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TSE Ontology (Draft)

Id:TSE-Ontology
Version:1.0
Description:

This is the ontology of Transmissible Spongiform Encephalopathies (TSEs) and the associated risks of transmission. In particular, this ontology focuses on source material, processing, and end-product use. This is a draft ontology and may change at any time.

Contact:Jeff Heflin (heflin@cs.umd.edu)
Revision Date:03 Feb 2000

Organization of this Document

This ontology is declared in this document both in human-readable form (what you see in front of you now) and machine-readable SHOE form (which you can see from viewing the html source of this document). The rest of this document is divided into the following sections:



Source Material


Material

Subcategories:

   Substance
      Liquid
         Body_Fluid (see Body_Fluid heading for details)
      Solid
         Tissue (see Tissue heading for details)
   End_Product

Relations:

   hasForm(Material, .STRING)
   materialWeight(Material, .NUMBER, Weight_Unit)
   volume(Material, .NUMBER, Volume_Unit)
   tissueSource(Tissue, Animal)

Notes:


Animal

Subcategories:

   Mammal
      Primate
         Human
      Ungulate
         Ruminant
            Bovine
            Ovine
            Caprine
         Porcine
         Equine
      Carnivore
      Rodent
         Mouse
-----------------
   Diseased_Animal

Relations:

   age(Animal, .NUMBER)
   weight(Animal, .NUMBER)
   geneticBackground(Animal, .STRING)
   methodOfDeath(Animal, .STRING)
   originatesFrom(Animal, Location)
   hasDisease(Diseased_Animal, Disease_Agent)
   exposureMethod(Diseased_Animal, Exposure_Route)
   composedOf(Animal, Tissue, .NUMBER(Percentage Weight)
   prpHomology(Animal(Source), Animal(Target))
   prpSequence(Animal, .STRING)
   commonName(Animal, .STRING)
   zoologicalName(Animal, .STRING)

Notes:


Body_Fluid

Subcategories:

   Blood
      Serum
   Cerebrospinal_Fluid
   Urine
   Secretion
      Bile
      Colostrum
      Milk
      Nasal_Mucosa
      Saliva
   Feces

Relations:

   to be determined

Notes:


Tissue

Subcategories:

   Circulatory_Tissue
      Heart
   Embryonic_Tissue
      Fetal_Tissue
      Placenta
   Endocrine_Tissue
      Adrenal_Gland
      Pituitary
      Thymus
      Thyroid_Gland
   Exocrine_Gland
      Mammary_Gland
      Salivary_Gland
   GI_Tissue
      Intestine
         Distal_Colon
         Ileum
         Proximal_Colon
      Liver
      Pancreas
   Immune_System_Tissue
      Bone_Marrow
      Lymph_Nodes
      Spleen
      Tonsil
   Musculoskeletal_Tissue
      Connective_Tissue
         Adipose_Tissue
         Cartilage
         Bone
            Skull
            Vertebral_Column
      Skeletal_Muscle
   Neurologic_Tissue
      Brain
         Dura_Mater
      Dorsal_Root_Ganglia
      Peripherhal_Nerve
      Sciatic_Nerve
      Spinal_Cord
      Trigeminal_Ganglia
   Reproductive_Tissue
      Ovary
      Testis
         Seminal_Testis
      Uterus
   Respiratory_Tissue
      Lung
   Sensory_Tissue
      Eyes
   Skin
      Hair
   Urinary_Tissue
      Kidney

Relations:

   none

Notes:


Location

Subcategories:

   BSE_Free_Zone
   BSE_Not_Indigenous_Zone
   BSE_Low_Incidence_Zone
   BSE_High_Incidence_Zone

Relations:

   contains(Location, Location)
   hasClimate(Location, .STRING)
   hasLegalSystem(Location, .STRING)
   hasGNP(Location, .NUMBER)
   hasEconomy(Location, .STRING)
   hasSurveillanceBy(Location, Organization)
   surveillanceLevel(Location, .NUMBER)
   mbmFeedBan(Location, .TRUTH)

Notes:


Disease_Agent

Subcategories:

   TSE
      CJD
         Genetic_CJD
         Spontaneous_CJD
         Iatrogenic_CJD
      GSS
      FFI
      Kuru
      BSE
         FSE
         NV-CJD
      Scrapie
      TME
      CWD

