MIxS

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Namespace URI: http://gensc.org/ns/mixs/ with preferred namespace prefix “mixs”.



 




Collections in MIxS:

MIxS Environment Vocabulary  •  MIxS Investigation Vocabulary  •  MIxS Nucleic Acid Sequence Source Vocabulary  •  MIxS Sequencing  •  mixs:air  •  mixs:built environment  •  mixs:host-associated  •  mixs:human-associated  •  mixs:human-gut  •  mixs:human-oral  •  mixs:human-skin  •  mixs:human-vaginal  •  mixs:microbial mat/biofilm  •  mixs:misc environment  •  mixs:miscellaneous natural or artificial environment  •  mixs:plant-associated  •  mixs:sediment  •  mixs:soil  •  mixs:wastewater/sludge  •  mixs:water

Concepts in MIxS (grouped by collection):

MIxS Environment Vocabulary

By concept name: mixs:alt elev  •  mixs:collection date  •  mixs:env biome  •  mixs:env feature  •  mixs:env material  •  mixs:env package  •  mixs:geo loc name  •  mixs:lat lon

MIxS Investigation Vocabulary

MIxS Nucleic Acid Sequence Source Vocabulary

MIxS Sequencing

By concept name: mixs:adapters  •  mixs:annot source  •  mixs:assembly  •  mixs:assembly name  •  mixs:chimera check  •  mixs:finishing strategy  •  mixs:lib const meth  •  mixs:lib reads seqd  •  mixs:lib screen  •  mixs:lib size  •  mixs:lib vector  •  mixs:mid  •  mixs:nucl acid amp  •  mixs:nucl acid ext  •  mixs:pcr cond  •  mixs:pcr primers  •  mixs:seq meth  •  mixs:sop  •  mixs:target gene  •  mixs:target subfragment  •  mixs:url

mixs:air

mixs:built environment

mixs:host-associated

mixs:human-associated

By label: IHMC ethnicity  •  IHMC medication code  •  amniotic fluid/color  •  amniotic fluid/foetal health status  •  amniotic fluid/gestation state  •  amniotic fluid/maternal health status  •  blood/blood disorder  •  chemical administration  •  drug usage  •  host HIV status  •  host age  •  host body product  •  host body site  •  host body temperature  •  host body-mass index  •  host diet  •  host disease status  •  host family relationship  •  host genotype  •  host height  •  host last meal  •  host occupation  •  host phenotype  •  host pulse  •  host sex  •  host subject id  •  host total mass  •  lung/nose-throat disorder  •  lung/pulmonary disorder  •  major diet change in last six months  •  medical history performed  •  miscellaneous parameter  •  organism count  •  oxygenation status of sample  •  perturbation  •  presence of pets or farm animals  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  smoker  •  study completion status  •  temperature  •  travel outside the country in last six months  •  twin sibling presence  •  urine/collection method  •  urine/kidney disorder  •  urine/urogenital tract disorder  •  weight loss in last three months

