TraitMech

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biological process

METPO:1000630 · CLASS · REVIEWED

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.

Biological process upper-class context

DOI-backed upper-ontology context graph linking biological process to molecular functions, gene products, and the non-environmental child metabolism class.

Biological process upper-class context Interactive directed graph showing evidence-backed causal relationships for biological process.

Edge evidence

  • gene product carries out molecular function

    Gene products are annotated to molecular functions that describe their activities.

    • DOI:10.1093/database/bat054 Elemental activities, such as catalysis or binding Supports molecular function as gene-product activity.
  • molecular function contributes to biological process RO:0002326

    Molecular functions collectively accomplish broader biological processes.

    • DOI:10.1093/database/bat054 Molecular Function, Biological Process and Cellular Component Supports GO annotation across molecular functions and biological processes.
  • metabolism specializes biological process rdfs:subClassOf

    In TraitMech, metabolism is the non-environmental child class under biological process.

    • DOI:10.1093/database/bat054 child term is a subtype of the parent term Supports parent-child is-a interpretation for GO-style process hierarchies.
  • molecular function part of biological process biolink:part_of

    GO Molecular Functions are linked to Biological Processes by mereological part_of relations.

    • DOI:10.1186/s40708-023-00208-5 a GO Molecular Function and a GO Biological Process (BP) are linked by mereological (part_of) relations
  • molecular function enabled by gene product

    A molecular function activity is enabled by a gene product (RO:0002333).

    • DOI:10.1186/s40708-023-00208-5 Essential GO-CAM mechanistic edge; figure example "glucokinase activity enabled by Hxk1".
  • molecular function occurs in cellular component biolink:occurs_in

    A molecular activity occurs in a cellular component (BFO:0000066).

    • DOI:10.1186/s40708-023-00208-5 Occurs in [BFO:0000066]; example "glucokinase activity occurs in cytosol".
  • molecular function has input chemical input entity

    A molecular activity has a chemical entity as input (RO:0002233).

    • DOI:10.1186/s40708-023-00208-5 Has input [RO:0002233]
  • molecular function has output chemical output entity

    A molecular activity has a chemical entity as output (RO:0002234).

    • DOI:10.1186/s40708-023-00208-5 Has output [RO:0002234]
  • molecular function causally upstream of or within downstream molecular function

    GO-CAMs causally link molecular functions into structured models of biological processes (RO:0002418).

    • DOI:10.1186/s40708-023-00208-5 GO-CAMs arrange GO annotations into structured models of biological processes by causally linking GO Molecular Functions

Provenance

Source
METPO (2025-11-25)
Definition source
DOI:10.1093/database/bat054

Children (1)

Cross-references

  • GO:0008150

kg-microbe context

Matched 1 kg-microbe node via direct_metpo.

  • METPO:1000630 [-0.906, -0.897, -0.035, -0.552, …]

512-dim DeepWalkSkipGramEnsmallen embedding from kg-microbe (2026-04-25).

Nearest neighbors in embedding space

Top-8 cosine-similar METPO traits from the 2026-04-25 deepwalk (512-D).

Curation history

  1. · SEEDED_FROM_METPO · seed_from_metpo

    imported from data/raw/metpo.owl (CLASS)

  2. · CURATED_UPPER_CONTEXT · codex

    Reviewed biological process as an upper classifier and added a DOI-backed context graph linking molecular functions, gene products, and the metabolism child class.

  3. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (RO:0002326×1).

  4. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 1 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (rdfs:subClassOf×1).

  5. · ENRICH_CAUSAL_GRAPH · claude

    Added 6 evidence-backed generic edges (4 new nodes) from the deep-research report.

  6. · GROUND_CAUSAL_PREDICATES · claude

    Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:part_of×1, biolink:occurs_in×1).

  7. · GROUND_CAUSAL_NODES · claude

    Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (GO:0005575×1).