4. MIxS controlled vocabularies - GenomicsStandardsConsortium/mixs GitHub Wiki

NOTE - This page was manually created using v5 of the checklist. We intend to replace this page with a page that will automatically update when we make a new MIxS release.

Whenever possible, MIxS metadata descriptors provide users a controlled vocabulary (CV) of terms as the value of a descriptor. A CV is an organized arrangement of words and phrases used to index content and/or to retrieve content through browsing or searching. The purpose of CVs is to organize information and to provide terminology to catalog and retrieve information. CVs promote consistency in preferred terms and the assignment of the same terms to similar content. While this might be restrictive, experience has shown that such CVs vastly enhance searching and automated retrieval of genomic datasets, as opposed to free text values. The CVs are dynamic, and are extended when required and requested.

The list below is all the MIxS descriptors that require the use of a CV, and their subsequent terms:

environmental package CV

 air|built environment|host-associated|human-associated|human-skin|human-oral|
 human-gut|human-vaginal|hydrocarbon resources-cores|hydrocarbon resources-fluids/swabs|
 microbial mat/biofilm|misc environment|plant-associated|sediment|
 soil|wastewater/sludge|water`

observed biotic relationship CV

 free living|parasitism|commensalism|symbiotic|mutualism

health or disease status of specific host at time of collection CV

 healthy|diseased|dead|disease-free|undetermined|recovering|resolving|
 pre-existing condition|pathological|life threatening|congenital

trophic level CV

 autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|
 chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|
 diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|
 methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|
 organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|
 photosynthetic|phototroph

relationship to oxygen CV

 aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|
 obligate anaerobe

taxa ID CV

16S rRNA gene|multi-marker approach|other

assembly quality CV
```
high|med|low
```

completeness approach CV
```
marker gene|reference based|other
```

contamination screening input CV
```
ref db|kmer|coverage|combination
```

decontamination software CV

checkm/refinem|anvi'o|prodege|bbtools:decontaminate.sh|acdc|combination

sorting technology CV

flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|
micromanipulation|other

single cell lysis approach CV

chemical|enzymatic|physical|combination

WGA amplication approach CV
```
pcr based|mda based
```

binning parameters CV

homology search|kmer|coverage|codon usage|combination

binning software CV

metabat|maxbin|concoct|groupm|esom|metawatt|combination|other

MAG coverage software CV
```
bwa|bbmap|bowtie|other
```

aerospace structure CV
```
plane|glider
```

architectural structure CV
```
building|shed|home
```

biological status CV

wild|natural|semi-natural|inbred line|breeder's line|hybrid|clonal selection|mutant

building occupancy type CV

office|market|restaurant|residence|school|residential|commercial|low rise|high rise|
wood framed|office|health care|school|airport|sports complex

building setting CV
```
urban|suburban|exurban|rural
```

built structure setting CV
```
urban|rural
```

ceiling condition CV

new|visible wear|needs repair|damaged|rupture

ceiling finish material CV

drywall|mineral fibre|tiles|PVC|plasterboard|metal|fiberglass|
stucco|mineral wool/calcium silicate|wood

ceiling signs of water/mold CV

presence of mold visible|no presence of mold visible

ceiling structure CV
```
wood frame|concrete
```

ceiling texture CV

crows feet|crows-foot stomp|double skip|hawk and trowel|knockdown|popcorn|
orange peel|rosebud stomp|Santa-Fe texture|skip trowel|smooth|stomp knockdown|swirl

