in the Built Environment Lynn M Schriml University of Maryland School of Medicine Institute for Genome Sciences Baltimore Maryland lschrimlsomumarylandedu Communitydriven solutions Sample and Sequence Metadata ID: 590241
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Slide1
Standardized Metadata
in the Built Environment
Lynn M. Schriml
University of Maryland School of MedicineInstitute for Genome SciencesBaltimore, Marylandlschriml@som.umaryland.eduSlide2
Community-driven solutions
Sample and Sequence Metadata
Biomedical Data
Data problem
Community
Standards
Implementation
Data AnalysisSlide3
17th Genomic Standards Consortium meeting
(GSC17) @ JGI May 4-6
th
, 2015
10 years, 28 meetings, 534 GSC Consortium members from 14 countries &
Areas of research
soil, water, environmental samples,
metagenomics
, microbiome, indoor
environment, human healthSlide4
Pelin
Yilmaz
- MIxSChecklist standards:
flexible and extensible, minimum information standards, fosters exchange and integration of genomic data and standardized descriptions
Built environment
MIxS: capture geographic and environmental context
MIxS
Shell Oil: hydrocarbon resourcesSlide5
MIxS
-BE: A MIxS extension defining the Minimal Metadata for the Built Environment
Minimal Information Checklist
MIxS Descriptors
MiXs
– air environmental package
p
roject name, sample environment, sequencing specifications
BE - core
carbon dioxide, ventilation type, organism count
BE – building properties
BE – sample properties
surface material, temperature, humidity, occupancy
r
oom type, HVAC system, light source
s
ample processing, occupancy load
Built Environment (BE) package
. The BE package represents a minimal metadata description of the built environment to be collected and reported for each sequenced sample.
http://gensc.org/gc_wiki/index.php/MIxS_extensionsSlide6
MIxS-BE:
Building Built Structure & Room Checklist
built structure
geographic location, region, city, state, countrysetting, built structure type, building identifier, net area of built structure
BE documentation: drawings, specifications, design,
construction
architectural elements
building: # floors, # rooms,
stairs, elevators
room: ID/name, floor, volume, condition, # windows
floors, walls, ceilings,
room, windows, shading devices, doors & archways, furnishings:
area, location, type, structure, material,
condition, age, signs of water/mold
building systems
heating, cooling, ventilation: system ID, delivery method
& locations
occupants and function
data types: manual,
automated counts, video, estimated, average daily, houseplants, cleaning & cooking frequency
building environmental conditions
temperature (globe, variance), humidity,
illuminations, solar radiation, air distribution
(Lynn Schriml & Jeff Kline)
extension
to capture breadth of study related metadataSlide7
MIxS
-BE: Building & RoomData Gathering
Scott Kelley, John Chase, Jeffrey Siegel, Greg
Caporaso
, Jack Gilbert, Kin Handley, Brent Stephens, Curtis
Huttenhower
, Regina
Joice
, Rachel Adams,
Seema
Bhangar
, Jean Francis Ruiz Calderon,
Atila Novoselec, Maria Gloria Dominguez-Bello, Humberto
Cavallin
Calanche
, Jessica Green, James Meadow, Jeff Kline, Jordan
Peccia
, Susan Lynch, Chris Johnson, Al LevinSlide8
building (collection location)
Age of building
building type
University housing
location
longitude
Train stop collection location
train line
Station collection location
latitude
urban/rural
architectural elements
number of bathrooms
number of bedrooms
flooring type
flooring material: vinyl tiles, carpeting
Flooring (carpet, hard-floor, throw-rug)
exterior siding
exterior siding: fiber-cement (HardiPlank)
building exterior material
Slope of roof
wall
wall material: painted sheetrock
Interior wall construction (drywall/plaster)
interior wall type
collection date
date
day
collection date
collection time
month
time
weekday
Season
humidity
average relative
humidity
humidity at time of sampling
humidity on sampling day
Indoor air absolute humidity (humidity ratio)
relative_humidity
RelHumid_mean
Indoor air relative humidity
Chamber
Temperature
/
relative humidity
occupancy
number of adults
number of children
Pets (# and kind)
Crowdedness
cleaning
frequency
Number of infrared beam breaks at patient room doorways (a metric of human occupancy/activity)
House occupied during the day (1-2, 3-4, or 7)
Times/week a meal is cooked (1-2, 3-4, or 7)
gender
Houseplant (yes/no
)
Pets
Usage
Indoor air CO2 concentration (patient rooms only)
Last time
swept
/mopped/vacuumed
Indoor
illumination levelsSlide9
structure
type
mechanical, architectural, aerospacebuilt structure
airport, bus, taxi, train, train stationgeographic locationUSA: New York City, New Yorklatitude longitude
sample ID
collection
date
June
20, 2015
environmental feature
park
[ENVO:00000562
]train station collection location
south station above ground, south station underground
train line
red, blue, green
indoor surface
turnstile, emergency exit, Metro Card kiosks, wooden
bench, metal bench, stairwell handrail, garbage can, train door, train poll, train handrail, train seat
surface
material
concrete, wood,
stone, tile, plastic, glass, metal, vinyl, carpet
collection method
Copan Liquid
Amies
Elution Swab 481C
DNA extraction method
MoBio
Powersoil
DNA isolation kit
Link to Ontologies
Develop a
MetaSub
metadata template, link to MIxS standardSlide10
Clinical
Biomedical
Research
Samples, Phenotypes, Ontology Team
Health DataSlide11
6,582
disease terms (38% defined)
37,988
xref
mappings
Human Disease Ontology
DO website: http://disease-
ontology.org