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genome

vr.tr.genome · thing-q7020

Let an agent explain genomes and their organisation, relay sizes, sequencing and organelle genomes from genomics references, describe applications in medicine and evolution, and distinguish genomes from genes, transcriptomes and proteomes.

Thing Registry Physical world and living systems PHY.OBJ
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 a genome is.

Definition

Definition and organisation.

Definition

Definition.

  1. What is a genome, and how are genes, regulatory and non-coding sequences organised in chromosomes? definition
  2. Is the question about a genome, a gene, the transcriptome or the proteome? boundary

Kinds

Kinds.

Kinds

Kinds.

  1. How do nuclear, bacterial, viral, mitochondrial, kinetoplast and chloroplast genomes differ? definition
  2. Which entry fits the specific genome? action
Study Sequencing and analysis.

Sequencing

Sequencing.

Sequencing

Sequencing.

  1. How are genomes sequenced, assembled and annotated? provenance
  2. Which references are standard? provenance

Comparison

Comparative genomics.

Comparison

Comparison.

  1. What do genome comparisons reveal about evolution and gene function? provenance
  2. Which entry fits comparative genomics? action
Apply Applications.

Medicine

Medicine.

Medicine

Medicine.

  1. How are genomes used in diagnosis, pharmacogenomics and personalised medicine, in general terms? provenance
  2. Is the user asking about their own genetic results, which need a clinician or genetic counsellor? boundary

Parasites

Parasite genomes.

Parasites

Parasites.

  1. What is known about Leishmania mitochondrial and kinetoplast genomes, and why do they matter? provenance
  2. Which sources are cited? provenance
Context Ethics and history.

Ethics

Privacy and ethics.

Ethics

Ethics.

  1. What privacy and ethical issues surround genomic data, with positions attributed? provenance
  2. Which entry fits genetic privacy? action

History

History.

History

History.

  1. How did genome sequencing develop from the first viral genome to the Human Genome Project and beyond? provenance
  2. Which entry fits the history of genomics? action

Classifiers Filled

Family
Thing Registry
Category
Physical world and living systems
Entry kind
thing
Plane
PHY
Domain
PHY.OBJ
Other names and narrower kinds
viral RNA, kinetoplast, mitochondrial DNA, Leishmania panamensis mitochondrial genome, Leishmania donovani mitochondrial genome, Leishmania tarentolae mitochondrial genome, Leishmania aethiopica mitochondrial genome, Leishmania tropica mitochondrial genome, Leishmania amazonensis mitochondrial genome, Selfish mitochondrial DNA, Leishmania peruviana mitochondrial genome, Leishmania lainsoni mitochondrial genome

What it is Filled

The complete set of genetic material of an organism or virus, comprising all its DNA or, in some viruses, RNA, including chromosomes in the nucleus and separate genomes of organelles such as mitochondrial DNA and the kinetoplast DNA of trypanosomatids like Leishmania, encoding genes and regulatory and non-coding sequences; genomes range from a few thousand bases in small viruses to billions in plants and animals, and are sequenced, annotated and compared in genomics.

Why it exists Filled

Let an agent explain genomes and their organisation, relay sizes, sequencing and organelle genomes from genomics references, describe applications in medicine and evolution, and distinguish genomes from genes, transcriptomes and proteomes.

Distinguishing features Filled

  • Complete genetic content
  • Nuclear and organelle parts
  • Huge size range
  • Sequenced and annotated

What robots and AI may and may not do Filled

Must not

  • Disclose or attempt to reidentify a person's genome without authorization.
  • Treat a genome sequence as a complete prediction of health, behavior or personal worth.
  • Represent a reference genome as the exact genome of every individual in a species.
  • Assist in using genomic information to discriminate against people or harm organisms.

Only with a human decision

  • An authorized human must decide whether identifiable genomic information may be shared or reused.
  • A qualified clinician must decide how genomic findings affect individual care.

May

  • Explain genome organization and distinguish nuclear, organellar and viral genomes.
  • Summarize authorized genome records while preserving uncertainty about sequence completeness and gene function.

Moral aspects Filled

  • Genomic disclosure can expose sensitive information about relatives who did not consent.
  • Genomic research can distribute benefits unfairly when contributing communities lack a meaningful voice.

Who is affected

  • People whose genomes are recorded and their biological relatives.
  • Communities contributing genomic information or biological resources.

Owners Filled

Steward

The authorized custodian of the genomic record, accountable to the people or communities with relevant rights.

Master systems

  • Public nucleotide sequence archives and curated genome assembly repositories.

Links to other meta-models Filled

parent

  • Q193395 - registry parent class

related

  • recording medium - in registry terms, though biologists treat it as genetic material
  • DNA - or RNA in some viruses
  • genomics - through sequencing
  • mitochondrial DNA - as an organelle genome

What else AI and robots need to interact with it Filled

Identity and identifiers required Filled

  • Vercy registry: vr.tr.genome
  • Wikidata: Q7020 (https://www.wikidata.org/wiki/Q7020)
  • MeSH: D016678 genome
  • GO: GO:0000229 and related genome components

Direct properties required Filled

  • human genome: about 3.1 billion base pairs
  • human mitochondrial genome: 16569 base pairs
  • first complete human genome: 2022 year - telomere to telomere

Recognition required Filled

  • Complete genetic material of an organism
  • Nuclear genomes, mitochondrial DNA, kinetoplast DNA, viral RNA genomes
  • A gene is one unit; the transcriptome is expressed RNA; the proteome is the proteins
  • Not a visible object; DNA or RNA sequences.

Capabilities and actions required Filled

  • explain organisation
  • relay sizes and sequencing
  • describe organelle genomes
  • distinguish from related concepts

Hazards and failure modes required Filled

  • Confusing genome with gene or DNA generally
  • Privacy risks of genomic data
  • Registry parent treating the genome as a recording medium

Standards and interfaces required Filled

  • Genome data sharing standards such as INSDC and GA4GH
  • Genetic privacy and data protection laws
  • Biobank and research ethics rules

Context of use required Filled

  • Not applicable; the genetic content of an organism.
  • nuclear genomes of eukaryotes
  • bacterial and archaeal genomes
  • viral DNA and RNA genomes
  • mitochondrial genomes including those of Leishmania species
  • kinetoplast DNA networks of trypanosomatids
  • chloroplast genomes
  • metagenomes of communities

Sources Filled

  1. Wikidata item Q7020: genome - identity and sense of the item
  2. Wikipedia: Genome - general description of the item

Open questions

  • Should mitochondrial DNA and human genome be separate primary entries?
  • How should genomics references be linked?
  • The registry entry has merged aliases naming specific Leishmania genomes; 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-q7020/spec.json