identifier: METPO:1000630
label: biological process
definition: A execution of a genetically-encoded biological module or program. It
  consists of all the steps required to achieve the specific biological objective
  of the module. A biological process is accomplished by a particular set of molecular
  functions carried out by specific gene products (or macromolecular complexes), often
  in a highly regulated manner and in a particular temporal sequence.
definition_source: DOI:10.1093/database/bat054
trait_category: UPPER
term_kind: CLASS
mapping_status: REVIEWED
xrefs:
- GO:0008150
evidence:
- reference: DOI:10.1093/database/bat054
  snippet: gene product can be associated to a GO term
  notes: Supports biological process as a Gene Ontology aspect used for annotating
    gene-product roles.
- reference: DOI:10.1093/database/bat054
  snippet: biological process, molecular function, or cellular component
  notes: Supports biological process as one of the core GO annotation aspects.
causal_graphs:
- graph_id: biological_process_go_upper_context
  title: Biological process upper-class context
  description: DOI-backed upper-ontology context graph linking biological process
    to molecular functions, gene products, and the non-environmental child metabolism
    class.
  nodes:
  - node_id: biological_process_trait
    label: biological process
    node_type: BIOLOGICAL_PROCESS
    grounding: METPO:1000630
    xrefs:
    - GO:0008150
    description: Upper-level process class for genetically encoded biological programs.
  - node_id: molecular_function
    label: molecular function
    node_type: MOLECULAR_FUNCTION
    grounding: GO:0003674
    description: Elemental molecular activity carried out by a gene product.
  - node_id: gene_product
    label: gene product
    node_type: GENE_OR_PROTEIN
    description: Gene, protein, RNA, or macromolecular complex annotated to GO.
  - node_id: metabolism_trait
    label: metabolism
    node_type: TRAIT
    grounding: METPO:1000060
    description: Non-environmental TraitMech child class under biological process.
  - node_id: cellular_component
    label: cellular component
    node_type: CELLULAR_LOCALIZATION
    description: GO cellular component where a molecular activity occurs.
    grounding: GO:0005575
  - node_id: chemical_input
    label: chemical input entity
    node_type: CHEMICAL
    description: Chemical entity consumed as input of a molecular activity.
  - node_id: chemical_output
    label: chemical output entity
    node_type: CHEMICAL
    description: Chemical entity produced as output of a molecular activity.
  - node_id: molecular_function_downstream
    label: downstream molecular function
    node_type: MOLECULAR_FUNCTION
    description: A molecular function causally downstream of another in a GO-CAM model.
  edges:
  - subject: gene_product
    predicate: carries out
    object: molecular_function
    description: Gene products are annotated to molecular functions that describe
      their activities.
    evidence:
    - reference: DOI:10.1093/database/bat054
      snippet: Elemental activities, such as catalysis or binding
      notes: Supports molecular function as gene-product activity.
  - subject: molecular_function
    predicate: contributes to
    object: biological_process_trait
    description: Molecular functions collectively accomplish broader biological processes.
    evidence:
    - reference: DOI:10.1093/database/bat054
      snippet: Molecular Function, Biological Process and Cellular Component
      notes: Supports GO annotation across molecular functions and biological processes.
    predicate_id: RO:0002326
  - subject: metabolism_trait
    predicate: specializes
    object: biological_process_trait
    description: In TraitMech, metabolism is the non-environmental child class under
      biological process.
    evidence:
    - reference: DOI:10.1093/database/bat054
      snippet: child term is a subtype of the parent term
      notes: Supports parent-child is-a interpretation for GO-style process hierarchies.
    predicate_id: rdfs:subClassOf
  - subject: molecular_function
    predicate: part of
    object: biological_process_trait
    description: GO Molecular Functions are linked to Biological Processes by mereological
      part_of relations.
    evidence:
    - reference: DOI:10.1186/s40708-023-00208-5
      notes: a GO Molecular Function and a GO Biological Process (BP) are linked by
        mereological (part_of) relations
    predicate_id: biolink:part_of
  - subject: molecular_function
    predicate: enabled by
    object: gene_product
    description: A molecular function activity is enabled by a gene product (RO:0002333).
    evidence:
    - reference: DOI:10.1186/s40708-023-00208-5
      notes: Essential GO-CAM mechanistic edge; figure example "glucokinase activity
        enabled by Hxk1".
  - subject: molecular_function
    predicate: occurs in
    object: cellular_component
    description: A molecular activity occurs in a cellular component (BFO:0000066).
    evidence:
    - reference: DOI:10.1186/s40708-023-00208-5
      notes: Occurs in [BFO:0000066]; example "glucokinase activity occurs in cytosol".
    predicate_id: biolink:occurs_in
  - subject: molecular_function
    predicate: has input
    object: chemical_input
    description: A molecular activity has a chemical entity as input (RO:0002233).
    evidence:
    - reference: DOI:10.1186/s40708-023-00208-5
      notes: Has input [RO:0002233]
  - subject: molecular_function
    predicate: has output
    object: chemical_output
    description: A molecular activity has a chemical entity as output (RO:0002234).
    evidence:
    - reference: DOI:10.1186/s40708-023-00208-5
      notes: Has output [RO:0002234]
  - subject: molecular_function
    predicate: causally upstream of or within
    object: molecular_function_downstream
    description: GO-CAMs causally link molecular functions into structured models
      of biological processes (RO:0002418).
    evidence:
    - reference: DOI:10.1186/s40708-023-00208-5
      notes: GO-CAMs arrange GO annotations into structured models of biological processes
        by causally linking GO Molecular Functions
curation_history:
- timestamp: '2026-05-05T01:35:46.866352+00:00'
  curator: seed_from_metpo
  action: SEEDED_FROM_METPO
  changes: imported from data/raw/metpo.owl (CLASS)
  llm_assisted: false
- timestamp: '2026-05-15T00:35:00-07:00'
  curator: codex
  action: CURATED_UPPER_CONTEXT
  changes: Reviewed biological process as an upper classifier and added a DOI-backed
    context graph linking molecular functions, gene products, and the metabolism child
    class.
  llm_assisted: true
- timestamp: '2026-05-20T03:35:32Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (RO:0002326×1).
  llm_assisted: true
- timestamp: '2026-05-23T08:21:50Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (rdfs:subClassOf×1).
  llm_assisted: true
- timestamp: '2026-06-23T00:00:00Z'
  curator: claude
  action: ENRICH_CAUSAL_GRAPH
  changes: Added 6 evidence-backed generic edges (4 new nodes) from the deep-research
    report.
  llm_assisted: true
- timestamp: '2026-06-24T17:21:15Z'
  curator: claude
  action: GROUND_CAUSAL_PREDICATES
  changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv
    (biolink:part_of×1, biolink:occurs_in×1).
  llm_assisted: true
- timestamp: '2026-06-24T17:23:35Z'
  curator: claude
  action: GROUND_CAUSAL_NODES
  changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv
    (GO:0005575×1).
  llm_assisted: true