TODO
Microorganism / Pathogen
vr.wm-liv-007 · wm-liv-007-microorganism-pathogen
Characterised microbial strains and isolates with identity, provenance, risk group and holding collection.
World Models Physical world and living systems PHY.LIV.MIC
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
3 bundles · 4 layers · 5 findings · 11 questions
Identity Which organism the record is about.
Taxonomy and strain
Taxonomic placement and strain or isolate designation.
Taxonomic placement
The accepted name and the authority that recognises it.
- Which accepted taxon name applies, and according to which taxonomic authority?
- Is the identification confirmed by sequencing, or only presumptive?
Strain designation
The strain or isolate name and where it is deposited.
- Which strain or isolate designation does this record refer to?
- Which culture collection or biobank holds it, under which accession number?
Significance and classification Why the organism matters and how it is classified.
Host and disease relation
Hosts affected and the conditions referenced.
Host association
Hosts in which the organism is known to occur or cause disease.
- Which hosts, human, animal or plant, is the organism associated with?
- Which diseases does the record reference, by link to the disease record?
Risk and regulatory status
Risk group and legal listings that govern the record.
Risk classification
The risk group assigned and the listings that apply.
- Which risk group does the applicable national classification assign to this organism?
- Is the organism notifiable, regulated or subject to export control in the relevant jurisdiction?
- Which authority maintains that classification, and when was it last reviewed?
Provenance and custody Where the material came from and who holds it.
Origin and legal terms
Isolation origin and access and benefit-sharing status.
Origin record
Source, place and time of isolation and the terms the material came under.
- From which source, place and time was the isolate obtained?
- Under which access and benefit-sharing terms was the material obtained and transferred?
Classifiers Filled
- Family
- World Models
- Category
- Physical world and living systems
- Entry kind
- standalone-mm
- Navigation path
- NAV.PHY.LIV.MIC
- Domain
- PHY.LIV.MIC
- Industry
- Cross-industry
- Tags
- microorganismpathogenphy.liv.mic
What it is Filled
A microorganism record describes a characterised strain or isolate of a microscopic organism, such as a bacterium, archaeon, microscopic fungus, protist or virus, with its taxonomy, where it is held and which risk classification applies to it. Where the organism can cause disease in a host it is also a pathogen; the disease itself, outbreaks and physical specimens are separate records.
Why it exists Filled
Characterised microbial strains and isolates with identity, provenance, risk group and holding collection.
Distinguishing features Filled
- The record describes the organism; the disease it can cause and any outbreak are separate records it links to.
- Identity is strain-level, because members of one species can differ greatly in behaviour and significance.
- Risk group and regulatory listing are part of the record and constrain who may hold or receive the material.
- Distinct from a microbiome, which describes a community, and from a clinical specimen, which is physical material.
What robots and AI may and may not do Filled
Must not
- Give procedures, conditions or quantities for culturing, propagating or modifying an organism.
- Provide any information that would help increase an organism's harmfulness or evade detection.
- Assert a risk group or regulatory status without an authoritative source for it.
- Arrange or facilitate transfer of material without the required permits and transfer agreement.
- Drop the origin and benefit-sharing terms recorded with the material.
Only with a human decision
- Assigning or changing a risk classification for a record.
- Approving any transfer, import or export of biological material.
- Deciding what may be published about a regulated or notifiable organism.
May
- Record taxonomy, strain designation, collection accession and risk classification from authoritative sources.
- Report the risk group and regulatory listings that apply in a stated jurisdiction.
- Link the record to disease, specimen and sequence records held elsewhere.
- Flag records whose identification or classification is unconfirmed or out of date.
Moral aspects Filled
- Information about pathogens can be misused, so records stay at identification and governance level.
- Material often originates in communities and countries whose contribution and rights must be respected.
- Public health depends on timely, accurate sharing of identification data between laboratories.
- Laboratory staff bear the risk when a record understates what an organism is.
Who is affected
- Laboratory and healthcare staff
- Patients and communities where the organism occurs
- Providers of the source material and their countries
- Public health and veterinary authorities
Owners Filled
Steward
The biosafety officer or collection curator who answers for the record and the material held.
Master systems
- Culture collection and biobank catalogues
- Taxonomic reference databases
- National notifiable disease and biosafety registers
Links to other meta-models Filled
references
- wm-liv-001-taxon - Taxonomic placement resolves to the taxon record.
- wm-liv-021-disease-biological-condition - Diseases the organism is associated with are described there.
related
- wm-liv-024-biobank-sample-repository - Repositories hold the deposited material the record refers to.
What else AI and robots need to interact with it Filled
Identity and identifiers required Filled
- A strain is identified by its culture collection accession number together with the collection's code.
- The taxon is identified by the accepted name and a taxonomic database identifier.
- Sequenced isolates are also identified by their sequence database accessions.
Direct properties required Filled
- The record states which property kinds identify the organism, each with its unit and method, rather than any values.
- Cell or particle size in micrometres or nanometres, from microscopy or sizing methods.
- Genome size in base pairs, from an assembled sequence.
- Growth requirements are recorded as categories, such as aerobic or anaerobic, without culturing conditions.
- All values must be read from the holding collection's catalogue entry rather than asserted here.
Recognition required Filled
- Identification is made in a laboratory by sequencing or validated identification systems, not by direct observation.
- A deposited strain is recognised in practice by its accession number on the vial and in the catalogue.
- Easily confused with closely related strains of the same species, which can differ in significance.
Capabilities and actions required Filled
- Records can be linked to sequences, specimens and disease records across databases.
- Classifications can be compared across jurisdictions for the same organism.
- Identification can be revised as taxonomy and sequence evidence change.
Hazards and failure modes required Filled
- An understated risk classification exposes laboratory staff to unexpected risk.
- Misidentification leads to wrong public health or veterinary decisions.
- Transfers without permits breach biosafety and benefit-sharing law.
- Detailed information about dangerous organisms can be misused, so records stay at governance level.
Standards and interfaces required Filled
- WHO Laboratory Biosafety Manual for risk group and containment concepts.
- Nagoya Protocol and the standard material transfer practice of culture collections.
- WFCC guidelines for culture collections and INSDC accessions for sequence references.
Context of use required Filled
- Used in clinical and veterinary diagnostics, public health surveillance, food safety and research collections.
- National biosafety, notifiable disease and export control law governs what may be held and shared.
Sources Filled
- Laboratory Biosafety Manual, World Health Organization
- Nagoya Protocol on Access to Genetic Resources and the Fair and Equitable Sharing of Benefits, Convention on Biological Diversity
- International Code of Nomenclature of Prokaryotes, International Committee on Systematics of Prokaryotes
Open questions
- Planned model: boundary questions, research and every section remain to be written.
Machine files
Provenance
planned (registry candidate) · todo
Built from: models/runtime-index.json, ver-cy/world-models/card-supplements/wm-liv-007-microorganism-pathogen.json
Planned entry, hidden from the catalogue until researched.