Elena Slavco PERSON: Saba Noor DECIDE Aquaculture and Livestock Ontology Elena Salvaco Miel Hostens Saba Noor DECIDE Aquaculture and Livestock Ontology This ontology was developed as part of the DECIDE EU 2020 project to support data integration, classification, and knowledge modeling in the domain of aquaculture. It provides a structured, upper-level framework for representing species (such as salmon, cattle, poultry, and pigs), production systems, measurement events, and health-related information including clinical signs, diagnostics, and interventions. The ontology is designed to be modular and extensible, and it can be adapted or reused for terrestrial livestock species such as cattle, poultry, and pigs. seeAlso: LivestockHealthOntology https://bioportal.bioontology.org/ontologies/LHO Its purpose is to facilitate harmonized data representation for improved disease surveillance, risk assessment, and decision support across livestock sectors. http://www.purl.org/decide# DECIDE Aquaculture and Livestock Ontology Extend DECIDE ontology for terrestrial livestock species such as cattle, poultry, and pigs. https://bioportal.bioontology.org/ontologies/LHO A textual abbreviation or acronym for a term, class, or property. has Abbrevation Information Artifact Ontology (IAO) A string that provides a usage example of a class, property, or other ontology element to help users understand how it is applied. example of usage Indicates the editorial or curation status of an ontology term or axiom. has curation status A textual definition that precisely specifies the meaning of a term or class definition A note or comment intended for ontology editors and maintainers, not for general users of the ontology. editor note The person primarily responsible for the creation or curation of a given ontology term. term editor 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 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. alternative term A reference (such as a publication, URL, or ontology) that identifies where the definition of a term originated from. definition source http://purl.obolibrary.org/obo/IAO_0000412 An annotation indicating the source ontology or resource from which a given term was imported. imported from Person who contribute to create and define ontology terms Persons involved to create ontology Ontology Name hasName Term Matching This document is about information artifacts and their representations A (currently) primitive relation that relates an information artifact to an entity. is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about Relates an event (such as a health check, sampling, diagnosis, or treatment) to the veterinarian who conducted it Relates a Farm to an Event that occurred at or is associated with that farm. Events may include veterinary visits, sampling, inspections, treatments, or production-related actions. Associates an Event with its EventType, describing the nature or category of the event (e.g., Sampling, Treatment, Inspection, Vaccination). Links an Event to one or more Measurement instances that record quantitative or qualitative observations made during the event. For Exmaple Antibiotic dosage, Body weight, Temperature, Pathogen load, Water quality indicators Associates a Measurement with a MeasurementType that describes what kind of value is being measured (e.g., body weight, temperature, pH level,) link Sample with SampleResults Relates an Event to a Sample collected or used during that event. Typical in sampling, diagnostic, or surveillance activities in livestock and aquaculture systems. Associates a Sample with a SampleType indicating the kind of material collected, such as blood, tissue, feces, or water. Links an Event to one or more Statistic instances that summarize outcomes or observations related to that event. This may include prevalence, mortality rate, average weight, or test positivity. Link Measurement to Unit Links a SampleResult to the Pathogen that was identified in the sample. This is used to record confirmed detections of pathogens through diagnostic testing. Relates an Event to the SpeciesGroup that was involved in or affected by the event. This helps to contextualize the event with respect to the biological group it targeted. measurement value has value Age data property Birthday data property data property to define event date A geographic location . Indentification of Farm or Spceis group Local Authority in region Particular Fame name Amount of animal in a farm, herd or group Farm Postal Code value data property A data property for SampleResult that is either 0 or 1 . Data property like Cattle, Poultry, Pig and Salmon belongs to Species Indicates the general production system or environment for a species, such as 'Aquaculture' or 'Terrestrial'. This property can be used to categorize species based on farming context. Farm location Latitude value Farm location longitude value 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. https://agrovoc.fao.org/browse/agrovoc/en/page/c_6145 Poultry 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. Atlantic salmon Pacific salmon https://agrovoc.fao.org/browse/agrovoc/en/page/c_6756 https://agrovoc.fao.org/browse/agrovoc/en/page/c_6756 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. Salmon The pig (Sus domesticus), often called swine, hog, or domestic pig Swine https://aims.fao.org/aos/agrovoc/c_7555.html