biological process
Let an agent handle biological processes as the general concept, routing to specific processes and linking to ontologies such as the Gene Ontology.
Research draft, second pass
A second pass drafted this model: the structure a model of this thing needs, and what is known about it in the world. The line under this one says how the second half was obtained - researched against sources, or recalled without web access, in which case nothing here was read anywhere and every claim is a lead to verify. Unreviewed either way.
written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify
Researched by: Claude
Purpose and description
Let an agent handle biological processes as the general concept, routing to specific processes and linking to ontologies such as the Gene Ontology.
Any process carried out by living organisms or their parts, such as metabolism, growth, reproduction, digestion, reflexes and cell signalling, as the general concept for biological processes.
What it is for: The entry above specific biological processes.
It can be classify a process; link to Gene Ontology terms; describe steps and regulation; find evidence for mechanisms.
Distinguishing features
Carried out by living systems
Levels from molecules to organisms
Regulated
Catalogued in ontologies
What it looks like
Not a single appearance; processes inside organisms and cells.
How it is recognised
Named processes such as digestion or reflex
GO biological process terms
Specific processes are separate entries
Related models
is a kind of - category
has kind - kinds
is catalogued in - ontology
is studied by - field
In practice
Families and kinds
metabolic processes
developmental processes
reproductive processes
signalling and regulation
organismal processes such as digestion
Identifiers
GO id GO:0008150 biological process root
Standards and regulation
Gene Ontology guidelines
Failure modes and hazards
Overstating mechanisms
Mixing levels of organisation
Where this came from
wikidata · CC0 1.0
Drafted structure
Bundle to layer to finding to question, as the second pass will find it: 4 bundles · 8 layers · 8 findings · 16 questions.
Kind Which process.
Kind leads to specific entries.
Type
Metabolic, developmental.
Type
Process type.
- Which biological process is meant? definition
- Which specific entry fits? action
Level
Molecule to organism.
Level
Level.
- At which level does it occur? definition
- In which organisms? definition
Mechanism How it works.
Mechanisms need evidence.
Steps
Sequence.
Steps
Steps.
- What are its main steps? definition
- How is it regulated? definition
Evidence
Studies.
Evidence
Evidence.
- What evidence supports the mechanism? provenance
- Which GO evidence codes apply? provenance
Ontology Terms.
Ontologies standardise.
GO term
Identifier.
GO
GO term.
- Which GO term matches it? provenance
- Where does it sit in the hierarchy? definition
Annotation
Genes.
Annotation
Gene annotation.
- Which genes are annotated to it? provenance
- In which species? definition
Health When it fails.
Disrupted processes cause disease.
Disease
Dysfunction.
Disease
Dysfunction.
- Which diseases involve disruption of this process? provenance
- Is this general information only? boundary
Research
Open questions.
Research
Research.
- What remains unknown? provenance
- Which reviews summarise it? provenance
What the second pass must settle
- How should the general entry organise children?
- How should GO terms be linked?
- How should evidence codes be recorded?