mixs:human-gut

mixs:human-oral

mixs:human-skin

mixs:human-vaginal

mixs:microbial mat/biofilm

By label: alkalinity  •  alkyl diethers  •  altitude  •  aminopeptidase activity  •  ammonium  •  bacterial carbon production  •  biomass  •  bishomohopanol  •  bromide  •  calcium  •  carbon/nitrogen ratio  •  chemical administration  •  chloride  •  chlorophyll  •  diether lipids  •  dissolved carbon dioxide  •  dissolved hydrogen  •  dissolved inorganic carbon  •  dissolved organic carbon  •  dissolved organic nitrogen  •  dissolved oxygen  •  elevation  •  geographic location (depth)  •  glucosidase activity  •  magnesium  •  mean friction velocity  •  mean peak friction velocity  •  methane  •  miscellaneous parameter  •  n-alkanes  •  nitrate  •  nitrite  •  nitrogen  •  organic carbon  •  organic matter  •  organic nitrogen  •  organism count  •  oxygenation status of sample  •  pH  •  particulate organic carbon  •  perturbation  •  petroleum hydrocarbon  •  phaeopigments  •  phosphate  •  phospholipid fatty acid  •  potassium  •  pressure  •  redox potential  •  salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  silicate  •  sodium  •  sulfate  •  sulfide  •  temperature  •  total carbon  •  total nitrogen  •  total organic carbon  •  turbidity  •  water content
By concept name: mixs:alkalinity  •  mixs:alkyl diethers  •  mixs:alt  •  mixs:aminopept act  •  mixs:ammonium  •  mixs:bacteria carb prod  •  mixs:biomass  •  mixs:bishomohopanol  •  mixs:bromide  •  mixs:calcium  •  mixs:carb nitro ratio  •  mixs:chem administration  •  mixs:chloride  •  mixs:chlorophyll  •  mixs:depth  •  mixs:diether lipids  •  mixs:diss carb dioxide  •  mixs:diss hydrogen  •  mixs:diss inorg carb  •  mixs:diss org carb  •  mixs:diss org nitro  •  mixs:diss oxygen  •  mixs:elev  •  mixs:glucosidase act  •  mixs:magnesium  •  mixs:mean frict vel  •  mixs:mean peak frict vel  •  mixs:methane  •  mixs:misc param  •  mixs:n alkanes  •  mixs:nitrate  •  mixs:nitrite  •  mixs:nitro  •  mixs:org carb  •  mixs:org matter  •  mixs:org nitro  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:part org carb  •  mixs:perturbation  •  mixs:petroleum hydrocarb  •  mixs:ph  •  mixs:phaeopigments  •  mixs:phosphate  •  mixs:phosplipid fatt acid  •  mixs:potassium  •  mixs:pressure  •  mixs:redox potential  •  mixs:salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:silicate  •  mixs:sodium  •  mixs:sulfate  •  mixs:sulfide  •  mixs:temp  •  mixs:tot carb  •  mixs:tot nitro  •  mixs:tot org carb  •  mixs:turbidity  •  mixs:water content

mixs:misc environment

By label:
  • No labels found in collection “mixs:misc environment”
By concept name:
  • No concepts found in collection “mixs:misc environment”

mixs:miscellaneous natural or artificial environment

By label: alkalinity  •  altitude  •  ammonium  •  biomass  •  bromide  •  calcium  •  chemical administration  •  chloride  •  chlorophyll  •  density  •  diether lipids  •  dissolved carbon dioxide  •  dissolved hydrogen  •  dissolved inorganic carbon  •  dissolved organic nitrogen  •  dissolved oxygen  •  elevation  •  geographic location (depth)  •  miscellaneous parameter  •  nitrate  •  nitrite  •  nitrogen  •  organic carbon  •  organic matter  •  organic nitrogen  •  organism count  •  oxygenation status of sample  •  pH  •  perturbation  •  phosphate  •  phospholipid fatty acid  •  potassium  •  pressure  •  salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  silicate  •  sodium  •  sulfate  •  sulfide  •  temperature  •  water current
By concept name: mixs:alkalinity  •  mixs:alt  •  mixs:ammonium  •  mixs:biomass  •  mixs:bromide  •  mixs:calcium  •  mixs:chem administration  •  mixs:chloride  •  mixs:chlorophyll  •  mixs:density  •  mixs:depth  •  mixs:diether lipids  •  mixs:diss carb dioxide  •  mixs:diss hydrogen  •  mixs:diss inorg carb  •  mixs:diss org nitro  •  mixs:diss oxygen  •  mixs:elev  •  mixs:misc param  •  mixs:nitrate  •  mixs:nitrite  •  mixs:nitro  •  mixs:org carb  •  mixs:org matter  •  mixs:org nitro  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:ph  •  mixs:phosphate  •  mixs:phosplipid fatt acid  •  mixs:potassium  •  mixs:pressure  •  mixs:salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:silicate  •  mixs:sodium  •  mixs:sulfate  •  mixs:sulfide  •  mixs:temp  •  mixs:water current

