biological pathway
Let an agent describe biological pathways, find them in curated databases with identifiers, and explain their components and roles in health and disease.
Bundle → Layer → Finding → Questions Filled
4 bundles · 8 layers · 8 findings · 16 questions
Identity Which pathway.
Database record
Database and ID.
Pathway record
Database, ID and version.
- Which database record describes the pathway? provenance
- Which version and species? provenance
Kind
Metabolic, signalling, regulatory.
Pathway kind
Kind.
- What kind of pathway is it? definition
- Which process does it serve? definition
Components Parts and steps.
Participants
Genes, proteins, metabolites.
Participant
Molecule and role.
- Which molecules take part? provenance
- In which roles? definition
Reactions
Steps and interactions.
Reaction
Reaction, direction, catalysts and regulators, compartment and cell context, experimental or inferred evidence.
- Which reactions make up the pathway? provenance
- What evidence supports each? provenance
Analysis Using pathways in data analysis.
Enrichment
Pathway enrichment.
Enrichment result
Method and statistics.
- Which method and database version were used? provenance
- What correction for multiple testing? measurement
Modelling
Quantitative models.
Model
Format and parameters.
- Is there a quantitative model? provenance
- In which format? provenance
Biomedical relevance Disease and drugs.
Disease
Pathway in disease.
Disease link
Disease and evidence.
- Which diseases involve the pathway? provenance
- What is the evidence? provenance
Drugs
Drug targets.
Drug target
Drug and target.
- Which drugs act on the pathway? provenance
- At which step? provenance
Classifiers Filled
- Family
- Thing Registry
- Category
- Activities and processes
- Entry kind
- thing
- Plane
- ACT
- Domain
- ACT.PRC
- Other names and narrower kinds
- anticoagulation, cellular pathway, transcriptional pathway, dispersal pathway, tumor invasion pathway, classic metabolic pathway, disease pathway, drug pathway, regulatory pathway, signaling pathway
What it is Filled
A set of interconnected molecular reactions and interactions in a cell or organism, such as metabolic, signalling or gene-regulatory pathways, delineated as a model for studying how biomolecules work together to produce a function.
Why it exists Filled
Let an agent describe biological pathways, find them in curated databases with identifiers, and explain their components and roles in health and disease.
Distinguishing features Filled
- A model: manually curated or computationally inferred, with boundaries set by each database and purpose.
- Metabolic pathways transform molecules; signalling pathways transmit information; regulatory pathways control gene expression.
- The same pathway can be represented differently in different databases.
What robots and AI may and may not do Filled
Must not
- present pathway models as complete reality
- give medical advice from pathway data
May
- describe pathways with database identifiers
Moral aspects Filled
- accuracy
- open data
Who is affected
- researchers
Owners Filled
Steward
nobody as a concept; each database curates its own pathway models
Master systems
- Reactome
- KEGG
- WikiPathways
Links to other meta-models Filled
parent
- Q2996394 - registry parent class
related
- biological process model - model
- pathway database - Reactome, KEGG, WikiPathways
- Gene Ontology biological process - annotation
contains
- biochemical reaction - steps
What else AI and robots need to interact with it Filled
Identity and identifiers required Filled
- Vercy registry: vr.tr.biological-pathway
- Wikidata: Q4915012 (https://www.wikidata.org/wiki/Q4915012)
- Reactome stable ID: R-HSA-<number>, optionally .<version> human pathways; check the record type is Pathway
- KEGG pathway ID: map##### or hsa#####
- WikiPathways ID: WP<number>, for example WP732 revision recorded separately
Direct properties not applicable Not applicable
Not applicable
A molecular model has no physical properties.
Recognition optional Filled
- Shown as diagrams of molecules connected by reactions and interactions
Capabilities and actions required Filled
- identify a pathway and its database records
- list components and steps
- explain pathway enrichment analysis in general terms
- link pathways to diseases and drugs with sources
Hazards and failure modes required Filled
- Over-interpreting enrichment results
- Mixing pathway versions and species
Standards and interfaces required Filled
- BioPAX and SBGN exchange and notation standards
- Systems Biology Markup Language (SBML)
Context of use required Filled
- Organising knowledge of molecular mechanisms for research, drug discovery and data analysis.
- metabolic pathway
- signalling pathway
- gene-regulatory pathway
- disease pathway
Sources Filled
- Q4915012 - identity of the registry item, labels and sitelinks
- Biological pathway - general description of the subject
- Biological Pathways Fact Sheet - Definition, metabolic and regulatory kinds, interconnected boundaries and disease and drug research applications.
- Explain the identifiers associated with entities and events - Stable identifier structure, versions, species codes and manually annotated versus computationally inferred events.
- KEGG PATHWAY Database - Pathway categories, reference and organism-specific maps, and prefix-plus-five-digit identifiers.
- WikiPathways identifier registry - Variable-length WikiPathways identifiers and revision-qualified forms.
- BioPAX Level 3 Documentation - Pathway exchange, molecular context and the complementary roles of BioPAX, SBGN and SBML.
- SBML Specifications - SBML as a model representation standard, including quantitative and qualitative model types.
Open questions
- The registry merges specific processes and ecological dispersal pathways; they need registry corrections.
Machine files
Provenance
thing registry research (pass 2) · unreviewed
Built from: models/things/publications/thing-q4915012/spec.json