User guide

Use OncoRoute for research discovery

OncoRoute helps researchers move from a cancer-focused question to live source records, reviewable cohorts, provenance, and reproducible export packs.

Start searching Check sources Privacy Terms

Core workflow

Search across live sources

Enter a research question such as BRAF V600E melanoma or KRAS pancreatic cancer RNA-seq survival. OncoRoute resolves genes, variants, diseases, assays, and therapy terms, then queries each connected source independently as live results return.

Review source coverage

The Source Coverage panel shows which source APIs are loading, which returned records, and which are limited or unavailable. Result counts update progressively, so you can start reviewing records while slower sources continue loading.

Build a cohort

Add relevant datasets to a local cohort from search results or the dataset browser. Cohorts can be used without an account, and signed-in users can keep workspace state for team workflows.

Export an analysis pack

Create a reproducible ZIP pack containing cohort tables, dataset snapshots, file manifests, provenance, and starter Python and R notebooks. Exports are intended to help you move from discovery into analysis.

Understanding result types

Datasets: Cohort-level studies, projects, series, and molecular datasets returned from sources such as GDC, GEO, cBioPortal, and related repositories.
Evidence: Research-context evidence records for genes, variants, diseases, and therapies. Evidence statements must be reviewed in the original source before use.
Trials: ClinicalTrials.gov records that mention relevant conditions, biomarkers, therapies, or study terms. OncoRoute does not determine patient eligibility.
Graph: Relationship context between resolved entities, source records, evidence, and trial references.

No account required: Search, review results, create local cohorts, and export local analysis packs without signing up.
Optional accounts: Create an account when you want persistent workspace identity, organization membership, or teammate invitations.
Team access: Organization owners can invite teammates. Invitations create a shared workspace context while preserving individual sessions.

Exports and provenance

Analysis packs: Signed-in exports are prepared server-side when available. Guest exports remain local in the browser so the research workflow does not require an account.
Manifest: Each pack includes cohort tables, file manifests, a manifest JSON, provenance JSON, citations, README, and starter Python and R notebooks.
Provenance: Every result keeps source, source record ID, source URL, retrieval timestamp, matched fields, adapter version, and source limitations where available.

Source limitations

GDC: Live project search returns project metadata first; case and file detail can require controlled-access authorization.
CDA: CDA subject searches are useful for cross-repository discovery, but some file and summary follow-up endpoints vary by data source.
GEO: GEO summaries identify series and samples; raw or supplementary files may require separate retrieval from NCBI/GEO.
cBioPortal: Study-level metadata loads first; molecular profiles and sample lists are hydrated as source detail is requested.
CIViC and Open Targets: Evidence records are research context and must be reviewed in the original source before publication or downstream use.
ClinicalTrials.gov: Trial records are registry metadata. OncoRoute never determines patient-specific eligibility.

Source status

Ok: The live contract monitor reached the upstream API and received the expected response shape.
Limited: The source is known to OncoRoute, but the production monitor cannot yet prove a live search integration for it. The status text explains what is missing.
Degraded: The upstream API or response contract did not pass the latest check. Results from that source may be incomplete until the upstream recovers.

Troubleshooting

No results: Check source status, broaden the query, or remove filters. Some sources return no records for very specific variant or assay combinations.
Export pending: Server exports are queued and may take a short time to complete. Refresh the exports page to check the latest job status.
Invitation token: If an emailed invitation link does not open, paste the token on the Settings page under account session.

Research-use boundary

OncoRoute is for research and education. It does not provide medical advice, diagnosis, treatment recommendations, or patient-specific clinical trial eligibility decisions.