mixs:plant-associated

By label: air temperature regimen  •  altitude  •  antibiotic regimen  •  chemical administration  •  chemical mutagen  •  climate environment  •  elevation  •  fertilizer regimen  •  fungicide regimen  •  gaseous environment  •  geographic location (depth)  •  gravity  •  growth hormone regimen  •  growth media  •  herbicide regimen  •  host age  •  host common name  •  host disease status  •  host dry mass  •  host genotype  •  host height  •  host infra-specific name  •  host infra-specific rank  •  host length  •  host life stage  •  host phenotype  •  host taxid  •  host total mass  •  host wet mass  •  humidity regimen  •  mechanical damage  •  mineral nutrient regimen  •  miscellaneous parameter  •  non-mineral nutrient regimen  •  organism count  •  oxygenation status of sample  •  pH regimen  •  perturbation  •  pesticide regimen  •  plant body site  •  plant product  •  radiation regimen  •  rainfall regimen  •  salt regimen  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  seasonal environment  •  standing water regimen  •  temperature  •  tissue culture growth media  •  water temperature regimen  •  watering regimen
By concept name: mixs:air temp regm  •  mixs:alt  •  mixs:antibiotic regm  •  mixs:chem administration  •  mixs:chem mutagen  •  mixs:climate environment  •  mixs:depth  •  mixs:elev  •  mixs:fertilizer regm  •  mixs:fungicide regm  •  mixs:gaseous environment  •  mixs:gravity  •  mixs:growth hormone regm  •  mixs:growth med  •  mixs:herbicide regm  •  mixs:host age  •  mixs:host common name  •  mixs:host disease stat  •  mixs:host dry mass  •  mixs:host genotype  •  mixs:host height  •  mixs:host infra specific name  •  mixs:host infra specific rank  •  mixs:host length  •  mixs:host life stage  •  mixs:host phenotype  •  mixs:host taxid  •  mixs:host tot mass  •  mixs:host wet mass  •  mixs:humidity regm  •  mixs:mechanical damage  •  mixs:mineral nutr regm  •  mixs:misc param  •  mixs:non mineral nutr regm  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:pesticide regm  •  mixs:ph regm  •  mixs:plant body site  •  mixs:plant product  •  mixs:radiation regm  •  mixs:rainfall regm  •  mixs:salt regm  •  mixs:samp salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:season environment  •  mixs:standing water regm  •  mixs:temp  •  mixs:tiss cult growth med  •  mixs:water temp regm  •  mixs:watering regm

