Download Organism Remodel Figures 20140619

Assumptions
• There is value in alignment with OBO/BIOTOP
• OBO - http://www.obofoundry.org/
• BIOTOP - http://www.obofoundry.org/
• The organism concepts describe organism populations not
biological taxa.
• The model will depend on class definitions that are intrinsic
to bacteria
• Shapes, staining characteristics, growth requirements
• Biologic functions (e.g. sugar fermentation)
• Living organisms participate in processes
• Proper physical parts (material entities) related however distantly
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to (human) anatomy.
Access this TOC in “slide show” mode:
• Model diagrams (12 slides)
• Quality Values (8 slides)
• Authorities (4 slides)
• Naming convention (1 slide)
• Concerns and limitations (4 slides)
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Bacteria quality model
Bacteria quality subtype
≡
Bacteria (organism)
bearer of
Some bacteria quality (e.g. shape)
Rod-shaped bacteria
≡
Bacteria (organism)
bearer of
rod shape
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Absolute nutritional requirement
Cysteine-requiring bacteria
≡
Bacteria (organism)
1
bearer of
Absolute nutritional requirement
towards
cysteine
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Bacteria function model
Bacteria functional subtype
≡
Bacteria (organism)
bearer of
Some biological function
Alternative that refers to process rather than function.
Bacteria functional subtype
≡
Bacteria (organism)
Participates in
Some biological process
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Aerobic bacteria
Aerobic bacteria
≡
Bacteria (organism)
bearer of
(bacterial?) aerobic respiration
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Resistant bacteria
Methicillin resistant S. aureus
≡
S. aureus (organism)
1
bearer of
Antimicrobial resistance
towards
Methicillin
Multi-drug resistant E. coli
≡
?
Can add a data property to assert “more than one,”
with value of “antimicrobial agent” in place of
Methicillin. Is this concept useful???
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Bacteria structure model
Bacteria structure subtype
≡
Bacteria (organism)
proper physical part
Some organism structure
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Gram negative bacteria
Gram negative bacteria
≡
Bacteria (organism)
proper physical part
Gram negative cell wall
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Organism serotype pattern
Organism serotype
≡
Organism (organism)
1
Proper physical Part
Antigen bearing structure (organism structure)
Component part
bacterial antigen (substance)
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Gram negative organism serotype pattern
Gram negative organism serotype
≡
Gram negative organism
1
2
Proper physical Part
Gram negative outer membrane (organism structure)
Component part
somatic antigen (substance)
Proper physical Part
Flagellum (organism structure)
Component part
Flagellar antigen (substance)
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Salmonella Serotype pattern
Salmonella serotype
≡
Salmonella subspecies
1
2
3
4
Proper physical Part
Gram negative outer membrane (organism structure)
Component part
Salmonella somatic antigen (substance)
Proper physical Part
H1 Flagellum (organism structure)
Component part
Salmonella flagellar antigen (substance)
Proper physical Part
H2 Flagellum (organism structure)
Component part
Salmonella flagellar antigen (substance)
Proper physical Part
H3 Flagellum (organism structure)
Component part
Salmonella flagellar antigen (substance)
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Salmonella I 2,12:g,m (Salmonella Nitra)
Salmonella I 2,12:g,m (Salmonella Nitra)
≡
Salmonella I
1
2
Proper physical Part
Gram negative outer membrane (organism structure)
Component part
Salmonella somatic antigen 2 (substance)
Component part
Salmonella somatic antigen 12 (substance)
Proper physical Part
H1 flagellum (organism structure)
Component part
Salmonella flagellar antigen g (substance)
Component part
Salmonella flagellar antigen m (substance)
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Salmonella I 1,4,[5],12:i:1,2 (Salmonella Typhimurium)
Salmonella I 1,4,[5],12:i:1,2 (Salmonella Typhimurium)
≡
Salmonella I
1
2
3
Proper physical Part
Gram negative outer membrane (organism structure)
Component part
Salmonella somatic antigen 1 (substance)
Component part
Salmonella somatic antigen 4 (substance)
Component part
Salmonella somatic antigen [5] (substance)
Component part
Salmonella somatic antigen 12 antigen (substance)
Proper physical Part
H1 Flagellum (organism structure)
Component part
Salmonella flagellar antigen i (substance)
Proper physical Part
H2 Flagellum (organism structure)
Component part
Salmonella flagellar antigen 1 (substance)
Component part
Salmonella flagellar
antigen
(substance)
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Values – Shapes
 Coccus
 Small coccus
 Large coccus
 Chaining coccus
 Diplococcus
 Bacillus
 Coccobacillus
 Sporing
 Various / irregular
 Spiral
 L-form?
