement represents the abundance of a specific cell-populations, expressed
as the percentage of the total number of nucleated cells (mostly useful for imaging assays) |
| percent-of-parent | float | one | | | Use this attribute if the measurement represents the abundance of a specific cell-populations, expressed
as the percentage of its parent population |
| percent-of-singlets | float | one | | | Use this attribute if the measurement represents the abundance of a specific cell-populations, expressed
as the percentage of the total number of singlets in the sample (mostly useful for flow cytometry assays |
| percent-of-total-cells | float | one | | | Use this attribute if the measurement represents the abundance of a specific cell-populations, expressed
as the percentage of the total number of cells in the sample (in [0, 1], mostly useful for flow cytometry assays) |
| pg-mL | float | one | | | Use this attribute if the measurement represents a concentration expressed as pg/mL |
| protein-array-log-intensity | float | one | | | Use this attribute if the measurement represents a log intensity equivalent to one channel protein expression array. |
| read-count | long | one | | | Use this attribute if the measurement represents the count of reads for a specific target |
| read-count-otu | long | one | | | Use this attribute if the measurement represents the count of reads for a specific OTU |
| read-count-otu-rarefied | long | one | | | Use this attribute if the measurement represents the rarefied count of reads for a specific OTU |
| region-of-interest | string | one | | | For imaging data, the region of interest that this measurement refers to |
| rpkm | float | one | | | Use this attribute if the measurement represents a RPKM value (Reads Per Kilobase Million, a measure
of gene expression in RNAseq experiments) |
| rsem-normalized-count | float | one | | | Use this attribute if the measurement represents the RSEM normalized count. This is a transformation where
for gene level estimates you divide all raw-count values by the 75th percentile of the column (after removing zeros) and multiply that by 1000. This
transforms each sample so that the values are relative the 75th percentile with a x1000 adjustment factor (see https://www.biostars.org/p/106127/).
Most papers that analyze TCGA data use log2(rsem-normalized-count + 1) |
| rsem-raw-count | float | one | | | Use this attribute if the measurement represents the RSEM raw count, i.e. the estimated number of fragments
derived from a given gene (see https://www.biostars.org/p/106127/) |
| rsem-scaled-estimate | float | one | | | Use this attribute if the measurement represents the RSEM scaled estimate, i.e. the fraction of transcripts
made up by a given gene (see https://www.biostars.org/p/106127/) |
| sample | sample | one | | | The biological sample this measurement was performed on |
| segment-mean-lrr | float | one | | | Use this attribute if the measurement represents the mean Log R Ratio (LRR) of a CNV (Copy Number Variation) segment. This is equal
to log2(copy-number / 2) for a genomic segment |
| singlets-count | long | one | | | Use this attribute if the measurement represents the number of singlets in a sample (mostly useful for
flow cytometry assays. Note that in this case the measurement will not target any specific cell-population |
| t-alt-count | long | one | | | Use this attribute if the measurement represents the read depth supporting the variant allele in the tumor sequencing output |
| t-depth | long | one | | | Use this attribute if the measurement represents the read depth across this locus in the tumor sequencing output |
| t-ref-count | long | one | | | Use this attribute if the measurement represents the read depth supporting the reference allele in the tumor sequencing output |
| tcr | tcr | one | | | The target T Cell Receptor (TCR) for this measurement |
| tcr-alpha-clonality | float | one | | | Use this attribute if the measurement represents the clonality (range 0-1) of TCR alpha sequences a sample.
This measurement type is common when TCR sequences are computationally derived from RNAseq data
and thus alpha and beta pairing is not known. |
| tcr-beta-clonality | float | one | | | Use this attribute if the measurement represents the clonality (range 0-1) of TCR alpha sequences a sample.
This measurement type is common when TCR sequences are computationally derived from RNAseq data
and thus alpha and beta pairing is not known. |
| tcr-clonality | float | one | | | Use this attribute if the measurement represents a TCR clonality measurement. Note that in this case
the entity will not have a specific TCR target. |
| tcr-count | long | one | | | Use this attribute if the measurement represents the counts of a specific T Cell Receptor (TCR) |
| tcr-d | string | many | | | Use this attribute if the measurement represents the hits for possible D gene segment linking to a specific T Cell Receptor (TCR) |
| tcr-frequency | float | one | | | Use this attribute if the measurement represents the frequency of a specific T Cell Receptor (TCR) |
| tcr-j | string | many | | | Use this attribute if the measurement represents the hits for possible J gene segment linking to a specific T Cell Receptor (TCR) |
| tcr-v | string | many | | | Use this attribute if the measurement represents the hits for possible V gene segment linking to a specific T Cell Receptor (TCR) |
| tmb-indel | float | one | | | Tumor mutational burden expressed as the total number of indels per Mb sequenced |
| tmb-snv | float | one | | | Tumor mutational burden expressed as the total number of SNVs per Mb sequenced |
| tmb-total | float | one | | | Tumor mutational burden expressed as the total number of mutations (SNVs + indels) per Mb sequenced |
| total-reads | long | one | | | Use this attribute if the measurement represents the total number of reads in a sample.
Note that in this case the measurement will not have any target |
| tpm | float | one | | | Use this attribute if the measurement represents a TPM value (Transcripts Per Kilobase Million, a measure
of gene expression in RNAseq experiments) |
| tss-score | float | one | | | Use this attribute if the measurement represents the TSS score of the sample (relevant for ATACseq data).
Note that in this case the measurement will not have any target |
| tumor-purity | float | one | | | Use this attribute if the measurement represents the tumor purity of a sample
(expressed as a number in [0, 1]). Note that in this case the measurement will not have any target |
| uid | [[* string]] | one | yes | | Synthetic unique ID for measurements |
| vaf | float | one | | | Use this attribute if the measurement represents the variant allele frequency of a variant |
| variant | variant | one | | | The target variant for this measurement |