mixs:sediment

By label: alkalinity  •  alkyl diethers  •  altitude  •  aminopeptidase activity  •  ammonium  •  bacterial carbon production  •  biomass  •  bishomohopanol  •  bromide  •  calcium  •  carbon/nitrogen ratio  •  chemical administration  •  chloride  •  chlorophyll  •  density  •  diether lipids  •  dissolved carbon dioxide  •  dissolved hydrogen  •  dissolved inorganic carbon  •  dissolved organic carbon  •  dissolved organic nitrogen  •  dissolved oxygen  •  elevation  •  geographic location (depth)  •  glucosidase activity  •  magnesium  •  mean friction velocity  •  mean peak friction velocity  •  methane  •  miscellaneous parameter  •  n-alkanes  •  nitrate  •  nitrite  •  nitrogen  •  organic carbon  •  organic matter  •  organic nitrogen  •  organism count  •  oxygenation status of sample  •  pH  •  particle classification  •  particulate organic carbon  •  perturbation  •  petroleum hydrocarbon  •  phaeopigments  •  phosphate  •  phospholipid fatty acid  •  porosity  •  potassium  •  pressure  •  redox potential  •  salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  sediment type  •  silicate  •  sodium  •  sulfate  •  sulfide  •  temperature  •  tidal stage  •  total carbon  •  total nitrogen  •  total organic carbon  •  turbidity  •  water content
By concept name: mixs:alkalinity  •  mixs:alkyl diethers  •  mixs:alt  •  mixs:aminopept act  •  mixs:ammonium  •  mixs:bacteria carb prod  •  mixs:biomass  •  mixs:bishomohopanol  •  mixs:bromide  •  mixs:calcium  •  mixs:carb nitro ratio  •  mixs:chem administration  •  mixs:chloride  •  mixs:chlorophyll  •  mixs:density  •  mixs:depth  •  mixs:diether lipids  •  mixs:diss carb dioxide  •  mixs:diss hydrogen  •  mixs:diss inorg carb  •  mixs:diss org carb  •  mixs:diss org nitro  •  mixs:diss oxygen  •  mixs:elev  •  mixs:glucosidase act  •  mixs:magnesium  •  mixs:mean frict vel  •  mixs:mean peak frict vel  •  mixs:methane  •  mixs:misc param  •  mixs:n alkanes  •  mixs:nitrate  •  mixs:nitrite  •  mixs:nitro  •  mixs:org carb  •  mixs:org matter  •  mixs:org nitro  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:part org carb  •  mixs:particle class  •  mixs:perturbation  •  mixs:petroleum hydrocarb  •  mixs:ph  •  mixs:phaeopigments  •  mixs:phosphate  •  mixs:phosplipid fatt acid  •  mixs:porosity  •  mixs:potassium  •  mixs:pressure  •  mixs:redox potential  •  mixs:salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:sediment type  •  mixs:silicate  •  mixs:sodium  •  mixs:sulfate  •  mixs:sulfide  •  mixs:temp  •  mixs:tidal stage  •  mixs:tot carb  •  mixs:tot nitro  •  mixs:tot org carb  •  mixs:turbidity  •  mixs:water content

mixs:soil

By label: altitude  •  composite design/sieving (if any)  •  current land use  •  current vegetation  •  current vegetation method  •  drainage classification  •  elevation  •  extreme_unusual_properties/Al saturation  •  extreme_unusual_properties/Al saturation method  •  extreme_unusual_properties/heavy metals  •  extreme_unusual_properties/heavy metals method  •  extreme_unusual_properties/salinity  •  extreme_unusual_properties/salinity method  •  geographic location (depth)  •  history/agrochemical additions  •  history/crop rotation  •  history/extreme events  •  history/fire  •  history/flooding  •  history/previous land use  •  history/previous land use method  •  history/tillage  •  horizon  •  horizon method  •  link to classification information  •  link to climate information  •  links to additional analysis  •  mean annual and seasonal precipitation  •  mean annual and seasonal temperature  •  microbial biomass  •  microbial biomass method  •  miscellaneous parameter  •  pH  •  pH method  •  pooling of DNA extracts (if done)  •  profile position  •  sample volume or weight for DNA extraction  •  slope aspect  •  slope gradient  •  soil type  •  soil type method  •  soil_taxonomic/FAO classification  •  soil_taxonomic/local classification  •  soil_taxonomic/local classification method  •  storage conditions (fresh/frozen/other)  •  texture  •  texture method  •  total nitrogen  •  total nitrogen method  •  total organic carbon  •  total organic carbon method  •  water content  •  water content method

