GenEpiO Scope

	A	B	C	D	E	F	G	H	I	J	K	L	M	N	O	Q	R	S	T	U	V	W	Y	Z	AA	AB	AC	AD	AE	AF	AG	AH	AJ	AL	AM	AN	AO	AP	AQ	AR	AS	AT	AU	AV	AW	AX	AZ	BC	BD	BE	BF	BG	BI	BL	BM
1		GenEpiO Upper-Level Schema and example terms
2		Selection examples are a small sample of anticipated terminology
3		Sample Collection														Repository or Naming Authority							Laboratory Testing										Project Data	Case Epidemiology (human and animal)													Epidemiology Investigation						Evolutionary Surveillance	Public Health Data Model
4		Includes generic epidemiology demographic inputs														Applies across sample gathering and analysis processes																																					Tracking mobile elements found in laboratory sample processing
5		environment			food				host organism						sample matrix																																			Surveillance Epidemiology (SurvO)
6												demographics				Handling and storage identification							testing (including date/time metrics)				results							host exposure event(s)			operational info		demographics	host medical events (history)							phylogeny - clustering	operational info		monitoring system				entity provider	entity
7		immediate feature	location (geography)	anthropogenic geographic feature	cooking method	packaging / container / wrapping	preservation method	product category (USDA example)	host taxonomy	sample by body part	sample by material type	phenotypic sex	age	host role		identifier role	stored entity type	entity storage details	issuing organization	collection or identifier name or type	package label technology		isolate extraction	test	test inputs	test prep	species	strain	quality control metrics	Anti-microbial resistance genes (in silico)	AMR Drug resistance	virulence (in silico)	project details	mode of transmission	source	location	contacts (incl. name, phone and email)	host identification		temporal data	symptom	disease	disease status	disease outcome	treatment			outbreak details	geography	information provider	regional scope	outbreak rules / thresholds
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9	SELECTION EXAMPLES	temperature of sample	geopolitical region	agricultural feature	dry heat	gas	spices or extracts	dairy and egg ...	Homo Sapiens	caecum	animal product	female		animal role	clinical material (human)	primary	container	refrigeration	[list of labs / institutions]	NCBI BioProject	barcode			whole genome sequencing	reference genome	sequencing platform	Bacterial		assembly status standard high quality ...				NCBI BioProject details	direct transmission	human	(could echo sample collection location, but also may be location pointing to group exposure)	attending physician (or veterinary contact!)	case ID	(See sample collection; + garnered from interview)	hospitalization admission date discharge date	abdominal symptom	disease by infectious agent	acute	chronic	anti-microbial agent			title		physician		pathogen time window x case reports x regional coverage		The specifications here detail how particular well known data providers and consumers map their own content entities - like NCBI BioProject and BioSample - over to GenEpiO content
10		temperature - average daily	[countries / cities / regions]	farm	moist heat	vaccume-packed	chemicals	spices and herbs ...		embryo	bronchoalveolar lavage	hermaphrodite		animal model	clinical material (human) - invasive	secondary	specimen	preservation life-span	NCBI	NCBI BioSample	QR (Quick Response) code					library prep	Proteobacteria		assembly contig count N50 N99	Resistome Gene Identifier?			investigation assay specification	congenital	exposure activity diaper changing		parent / caregiver	health authority	(See sample collection; + garnered from interview)	symptom onset date symptom duration symptom cessation date	abdominal cramp	bacterial	chronic	dead	antibiotic			start (date of notification)		epidemiologist
11		bacterial density		fish farm	steam	bag / box	antibiotics	baby foods ...	Gallus Gallus	heart	cerebrospinal fluid	male		animal, laboratory	matrix - fluid	discontinued / previous	sample	received date isolation date frozen date sequencing run date upload date	Canadian National Microbiology Laboratory	GenBank						assembly	Campylobacter		coverage				array	contact	social role aquaintance child parent spouse		interviewer	case status no further action taken review/report outbreak investigation	birth date death date	case notification date diagnosis date disease outcome date treatment date	asymptomatic host of infectious agent	commensal	congenital	healthy	vaccine			date of most recent case	common events / location(s)	laboratory				NCBI	NCBI BioProject
12		collection depth		plantation	water	can / bottle / jar	organic acids or salts	fats and oils ...	...	lung	down feather	missing		animal, wild	matrix - solid		isolate	sample / specimen collection date									Enterobacteriaceae						sequencing	droplet spread					food allergy		digestive system symptom	toxic shock	healthy	recovering				end							NCBI BioSample
13		ph		constructed feature	fat or oil		inorganic acids or salts	poultry products ...		organ	feces	neuter		livestock	plant rinse		digital dna sequence									annotation	Escherichia coli		(for amr / virulence)				project relevance	indirect transmission							bloating	primary	pathological					outbreak_id	geographic distribution						SRA
14		turbidity		building	microwave		chemical treatment	soups, sauces, and gravies		stomach	muscle tissue	pooled male and female		pet	swab		digital rna sequnce							CGF????			Salmonella						agricultural	common vehicle transmission	human contact type close household individuals with diarrhea				pregnancy date of conception pregnancy outcome (+ date)		feces and droppings symptom	botulism	recovering					number of cases within time threshold (e.g. 2 weeks)	health agencies involved					PHE
15		precipitation		hospital	...		chilling or freezing	fruits and fruit juices		vertebral column	peritoneal fluid	pseudohermaphrodite		domesticated, avian	food contact surface									MLST			Viral						environmental	inhalation	food						nausea	viral infectioius disease	recurrence					Investigation status solved not solved	multi-regional distribution					PulseNet	PulseNet Submission Model
16		nitrate concentration		house			fermentation	finfish and shellfish			yolk			wild, avian	inanimate object surface																		medical	vehicle-born ingestion	travel (incl. mode and reason)						vomiting	severe acute respiratory syndrome	remission					time elapsed (from notification to most recent case)	travel / immigration					BCCDC-Oxford Tuberculosis
17		nitrite concentration		industrial building			filtration	legumes and legume products			plant product			N/A - inanimate environment (swab or sampling)	meat									MLVA			Fungal						model organism		animal							disease of anatomical entity												IRIDA
18				bakery			irradiation	lamb, veal and game products			compost			N/A - substance as food role	rectal									PFGE									specification of data to be generated in an investigation		exposure location							gastrointestinal ...						epidemiological link
19				dairy			heat treatment	...				not applicable / not collected / not determined		human role (clinical material)																			title		agricultural fair farm petting zoo							immune system ...
20				retirement home			modified atmosphere					(Above apply to most columns)		pregnant femaie role																					water related							nervous system ...
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22	Ontology	PATO	GEO or GAZETTEER	ENVO	FOODON / LANGUAL	FOODON / LANGUAL	FOODON / LANGUAL	FOODON / LANGUAL	NCBITaxon	UBERON	UBERON	PATO		GENEPIO		GENEPIO	GENEPIO			GENEPIO		GENEPIO	GENEPIO	GENEPIO		GENEPIO	NCBITaxon			ARO	ARO	MobiO	GENEPIO	TRANS	GENEPIO		GENEPIO	GENEPIO	GENEPIO		HP	DOID	NDF-RT	NDF-RT		CHEBI
23		FIX								BTO	BTO	GENEPIO		MESH									CHMO											EO					VIVO		IDO		SIO	SIO		VO
24		EVS												EVS									UBERON											ExO									OAE	GENEPIO
25		GENEPIO												CHEBI																													GENEPIO
26																																											CVDO
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