ceiling type CV

cathedral|dropped|concave|barrel-shaped|coffered|cove|stretched

current land use CV

cities|farmstead|industrial areas|roads/railroads|rock|sand|gravel|mudflats|
salt flats|badlands|permanent snow or ice|saline seeps|mines/quarries|oil waste areas
|small grains|row crops|vegetable crops|horticultural plants (e.g. tulips)|marshlands 
(grass,sedges,rushes)|tundra (mosses,lichens)|rangeland|pastureland (grasslands used for livestock 
grazing)|hayland|meadows (grasses,alfalfa,fescue,bromegrass,timothy)|shrub land
(e.g. mesquite,sage-brush,creosote bush,shrub, oak,eucalyptus)|successional shrub land (tree 
saplings,hazels,sumacs,chokecherry,shrub dogwoods,blackberries)|shrub crops (blueberries,nursery 
ornamentals,filberts)|vine crops (grapes)|conifers (e.g. pine,spruce,fir,cypress)|
hardwoods (e.g. oak,hickory,elm,aspen)|intermixed hardwood and conifers|tropical
(e.g. mangrove,palms)|rainforest (evergreen forest receiving >406 cm annual rainfall)|
swamp (permanent or semi-permanent water body dominated by woody plants)|crop trees 
(nuts,fruit,christmas trees,nursery trees)

depositional environment CV

Continental - Alluvial|Continental - Aeolian|Continental - Fluvial|
Continental - Lacustrine|Transitional - Deltaic|Transitional - Tidal|
Transitional - Lagoonal|Transitional - Beach|Transitional - Lake|Marine - Shallow|
Marine - Deep|Marine - Reef|Other - Evaporite|Other - Glacial|Other - Volcanic|other

design, construction, and operation documents CV

building information model|commissioning report|complaint logs|contract administration|
cost estimate|janitorial schedules or logs|maintenance plans|schedule|sections|
shop drawings|submittals|ventilation system|windows

dominant hand CV
```
left|right|ambidextrous
```

door condition CV

damaged|needs repair|new|rupture|visible wear

door direction of opening CV
```
inward|outward|sideways
```

door location CV
```
north|south|east|west
```

door material CV

aluminum|cellular PVC|engineered plastic|fiberboard|fiberglass|metal|
thermoplastic alloy|vinyl|wood|wood/plastic composite

door movement CV

collapsible|folding|revolving|rolling shutter|sliding|swinging

door signs of water/mold CV

presence of mold visible|no presence of mold visible

door type CV
```
composite|metal|wooden
```

door type, composite CV

metal covered|revolving|sliding|telescopic

door type, metal CV

collapsible|corrugated steel|hollow|rolling shutters|steel plate

door type, wood CV

bettened and ledged|battened|ledged and braced|battened|ledged and framed|battened|
ledged, braced and frame|framed and paneled|glashed or sash|flush|louvered|wire gauged

drainage classification CV

very poorly|poorly|somewhat poorly|moderately well|well|excessively drained

drawings CV

operation|as built|construction|bid|design|building navigation map|diagram|sketch

filter type CV

particulate air filter|chemical air filter|low-MERV pleated media|HEPA|
electrostatic|gas-phase or ultraviolet air treatments

fireplace type CV
```
gas burning|wood burning
```

floor condition CV

new|visible wear|needs repair|damaged|rupture

floor finish material CV

tile|wood strip or parquet|carpet|rug|laminate wood|lineoleum|vinyl composition tile|
sheet vinyl|stone|bamboo|cork|terrazo|concrete|none;specify unfinished|sealed|
clear finish|paint

floor signs of water/mold CV

mold odor|wet floor|water stains|wall discoloration|floor discoloration|
ceiling discoloration|peeling paint or wallpaper|bulging walls|condensation

floor structure CV

balcony|floating floor|glass floor|raised floor|sprung floor|wood-framed|concrete

furniture CV
```
cabinet|chair|desks
```

gender of restroom CV
```
male|female
```

growth habit CV
```
erect|semi-erect|spreading|prostrate
```

growth media CV
```
soil|liquid
```

handidness CV

ambidexterity|left handedness|mixed-handedness|right handedness

heating and cooling system type CV

radiant system|heat pump|forced air system|steam forced heat|wood stove

heating delivery locations CV
```
north|south|east|west
```

heating system delivery method CV
```
conductive|radiant
```

history/tillage CV

drill|cutting disc|ridge till|strip tillage|zonal tillage|chisel|tined|mouldboard|
disc plough