mixs:wastewater/sludge

mixs:water

By label: alkalinity  •  alkyl diethers  •  altitude  •  aminopeptidase activity  •  ammonium  •  atmospheric data  •  bacterial carbon production  •  bacterial production  •  bacterial respiration  •  biomass  •  bishomohopanol  •  bromide  •  calcium  •  carbon/nitrogen ratio  •  chemical administration  •  chloride  •  chlorophyll  •  conductivity  •  density  •  diether lipids  •  dissolved carbon dioxide  •  dissolved hydrogen  •  dissolved inorganic carbon  •  dissolved inorganic nitrogen  •  dissolved inorganic phosphorus  •  dissolved organic carbon  •  dissolved organic nitrogen  •  dissolved oxygen  •  downward PAR  •  elevation  •  fluorescence  •  geographic location (depth)  •  glucosidase activity  •  light intensity  •  magnesium  •  mean friction velocity  •  mean peak friction velocity  •  miscellaneous parameter  •  n-alkanes  •  nitrate  •  nitrite  •  nitrogen  •  organic carbon  •  organic matter  •  organic nitrogen  •  organism count  •  oxygenation status of sample  •  pH  •  particulate organic carbon  •  particulate organic nitrogen  •  perturbation  •  petroleum hydrocarbon  •  phaeopigments  •  phosphate  •  phospholipid fatty acid  •  photon flux  •  potassium  •  pressure  •  primary production  •  redox potential  •  salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  silicate  •  sodium  •  soluble reactive phosphorus  •  sulfate  •  sulfide  •  suspended particulate matter  •  temperature  •  tidal stage  •  total depth of water column  •  total dissolved nitrogen  •  total inorganic nitrogen  •  total nitrogen  •  total particulate carbon  •  total phosphorus  •  water current
By concept name: mixs:alkalinity  •  mixs:alkyl diethers  •  mixs:alt  •  mixs:aminopept act  •  mixs:ammonium  •  mixs:atmospheric data  •  mixs:bac prod  •  mixs:bac resp  •  mixs:bacteria carb prod  •  mixs:biomass  •  mixs:bishomohopanol  •  mixs:bromide  •  mixs:calcium  •  mixs:carb nitro ratio  •  mixs:chem administration  •  mixs:chloride  •  mixs:chlorophyll  •  mixs:conduc  •  mixs:density  •  mixs:depth  •  mixs:diether lipids  •  mixs:diss carb dioxide  •  mixs:diss hydrogen  •  mixs:diss inorg carb  •  mixs:diss inorg nitro  •  mixs:diss inorg phosp  •  mixs:diss org carb  •  mixs:diss org nitro  •  mixs:diss oxygen  •  mixs:down par  •  mixs:elev  •  mixs:fluor  •  mixs:glucosidase act  •  mixs:light intensity  •  mixs:magnesium  •  mixs:mean frict vel  •  mixs:mean peak frict vel  •  mixs:misc param  •  mixs:n alkanes  •  mixs:nitrate  •  mixs:nitrite  •  mixs:nitro  •  mixs:org carb  •  mixs:org matter  •  mixs:org nitro  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:part org carb  •  mixs:part org nitro  •  mixs:perturbation  •  mixs:petroleum hydrocarb  •  mixs:ph  •  mixs:phaeopigments  •  mixs:phosphate  •  mixs:phosplipid fatt acid  •  mixs:photon flux  •  mixs:potassium  •  mixs:pressure  •  mixs:primary prod  •  mixs:redox potential  •  mixs:salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:silicate  •  mixs:sodium  •  mixs:soluble react phosp  •  mixs:sulfate  •  mixs:sulfide  •  mixs:suspend part matter  •  mixs:temp  •  mixs:tidal stage  •  mixs:tot depth water col  •  mixs:tot diss nitro  •  mixs:tot inorg nitro  •  mixs:tot nitro  •  mixs:tot part carb  •  mixs:tot phosp  •  mixs:water current


Dynamic Term List

Note that only term definitions of 17 collections out of 20 can be displayed here in detail, the remaining collections can be accessed on further result pages (the link at the bottom of this page).

Index to concepts (all collections combined)