Relations:

   transmissibility(Disease_Agent, Animal)
   lethalDose(Disease_Agent, Animal, Tissue, .NUMBER)
   latency(Disease_Agent, .NUMBER)
   timeToDeath(Disease_Agent, .NUMBER)
   mayOriginateFrom(Disease_Agent, Disease_Agent, .NUMBER(Qualitative Scale))  
   documentedCases(Disease_Agent, Location, .NUMBER)
   transmissionMethod(Disease_Agent, Exposure_Route)
   mouse_LD_Titer(Disease_Agent, Animal, Tissue, .NUMBER)
   discoveryDate(Disease_Agent, .DATE)
   hasSymptom(Disease_Agent, .STRING)
   strain(Disease_Agent, .STRING)
   heritability(Disease_Agent, .TRUTH)
   hasSpeciesBarrier(Disease_Agent, .TRUTH)
   onsetAge(Disease_Agent, .NUMBER)
   incidenceRate(Disease_Agent, .NUMBER)
   qualtitativeInfectivity(Disease_Agent, Tissue, .STRING)
   infectivityDensity(Disease_Agent, Tissue, .NUMBER)

Notes:





Processing


Process

Subcategories:

   Basic_Process
      Separation
         Filtration
         Partitioning
         Absorption
	 Extraction
	 Precipitation
      Dilution
      Concentration
      Chemical_Treatment
      Thermal_Treatment
      Pressure_Treatment
      Storage
   Applied_Process
      Health_Care_Process
         Phlebotomy
         Surgery
	    Autopsy
            Dural_Implantation
            Neurosurgery
      Household_Goods_Manufacture
         Cosmetics_Manufacture
         Soap_Manufacture
      Industrial_Process
         Chemical_Industry_Process
         Drug_Industry_Process
            Capsule_Making
         Food_Industry_Process
            Slaughter
               Stunning
	       Exsanguination
	       Skinning
	       Splitting
            Butchering
            Rendering
	       Grinding
               Cooking
	       Pressing
	       Drying
	       Milling
	       Centrifugation
	       Polishing
	       Rendered_Storage
            Feed_Manufacture

Relations:

   duration(Process, .NUMBER, Time_Unit)
   hydrolysis(Process, .NUMBER)
   denaturation(Process, .NUMBER)
   hasInput(Process, Material)
   hasOutput(Process, Material)
   hasStep(Process, Process)
   precedes(Process, Process)
   follows(Process, Process)  
   inactivatesAgent(Process, Disease_Agent, .TRUTH)
   inactivationDegree(Process, Disease_Agent, .NUMBER)
   concentration(Chemical_Treatment, .NUMBER)
   pH(Chemical_Treatment, .NUMBER)
   temperature(Thermal_Treatment, .NUMBER)
   humidity(Thermal_Treatment, .NUMBER)
   heatCapacity(Thermal_Treatment, .NUMBER)
   lipidFraction(Thermal_Treatment, .NUMBER)
   deltaPascal(Pressure_Treatment, .NUMBER)
   particleSize(Process, .NUMBER, Length_Unit)

Renames:

   name from base.name

Notes:





End-Product Use


End_Product

Subcategories:

   Animal_Feed
   Human Food
      Processed_Meat
      Food_Gelatin
      Dietary_Supplement
   Drug
      Drug_Capsule
   Biologic
      Blood_Product
      Allograft
         Dura_Mater_Allograft
   Medical_Device
   Household_Product
      Cosmetic
         Baby_Product
         Bath_Preparation
         Eye_Makeup_Preparation
         Fragance_Preparation
         Hair_Preparation
         Hair_Coloring_Preparation
         Makeup_Preparation
         Manicuring_Preparation
         Oral_Hygiene_Product
         Personal_Cleanliness_Product
         Shaving_Preparation
         Skin_Care_Preparation
         Suntan_Preparation
      Detergent
      Soap
   Industrial_Product
   Agricultural_Product

Relations:

   hasForm(Material, .STRING)
   materialWeight(Material, .NUMBER, Weight_Unit)
   volume(Material, .NUMBER, Volume_Unit)
   usedVia(End_Product, Exposure_Route)
   madeFrom(Material, Material)
   consumedBy(End_Product, Animal)
   averageConsumption(End_Product, .NUMBER)

Notes:


Exposure_Route

Subcategories:

   Oral_Exposure
   Topical_Exposure
   Occular_Exposure (a.k.a. opthalmic)
   Parenteral_Exposure
      Implant_Exposure
      Injection_Exposure
      Transplant_Exposure
   Inhalation_Exposure
   Genetic_Exposure
   Spontaneous_Exposure

