LHO
LHO, guided by OBO Foundry principles, integrates domain knowledge and data for livestock health. The ontology covers farms, samples, geolocation, breed, diagnostic tests, and pathogen identification, including bacteria like Histophilus somni, Mannheimia haemolytica, Pasteurella multocida, Bovine coronavirus, bacterial mycoplasma, and aerobic culture results in cattle. For pigs, it includes FarmType, age, weight, and pathogens like PRRS, SI and M_Hyponemoniea. In poultry, LHO incorporates FarmType, with specific pathogen names such as Infectious Bronchitis (IB), providing a concise overview of health aspects across livestock species.
An extension of DECIDE ontology https://bioportal.bioontology.org/ontologies/DECIDE?p=summary
LiveStock HealthOntology
A string that provides a usage example of a class, property, or other ontology element to help users understand how it is applied.
For example, in the context of cattle, breeds can be categorized as meat, dairy, or mixed breeds, each breed for specific agricultural or culinary purposes. Similarly, in the context of poultry, breeds can be categorized as meat breeds or egg-laying breeds. Pigs are also breed for meat production. The 'Breed' class serves as a foundational concept for classifying and organizing various animal breeds within the ontology.
The person primarily responsible for the creation or curation of a given ontology term.
A term or phrase that may be used as a synonym or alternate label for a given ontology entity, especially useful for searching and term matching.
A reference (such as a publication, URL, or ontology) that identifies where the definition of a term originated from.
An annotation indicating the source ontology or resource from which a given term was imported.
Exact synonyms are words that have completely identical or nearly identical meanings in given contexts
resource from where ontology is imported
hasPrevalence
Links a region to BRD case records.
hasBRDCase
Links a region to a specific time period.
hasTimePeriod
Links a farm to one or more houses within it.
hasHouse
Links a house to one or more flocks within it.
hasFlock
Links a flock to its associated poultry sample.
hasSample
infer farm identification for particular poultry house
hasAssociatedFlock
Links a production stage to a concept representing the time duration of that stage.
hasCycleTime
causedBy
Object property linked Salmon sample with Actual Biomass property
hasActualBiomass
object property that link Salmon sample with water type for eaxmple Freshwater, Seawater, BrackishWater
hasWaterType
Object property that link Salmon sample with Salmon mortality per sample?
hasMortality
Object property that link physical region or location
hasLocalAuthority
Object property that links a unique identifier specific to poultry farms, used for traceability and health monitoring purposes.
hasPoultryFarmIdentification
Links a pathogen, breed, sample type, or country to the species it applies to. Used to filter species-specific categories in a multi-species ontology.
affectsSpecies
Links a pathogen to the type of disease it causes. Used to classify pathogens into Viral or Bacterial groups for graph construction.
causesDisease
Link a sample to specific animal breed.
link sample to event at which it perform
Links a sample or a farm to unique farm ID
Symmetric property indicating two countries share a geographic land border. Used to create geographic adjacency edges in the knowledge graph.
hasGeographicNeighbor
Link Lab reference,for identification and tracking within a laboratory or data system if Farm Identification is not available
link sample to its unique sample Number if available
Link Sample to result postive 1 or negative 0
Associates a Sample with a SampleType indicating the kind of material collected, such as blood, tissue, feces, or water.
Time unit like Months, days, minutes etc...
A unit of measurement used to express the weight or mass of an animal, feed, or product. Common examples include kilogram (kg), gram (g), and tonne (t).
data type vlaue Represents the prevalence rate of a pathogen in a province.
hasProvincePathogenPrevalence
hasProvinceNoOfBRD
percentage % of cases in a country.
hasCountryPathogenPrevalence
Count of positive BRD cases in a country.
hasCountryNoOfBRD
hasQuarterPathogenPrevalence
hasQuarterNoOfBRD
A data property that tells whether a sample tested positive (1) or negative (0).
result
date
hasSampleNumber
Unique identifier for a flock.
hasFlockID
Identifier for the veterinarian responsible for the flock.
hasVetID
hasHatchDate
Date when the flock was removed from the house or farm.
hasRemovalDate
Records the growth pattern of the flock over time.
hasGrowthCurve
A data property that indicates whether the flock has undergone thinning (removal of some birds before full harvest).
hasThinned
houseNumber
data type property that represent mortality in KG
mortality
data type that Represents breed like beef, mixed, Veal, suckler
A data property that discribes a name of the pathogen in animal sample
BRSV
Bovine Respiratory Syncytial Virus (BRSV) is a major cause of respiratory disease in cattle, characterized by coughing, nasal discharge, and increased respiratory rate.
BovineRespiratorySyncytialVirus
Lepeophtheirus salmonis (Sea Lice): A parasitic copepod that infests salmon, causing significant issues in aquaculture
Mycoplasma bovis is a bacterial pathogen that primarily affects cattle, causing respiratory disease, arthritis, mastitis, and other systemic infections.
MycoplasmaBovis
M_Hyopneumoniae
Mycoplasma hyopneumoniae is a bacterium causing swine enzootic pneumonia, a respiratory disease in pigs, characterized by coughing and impaired respiratory function.
MycoplasmaHyopneumoniae
Causes Infectious Salmon Anemia (ISA), a serious viral disease in Atlantic salmon
Haemophilus somnus classified as Histophilus somni, is a Gram-negative bacterium that can cause respiratory and systemic infections in cattle and other domestic and farm animals
HistophilusSomnus
Pasteurella haemolytica is a Gram-negative bacterium associated with respiratory infections, particularly in cattle, causing bovine respiratory disease complex (BRDC) or shipping fever.
PasteurellaHaemolytica
PRRS
Porcine Reproductive and Respiratory Syndrome (PRRS) is a viral disease in pigs, causing reproductive failure in sows and respiratory symptoms in pigs of all ages.
PorcineReproductiveAndRespiratorySyndromeVirus
All domesticated birds used for the production of meat or eggs for consumption, for the production of other commercial products, for restocking, supplies of game, or for breeding these categories of birds.
Poultry
Swine Influenza is a respiratory viral infection in pigs, characterized by coughing, sneezing, and fever, with potential transmission to humans.
SwineInfluenzaVirus
The pig (Sus domesticus), often called swine, hog, or domestic pig
Pig
pig
Damage on the health. The modifications of an organism defending itself against an infection or another damager factor. Perturbation of the animal's normal functions.
Disease
Infectious disease class includes diseases caused by pathogens such as viruses, bacteria, fungi, or parasites that can spread between animals, humans, or both
BCV
Bovine coronavirus primarily causes enteric (intestinal) infections in calves, leading to diarrhea.
BovineCoronaVirus
Infectious bronchitis is a highly contagious viral respiratory disease in chickens, characterized by respiratory distress and egg production drops.
InfectiousBrochistVirus
Mannheimia haemolytica is a bacterium associated with bovine respiratory disease in cattle, causing pneumonia and respiratory distress.
MannheimiaHaemolytica
Pasteurella multocida is a bacterial pathogen in cattle associated with respiratory infections, causing pneumonia and other respiratory symptoms.
PasteurellaMultocida
obo:IAO_0000119 "http://purl.obolibrary.org/obo/iao.owl" .
An information content entity that specifies how a realizable entity is concretized, and that is not concretized in the specification itself."
Location refers to a specific place or area where an event, object, or entity exists or occurs.
Location
COUNTRY; Country
Country
Cattle
A class representing any occurrence or activity related to aquaculture or livestock management, such as disease outbreaks, treatments, movements, or inspections.
It refer to different types of events related to livestock or farming. For example, "slaughter" could be one event type, and "birth," "vaccination," or "disease outbreak" could be other event types.
A farm is an agricultural or aquacultural establishment where crops are cultivated, terrestrial livestock and/or aquatic species (such as fish or shellfish) are raised for food production or other commercial, research, or conservation purposes.
A record of an observed or measured value related to a specific characteristic (such as weight, age, or temperature) of an animal, population, environment, or system, applicable to both terrestrial livestock and aquaculture species
A classification of measurement, such as weight or age
A pathogen is a microorganism, such as a bacterium or virus, that causes disease in its host, be it plants, animals, or humans.
Pathogen
ProductionCycleTime refers to the duration of a specific production stage or the entire production process in aquaculture or livestock farming. It is used to describe the time span from the beginning to the end of a defined stage (e.g., nursery, finishing) or the complete cycle.
A sample, such as a CattleSample, PigSample, or PoultrySample, refers to a specimen collected from respective animals for diagnostic or research purposes, often involving testing for diseases or analyzing biological parameters.
Sample
SampleResult represents the outcome or findings derived from analyzing a specimen, providing valuable information about the health or characteristics of the sampled subject, whether it be cattle, pig, poultry, or another source.
SampleType
SampleType describes the kind of material or source from which a sample is collected for analysis. Examples include blood, tissue, feces, milk, water, feed, or environmental swabs. It is used to classify samples according to their origin and is essential for interpreting diagnostic and surveillance data.
SpeciesGroup represents a group of animals belonging to the same species or production category (e.g., Atlantic salmon, broiler chickens, weaned piglets, dairy cattle). It is used to describe the target population involved in events such as sampling, treatment, or observation.
The class representing a unit of measurement or denomination. Instances of this class may include various units such as length units, weight units, time units, etc. It serves as a general category for expressing quantitative values in a standardized manner across different domains.
A Veterinarian is a qualified and licensed professional responsible for the health and welfare of animals. Veterinarians perform clinical examinations, diagnose diseases, prescribe treatments, and provide guidance on prevention, vaccination, and biosecurity in livestock and aquaculture settings.
Represents the total measured live body weight of the sampled population in kilograms at a specific timepoint.
Beef
Birth event refers to the occurrence of a living being coming into the world.
Blood is a SampleType. A blood sample is a specimen collected from an organism, typically through venipuncture, and is used for diagnostic or research purposes, providing insights into the health and physiological parameters of the individual.
Breeds are used to categorize and classify animals based on specific characteristics, traits, and purposes.
Breed
Birds (hens and roosters) are raised for reproduction to produce fertilized eggs for hatching.
Pid production Breeding stage in pigs involves reproductive activities where a sow (mature female), boar (male pig), and gilt (young female yet to farrow but ready to breed) participate in the mating process.
A Breedingfarm" may focus on breeding and raising animals for specific traits.
Represents a housing unit within a farm where a poultry flock is kept.
House
A time-based unit representing one-fourth of a year, typically spanning three months.
Quarter
Represents the number of BRD cases in a region/time.
BRDCasesObservation
Represents disease outbreaks linked to regions, time, and pathogens.
DiseaseOutBreak
Bovine respiratory disease +ev cases in animal sample at particualr time and region
BRDCaseOutbreak
Represents a group of poultry birds in a specific house at a farm, forming a distinct management unit.
Flock
A unique identifier specific to poultry farms, used for traceability and health monitoring purposes.
PoultryFarmIdentification
Prevalence refers to the proportion of a population that has a specific characteristic or condition at a given time. It is often used in public health to indicate how widespread a disease is within a population.
Prevelance
Livestock production stages are the sequential phases in the life and management of farm cattles
CattleSamples are the "n" number of observations for Cattle
A unit of time equal to 24 hours, used for short-term measurements or daily records
Diagnostic tests, such as PCR and culture, are utilized in pigs, poultry, and cattle to identify and analyze pathogens, aiding in disease detection and management.
DiagnosticTest
Egg-laying breed refers to a type of poultry, for example chickens, that is specifically raised for producing a high number of eggs.
Farm identification involves assigning a unique code or name to a specific agricultural property, facilitating tracking and management for regulatory, organizational, or administrative purposes.
FarmIdentification
FarmType categorizes the nature or focus of a farm, specifying whether it is oriented towards crop cultivation, livestock raising, or a combination of both, providing a classification for agricultural purposes.
FarmType
A sample of solid waste (stool) used to detect gastrointestinal pathogens, parasites, or digestive disorders.
A Feedlot typically emphasizes the finishing stage of livestock for meat production,
A general term for bodily fluids (e.g., urine, pleural fluid, synovial fluid) used to test for infections or other abnormalities.
H1N1 is a subtype of the influenza a virus, and it has been responsible for influenza outbreaks in both humans and pigs. In the context of livestock health ontology or any ontology dealing with diseases, H1N1 would be classified as a pathogen.
H1N2 is a swine influenza subtype, resulting from the reassortment of genetic material from human, swine, and avian influenza viruses.
H3N2 is a subtype of the influenza a virus
Fertilized eggs are incubated under controlled conditions until chicks hatch, usually in 21 days.
Lab reference, often a unique number, is assigned to data related to farm animals for identification and tracking within a laboratory or data system.
LabReference
Pullets (young hens) are raised to become layers, producing eggs regularly starting around 18–20 weeks.
The Live Stock Health Ontology (LHO), an extension of the DECIDE ontology, serves as a structured framework for organizing information related to the health and well-being of livestock species, encompassing cattle, poultry, pig, and salmon. LHO facilitates the integration of domain knowledge and data, offering explicit representations of various aspects. In the development process, insights from domain experts contribute to the creation of a prototype designed for reasoning and planning of data, particularly concerning cattle. Within LHO, concepts include farms with identifications, samples, geolocation, breed, diagnostic tests, and pathogen identifications. Notably, specific bacteria like Histophilus somni (HS), Mannheimia haemolytica (MH), Pasteurella multocida (PM), Bovine coronavirus (BCV), bacterial mycoplasma, and aerobic culture results for the respiratory tract in cattle are covered. For pigs, additional details encompass FarmType, age, weight-related information, and pathogen names such as Porcine Reproductive and Respiratory Syndrome (PRRS), Swine Infuenza(SI), and Mycoplasma hyopneumoniae are included. This enhanced representation facilitates a comprehensive understanding of pig health, covering aspects of farm classification, age or weight specifics, and the presence of specific pathogens. Similarly, for poultry, LHO incorporates FarmType along with specific pathogen names like Infectious Bronchitis (IB), offering a detailed perspective on poultry health, including farm categorization and information on prevalent diseases.
LivestockHealthOntology
Livestock production stages are the sequential phases in the life and management of farm animals, includingbreeding, birth, suckling, weaning, growing, finishing, and reproduction.
For example for Scotland local authority council example areas are Highland, Argyll and Bute, or Glasgow City etc...
An administrative council area that governs and delivers public services for a defined local community region.
A time unit based on calendar months, typically used for monthly reporting or trends.
Mortality represents the death of one or more individuals in a given animal population, often measured over a specified time frame, due to natural causes, disease, management practices, or environmental factors.
Nursery stage is the post-weaning phase (4–10 weeks) where piglets are housed separately, given special feed, and undergo rapid growth, socialization, and health care.
Pig production stages focused on growth and productivity
PigSample is n number of observations for Pig and piglets
Poultry production stages are the key phases in the lifecycle and management of birds raised for eggs or meat, including breeding, hatching, growing, laying, and processing.
PoultrySample is "n" number of observation for Poultry data.
PoultrySample is associated with a specific flock, linking pathogen data, diagnostic tests, and geolocation.
Mature birds are slaughtered, cleaned, and prepared for meat production or market.
A province is an administrative region or territorial division within a country, typically with its own government and administrative structure.
Atlantic salmon (Salmo salar) are frequently farmed in marine cages and monitored for growth, health, and disease events such as sea lice infestation or viral infections.
A common name for several species of ray-finned fish in the family Salmonidae, widely farmed in aquaculture systems for food production. Salmon are anadromous, meaning they hatch in freshwater, migrate to the ocean, and return to freshwater to spawn.
SalmonSample is "n" number of observation for Salmon data.
A SalmonSample represents a biological sample collected from a salmon individual, associated with pathogen detection, diagnostic tests, and location data, Mortality rate, actual biomass and water type.
SampleNumber is a unique identifier assigned to a specimen collected from livestock or other sources for purposes such as diagnostics or research, facilitating individual sample tracking and data organization.
SampleNumber
Slaughter event refers to the process of killing animals, usually for meat production or other purposes.
Cattle, pig, and poultry represent distinct species within the animal kingdom commonly raised for agricultural purposes, including meat production.
Livestock species classification
Species
Suckling stage begins at birth and lasts for about 21–28 days (3–4 weeks), during which piglets nurse from the sow. They are born small (2–3 pounds), blind, and hairless but quickly develop eyesight, teeth, and mobility. By around 3 weeks, they begin nibbling on solid feed alongside milk as they prepare for weaning.
A swab is a sample collection method involving a small absorbent tool, often a cotton-tipped applicator, used to collect specimens from surfaces or body areas, such as the throat or nasal cavity, for diagnostic or research purposes.
Vaccination event refers to the process of giving vaccines to individuals or animals to protect them from specific diseases.
In aquaculture (fish farming, like salmon farming), WaterType refers to the kind of water environment (freshwater, seawater, or brackish) the animals are raised in.
A measurement unit used to quantify mass or weight, such as grams, kilograms, or pounds.
A unit of time representing 12 months, often used for annual summaries or long-term analysis.
An individual representing different Local Authorities in UK.
Bovine Coronavirus (BCV) is a viral pathogen causing respiratory and enteric diseases in cattle.
Belgium - European country with land borders to France and The Netherlands.
Belgium
CattleSample01
Suckler cattle are breeds raised primarily for meat production, where calves are nursed by their mothers until weaning.
Suckler
an individual (entity) that represent PCR
PCR
Veal cattle are young calves (typically under 8 months) raised for veal meat production. Often includes male dairy calves or crossbred calves from dairy herds
Veal
Unknown breed category used when the specific breed information is not available or not recorded in the sample data
Unknown
Nasopharyngeal Swab
Nasopharyngeal Swab (NPS) is a sample collection method where a swab is inserted through the nostril to collect secretions from the nasopharynx. Commonly used for detecting respiratory pathogens
Nps
Trans-tracheal Aspirate (TTA) is a diagnostic sample collected by inserting a catheter through the trachea to obtain lower respiratory tract secretions. Used for accurate identification of bacterial pathogens
Tta
is an individual instance representing a specific, uniquely identified flock entity used to associate birds with a defined production or health unit or samples
PoultrySample101
an individual (entity) that represent Infectious Bronchis pathogen
Missing
an individual or instance type of Disease
BRSVDisease
SwineInfluenzaDisease
Lawsonia intracellularis
Freshwater
ISAV
An individual that represent an infectious disease in salmon caused by parasitic copepods Lepeophtheirus salmonis
SeaLiceInfestation
The prevalence of Bovine Respiratory Disease (BRD) in cattle varies significantly across different regions, age groups, and diagnostic methods. BRD is estimated to affect 2.1% to 20.2% of cattle, with higher rates observed in winter months. The disease is a leading cause of morbidity and mortality in pre-weaned dairy calves, and its economic impact is substantial, leading to mortality, reduced growth, and lower carcass value.
BRD_Prevalence
The prevalence of Porcine Respiratory Disease Complex (PRDC)
PRDC_Prevalence
Bovine species - cattle, cows, calves
This is a general Farm ID
This is a Poultry Farm ID
PF_ID_38236
PF_ID_38423
PF_ID_38543
PF_ID_38615
PF_ID_39044
PF_ID_39105
PF_ID_39488
PF_ID_40458
PF_ID_40981
An individual instance representing a specific, uniquely identified flock entity used to associate birds with a defined production or health unit or samples
France - European country with land border to Belgium.
France
An individual representing different Province.
Histophilus somni (member of the Pasteurellaceae family)
House (like 1, 2, 3) appears in many farms, but it's contextual.That means Farm A might have House 1, and Farm B also might have its own House 1 — but they're not the same. so we model House individuals uniquely per Farm or PoultryFarm (e.g., House_Farm2214740_1).
Ireland - Island nation with no land borders to other countries in this dataset.
Ireland
An individual representing a sample from a cattle.
An individual representing a sample from a Poultry or Chiken.
An individual representing a sample from a Salmon.
An individual representing a sample from a Pig and Piglets.
Mannheimia haemolytica (member of the Pasteurellaceae family, two major genotypes (1 and 2))
An individual representing Polutry Pathogen.
An individual representing Breed Type.
An individual representing a cattle breed of mixed meat and dairy type.
An individual representing Pig pathogen.
Mycoplasma hyopneumoniae
PI3
Parainfluenza-3
Parainfluenza-3 Virus (PI3) is a viral respiratory pathogen in cattle belonging to the Paramyxoviridae family. It causes upper respiratory tract infections and is a common contributor to the Bovine Respiratory Disease (BRD) complex.
Pasteurella multocida
Porcine species - pigs, swine
Avian species - chickens, turkeys, ducks
An individual representing SampleType for Poultry.
An individual representing different Countries.
An individual that represents the water type for salmon.
An individual representing Country.
The Netherlands - European country with land border to Belgium.
TheNetherlands
An individual representing Actual biomass of salmon.
An individual sample representing Salmon Mortality.
An individual representing Lab refence
An individual representing a Particular Date.
An individual representing the sampling date.
Viral disease is an illness caused by a virus, where the virus invades living cells to reproduce, often leading to symptoms like fever, cough, or organ damage.
Bacterial disease is an illness caused by pathogenic bacteria, such as Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, or Mycoplasma bovis in cattle.
Bacterial Disease
An autopsy sample refers to tissues or specimens collected during a post-mortem examination, conducted to investigate the cause of death or study pathological conditions in animals or humans.
Bronchoalveolar Lavage is a fluid sample collected from the lungs by flushing and retrieving liquid through a bronchoscope to examine respiratory infections.
Chicks raised specifically for meat production grow rapidly and are typically processed within 6–8 weeks.
Mixed breed cattle are crossbred animals that do not belong to a single pure breed category. May include dairy-beef crosses or other hybrid breeding combinations
Dairy breed refers to a type of livestock, for example cows, that is specifically raised for milk production
Finishing stage in pigs is the final growth phase, typically from 10 to 25 weeks of age, where pigs grow from about 20–25 kg to 100–110+ kg before market.
A tissue sample is a specimen composed of cells derived from an organism's body, collected for diagnostic or research purposes to study cellular structures, functions, or identify potential abnormalities.
Weaning stage (4–8 weeks) is when piglets are separated from the sow and transition fully to solid food, ending milk consumption.