Fernanda Dórea (nanda@datadrivensurveillance.org), Crawford Revie, Ann Lindberg, Eva Blomqvist
Flavie Vial, Karl Hammar, Patrick Lambrix, Noel Kennedy, Victor Oliveira
0.1.0
This is an ontology for health surveillance, assuming that surveillance data is recorded at three main levels:
SAMPLE data - data about specific collected samples; OBSERVATIONS, which can aggregate several samples; and OBSERVATIONAL CONTEXT, which is the context in which the observations were made (for instance clinical observation, surveillance sampling, etc).
HEALTH EVENT is the occurrence in the real World to be modeled. This occurrence is an abstract concept, as it generally cannot be determined what are its boundaries in time, space, or population units.
We assume that several OBSERVATIONS are derived from each health event, and recorded in the same or different databases - for instance clinical journal, laboratory database, abattoir. At the same time or not.
AHSO attempts to model these time specific observations. The ontology is focused on the modeling of the animal and health information connected to a single observation, made at a specific point on time. All the information recorded is relative to that specific point in time.
For instance, an animal belongs to a herd, which belongs to an owner, AT THE TIME OF THE OBSERVATION. We do not attempt to model how that animal changed herds on time. Similarly, we do not model clinical progression. It is up to those using the data to create definitions of when two observations should be connected to the same event.
An ontology to support the use of animal health data for data-driven surveillance ontology. Mode details at http://datadrivensurveillance.org.
Animal Health Surveillance Ontology (AHSO)
example
A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not
A phrase describing how a term should be used and/or a citation to a work which uses it. May also include other kinds of examples that facilitate immediate understanding, such as widely know prototypes or instances of a class, or cases where a relation is said to hold.
PERSON:Daniel Schober
GROUP:OBI:<http://purl.obolibrary.org/obo/obi>
example of usage
From the European Food Safety Agency (EFSA):
https://zenodo.org/record/344473#.WzvvyvkzYkV
The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research.
DCF_catalogues file contains all the valid catalogues published in the DCF.
The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives.
This annotation points to the specific catalague, within SSD2, form which terms were imported.
From the European Food Safety Agency (EFSA):
https://zenodo.org/record/344473#.WzvvyvkzYkV
The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research.
DCF_catalogues file contains all the valid catalogues published in the DCF.
The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives.
This annotation gives the specific code for the concept include din the ontology. Look for this code in the specific catalogue via the annotation property "SSD_catalogue".
Full names are stored in the property "SSD_termExtendedName".
From the European Food Safety Agency (EFSA):
https://zenodo.org/record/344473#.WzvvyvkzYkV
The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research.
DCF_catalogues file contains all the valid catalogues published in the DCF.
The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives.
This annotation gives the specific term name for the concept include din the ontology. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode".
From the European Food Safety Agency (EFSA):
https://zenodo.org/record/344473#.WzvvyvkzYkV
The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research.
DCF_catalogues file contains all the valid catalogues published in the DCF.
The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives.
This annotation gives any additional notes. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode".
