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.
LiveStock HealthOntology
Saba Noor for more information please contact at this email: saba.noor@ugent.be / sabanoor8867@gmail.com
LHO
hasMeasurementUnit
Aquaculture / Fish Management LiveStock Species
hasSpeciesType
hasExternalParasites
Animal breed type. for example for cattle its veal, diary, beef or mixed for poultry its egglaying.
animal diagnostic test which is PCR or Culture or any other?
could be any event like slughter event, birth event etc..
link animal species sample to particular pathogen
Bovine Respiratory Syncytial Virus (BRSV) is a major cause of respiratory disease in cattle, characterized by coughing, nasal discharge, and increased respiratory rate.
BovineRespiratorySyncytialVirus
BRSV
Mycoplasma bovis is a bacterial pathogen that primarily affects cattle, causing respiratory disease, arthritis, mastitis, and other systemic infections.
MycoplasmaBovis
Mycoplasma hyopneumoniae is a bacterium causing swine enzootic pneumonia, a respiratory disease in pigs, characterized by coughing and impaired respiratory function.
MycoplasmaHyopneumoniae
M_Hyopneumoniae
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
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.
PorcineReproductiveAndRespiratorySyndrome
PRRS
Poultry
Swine Influenza is a respiratory viral infection in pigs, characterized by coughing, sneezing, and fever, with potential transmission to humans.
SwineInfluenza
Pig
pig
Bovine coronavirus primarily causes enteric (intestinal) infections in calves, leading to diarrhea.
BovineCoronaVirus
BCV
Infectious bronchitis is a highly contagious viral respiratory disease in chickens, characterized by respiratory distress and egg production drops.
InfectiousBrochist
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
Country
COUNTRY; Country
Cattle
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 establishment where crops are cultivated, and livestock may be raised for food production or other purposes.
A pathogen is a microorganism, such as a bacterium or virus, that causes disease in its host, be it plants, animals, or humans.
Pathogen
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 categorizes the nature of a specimen, including blood, tissue, bronchoalveolar lavage (BAL) fluid, swab, feces, etc., providing crucial information for diagnostic and research purposes in the context of animals or other biological systems.
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.
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.
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.
A class representing different breeds of animals, such as cattle, poultry, and pigs. Breeds are used to categorize and classify animals based on specific characteristics, traits, and purposes. For example, in the context of cattle, breeds can be categorized as meat, beef, 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.
Breed
A Breedingfarm" may focus on breeding and raising animals for specific traits.
CattleSamples are the "n" number of observations for Cattle
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
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 Feedlot typically emphasizes the finishing stage of livestock for meat production,
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.
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
The Live Stock Health Ontology (LHO), an extension of the DECIDE ontology following OBO Foundry guidelines, 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
PigSample is n number of observations for Pig and piglets
PoultrySample is "n" number of aobservation for Poultry data.
A province is an administrative region or territorial division within a country, typically with its own government and administrative structure.
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
Cattle, pig, and poultry represent distinct species within the animal kingdom commonly raised for agricultural purposes, including meat production.
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.
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.
An individual representing different Province.
An individual representing a cattle breed of Beef.
An individual representing Pig pathogen.
H3N2 is a subtype of the influenza A virus, primarily associated with swine influenza, characterized by genetic material derived from human and avian influenza viruses.
An individual representing a sample from a cattle.
An individual representing a sample from a Pig and Piglets.
An individual representing Poultry Pathogen.
An individual representing SampleType for Poultry.
An individual representing a particular Date.
An individual representing a sample from Poultry or Chicken.
An individual describes the type of farm or facility from which the samples were collected.Breeding Farm: If the farm is primarily focused on breeding animals, Feedlot : If the farm is a feedlot or facility where animals are raised for fattening, Mixed Farm: If the farm has a combination of activities, such as breeding and fattening
An individual representing a Piglet Sampling Method for diagnosing Disease.
An individual representing a Piglet breed which is Meat.
An individual representing a missing or unspecified cattle sample type.
An individual representing different Countries.
An individual representing Age: 100 Kg.
An individual representing Age .
An individual representing Age: 2.0 months.
An individual representing Age: 20 Kg.
An individual representing Age: 20 days.
An individual representing Age: 3 months.
An individual representing Age: 3.5 months.
An individual representing Age: 30 Kg.
An individual representing Age: 30-40 Kg.
An individual representing Age: 4 months.
An individual representing Age: 4-5 months.
An individual representing Age: 45-50 days.
An individual representing Age: 48 days.
An individual representing Age: 5 months.
An individual representing Age: 50 Kg.
An individual representing Age: 6 months.
An individual representing Age: 60 Kg.
An individual representing Age: 8-9 weeks.
An individual representing Age: 9-10 weeks.
SalmonSample01
MeasurementFishFarm
Sealice
A mixed sample type comprises a combination of different specimen components, potentially including blood, tissue, swabs, etc., providing a comprehensive source for varied analyses in diagnostic or research contexts.