Relations:

   none

Notes:


Risk

Subcategories:

   None

Relations:

   riskDisease(Risk, Disease_Agent)
   riskMethod(Risk, Exposure_Route)
   riskMaterial(Risk, Material)
   riskSubject(Risk, Animal)
   riskReductionStep(Risk, Process, .STRING(Helpful?))
   qualitativeRisk(Risk, .STRING)
   quantitativeRisk(Risk, .NUMBER)
   riskFactors(Risk, .STRING)
   riskFactorExceptions(Risk, .STRING)

Notes:





General


Event

Subcategories:

   Disease_Incident

Relations:

   eventDate(Event, .DATE)
   eventLocation(Event, Location)
   contaminationSource(Disease_Incident, base.SHOEEntity)
   contaminationMode(Disease_Incident, base.SHOEEntity)
   numberContaminated(Disease_Incident, .NUMBER)
   incidenceDisease(Disease_Incident, Disease_Agent)
   contaminatedSpecies(Disease_Incident, Animal)

Notes:


Organization

Subcategories:

   Government
   Commitee

Relations:

   establishes(Organization, Organization)
   hasSurveillanceOf(Organization, Disease_Agent)
   governs(Government, Location)

Person

Subcategories:

   none

Relations:

   memberOf(Person, Organization)

Publication

Subcategories:

   Abstract
   Comment
   Dictionary
   Editorial
   Guideline
   Journal
   Journal_Article
   Lecture
   Regulation
   Review
   Technical_Report
   others to be determined

Relations:

   publicationAuthor(Publication, Person)
   publicationOrg(Publication, Organization)
   publicationDate(Publication, .DATE)
   publicationTitle(Publication, .STRING)
   publishedIn(Publication, Publication)
   publicationVolume(Journal, .NUMBER)
   publisher(Publication, Organization)
   topic(Publication, .SHOEEntity)

Research

Subcategories:

   Diagnosis
   Epidemiology
   Pathogenesis
   Prevention
     Sourcing
     Inactivation
   Risk Assessment
   Transmission
   Treatment

Relations:

   to be determined

Measurement_Unit

Subcategories:

   Length_Unit
   Time_Unit
   Volume_Unit
   Weight_Unit

Constants:

   (Length_Unit)
     MM
     CM
     M
     KM
   (Time_Unit)
     SEC
     MIN
     HOUR
     DAY
     MONTH
     YEAR
   (Volume_Unit)
     MM^3
     CM^3
     M^3
   (Weight_Unit)
     GRAM
     KG

Relations:

   none




Definitions

This section contains an incomplete list of definitions for elements of this ontology

Categories

Allograft
A graft of tissue between allogeneic individuals of the same species.
FFI
Familial Fatal Insomnia.
Genetic_Exposure
A type of exposure in which the disease is contract by genetic predisposition.
Iatrogenic_CJD
A form of CJD caused by human intervention.
Liquid
A substance in the fluid state of matter having no fixed shape but a fixed volume.
Material
A physical object.
Pathogenesis
The study of the orgin and development of a disease.
Process
A particular course of action intended to achieve a result.
Spontaneous_Exposure
A type of exposure in which the disease is contracted by spontaneous mutation (pathogenesis).
Substance
A physical object that cannnot be referred to as an individual. In other words, a mass noun such as butter, water, hydrogen and dirt.

Relations

composedof
The weight of a tissue as a percentage of the total animal.
denaturation
The change of a protein structure to an unnatural state.
documentedCases
The number of case of a particular disease reported in a given location.
duration
The duration of a process in the units identified by the third argument.
hasForm
The physical form of the substance, such as liquid, solid, or gas.
inactivationDegree
The degree to which a process inactivates a disease agent.
incidenceRate
The number of persons per million that are contaminated by the disease.
infectivityDensity
The animal oral infectious dose 50% per gram of the specified tissue.
materialWeight
The weight of the material in the units identified by the third argument.
mouse_LD_Titer
The does at which 50% of mice die after having material from the given tissue contaminated with a given disease implanted.
particleSize
The diameter of the input particle in the units identified by the third argument.
temperature
The final temperature of a process in degrees celsius.
transmissibility
The animals that can contract a given disease.
volume
The volume of the material in the units identified by the third argument.
weight
The weight of an animal in kilograms.

Change History: