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Reactome: Database organization, Database content & Overview

Reactome is a free online database of biological pathways. It is manually curated and authored by PhD-level biologists, in collaboration with Reactome editorial staff. The content is cross-referenced to many bioinformatics databases. The rationale behind Reactome is to visually represent biological pathways in full mechanistic detail, while making the…

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Reactome topic overview

The analysis highlights Database organization, Database content and Overview as prominent areas in the source structure around Reactome.

Related topics
13
Source areas
3
Connected nodes
16
Extracted relationships
34
Concept neighborhoods
9
Bridge connections
16

What this topic covers Research coverage

Source areas are shown by the number of related topics found in each part of the analysis. Use smaller areas too: they can reveal specialized angles and content gaps.

Overview · 7 topics
Database organization · 4 topics
Database content · 2 topics

Smaller areas are not necessarily less important. They contain fewer connections in this analysis and can be useful for finding specialized angles or coverage gaps.

Key facts & relationships

High-confidence facts extracted from structured source data. Use them as anchors for further research.

Data format
BioPAX SBML
Data release frequency
https://reactome.org/about/release-calendar
Description
Reactome: a database of reactions, pathways and biological processes.
Download URL
https://reactome.org/download-data
License
https://reactome.org/license
Web service URL
https://reactome.org/ContentService/

Explore all related topics Closing gaps

Browse the complete topic structure, not only the most central items. Less prominent entities and concepts can reveal missing angles, specialized context and useful research gaps. Each item opens a new analysis centered on that subject.

Overview

Database organization

Database content

Advanced semantic analysis

Deeper signals for content research, entity SEO and topical coverage. The plain-language headings explain what each technical view is useful for.

How Reactome connects Entity context

The extracted context around Reactome shows recurring relationship patterns in the source. For example, Reactome → ChEBI, Expression, GWAS, If, Mixed, Over-representation, The, There, Uniprot Another extracted example is Reactome → BioCyc, Comparative Toxicogenomics Database, Genes, Genomes, Pathway CommonsKEGG, The BRaunschweig ENzyme DAtabase, The Kyoto Encyclopedia, WikiPathways. Use these groups to spot repeated connection types before inspecting the individual relationships.

Reactome

Top relations

related to Tools · 9
Reactome → ChEBI, Expression, GWAS, If, Mixed, Over-representation, The, There, Uniprot
see also · 8
Reactome → BioCyc, Comparative Toxicogenomics Database, Genes, Genomes, Pathway CommonsKEGG, The BRaunschweig ENzyme DAtabase, The Kyoto Encyclopedia, WikiPathways
related to Database content · 5
Reactome → DOI, Each, ORCID, Reviewers, The
related to Database organization · 2
Reactome → In Reactome, Like
Data format · 1
Reactome → BioPAX SBML
Data release frequency · 1
Reactome → https://reactome.org/about/release-calendar
Description · 1
Reactome → Reactome: a database of reactions, pathways and biological processes.
Download URL · 1
Reactome → https://reactome.org/download-data
License · 1
Reactome → https://reactome.org/license
Primary citation · 1
Reactome → .mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:r…

Important terminology

Use these terms to understand the vocabulary surrounding the topic, not as a checklist for keyword stuffing.

Important terminology

pathways data pathway biological database reactions molecules human tools molecular analysis entities processes used process contain expression proteins format website

Reactome relationships Subject–Predicate–Object triples

TTTA extracted 34 structured relationships around Reactome. Examples in this analysis include Reactome → Data format → BioPAX SBML and Reactome → Data release frequency → https://reactome.org/about/release-calendar. The table shows each extracted connection, where it came from and its confidence.

SubjectPredicateObjectConfidenceSrc
ReactomeData formatBioPAX SBML1.00infobox
ReactomeData release frequencyhttps://reactome.org/about/release-calendar1.00infobox
ReactomeDescriptionReactome: a database of reactions, pathways and biological processes.1.00infobox
ReactomeDownload URLhttps://reactome.org/download-data1.00infobox
ReactomeLicensehttps://reactome.org/license1.00infobox
ReactomePrimary citation.mw-parser-output cite.citation{font-style:inherit;word-wrap:break-word}.mw-parser-output .citation q{quotes:"\"""\"""'""'"}.mw-parser-output .citation:target{background-color:r…1.00infobox
ReactomeWeb service URLhttps://reactome.org/ContentService/1.00infobox
ReactomeWebsitehttps://reactome.org1.00infobox
Reactomeis afree online database of biological pathways0.90text
the activation of a protein by cleavage of one or more of its peptide bondsinstance ofand events0.80text
Reactomerelated to Database contentThe0.60section
Reactomerelated to Database contentReviewers0.60section

Related concept clusters Concept neighborhoods

The concept neighborhoods around Reactome bring nearby vocabulary together. In this analysis, examples include Processes, Also and Molecular. Use the clusters to find adjacent concepts and terminology that may deserve separate research.

  • biological pathways
    • Processes
    • Reactome
    • Reactions
    • Pathways
    • Database
    • Molecules
    • Pathway
    • Accessible
    • External
    • Analysis
    • Tools
    • Human
  • database content
    • Processes
    • Biological
    • Reactome
    • Also
    • Databases
    • External
    • Pathways
    • Molecular
    • Reactions
    • Tools
    • Biopax
    • Citation
  • database organization
    • Processes
    • Biological
    • Reactome
    • Pathways
    • Molecular
    • Reactions
    • Biopax
    • Citation
    • Content
    • Sbml
    • Also
    • Contain
  • Reactome
    • Processes
    • Also
    • Molecular
    • Tools
    • External
    • Website
    • Human
    • Sbml
    • Verification
    • Databases
    • Process
    • Using
  • reactome
    • Processes
    • Also
    • Molecular
    • Tools
    • External
    • Website
    • Human
    • Sbml
    • Verification
    • Databases
    • Process
    • Using
  • human genome
    • Processes
    • Molecules
    • Manually
    • Verification
    • Process
    • Small
    • Using
    • Proteins
    • Used
    • Molecular
    • Pathways
    • Reactome
  • biopax
    • Sbml
    • Citation
    • Contain
    • Format
    • Website
    • Data
    • Database
    • Reactome
  • molecular
    • Processes
    • Reactions
    • Databases
    • Reactome
    • Used
    • Molecules
    • Pathway
    • Pathways

Connections between topic areas Semantic bridges

For Reactome, one of the stronger structural bridges in this analysis connects Reactome with Overview. Bridges highlight paths between different parts of the map and can reveal research angles that are easy to miss in a flat list.

Min side: 3
Reactome — Overview · splits 9 ⟂ 8
Reactome — Database organization · splits 12 ⟂ 5
Reactome — Database content · splits 14 ⟂ 3

Map overview Semantic statistics

Reactome

Nodes17
Edges16
Triples34
Avg. degree1.88
Density0.117647
Components1

Source & methodology

TTTA analyzes the structure around Reactome to surface related topics, entities, relationships, concept neighborhoods and bridge connections. Use the map to explore areas such as Database organization, Database content & Overview, including less central topics that may reveal useful research gaps. Automatically extracted connections are research leads rather than rewritten encyclopedia content.

Source: Wikipedia — Reactome · EN edition · Analysis: TopicsToTalkAbout

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