Indago Life sciences bundle
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Bundle 04 · Life SciencesAudience · genomics, biochem, computational biology

Pathway, sequence,
gene-name reality checks.

Catch sequence, symbol & pathway bugs before they reach the manuscript — on your workstation.

Early access · Audit a supplementary table in 90 seconds
See the demosJoin the waitlist →
THE GENOMESequence, indexed.
Retraction preventedExcel-coerced gene symbols ("SEPT2 → 2-Sep") caught in the supplementary, not the corrigendum.
200 M+ proteinsUniProt + KEGG + Reactome + bioRxiv · delta-refreshed · < 2 ms lookup · anti-fab gated.
Pathway sanityManuscript figures cross-checked against canonical KEGG pathways before submission.
Zero data leavesFASTQ / BAM / VCF stay on the workstation. Free trial. Same answer in 6 months. Try yourself for free →

The collision that turns into a retraction.

A gene symbol auto-corrected to a date. A pathway map that contradicts the canonical one in KEGG. A sequence read whose quality dropped silently below threshold. Indago indexes UniProt, KEGG, Reactome and bioRxiv alongside your pipeline output and runs the bio-anomaly scans automatically — flagged before submission. Every cited chunk_id resolves; emit is rejected otherwise.

I · Three questions a working bio team asks

From pathway to sequence to symbol audit.

Demo 1 · Pathway lookup with consistency check1.4 ms · local
pathway · mTORC1 · upstream regulators · vertebrate · consistent with KEGG hsa04150
01
Canonical · RHEB → mTORC1; TSC1/TSC2 GAP activity, Akt-mediated TSC inhibition. KEGG · hsa04150 · 2025 · node 23
0.96
02
XLSX gene table — SEPT2 → 2-Sep Excel coercion flagged. file://lab/draft-v3/supp_genes.xlsx · 2026-04 · scan · anomaly.bio.excel-coerce
0.88
03
Review · "RHEB-independent mTOR activation under amino-acid deprivation". PubMed · PMID 38… · 2024 · Sect. 3.2
0.83
KEGG + local figure + literaturescan flagged before submission
Demo 2 · Gene-symbol audit across the supplementary tablesscan · per-file
audit · all gene symbols in supplementary/*.xlsx · flag Excel-coerced dates
01
SEPT2 → "2-Sep" coercion in 14 rows of supp_table_3.xlsx. scan · life.symbol.excel-coerce · file://supp/table_3.xlsx
0.99
02
MARCH1 / MARCHF1 nomenclature drift across tables — HGNC update 2020. UniProt mapping · 2020 release · 3 affected rows
0.91
14 + 3 corrected referencesdelta report exported to PRJ folder

Demos illustrative. The engine indexes your pipeline output locally — sequence FASTQs are not re-uploaded.

II · What's included

UniProt, KEGG, Reactome, bioRxiv — plus your pipeline.

Pair with Medical when work crosses into clinical evidence; with Research for the broader scholarly graph.

  • UniProt · KEGG · Reactome · bioRxivauthenticated bulk · delta updates · 200 M+ proteins
  • Native renderers
    materials-regulatory-card · sota-survey-map · claims-ledger aggregator profile materials.29-template surface
  • Anti-fabrication rail
    indago_finding_emit rejects unresolvable chunk-ids — no fabricated accession numbers.guard at emit
  • Gene-symbol drift · Excel-coercescan · anomaly.bio.symbol-collision · anomaly.bio.excel-coerce
  • Sequence-quality & integrityFASTQ phred drop · adapter contamination · duplication rate
  • Local pipeline indexingFASTQ · BAM · VCF metadata · notebook outputs
Sources of recordUniProtKEGGReactomebioRxiv

Need ChEMBL, HGNC or RCSB PDB? Indago can ingest any of them via URL on demand (indago_learn), but they are not first-class registered sources in this bundle today.

II.5 · Sample workflows

Real workflows. Real numbers.

Three workflows shaped for this bundle. Where the box reads Verified, the numbers come from a real run logged in this codebase. Where it reads Pending validation, the workflow shape is implemented and we are still gathering the headline numbers before we publish them.

Workflow 01 Pending validation

Supplementary-table symbol audit

Genomics core
  1. InputA manuscript supplementary directory of XLSX/CSV gene-list tables.
  2. Methodanomaly.bio.excel-coerce + UniProt cross-reference + chunk-resolved citation per coerced row.
  3. OutputPer-file delta report listing every coerced symbol ("SEPT2 → 2-Sep" class) plus suggested rewrites.
Excel-coerce trap Scan shape is implemented; pending validation on a real supplementary dataset before publishing a hit-rate.
Workflow 02 Pending validation

Pathway consistency check

Computational biologists
  1. InputA draft manuscript figure (PDF/SVG) plus the cited pathway ID.
  2. MethodCross-reference against KEGG canonical + literature search for known deviations.
  3. OutputAnnotated figure diff with each missing / extra edge flagged against KEGG.
Pre-submission catch Pending bio-team end-to-end test on a real draft figure before quoting precision.
Workflow 03 Pending validation

Sequence-quality batch QC

Sequencing pipelines
  1. InputA directory of FASTQ + a quality threshold.
  2. Methodlife.sequence.phred-drop + adapter-contamination + duplication-rate scans.
  3. OutputPer-file QC card and a single summary CSV for the LIMS.
Pipeline gate Workflow runs against synthetic FASTQ today — pending a real wet-lab batch for the quote-worthy numbers.

Verified workflows are reproducible against the index hash listed in each run. Pending workflows are a written commitment, not a customer quote — we publish numbers only when we have measured them.

Life sciences bundle · from€499/ seat / month· institutional rollouts · scan family included
III · Also useful
MED · MedicalClinical evidencePubMed · CT.gov · Cochrane · ICTRP · EU CTR for translational work. RES · ResearchBroad scholarly graphOpenAlex · arXiv quant-bio · Semantic Scholar. DEV · CodePipeline sourceIndex your Nextflow / Snakemake / Python pipelines alongside the bio data.