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Values – growth requirements, preferences,
tolerances
• Growth requirements
• X&V
• Cysteine
• Charcoal yeast agar with iron AND
cysteine
• Temperature
• Thermophilic
• Mesophilic
• Psychrotrophic
• Aerophilicity
• Aerobic
• Anaerobic
• Microaerophilic
• Aerotolerant
• Facultative anaerobic
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Values – Flagella and Capsules
• Flagellar distribution
• Monotrichous
• Polar
• Lophotrichous
• Amphitrichous
• Peritrichous
• Capsules
• Encapsulated (smooth)
• Non-encapsulated (rough)
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Values – Gram stain
•
Gram stain retention
• Gram negative
• Gram positive
• Gram variable
•
Cell wall type
• Gram negative
• Gram positive
• Gram variable
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Values
• Biochemistry
• Catalase (+/-)
• Coagulase (+/-)
• Oxidase (+/-)
• Urease (+/-)
• Sugar fermentation
• Lactose (+/-)
• Glucose (+/-)
• Maltose (+/-)
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Values – activities demonstrated by colonies
• “Activity”
• Hemolysis
• β - hemolysis
• α - hemolysis
• γ - hemolysis
• Motility
• Motile
• Non motile
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Values – Serotypes & Susceptibility
 Surface structures
 Antigens
 Antimicrobial resistance
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Values – “Biotype”
• Yersinia (example)
• Pathogenic
• Non-pathogenic
• Pathogenic activity (?)
• Enterotoxin production
• Exotoxin production
• Diarrheagenic
• Caseating
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Locations for values
• Values for “bearer of” role
• Shapes (e.g. round) are qualifier values, is coccus-shaped just a specialization of
round?
• Nutritional requirements?
• Functions and processes?
• Values for “proper physical part” role
• Currently cell structures in “Anatomical structure” hierarchy
• Suggest a “prokaryotic cell structure” grouping
• Values for “component part” role
• Current proposal is substances
• Current “bacterial antigen” placement is questionable
• Bacterial antigens are not thought of (first) as allergens.
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Authorities
• Bacterial nomenclature:
• Very mature systems for identifying and maintaining
• Probably why Bacteria hierarchy in SNOMED is as up-to-date as it is
• LPSN (http://www.bacterio.net/) - aligned with IJSEM.
• DSMZ-Prokaryotic Nomenclature Up-to-date (https://www.dsmz.de/bacterialdiversity/prokaryotic-nomenclature-up-to-date.html) -- used by the WHO for WHONET
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Authorities
• Viruses
• CONSIDERABLE IMPROVEMENT in taxonomic alignment (with other
organisms) and published maintenance principles
• Would rate this as reliable.
• available Virus taxonomy resource is greatly improved
• http://www.ictvonline.org/virusTaxonomy.asp
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Authorities
• Fungus
• Detailed analysis has not been done at this time.
• http://www.mycobank.org/
• www.doctorfungus.org (used for WHONET)
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Authorities
• Parasites
•
•
•
•
An orthogonal way to classify organisms (sibling of ‘infectious agent’)
Parasites in what biological system? Represent aberrant parasitism?
A list of Linnaean classes that can be represented.
Modeling and editing tasks would be MASSIVE
• All classes that might logically be grouped here are large
• Near term activity – correct an all primitive subtype hierarchy
• http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/
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Naming convention
• Strictly follow LPSN?
• Custom naming for SNOMED and users?
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Concerns – Complexity and Uncertainty
• To some extent (especially among enterobacteriaceae), bacterial
identification is probability based. (e.g., 50% of E. coli are sucrose
fermenters). See:
• J J Farmer 3rd, B R Davis, F W Hickman-Brenner, A McWhorter, G P HuntleyCarter, M A Asbury, C Riddle, H G Wathen-Grady, C Elias and G R Fanning. J.
Clin. Microbiol. 1985, 21(1):46.
• Need copy of Bergey’s to evaluate ability to produce solid “always true”
differentia for bacteria classes
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Concerns – genetic identification
• There is fairly clearly a shift going on towards genetic identification
(e.g., PCR) and away identification by classic .
• Does this mean genetic CLASSIFICATION or does it just mean “shortcut” to the
existing phenotypic classification ?
• Facilitate automation and speeds detection/screening methodologies.
• Impact on phenotypic hierarchy is unclear at this time.
• Have seen nothing to suggest that the bacteria hierarchy will undergo
wholesale change
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Concerns – Groups and complexes
• Unable to identify a reliable reference concerning CDC “biogroups.”
SNOMED has 30+ of these already. There seem to be more (SNOMED
has 1 under proteobacteria, as many as 11 exist) I believe these to be
of two types.
• For newly discovered / unclassified organisms
• Many now have names (not clear if CDC still uses or expects use)
• See Bruckner and Colona
• CDC Enteric Group 59 = Buttiauxella noackiae ?
• Importance of cross-reference unclear
• CDC policies on use of these names vs. “official” names are unknown. (requirements to
submit?)
• For organisms that CDC wants submitted before classification is complete.
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Concerns - miscellaneous
• Interest has been expressed in an ability to track “previous names /
historical names”
• Unordered synonyms?
• Concept retirements and referrals
• Concepts with non-specific references to attributes (e.g., Mutiple
antimicrobial resistant X)
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