By label: HRT  •  IHMC ethnicity  •  IHMC medication code  •  absolute air humidity  •  adapters  •  air temperature regimen  •  alkalinity  •  alkyl diethers  •  altitude  •  altitude  •  aminopeptidase activity  •  ammonium  •  amniotic fluid/color  •  amniotic fluid/foetal health status  •  amniotic fluid/gestation state  •  amniotic fluid/maternal health status  •  annotation source  •  antibiotic regimen  •  assembly  •  assembly name  •  atmospheric data  •  bacterial carbon production  •  bacterial production  •  bacterial respiration  •  barometric pressure  •  biochemical oxygen demand  •  biomass  •  birth control  •  bishomohopanol  •  blood/blood disorder  •  bromide  •  building occupancy type  •  building setting  •  calcium  •  carbon dioxide  •  carbon monoxide  •  carbon/nitrogen ratio  •  chemical administration  •  chemical mutagen  •  chemical oxygen demand  •  chimera check  •  chloride  •  chlorophyll  •  climate environment  •  collection date  •  composite design/sieving (if any)  •  conductivity  •  current land use  •  current vegetation  •  current vegetation method  •  density  •  dermatology disorder  •  dew point  •  diether lipids  •  dissolved carbon dioxide  •  dissolved hydrogen  •  dissolved inorganic carbon  •  dissolved inorganic nitrogen  •  dissolved inorganic phosphorus  •  dissolved organic carbon  •  dissolved organic nitrogen  •  dissolved oxygen  •  dominant hand  •  douche  •  downward PAR  •  drainage classification  •  drug usage  •  efficiency percent  •  elevation  •  emulsions  •  encoded traits  •  environment (biome)  •  environment (feature)  •  environment (material)  •  environmental package  •  estimated Size  •  experimental factor  •  extrachromosomal elements  •  extreme_unusual_properties/Al saturation  •  extreme_unusual_properties/Al saturation method  •  extreme_unusual_properties/heavy metals  •  extreme_unusual_properties/heavy metals method  •  extreme_unusual_properties/salinity  •  extreme_unusual_properties/salinity method  •  fertilizer regimen  •  filter type  •  finishing strategy  •  fluorescence  •  fungicide regimen  •  gaseous environment  •  gaseous substances  •  gastrointestinal tract disorder  •  geographic location (altitude/elevation)  •  geographic location (country and/or sea,region)  •  geographic location (depth)  •  geographic location (latitude and longitude)  •  glucosidase activity  •  gravidity  •  gravity  •  growth hormone regimen  •  growth media  •  gynecological disorder  •  health or disease status of specific host at time of collection  •  heating and cooling system type  •  herbicide regimen  •  history/agrochemical additions  •  history/crop rotation  •  history/extreme events  •  history/fire  •  history/flooding  •  history/previous land use  •  history/previous land use method  •  history/tillage  •  horizon  •  horizon method  •  host HIV status  •  host age  •  host blood pressure diastolic  •  host blood pressure systolic  •  host body habitat  •  host body product  •  host body site  •  host body temperature  •  host body-mass index  •  host color  •  host common name  •  host diet  •  host disease status  •  host dry mass  •  host family relationship  •  host genotype  •  host growth conditions  •  host height  •  host infra-specific name  •  host infra-specific rank  •  host last meal  •  host length  •  host life stage  •  host occupation  •  host phenotype  •  host pulse  •  host sex  •  host shape  •  host specificity or range  •  host subject id  •  host substrate  •  host taxid  •  host total mass  •  host wet mass  •  humidity  •  humidity regimen  •  hysterectomy  •  indoor space  •  indoor surface  •  industrial effluent percent  •  inorganic particles  •  investigation type  •  isolation and growth condition  •  known pathogenicity  •  library construction method  •  library reads sequenced  •  library screening strategy  •  library size  •  library