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protein

vr.tr.protein · thing-q8054

Let an agent handle proteins by identity, sequence, structure, function and organism, using standard identifiers, and nutrition as a separate sense.

Thing Registry Physical world and living systems PHY.MAT
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

Identity Which protein.

Accession

UniProt and gene.

Accession

Identifiers.

  1. What is its UniProt accession and gene name? provenance
  2. Which organism? definition

Sequence

Amino acid sequence.

Sequence

The sequence.

  1. What is its sequence and length? measurement
  2. Which isoform? boundary
Structure Shape.

Experimental

PDB.

Structure

Experimental structures.

  1. Is there an experimental structure, at what resolution? provenance
  2. Which method? provenance

Predicted

Models.

Prediction

Predicted models.

  1. Is a predicted model available, and how confident is it? measurement
  2. Where might it be wrong? boundary
Function What it does.

Role

Molecular function.

Function

Molecular and biological role.

  1. What does the protein do? definition
  2. How is that known? provenance

Disease

Links to disease.

Disease links

Disease associations.

  1. Is it linked to disease? provenance
  2. Is it a drug target? provenance
Use Production and diet.

Production

Recombinant.

Production

How it is produced.

  1. How is it produced for use? definition
  2. Which rules apply? provenance

Diet

Nutrition and allergy.

Nutrition

Dietary aspects.

  1. Is it a food allergen? boundary
  2. How much dietary protein is recommended, by whom? provenance

Classifiers Filled

Family
Thing Registry
Category
Physical world and living systems
Entry kind
thing
Plane
PHY
Domain
PHY.MAT

What it is Filled

A biomolecule or biomolecule complex largely consisting of one or more chains of amino acid residues, with folded regions, intrinsically disordered regions or both, carrying out functions such as catalysis, structure, transport and signalling.

Why it exists Filled

Let an agent handle proteins by identity, sequence, structure, function and organism, using standard identifiers, and nutrition as a separate sense.

Distinguishing features Filled

  • Proteins consist largely of amino acid chains that may be folded, intrinsically disordered or both.
  • Function depends on sequence, structure and molecular dynamics.
  • Proteins are encoded by genes.
  • Dietary protein is a nutrition concept.

What robots and AI may and may not do Filled

Must not

  • Assist in designing or producing proteins intended to harm people, such as toxins.
  • Present predicted structures as experimentally confirmed.
  • Give personal dietary or supplement advice to a person with a medical condition.
  • Misattribute data from shared databases.

Only with a human decision

  • Releasing designs or data for proteins with possible dual use.

May

  • Describe proteins' structure and function from cited databases and literature.
  • Report dietary protein content from food composition data.

Moral aspects Filled

  • Protein science serves medicine but some proteins are toxins with misuse potential.
  • Shared databases rely on honest attribution and accuracy.

Who is affected

  • Patients
  • Researchers
  • The public

Owners Filled

Steward

Nobody owns proteins in nature; protein data banks curate shared records.

Master systems

  • Protein sequence and structure databases

Links to other meta-models Filled

parent

  • Q3084232 - registry parent class
  • Q422649 - registry parent class
  • Q424689 - registry parent class
  • Q66560214 - registry parent class

related

  • amino acids - monomers
  • gene - DNA
  • cell - context
  • food - dietary protein

What else AI and robots need to interact with it Filled

Identity and identifiers required Filled

  • Vercy registry: vr.tr.protein
  • Wikidata: Q8054 (https://www.wikidata.org/wiki/Q8054)
  • UniProt accession: for example P69905 protein sequence and function
  • PDB id: four characters structures

Direct properties required Filled

  • length: 50-35000 amino acids - titin is the largest
  • mass: 5-3800 kDa

Recognition required Filled

  • UniProt accession and gene name
  • PDB structures
  • Dietary protein on labels is a nutrient, not a specific protein
  • Invisible to the eye; shown as structure models, sequences or bands on gels.

Capabilities and actions required Filled

  • identify it, by sequence and accession
  • determine its structure
  • study its function
  • produce it, recombinantly, under biosafety rules

Hazards and failure modes required Filled

  • Allergenic proteins in food
  • Misfolding diseases
  • Confusing orthologs across species

Standards and interfaces required Filled

  • Biosafety rules for recombinant proteins
  • Medicines regulation for protein therapeutics
  • Food labelling rules on protein content

Context of use required Filled

  • Proteins do most of the work in cells; in diets, protein supplies amino acids.
  • enzymes
  • structural proteins
  • transport proteins
  • signalling proteins and receptors
  • antibodies

Sources Filled

  1. Wikidata item Q8054: protein - identity and sense of the item
  2. Wikipedia: Protein - general description of the item

Open questions

  • Should proteins be instances with UniProt accessions?
  • How should dietary and biochemical senses be separated?
  • How should predicted structures be marked?

Machine files

Card as JSON Specification Card backlog vercy.card/1

Provenance

thing registry research (pass 2) · unreviewed

Built from: models/things/publications/thing-q8054/spec.json