RCDome · Scientific Module

RCDome Operational Definitions

Browse the 53 canonicalized RCD-related entities and their curated operational definitions, ontological classification, key molecules, evidence, and adjudication gates, sourced from the RCDome decoder.
Ontology levels
L1 Modalities — bona fide cell-death modalities (apoptosis, necroptosis, ferroptosis…)
L2 Subtypes — a subtype of a modality (e.g., extrinsic apoptosis)
L3 Triggers — a trigger or mechanism (e.g., MPT)
L4 Functional/contextual — context-dependent or functional forms
L5 Generic/umbrella/taxon — generic, umbrella, legacy, taxon, or emerging terms
RCDome · Scientific Module

RCDome Operational Definition Comparator

The operational definitions of the 53 RCD entities overlap heavily in wording, and their differences are what make each entity distinct. Compare two or more entities side-by-side to disambiguate similar modalities (apoptosis vs necroptosis vs ferroptosis), understand their ontological relations (subtype, trigger, parent), weigh their evidence maturity and NCCD status, and audit the definitions for consistency. Differing values are highlighted so the contrasts stand out immediately.

RCD Entity Deep Dive

Human-curated, anti-hallucination-audited narrative beyond the operational definition. Every claim is traceable: the in-text [n] points to its reference, and each DOI/PMID opens the source.

Gene Catalog

9,265 HGNC-validated genes · 53 RCD-related entities · 21,568 unique gene–RCD pairs

Evidence-first: 5,138 mechanistic · 225 executors · 4,606 regulators · verbatim-grounded

DeepSeek: 9,785 mechanistic · 469 executor pairs · 9,311 regulator pairs · complete (100% classified)

Compiled gene role: 320 executor pairs · 3,235 regulator pairs · source-derived role

Click a row to see detailed information for that gene.

Direction/Role source:
Download death core (CSV)
Download Download RCDome matrix (CSV)

22,473 rows shown = 21,568 unique gene-RCD pairs + 905 rows of multi-database corroboration (same gene+entity reported by 2+ databases).

RCD Entities — Compiled gene role vs DeepSeek (executors / regulators)

Download comparison table (CSV)

Discrepancy Radar

The knowledge frontier: Where the three classifiers disagree, RCDome shows the conflict instead of hiding it. Each row carries the divergent verdicts, the GPT arbitration, the two curator votes, and the evidence-first verdict that resolved it from the verbatim.

Discovery Timeline

From 1859 to 2025: the 53 RCD-related entities plotted by founding year, one lane per ontological level. Hover a point for its founding citation; click it to open the discovery card.

RCDome · Scientific Module

RCDome Digital Molecular Board

A regulated-cell-death (RCD) interpretation module built for educational use and scientific interrogation. It translates the RCDome database (22,473 gene–RCD associations across 53 RCD-related entities) and the RCDome decoder (curated operational definitions and ontological classification) into a sourced, hedged prose synthesis — then supports structured follow-up questions about gene associations, mechanistic roles, regulatory directions, evidence maturity, key molecules, and ontological relationships, through the RCDome Q&A AI.
RCDome dome
What the Board integrates
RCDome database
Gene–RCD associations with evidence tier, role, direction, mechanistic classification, and verified PMIDs.
RCDome decoder
53 canonicalized RCD-related entities with operational definitions, key molecules, core mechanisms, hard-gate status, and founding references.
RCDome Q&A AI
A governed follow-up dialogue: genes associated, required genes, evidence maturity, key molecules, and ontological relationships.
How to use it
1. Select
Choose an RCD entity (and optionally a single gene) from the dropdowns.
2. Generate
The AI agent produces a prose synthesis sourced from the database and decoder.
3. Question
The three suggested queries appear in the Q&A module; ask any follow-up within scope.
RQ
RCDome Q&A AI
RCDome Q&A answers from the RCDome database and decoder. Enter to send.
Try an example query

Gene × RCD Entity Network

Click a gene (circle) for literature evidence. Click an RCD logo for its top-pair evidence trail.

Entity level L1 Modalities L2 Subtypes L3 Triggers L4 Functional/contextual L5 Generic/umbrella/taxon
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Gene role EXECUTOR REGULATOR MARKER UNCERTAIN
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Edge → PROMOTES ⊣ PROTECTS ET1 ET2 ET3 ET4 legacy form

About

The RCDome Atlas — a multi-database human gene atlas of regulated cell death.

Who built RCDome

Related platforms

Other tools from LBTGenomica/UENF

CancerRCDShiny cancerrcdshiny.shinyapps.io OncometabolismGPS oncometabolismgps.be SigPolytope sigpolytope.shinyapps.io/geometricatlas CancerRCDPredictor lbtgenomica.uenf.br

Data provenance

Where each gene–RCD association comes from