https://aims.fao.org/aos/agrovoc/c_7555.html Pig IAO:0000027 obo:IAO_0000119 "http://purl.obolibrary.org/obo/iao.owl" . A data item is an information content entity that is part of a dataset, record, or other data structure, and typically expressed in a structured format such as a number, string, or symbol. data item IAO:0000109 IAO_0000109 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." measurement datum OBI:0000679 average value A data item that is produced as the output of an averaging data transformation and represents the average value of the input data. PERSON: James Malone PERSON: Monnie McGee arithmetic mean average value VO:0000150 A measurement result that reflects the level of antibodies in a sample (usually blood), often after vaccination or infection antibody titer VO:0000555 A titer (or titre) is a measure of concentration. Titer testing employs serial dilution to obtain approximate quantitative information from an analytical procedure that inherently only evaluates as positive or negative. The titer corresponds to the highest dilution factor that still yields a positive reading; for example, positive readings in the first 8 serial twofold dilutions translate into a titer of 1:256. YH WEB:http://en.wikipedia.org/wiki/Titer http://purl.obolibrary.org/obo/vo.owl titer https://agrovoc.fao.org/browse/agrovoc/en/page/c_1391 https://agrovoc.fao.org/browse/agrovoc/en/page/c_1391 A collective term for bovine livestock. Cattle decide:Event A class representing any occurrence or activity related to aquaculture or livestock management, such as disease outbreaks, treatments, movements, or inspections. PERSON: Miel PERSON: Saba https://github.com/BFO-ontology/BFO A class representing any occurrence or activity related to aquaculture or livestock management, such as disease outbreaks, treatments, movements, or inspections. Event decide:EventType PERSON: Miel PERSON: Saba Class Event has Event Type and 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. EventType decide:Farm PERSON: Saba 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. decide:Measurement PERSON: Saba 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 decide:MeasurementType PERSON: Saba A classification of measurement, such as weight or age decide:Pathogen A material entity with a pathogenic disposition. http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C80324 http://purl.obolibrary.org/obo/IDO_0000528 http://www.purl.org/infection_trans#Pathogen https://agrovoc.fao.org/browse/agrovoc/en/page/c_5630 http://purl.obolibrary.org/obo/IDO_0000528 A pathogen is a microorganism, such as a bacterium or virus, that causes disease in its host, be it plants, animals, or humans. http://purl.obolibrary.org/obo/IDO_0000528 http://www.purl.org/infection_trans#Pathogen decide:ProductionCycleTime PERSON: Saba 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. decide:Sample PERSON:Elena 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 decide:SampleResult PERSON: Saba SampleResult represents the outcome or findings derived from analyzing a specimen. It includes diagnostic findings, laboratory test values, pathogen detections, or other observed indicators used for decision-making in animal health and production contexts. decide:SampleType PERSON: Saba 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. decide:SpeciesGroup PERSON: Saba SpeciesGroup represents a group of animals belonging to the same species or production category (e.g., salmon, broiler chickens, weaned piglets, dairy cattle). It is used to describe the target population involved in events such as sampling, treatment, or observation. decide:Statistics PERSON: Saba Statistic represents a quantitative summary derived from one or more observations or measurements. It includes values such as averages, percentages, rates, ratios, and counts used for describing or analyzing trends in animal health, disease, production, or diagnostic results. decide:Unit PERSON: Saba 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. decide:Veterinarian PERSON: Elena 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. degrees Celsius kilogram milligram Per Cubicmetre tonne kg/m3 mass density part per Trillion rate per 1000 Elena Slavco PERSON: Saba Noor DECIDE Aquaculture and Livestock Ontology Elena Salvaco Miel Hostens Saba Noor DECIDE Aquaculture and Livestock Ontology This ontology was developed as part of the DECIDE EU 2020 project to support data integration, classification, and knowledge modeling in the domain of aquaculture. It provides a structured, upper-level framework for representing species (such as salmon, cattle, poultry, and pigs), production systems, measurement events, and health-related information including clinical signs, diagnostics, and interventions. The ontology is designed to be modular and extensible, and it can be adapted or reused for terrestrial livestock species such as cattle, poultry, and pigs. seeAlso: LivestockHealthOntology https://bioportal.bioontology.org/ontologies/LHO Its purpose is to facilitate harmonized data representation for improved disease surveillance, risk assessment, and decision support across livestock sectors. http://www.purl.org/decide# DECIDE Aquaculture and Livestock Ontology Extend DECIDE ontology for terrestrial livestock species such as cattle, poultry, and pigs. https://bioportal.bioontology.org/ontologies/LHO