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Datasets/HTA15

SRRS

MixedMachine-extracted
Human Tumor Atlas NetworkAvailable from HTANCU Anschutz Medical Campus
Can it answer my research question?Who has used itGet the data

Can it answer your research question?

0 of 6 supported

  • Overall survival

    Not measured

    This field was not among those probed for this repository.

  • Progression or recurrence

    Not measured

    This field was not among those probed for this repository.

  • Treatment response

    Not measured

    This field was not among those probed for this repository.

  • Which drug was given

    Not measured

    This field was not among those probed for this repository.

  • Stage-adjusted modelling

    Not measured

    This field was not among those probed for this repository.

  • Analysis by race or ethnicity

    Not measured

    This field was not among those probed for this repository.

Judged from the repository’s own field completeness (thresholds). “Not measured” means we have not probed that field for this record, not that the data lack it.

At a glance

Every percentage is the repository’s own record of what is filled in
CasesAPI
-
samples; case count not published
Measurement types
3
654 files
Follow-upAPI
None recorded
no survival endpoint
Treatment responseAPI
Unknown

SubjectCALC

Subject derived from title

Derived from the title, not stated by the repository, and never used to place this dataset in an answer shortlist.

As filed by the repository

The repository publishes no disease classification.

Who is in the cohort

The repository’s harmonized records carry no demographics for this dataset.

What was measured, and on how many

3 measurement types, and no case count to measure their coverage against.

  • Multiplexed tissue imagingscarcecount not published
  • Single-cell / single-nucleus RNA sequencingcount not published
  • Single-cell ATAC sequencingscarcecount not published
Platform, files and data levels
AssayPlatformFilesLevels
Multiplexed tissue imagingAPI-143level 2
Single-cell / single-nucleus RNA sequencingAPI-63level 1
Single-cell ATAC sequencingAPI-56level 1
How complete the one clinical field is - 1 informative for at least 80% of cases

A field counts as informative only when it holds a real value. “Not reported” blocks an analysis just as a missing field does. Fields marked 1:n can hold several records per case, so they show the share of cases with any record.

Informative - a usable valuePresent but uninformative - “not reported” or “unknown”Absent - no value recorded

Other

  • Extended clinical data (tier 2)API100%

Access

MixedSome components are open; others need approval.API

Level 1-2 sequencing data are controlled through dbGaP; level 3-4 derived data and most imaging are downloadable from Synapse after registering and accepting the HTAN data use terms.

Open components
level 3-4 derived data; most imaging
Controlled components
level 1-2 sequencing (dbGaP)
License
HTAN data use terms; CC BY 4.0 for many level 3-4 products
Citation requirement
Cite the atlas publication and acknowledge HTAN per the network's publication policy.

What it is good for

Written and checked by a reviewer, not generated from metadata.

No reviewed research questions yet. The measurements and field completeness above are machine-extracted and still useful for judging fit.

What it cannot tell you

Written by a reviewer against the source, not inferred from what is missing.

No reviewed limitations yet. Check the field completeness chart above before committing to an analysis. Low coverage on an endpoint you need is the most common blocker.

Who has used it

Articles that analyzed these data, counted separately from articles that only cited the paper. Only the first counts as reuse.

Analyzed the dataCALC
-
could not be measured for this dataset
Declared using it
-
named in a data availability statement
Cited the paper
-
attention to the publication, not reuse of the data
Against expectation
Not assessed
Reuse cannot be traced for this dataset
No accession is specific enough to search the literature for, so we cannot tell how often these data have been reused. That is a limit of the measurement, not a finding about the dataset. It is also a barrier in itself: a researcher cannot find prior work to build on.
Reuse assessment
  • Not assessed: this dataset has no accession specific enough for citation-based reuse tracing, so a shortfall cannot be measured.

Compared against rgi-huber-v2. See Methods for the model.

Articles that analyzed the data

Not searchable. See the note above.

Community examples

Share your example

Analyses someone ran on these data end to end, each with a receipt recording when it ran, against which packages and for how long.

Nobody has shared an analysis of this dataset yet. The examples on other datasets cover the common patterns and can be adapted - and if you adapt one, it belongs here.

Start here

Starter code generated from this record’s own identifiers, then the access steps.

Get the data in code

HTAN: fetch files from Synapsepython

pip install synapseclient. Register at synapse.org and accept the HTAN terms first. Level 1 and 2 sequencing is controlled through dbGaP.

import synapseclient

syn = synapseclient.login()          # uses ~/.synapseConfig or SYNAPSE_AUTH_TOKEN
for sid in ["syn50295784","syn51607133","syn51607146","syn51757887"]:
    entity = syn.get(sid, downloadLocation="./htan")
    print(sid, entity.name)
# Browse the atlas at https://humantumoratlas.org/explore
This page as data: limitations firstbash
curl -s https://cd2s.vercel.app/data/datasets/htan-srrs.json | python3 -c '
import json, sys
r = json.load(sys.stdin)
for l in r["limitations"]:
    print(l["severity"].upper(), "-", l["statement"][:120])
print("survival endpoint:", r["longitudinal"]["has_survival_endpoint"], "| treatment response:", r["longitudinal"]["has_treatment_response"])'

Access steps

  1. 1
    Register at Synapse and accept the HTAN termsFor people15 minutes

    One free account covers the atlas; the terms are click-through, not a data access request.

    Requires: Synapse account

    https://humantumoratlas.org/data-access

    Generated from repository policy. Check the linked policy before downloading.

  2. 2
    Download the available files from SynapseFor peopleminutes to hours

    Derived data and other released files become available after the terms are accepted.

    synapse get syn50295784
    https://help.synapse.org/docs/Getting-Started.2055471150.html

    Generated from repository policy. Check the linked policy before downloading.

  3. 3
    Request controlled sequencing through dbGaP when neededFor peopledays to a few weeks

    Raw and aligned sequencing may require an approved request; derived analyses often do not.

    Requires: eRA Commons account, approved dbGaP request

    https://humantumoratlas.org/data-access

    Generated from repository policy. Check the linked policy before downloading.

  4. 4
    Give an agent a Synapse token, not a passwordFor agents

    Unauthenticated calls return metadata and no files, so an agent should report the credential requirement explicitly.

    Requires: SYNAPSE_AUTH_TOKEN

    export SYNAPSE_AUTH_TOKEN=...
synapse get syn50295784
    https://help.synapse.org/docs/Getting-Started.2055471150.html

    Generated from repository policy. Check the linked policy before downloading.

Provenance

All of it, and more, is in this record’s JSON.

Identifiers

Versions and verification

Metadata retrieved
18 Sept 2026
Review status
Machine-extracted
Data generation funding
Funded data generation

For softwarerecord JSON