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4. MIxS controlled vocabularies

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pyilmaz edited this page Aug 30, 2017 · 24 revisions

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:

  1. 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`

  1. observed biotic relationship CV

     free living|parasitism|commensalism|symbiotic|mutualism

  1. 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

  1. 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

  1. relationship to oxygen CV

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

  1. taxa ID CV

     16S rRNA gene|multi-marker approach|other

  1. assembly quality CV

     high|med|low

  1. completeness approach CV

     marker gene|reference based|other

  1. contamination screening input CV

     ref db|kmer|coverage|combination

  1. decontamination software CV

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

  1. sorting technology CV

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

  1. single cell lysis approach CV

    chemical|enzymatic|physical|combination

  1. WGA amplication approach CV

    pcr based|mda based

  1. binning parameters CV

    homology search|kmer|coverage|codon usage|combination

  1. binning software CV

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

  1. MAG coverage software CV

    bwa|bbmap|bowtie|other

  1. aerospace structure CV

    plane|glider

  1. architectural structure CV

    building|shed|home

  1. biological status CV

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

  1. building occupancy type CV

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

  1. building setting CV

    urban|suburban|exurban|rural

  1. built structure setting CV

    urban|rural

  1. ceiling condition CV

    new|visible wear|needs repair|damaged|rupture

  1. ceiling finish material CV

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

  1. ceiling signs of water/mold CV

    presence of mold visible|no presence of mold visible

  1. ceiling structure CV

    wood frame|concrete

  1. 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

  1. ceiling type CV

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

  1. 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)

  1. 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

  1. 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

  1. dominant hand CV

    left|right|ambidextrous

  1. door condition CV

    damaged|needs repair|new|rupture|visible wear

  1. door direction of opening CV

    inward|outward|sideways

  1. door location CV

    north|south|east|west

  1. door material CV

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

  1. door movement CV

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

  1. door signs of water/mold CV

    presence of mold visible|no presence of mold visible

  1. door type CV

    composite|metal|wooden

  1. door type, composite CV

    metal covered|revolving|sliding|telescopic

  1. door type, metal CV

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

  1. 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

  1. drainage classification CV

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

  1. drawings CV

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

  1. filter type CV

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

  1. fireplace type CV

    gas burning|wood burning

  1. floor condition CV

    new|visible wear|needs repair|damaged|rupture

  1. 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

  1. 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

  1. floor structure CV

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

  1. furniture CV

    cabinet|chair|desks
  1. gender of restroom CV male|female

  1. growth habit CV

    erect|semi-erect|spreading|prostrate

  1. growth media CV

    soil|liquid

  1. handidness CV

    ambidexterity|left handedness|mixed-handedness|right handedness

  1. heating and cooling system type CV

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

  1. heating delivery locations CV

    north|south|east|west

  1. heating system delivery method CV

    conductive|radiant

  1. history/tillage CV

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

  1. horizon CV

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

  1. host sex CV

    male|female|neuter|hermaphrodite|not determined

  1. hydrocarbon resource geological age CV

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

  1. hydrocarbon resource type CV

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

  1. hydrocarbon type produced CV

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

  1. indoor space CV

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

  1. indoor surface CV

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

  1. interior wall condition CV

    new|visible wear|needs repair|damaged|rupture

  1. light type CV

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

  1. lithology CV

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

  1. mechanical structure CV

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

  1. occupancy documentation CV

    automated count|estimate|manual count|videos

  1. organism count CV

    qPCR|ATP|MPN|other

  1. orientations of exterior wall CV

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

  1. orientations of exterior window CV

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

  1. oxygenation status of sample CV

    aerobic|anaerobic|other

  1. 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

  1. presence of pets, animals, or insects CV

    cat|dog|rodent|snake|other

  1. profile position CV

    summit|shoulder|backslope|footslope|toeslope

  1. quadrant position CV

    North side|West side|South side|East side

  1. relative sampling location CV

    edge of car|center of car|under a seat

  1. room condition CV

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

  1. room location in building CV

    corner room|interior room|exterior wall

  1. room sampling position CV

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

  1. 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

  1. rooms connected by a doorway CV

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

  1. sample capture status CV

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

  1. sample collection point CV

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

  1. sample measured depth CV

    GL|DF|RT|KB|MSL|other

  1. sample subtype CV

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

  1. 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

  1. sampling day weather CV

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

  1. sampling floor CV

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

  1. season CV

    Spring|Summer|Fall|Winter

  1. seasonal use CV

    Spring|Summer|Fall|Winter

  1. secondary and tertiary recovery methods CV

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

  1. sediment type CV

    biogenous|cosmogenous|hydrogenous|lithogenous

  1. shading device condition CV

    damaged|needs repair|new|rupture|visible wear

  1. shading device location CV

    exterior|interior

  1. shading device signs of water/mold CV

    presence of mold visible|no presence of mold visible

  1. shading device type CV

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

  1. soil_taxonomic/FAO classification CV

  2. source rock depositional environment CV

    Lacustine|Fluvioldeltaic|Fluviomarine|Marine|other

  1. source rock geological age CV Archean|Cambrian|Carboniferous|Cenozoic|Cretaceous|Devonian|Jurassic|Mesozoic|Neogene|Ordovician|Paleogene|Paleozoic|Permian|Precambrian|Proterozoic|Silurian|Triassic|other

  1. source rock kerogen type CV

    Type I|Type II|Type III|Type IV|other

  1. source rock lithology CV

    Clastic|Carbonate|Coal|Biosilicieous|other

  1. space typical state CV typical occupied|typically unoccupied

  1. special diet CV

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

  1. specifications CV operation|as built|construction|bid|design|photos

  1. substructure type CV

    crawlspace|slab on grade|basement

  1. surface material CV

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

  1. surface-air contaminant CV

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

  1. tidal stage CV

    low|high

  1. train line CV

    red|green|orange

  1. train station collection location CV

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

  1. train stop collection location CV

    end|mid|downtown

  1. urine/collection method CV

    clean catch|catheter

  1. visual media CV

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

  1. wall construction type CV

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

  1. wall finish material CV

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

  2. wall location CV

    north|south|east|west

  1. wall signs of water/mold CV

    presence of mold visible|no presence of mold visible

  1. wall surface treatment CV

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

  1. 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

  1. water feature type CV

    fountain|pool|standing feature|stream|waterfall

  1. weekday CV

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

  1. window condition CV

    damaged|needs repair|new|rupture|visible wear

  1. window covering CV

    blinds|curtains|none

  1. window horizontal position CV

    left|middle|right

  1. window location CV

    north|south|east|west

  1. window material CV

    clad|fiberglass|metal|vinyl|wood

  1. window signs of water/mold CV

      presence of mold visible|no presence of mold visible

  1. window status CV

    closed|open

  1. window type CV

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

  1. window vertical position CV

    bottom|middle|top|low|middle|high

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