horizon CV

O horizon|A horizon|E horizon|B horizon|C horizon|R layer|Permafrost

host sex CV

male|female|neuter|hermaphrodite|not determined

hydrocarbon resource geological age CV

Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|
Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other

hydrocarbon resource type CV

Oil Reservoir|Gas Reservoir|Oil Sand|Coalbed|Shale|Tight Oil Reservoir|
Tight Gas Reservoir|other

hydrocarbon type produced CV

Oil|Gas-Condensate|Gas|Bitumen|Coalbed Methane|other

indoor space CV

bedroom|office|bathroom|foyer|kitchen|locker room|hallway|elevator

indoor surface CV

counter top|window|wall|cabinet|ceiling|door|shelving|vent cover

interior wall condition CV

new|visible wear|needs repair|damaged|rupture

light type CV

natural light|electric light|desk lamp|flourescent lights|natural light|none

lithology CV

Basement|Chalk|Chert|Coal|Conglomerate|Diatomite|Dolomite|Limestone|Sandstone|Shale|
Siltstone|Volcanic|other

mechanical structure CV

subway|coach|carriage|elevator|escalator|boat|train|car|bus

occupancy documentation CV

automated count|estimate|manual count|videos

organism count CV
```
qPCR|ATP|MPN|other
```

orientations of exterior wall CV

north|south|east|west|northeast|southeast|southwest|northwest

orientations of exterior window CV

north|south|east|west|northeast|southeast|southwest|northwest

oxygenation status of sample CV
```
aerobic|anaerobic|other
```

plant sex CV

Androdioecious|Androecious|Androgynous|Androgynomonoecious|Andromonoecious|
Bisexual|Dichogamous|Diclinous|Dioecious|Gynodioecious|Gynoecious|Gynomonoecious|
Hermaphroditic|Imperfect|Monoclinous|Monoecious|Perfect|Polygamodioecious|
Polygamomonoecious|Polygamous|Protandrous|Protogynous|Subandroecious|Subdioecious|
Subgynoecious|Synoecious|Trimonoecious|Trioecious|Unisexual

presence of pets, animals, or insects CV
```
cat|dog|rodent|snake|other
```

profile position CV

summit|shoulder|backslope|footslope|toeslope

quadrant position CV

North side|West side|South side|East side

relative sampling location CV
```
edge of car|center of car|under a seat
```

room condition CV

new|visible wear|needs repair|damaged|rupture|visible signs of mold/mildew

room location in building CV

corner room|interior room|exterior wall

room sampling position CV

north corner|south corner|west corner|east corner|northeast corner|
northwest corner|southeast corner|southwest corner|center

room type CV

attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|
mail room|private office|open office|stairwell|,restroom|lobby|vestibule|
mechanical or electrical room|data center|laboratory_wet|laboratory_dry|
gymnasium|natatorium|auditorium|lockers|cafe|warehouse

rooms connected by a doorway CV

attic|bathroom|closet|conference room|elevator|examining room|hallway|kitchen|
mail room|office|stairwell

sample capture status CV

active surveillance in response to an outbreak|
active surveillance not initiated by an outbreak|
farm sample|market sample|other

sample collection point CV

well|test well|drilling rig|wellhead|separator|storage tank|other

sample measured depth CV
```
GL|DF|RT|KB|MSL|other
```

sample subtype CV

oil phase|water phase|biofilm|not applicable|other

sample type CV

core|rock trimmings|drill cuttings|piping section|coupon|pigging debris|solid deposit|
produced fluid|produced water|injected water|water from treatment plant|fresh water|
sea water|drilling fluid|procedural blank|positive control|negative control|other

sampling day weather CV

clear sky|cloudy|foggy|hail|rain|snow|sleet|sunny|windy

sampling floor CV

lobby|basement|1st floor|2nd floor|{integer} floor

season CV
```
Spring|Summer|Fall|Winter
```

seasonal use CV
```
Spring|Summer|Fall|Winter
```

secondary and tertiary recovery methods CV

Water Injection|Dump Flood|Gas Injection|Wag Immiscible Injection|Polymer Addition|
Surfactant Addition|Not Applicable|other