vector  •  light intensity  •  light type  •  link to classification information  •  link to climate information  •  links to additional analysis  •  liver disorder  •  lung/nose-throat disorder  •  lung/pulmonary disorder  •  magnesium  •  major diet change in last six months  •  mean annual and seasonal precipitation  •  mean annual and seasonal temperature  •  mean friction velocity  •  mean peak friction velocity  •  mechanical damage  •  medical history performed  •  menarche  •  menopause  •  methane  •  microbial biomass  •  microbial biomass method  •  mineral nutrient regimen  •  miscellaneous parameter  •  multiplex identifiers  •  n-alkanes  •  nitrate  •  nitrite  •  nitrogen  •  non-mineral nutrient regimen  •  nose/mouth/teeth/throat disorder  •  nucleic acid amplification  •  nucleic acid extraction  •  number of replicons  •  observed biotic relationship  •  occupancy at sampling  •  occupant density at sampling  •  organic carbon  •  organic matter  •  organic nitrogen  •  organic particles  •  organism count  •  oxygen  •  oxygenation status of sample  •  pH  •  pH method  •  pH regimen  •  particle classification  •  particulate organic carbon  •  particulate organic nitrogen  •  pcr conditions  •  pcr primers  •  perturbation  •  pesticide regimen  •  petroleum hydrocarbon  •  phaeopigments  •  phosphate  •  phospholipid fatty acid  •  photon flux  •  plant body site  •  plant product  •  ploidy  •  pollutants  •  pooling of DNA extracts (if done)  •  porosity  •  potassium  •  pre-treatment  •  pregnancy  •  presence of pets or farm animals  •  pressure  •  primary production  •  primary treatment  •  profile position  •  project name  •  propagation  •  radiation regimen  •  rainfall regimen  •  reactor type  •  redox potential  •  reference for biomaterial  •  relationship to oxygen  •  relative air humidity  •  relevant electronic resources  •  relevant standard operating procedures  •  respirable particulate matter  •  salinity  •  salt regimen  •  sample collection device or method  •  sample material processing  •  sample salinity  •  sample size  •  sample size sorting method  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  seasonal environment  •  secondary treatment  •  sediment type  •  sequencing method  •  sewage type  •  sexual activity  •  silicate  •  slope aspect  •  slope gradient  •  sludge retention time  •  smoker  •  sodium  •  soil type  •  soil type method  •  soil_taxonomic/FAO classification  •  soil_taxonomic/local classification  •  soil_taxonomic/local classification method  •  solar irradiance  •  soluble inorganic material  •  soluble organic material  •  soluble reactive phosphorus  •  source material identifiers  •  space typical state  •  special diet  •  specific host  •  standing water regimen  •  storage conditions (fresh/frozen/other)  •  study completion status  •  submitted to insdc  •  subspecific genetic lineage  •  substructure type  •  sulfate  •  sulfide  •  surface humidity  •  surface material  •  surface moisture  •  surface moisture pH  •  surface temperature  •  surface-air contaminant  •  suspended particulate matter  •  suspended solids  •  target gene  •  target subfragment  •  temperature  •  tertiary treatment  •  texture  •  texture method  •  tidal stage  •  time since last toothbrushing  •  time since last wash  •  tissue culture growth media  •  total carbon  •  total depth of water column  •  total dissolved nitrogen  •  total inorganic nitrogen  •  total nitrogen  •  total nitrogen method  •  total organic carbon  •  total organic carbon method  •  total particulate carbon  •  total phosphate  •  total phosphorus  •  travel outside the country in last six months  •  trophic level  •  turbidity  •  twin sibling presence  •  typical occupant density  •  urine/collection method  •  urine/kidney disorder  •  urine/urogenital tract disorder  •  urogenital disorder  •  ventilation rate  •  ventilation type  •  volatile organic compounds  •  wastewater type  •  water content  •  water content method  •  water current  •  water temperature regimen  •  watering regimen  •  weight loss in last three months  •  wind direction  •  wind speed
