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:

  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|

  1. observed biotic relationship CV

     free living|parasitism|commensalism|symbiotic|mutualism

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

     pre-existing condition|pathological|life threatening|congenital

  1. trophic level CV


  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


  1. completeness approach CV

    marker gene|reference based|other

  1. contamination screening input CV

    ref db|kmer|coverage|combination

  1. decontamination software CV


  1. sorting technology CV

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

  1. single cell lysis approach CV


  1. WGA amplication approach CV

    pcr based|mda based

  1. binning parameters CV

    homology search|kmer|coverage|codon usage|combination

  1. binning software CV


  1. MAG coverage software CV


  1. aerospace structure CV


  1. architectural structure CV


  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


  1. built structure setting CV


  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


  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


  1. door condition CV

    damaged|needs repair|new|rupture|visible wear

  1. door direction of opening CV


  1. door location CV


  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


  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


  1. gender of restroom CV


  1. growth habit CV


  1. growth media CV


  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


  1. heating system delivery method CV


  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


  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


  1. mechanical structure CV


  1. occupancy documentation CV

    automated count|estimate|manual count|videos

  1. organism count CV


  1. orientations of exterior wall CV


  1. orientations of exterior window CV


  1. oxygenation status of sample CV


  1. plant sex CV


  1. presence of pets, animals, or insects CV


  1. profile position CV


  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|

  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


  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


  1. seasonal use CV


  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


  1. shading device condition CV

    damaged|needs repair|new|rupture|visible wear

  1. shading device location CV


  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 screen|tree|trellis|venetian awning

  1. soil_taxonomic/FAO classification CV


  1. source rock depositional environment CV


  1. source rock geological age CV


  1. source rock kerogen type CV

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

  1. source rock lithology CV


  1. space typical state CV

      typically 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

      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 tide|ebb tide|flood tide|high tide

  1. train line CV


  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


  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

  1. wall location CV


  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


  1. window condition CV

      damaged|needs repair|new|rupture|visible wear

  1. window covering CV


  1. window horizontal position CV


  1. window location CV


  1. window material CV


  1. window signs of water/mold CV

      presence of mold visible|no presence of mold visible

  1. window status CV


  1. window type CV

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

  1. window vertical position CV