GC_ID:1
ncbi_taxonomy
biota
cellular organisms
GC_ID:11
PMID:11542086
PMID:12361288
PMID:16627635
PMID:1704793
PMID:19801389
PMID:29034857
ncbi_taxonomy
Ampylobacter
Campylobacter
RF-00000042-MCG
GC_ID:11
PMID:10425795
PMID:10425796
PMID:10425797
PMID:10490293
PMID:10843050
PMID:10939651
PMID:10939673
PMID:10939677
PMID:11211268
PMID:11321083
PMID:11321113
PMID:11411719
PMID:11540071
PMID:11542017
PMID:11542087
PMID:11760965
PMID:12054223
PMID:2112744
PMID:270744
PMID:8123559
PMID:8590690
PMID:9103655
PMID:9336922
eubacteria
ncbi_taxonomy
Monera
Procaryotae
Prokaryota
Prokaryotae
bacteria
not Bacteria Haeckel 1894
prokaryote
prokaryotes
Bacteria
Detection
ANLYTYP
AT01A
Detection
Serotyping
AT02A
Serotyping
Phagetyping
AT03A
Phagetyping
Susceptibility test
AT04A
Susceptibility test
Speciation
AT05A
Speciation
Screening
AT06A
Screening
Quantification
AT07A
Quantification
Confirmation
AT08A
Confirmation
Determination
AT09A
Determination
Enumeration
AT10A
Enumeration
Isolate characterisation
AT11A
Isolate characterisation
Discriminatory test
AT12A
Discriminatory test
Molecular characterisation/genotyping
AT13A
Molecular characterisation/genotyping
establishments
SAMPNT
Microbiological tests
ANLYMD
F099A
Microbiological tests
Hazard
Health Finding
Laboratorial analysis
from the RAKIP project: https://goo.gl/wbFoZU
Microorganisms
Human (as organism)
MTX
A056J
Human (as organism)
Humans as living organisms of the taxonomic group Homo sapiens (family Hominidae). The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Human
Gallus gallus broiler
MTX
A0C78
Gallus gallus broiler
Gallus gallus animals raised for meat production purposes. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Broiler
RF-00000044-MCG
Slaughterhouse
SAMPNT
E311A
Slaughterhouse
ISO 10272-1:2006 Campylobacter
ANLYMD
F163A
ISO 10272-1:2006 Campylobacter
Microbiology of food and animal feeding stuffs -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 1: Detection method
individual
animal
slaughter batch
G200A
slaughter batch
Clinical investigations
PRGTYP
K020A
Clinical investigations
clinical investigation in animals is considered as a selective way of sampling and results in a number of samples obtained in a passive way. The samples obtained and analysed via clinical investigations are heterogeneous with relation to the species (matrix) as well as type of samples. The reason for the analysis of the samples is very often a clinical examination of (diseased) animals by a veterinarian and/or specific clinical signs observed by the farmer and/or veterinarian.
Monitoring - active
PRGTYP
K023A
Monitoring - active
active monitoring programme of zoonotic agents or antimicrobial resistance in food and animals, based on random sampling strategies of the population of interest, stratified according to the relevant subcategories of the population. The sampling strategy should ensure that the sample is representative of the population of interest and that the sampling method is robust. A planned monitoring of wild life for e.g Trichinella or Echinococcus via organised hunting schemes should be considered as active monitoring.
Monitoring - passive
PRGTYP
K024A
Monitoring - passive
passive monitoring programme of zoonotic agents or antimicrobial resistance that includes information from diagnostic testing, or a representative selection of this information. Data on the prevalence of the zoonotic agents and on antimicrobial resistance provided by passive monitoring programmes are typically derived from diseased animals (clinical investigations, observed syndromes, etc).
animal sample - caecum
ZOO_CAT_SMPTYP
S002A
animal sample - caecum
animal sample - caecum
animal sample - faeces
ZOO_CAT_SMPTYP
S005A
animal sample - faeces
animal sample - faeces
Sweden
COUNTRY
Selective sampling
SAMPSTR
ST20A
Selective sampling
Selective sampling—planned strategy whereby the selection of the sample is from previously defined ‘high-risk’ population groups. Samples are normally selected to either illustrate or document unsatisfactory conditions or suspected adulteration of a product. The sampling is deliberately biased and is directed at the particular products or manufacturers. The sampling procedure can be random or not. The specification of the ‘high-risk’ population comes from either scientific studies or previous analysis and information of other regions or countries. The comparability of the results lies on both the definition of the population to be analysed and the way the samples have been drawn
Suspect sampling
SAMPSTR
ST30A
Suspect sampling
Suspect sampling—unplanned selection of a sample whereby the individual units are selected based on the recent judgement and experience regarding the population, lot or sampling frame, e.g. earlier positive samples. The samples obtained from this procedure are not randomly extracted.
Census
SAMPSTR
ST50A
Census
Census—strategy whereby all units of the population are sampled