GenEpiO Scope
 Share
The version of the browser you are using is no longer supported. Please upgrade to a supported browser.Dismiss

 
View only
 
 
Still loading...
ABCDEFGHIJKLMNOPQRSTUVWXYZAAABACADAEAFAGAHAIAJAKALAMANAOAPAQARASATAUAVAWAXAYAZBABBBCBDBEBFBGBHBIBJBKBLBMBN
1
GenEpiO Upper-Level Schema and example terms
2
Selection examples are a small sample of anticipated terminology
3
Sample CollectionRepository or Naming AuthorityLaboratory TestingProject DataCase Epidemiology (human and animal)Epidemiology InvestigationEvolutionary SurveillancePublic Health Data Model
4
Includes generic epidemiology demographic inputsApplies across sample gathering and analysis processesTracking mobile elements found in laboratory sample processing
5
environmentfoodhost organism
sample matrix
Surveillance Epidemiology (SurvO)
6
demographicsHandling and storage identificationtesting (including date/time metrics)resultshost exposure event(s)operational info
demographics
host medical events (history)phylogeny - clusteringoperational infomonitoring systementity providerentity
7
immediate featurelocation (geography)anthropogenic geographic featurecooking methodpackaging / container / wrappingpreservation methodproduct category
(USDA example)
host taxonomysample by body partsample by material typephenotypic sexagehost roleidentifier rolestored entity typeentity storage detailsissuing organizationcollection or identifier name or typepackage label technologyisolate extractiontesttest inputstest prepspeciesstrainquality control metricsAnti-microbial resistance genes (in silico)AMR Drug resistancevirulence (in silico)project detailsmode of transmissionsourcelocationcontacts (incl. name, phone and email)host identificationtemporal datasymptomdiseasedisease statusdisease outcometreatmentoutbreak detailsgeographyinformation providerregional scopeoutbreak rules / thresholds
8
9
SELECTION EXAMPLEStemperature of samplegeopolitical regionagricultural featuredry heatgasspices or extractsdairy and egg ...Homo Sapienscaecumanimal productfemaleanimal roleclinical material (human)primarycontainerrefrigeration[list of labs / institutions]NCBI BioProjectbarcodewhole genome sequencingreference genomesequencing platformBacterialassembly status
standard
high quality ...
NCBI BioProject detailsdirect transmissionhuman (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 symptomdisease by infectious agentacutechronicanti-microbial agenttitlephysicianpathogen
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] farmmoist heatvaccume-packedchemicalsspices and herbs ...embryo bronchoalveolar lavagehermaphrodite animal modelclinical material (human) - invasivesecondaryspecimenpreservation life-spanNCBINCBI BioSampleQR (Quick Response) codelibrary prep Proteobacteriaassembly
contig count
N50
N99
Resistome Gene Identifier? investigation assay specification congenital exposure activity
diaper changing
parent / caregiverhealth authoritysymptom onset date
symptom duration
symptom cessation date
abdominal cramp bacterialchronicdead antibioticstart (date of notification)epidemiologist
11
bacterial density fish farm steambag / box antibioticsbaby foods ...Gallus Gallusheart cerebrospinal fluidmale animal, laboratorymatrix - fluiddiscontinued / previoussamplereceived date
isolation date
frozen date
sequencing run date
upload date
Canadian National Microbiology LaboratoryGenBankassembly 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 commensalcongenitalhealthyvaccinedate of most recent casecommon events / location(s)laboratoryNCBINCBI BioProject
12
collection depth plantation watercan / bottle / jar organic acids or saltsfats and oils ......lung down feather missing animal, wildmatrix - solidisolatesample / specimen collection date Enterobacteriaceae sequencing droplet spreadfood allergydigestive system symptom toxic shockhealthyrecoveringendNCBI BioSample
13
phconstructed featurefat or oil inorganic acids or saltspoultry products ...organ fecesneuter livestockplant rinsedigital dna sequenceannotation Escherichia coli(for amr / virulence) project relevanceindirect transmission bloating primarypathologicaloutbreak_idgeographic distributionSRA
14
turbidity buildingmicrowave chemical treatmentsoups, sauces, and graviesstomach muscle tissue
pooled male and female
petswabdigital rna sequnceCGF???? Salmonella agricultural common vehicle transmission
human contact type
close
household
individuals with diarrhea
pregnancy
date of conception
pregnancy outcome (+ date)
feces and droppings symptom botulismrecoveringnumber of cases within time threshold (e.g. 2 weeks)health agencies involvedPHE
15
precipitation hospital...chilling or freezingfruits and fruit juicesvertebral column peritoneal fluidpseudohermaphrodite domesticated, avian food contact surfaceMLSTViral environmental inhalationfood nausea viral infectioius diseaserecurrenceInvestigation status
solved
not solved
multi-regional distribution
PulseNetPulseNet Submission Model
16
nitrate concentration housefermentationfinfish and shellfish yolk wild, avian inanimate object surface medical vehicle-born ingestiontravel (incl. mode and reason) vomiting severe acute respiratory syndromeremissiontime elapsed (from notification to most recent case)travel / immigrationBCCDC-Oxford Tuberculosis
17
nitrite concentration industrial buildingfiltrationlegumes and legume productsplant productN/A - inanimate environment (swab or sampling) meatMLVAFungal model organismanimaldisease of anatomical entityIRIDA
18
bakeryirradiationlamb, veal and game products compostN/A - substance as food role rectalPFGE specification of data to be generated in an investigation exposure location gastrointestinal ...epidemiological link
19
dairyheat treatment...not applicable / not collected / not determinedhuman role (clinical material)title agricultural fair
farm
petting zoo
immune system ...
20
retirement homemodified atmosphere(Above apply to most columns) pregnant femaie rolewater related nervous system ...
21
22
OntologyPATOGEO or GAZETTEERENVOFOODON / LANGUALFOODON / LANGUALFOODON / LANGUALFOODON / LANGUALNCBITaxonUBERONUBERONPATOGENEPIOGENEPIOGENEPIOGENEPIOGENEPIOGENEPIOGENEPIOGENEPIONCBITaxonAROAROMobiOGENEPIOTRANSGENEPIOGENEPIOGENEPIOGENEPIOHPDOIDNDF-RTNDF-RTCHEBI
23
FIXBTOBTOGENEPIOMESHCHMOEOVIVOIDOSIOSIOVO
24
EVSEVSUBERONExOOAEGENEPIO
25
GENEPIOCHEBIGENEPIO
26
CVDO
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
Loading...
 
 
 
Sheet1