sediment type CV

biogenous|cosmogenous|hydrogenous|lithogenous

shading device condition CV

damaged|needs repair|new|rupture|visible wear

shading device location CV
```
exterior|interior
```

shading device signs of water/mold CV

presence of mold visible|no presence of mold visible

shading device type CV

bahama shutters|exterior roll blind|gambrel awning|hood awning|
porchroller awning|sarasota shutters|slatted aluminum|solid aluminum awning|
sun screen|tree|trellis|venetian awning

soil_taxonomic/FAO classification CV

Acrisols|Andosols|Arenosols|Cambisols|Chernozems|Ferralsols|Fluvisols|
Gleysols|Greyzems|Gypsisols|Histosols|Kastanozems|Lithosols|Luvisols|
Nitosols|Phaeozems|Planosols|Podzols|Podzoluvisols|Rankers|Regosols|
Rendzinas|Solonchaks|Solonetz|Vertisols|Yermosols

source rock depositional environment CV

Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other

source rock geological age CV

Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|
Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|
Triassic|other

source rock kerogen type CV
```
Type I|Type II|Type III|Type IV|other
```

source rock lithology CV

 Clastic|Carbonate|Coal|Biosilicieous|other

space typical state CV

  typically occupied|typically unoccupied

special diet CV

  low carb|reduced calorie|vegetarian|other(to be specified)

specifications CV

  operation|as built|construction|bid|design|photos

substructure type CV
```
  crawlspace|slab on grade|basement
```

surface material CV

  concrete|wood|stone|tile|plastic|glass|vinyl|metal|carpet|
  stainless steel|paint|cinder blocks|hay bales|stucco|adobe

surface-air contaminant CV

  dust|organic matter|particulate matter|volatile organic compounds|
  biological contaminants|radon|nutrients|biocides

tidal stage CV

  low tide|ebb tide|flood tide|high tide

train line CV
```
  red|green|orange
```

train station collection location CV

  south station above ground|south station underground|south station amtrak|
  forest hills|riverside

train stop collection location CV
```
  end|mid|downtown
```

urine/collection method CV
```
  clean catch|catheter
```

visual media CV

  photos|videos|commonly of the building|site context (adjacent buildings,
  vegetation, terrain, streets)|interiors|equipment|3D scans

wall construction type CV

  frame construction|joisted masonry|light noncombustible|masonry noncombustible|
  modified fire resistive|fire resistive

wall finish material CV

  plaster|gypsum plaster|veneer plaster|gypsum board|tile|terrazzo|
  stone facing|acoustical treatment|wood|metal|masonry

wall location CV
```
  north|south|east|west
```

wall signs of water/mold CV

  presence of mold visible|no presence of mold visible

wall surface treatment CV

  painted|wall paper|no treatment|paneling|stucco|fabric

wall texture CV

  crows feet|crows-foot stomp||double skip|hawk and trowel|knockdown|popcorn|orange peel|rosebud stomp|Santa-Fe 
  texture|skip trowel|smooth|stomp knockdown|swirl

water feature type CV

  fountain|pool|standing feature|stream|waterfall

weekday CV

  Monday|Tuesday|Wednesday|Thursday|Friday|Saturday|Sunday

window condition CV

  damaged|needs repair|new|rupture|visible wear

window covering CV
```
  blinds|curtains|none
```

window horizontal position CV
```
  left|middle|right
```

window location CV
```
  north|south|east|west
```

window material CV
```
  clad|fiberglass|metal|vinyl|wood
```

window signs of water/mold CV

  presence of mold visible|no presence of mold visible

window status CV
```
  closed|open
```

window type CV

  single-hung sash window|horizontal sash window|fixed window

window vertical position CV
```
  bottom|middle|top|low|middle|high
```