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.

Select 2 to 4 RCD entities to compare

Display

All fields Differing fields only Identical fields only

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 · 4,455 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 (applies only to the Role and Direction columns):

Evidence-first DeepSeek Compiled gene role Consensus GPT Curator 1 Curator 2 Download death core (CSV)

Gene

RCD entity

Biotype

Cancer Gene

Source DBs

Confidence Tier

Mechanistic

Role

Direction

Adjudication

Format:

Download Download RCDome matrix (CSV)

Total corpus: 22,473 rows = 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)

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.

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.

1. RCD entity

2. Gene (optional)

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.

Filter by RCD entity:

Search gene:

Edge classification sources (1 = single, 2+ = compare):

Evidence-first DeepSeek Compiled gene role Consensus GPT Curator 1 Curator 2

Filter by level:

Filter by gene role:

Filter by mechanistic class:

Max genes per entity (top by evidence tier):

Entity level L1 Modalities L2 Subtypes L3 Triggers L4 Functional/contextual L5 Generic/umbrella/taxon

Gene role EXECUTOR REGULATOR MARKER UNCERTAIN

Edge → PROMOTES ⊣ PROTECTS ET1 ET2 ET3 ET4 legacy form

Multimedia

Video and audio presentations covering the core concepts and findings of RCDome.

🎧 Podcast

RCDome: How AI Audited Cell Death Databases

Emanuell Rodrigues de Souza · Victor dos Santos Lopes · Higor Almeida Cordeiro Nogueira · Enrique Medina-Acosta

October 2026 · ResearchGate

DOI: https://doi.org/10.13140/RG.2.2.33863.25763

How to Cite

Rodrigues de Souza E, dos Santos Lopes V, Almeida Cordeiro Nogueira H, Medina-Acosta E. (2026). RCDome: How AI Audited Cell Death Databases [Audio podcast]. ResearchGate. https://doi.org/10.13140/RG.2.2.33863.25763

🎬 Video Presentation

RCDome: A Multi-Database Human Gene Atlas of Regulated Cell Death

Emanuell Rodrigues de Souza · Victor dos Santos Lopes · Higor Almeida Cordeiro Nogueira · Enrique Medina-Acosta

October 2026 · ResearchGate

DOI: https://doi.org/10.13140/RG.2.2.10375.15527

How to Cite

Rodrigues de Souza E, dos Santos Lopes V, Almeida Cordeiro Nogueira H, Medina-Acosta E. (2026). RCDome: A Multi-Database Human Gene Atlas of Regulated Cell Death [Scientific video]. ResearchGate. https://doi.org/10.13140/RG.2.2.10375.15527

Infographics

Regulated Cell Death Atlas — overview of the information sources behind the RCDome scientific podcast.

Regulated Cell Death Atlas Overview infographic

Cite RCDome

Bibliographic references for the RCDome manuscript, software, and dataset.

Manuscript

Preprint — bioRxiv. doi: 10.64898/2026.10.29.761548

Rodrigues de Souza E, dos Santos Lopes V, Almeida Cordeiro Nogueira H, Medina-Acosta E. RCDome: A Multi-Database Human Gene Atlas of Regulated Cell Death. Preprint at bioRxiv. 2026. doi: 10.64898/2026.10.29.761548. Available at: https://www.biorxiv.org/content/10.64898/2026.10.29.761548v1.

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