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secondary metabolic process

vr.tr.secondary-metabolic-process · thing-q22274727

Let an agent explain secondary metabolic processes as an ontology class, relay biochemistry, gene clusters and examples from biology references, describe applications in medicine and agriculture, and distinguish secondary from primary metabolism and the ontology term from specific pathways.

Thing Registry Activities and processes ACT.PRC
Bundle → Layer → Finding → QuestionsClassifiersWhat it isWhy it existsDistinguishing featuresWhat robots and AI may and may not doMoral aspectsOwnersLinks to other meta-modelsIdentity and identifiersDirect propertiesRecognitionCapabilities and actionsHazards and failure modesStandards and interfacesContext of useSources

Bundle → Layer → Finding → Questions Filled

4 bundles · 8 layers · 8 findings · 16 questions

Understand What secondary metabolism is.

Definition

Definition.

Definition

Definition.

  1. What is a secondary metabolic process, and how does it differ from primary metabolism? definition
  2. Is the question about the ontology class, a compound class or a specific pathway? boundary

Examples

Examples.

Examples

Examples.

  1. What are pheromone, fumagillin, helvolic acid, ochratoxin A and protostadienol processes? definition
  2. Which entry fits the specific compound? action
Biology Biochemistry and genetics.

Pathways

Pathways.

Pathways

Pathways.

  1. How do polyketide, terpenoid, alkaloid and peptide pathways build secondary metabolites? provenance
  2. Which references are standard? provenance

Clusters

Gene clusters.

Clusters

Clusters.

  1. How are biosynthetic gene clusters organised and regulated? provenance
  2. Which sources are cited? provenance
Use Applications.

Medicine

Medicine.

Medicine

Medicine.

  1. How do secondary metabolites provide antibiotics and drugs? provenance
  2. Which entry fits natural product drug discovery? action

Agriculture

Agriculture and food.

Agriculture

Agriculture.

  1. How do mycotoxins and plant defence compounds matter in agriculture and food safety? provenance
  2. Which entry fits mycotoxin? action
Context Ontology and ecology.

Ontology

Gene Ontology.

Ontology

Ontology.

  1. How does the Gene Ontology organise metabolic process terms? provenance
  2. Which entry fits Gene Ontology? action

Ecology

Ecology.

Ecology

Ecology.

  1. What ecological roles do secondary metabolites play in defence and signalling? provenance
  2. Which entry fits chemical ecology? action

Classifiers Filled

Family
Thing Registry
Category
Activities and processes
Entry kind
thing
Plane
ACT
Domain
ACT.PRC
Other names and narrower kinds
secondary metabolite biosynthetic process, pheromone metabolic process, fumagillin biosynthetic process, helvolic acid metabolic process, (17Z)-protosta-17(20),24-dien-3beta-ol metabolic process, ochratoxin A metabolic process, toxin metabolic process, secondary metabolite catabolic process, polyketide metabolic process, dehydroaustinol metabolic process, arugosin metabolic process, melanin metabolic process

What it is Filled

A metabolic process, in the Gene Ontology sense, that produces or transforms secondary metabolites, compounds not necessarily required for growth and maintenance of cells but important for defence, signalling and ecological interaction, including the biosynthesis of pheromones, fungal products such as fumagillin, helvolic acid and ochratoxin A, and sterol intermediates such as protostadienol; secondary metabolism underlies antibiotics, toxins, pigments and many drugs.

Why it exists Filled

Let an agent explain secondary metabolic processes as an ontology class, relay biochemistry, gene clusters and examples from biology references, describe applications in medicine and agriculture, and distinguish secondary from primary metabolism and the ontology term from specific pathways.

Distinguishing features Filled

  • The compounds involved are not necessarily required for growth and maintenance of cells.
  • Secondary metabolites have ecological roles.
  • Genes involved in secondary metabolism can occur in clusters.
  • Secondary metabolism is a source of drugs.

What robots and AI may and may not do Filled

Must not

  • Present the ontology class as a single pathway.
  • Give procedures for producing toxic secondary metabolites such as mycotoxins.
  • Annotate a gene to the class without supporting evidence.
  • Present traces of a mycotoxin in food as harmless without data.

Only with a human decision

  • Using annotations to guide engineering of organisms that produce toxins.

May

  • Explain secondary metabolism and the Gene Ontology class in general terms.
  • Annotate genes to the class following ontology rules and evidence codes.

Moral aspects Filled

  • Mycotoxins contaminate food and harm health, especially in poorer regions.
  • Ontology errors spread through many downstream analyses.

Who is affected

  • Consumers of contaminated food
  • Farmers
  • Researchers

Owners Filled

Steward

The Gene Ontology consortium maintains the class.

Master systems

  • Gene Ontology

Links to other meta-models Filled

parent

  • Q1057 - registry parent class

related

  • metabolism - in registry terms
  • secondary metabolite - as its product
  • primary metabolism - for growth and energy
  • Gene Ontology - as a biological process term

What else AI and robots need to interact with it Filled

Identity and identifiers required Filled

  • Vercy registry: vr.tr.secondary-metabolic-process
  • Wikidata: Q22274727 (https://www.wikidata.org/wiki/Q22274727)
  • GO: GO:0019748 secondary metabolic process

Direct properties not applicable Not applicable

  • major classes: terpenoids, alkaloids, polyketides, non-ribosomal peptides, phenylpropanoids list
  • known plant secondary metabolites: over 200000 count - estimates

Plane ACT: no invented physical properties.

Recognition optional Filled

  • It concerns the metabolism of specialised compounds not necessarily required for growth and maintenance of cells.
  • Examples include pheromone, fumagillin, helvolic acid, ochratoxin A and protostadienol metabolic processes.
  • Primary metabolism supplies energy and building blocks, while this ontology term describes a class rather than one pathway.
  • Not a visible object; biochemical pathways.

Capabilities and actions required Filled

  • explain the class
  • relay biochemistry and examples
  • describe applications
  • distinguish related terms

Hazards and failure modes required Filled

  • Confusing the ontology class with a single pathway
  • Registry aliases naming obscure compound processes
  • Mycotoxin contamination of food

Standards and interfaces required Filled

  • Gene Ontology term definitions
  • Food safety limits for mycotoxins such as ochratoxin A

Context of use required Filled

  • Not applicable; a biological process class.
  • secondary metabolite biosynthetic processes
  • pheromone metabolic processes
  • fungal polyketide and terpenoid processes such as fumagillin and helvolic acid
  • mycotoxin processes such as ochratoxin A
  • sterol and triterpenoid intermediates such as protostadienol
  • plant secondary metabolism

Sources Filled

  1. Wikidata item Q22274727: secondary metabolic process - identity and sense of the item
  2. Wikipedia: Secondary metabolism - general description of the item

Open questions

  • Should secondary metabolite and mycotoxin be the primary linked entries?
  • How should ontology and biochemistry sources be linked?
  • The registry entry has merged aliases naming specific compound processes; should they be split off?

Machine files

Card as JSON Specification Card backlog vercy.card/1

Provenance

thing registry research (pass 2) · unreviewed

Built from: models/things/publications/thing-q22274727/spec.json