By concept name: mixs:abs air humidity  •  mixs:adapters  •  mixs:agrochem addition  •  mixs:air temp regm  •  mixs:al sat  •  mixs:al sat meth  •  mixs:alkalinity  •  mixs:alkyl diethers  •  mixs:alt  •  mixs:alt elev  •  mixs:altitude  •  mixs:aminopept act  •  mixs:ammonium  •  mixs:amniotic fluid color  •  mixs:annot source  •  mixs:annual season precpt  •  mixs:annual season temp  •  mixs:antibiotic regm  •  mixs:assembly  •  mixs:assembly name  •  mixs:atmospheric data  •  mixs:bac prod  •  mixs:bac resp  •  mixs:bacteria carb prod  •  mixs:barometric press  •  mixs:biochem oxygen dem  •  mixs:biomass  •  mixs:biotic relationship  •  mixs:birth control  •  mixs:bishomohopanol  •  mixs:blood blood disord  •  mixs:bromide  •  mixs:build occup type  •  mixs:building setting  •  mixs:calcium  •  mixs:carb dioxide  •  mixs:carb monoxide  •  mixs:carb nitro ratio  •  mixs:chem administration  •  mixs:chem mutagen  •  mixs:chem oxygen dem  •  mixs:chimera check  •  mixs:chloride  •  mixs:chlorophyll  •  mixs:climate environment  •  mixs:collection date  •  mixs:conduc  •  mixs:crop rotation  •  mixs:cur land use  •  mixs:cur vegetation  •  mixs:cur vegetation meth  •  mixs:density  •  mixs:depth  •  mixs:dermatology disord  •  mixs:dew point  •  mixs:diet last six month  •  mixs:diether lipids  •  mixs:diss carb dioxide  •  mixs:diss hydrogen  •  mixs:diss inorg carb  •  mixs:diss inorg nitro  •  mixs:diss inorg phosp  •  mixs:diss org carb  •  mixs:diss org nitro  •  mixs:diss oxygen  •  mixs:dominant hand  •  mixs:douche  •  mixs:down par  •  mixs:drainage class  •  mixs:drug usage  •  mixs:efficiency percent  •  mixs:elev  •  mixs:emulsions  •  mixs:encoded traits  •  mixs:env biome  •  mixs:env feature  •  mixs:env material  •  mixs:env package  •  mixs:estimated size  •  mixs:experimental factor  •  mixs:extrachrom elements  •  mixs:extreme event  •  mixs:extreme salinity  •  mixs:fao class  •  mixs:fertilizer regm  •  mixs:filter type  •  mixs:finishing strategy  •  mixs:fire  •  mixs:flooding  •  mixs:fluor  •  mixs:foetal health stat  •  mixs:fungicide regm  •  mixs:gaseous environment  •  mixs:gaseous substances  •  mixs:gastrointest disord  •  mixs:geo loc name  •  mixs:gestation state  •  mixs:glucosidase act  •  mixs:gravidity  •  mixs:gravity  •  mixs:growth hormone regm  •  mixs:growth med  •  mixs:gynecologic disord  •  mixs:health disease stat  •  mixs:heat cool type  •  mixs:heavy metals  •  mixs:heavy metals meth  •  mixs:herbicide regm  •  mixs:horizon  •  mixs:horizon meth  •  mixs:host age  •  mixs:host blood press diast  •  mixs:host blood press syst  •  mixs:host body habitat  •  mixs:host body mass index  •  mixs:host body product  •  mixs:host body site  •  mixs:host body temp  •  mixs:host color  •  mixs:host common name  •  mixs:host diet  •  mixs:host disease stat  •  mixs:host dry mass  •  mixs:host family relationship  •  mixs:host genotype  •  mixs:host growth cond  •  mixs:host height  •  mixs:host hiv stat  •  mixs:host infra specific name  •  mixs:host infra specific rank  •  mixs:host last meal  •  mixs:host length  •  mixs:host life stage  •  mixs:host occupation  •  mixs:host phenotype  •  mixs:host pulse  •  mixs:host sex  •  mixs:host shape  •  mixs:host spec range  •  mixs:host subject id  •  mixs:host substrate  •  mixs:host taxid  •  mixs:host tot mass  •  mixs:host wet mass  •  mixs:hrt  •  mixs:humidity  •  mixs:humidity regm  •  mixs:hysterectomy  •  mixs:ihmc ethnicity  •  mixs:ihmc medication code  •  mixs:indoor space  •  mixs:indoor surf  •  mixs:indust eff percent  •  mixs:inorg particles  •  mixs:investigation type  •  mixs:isol growth condt  •  mixs:kidney disord  •  mixs:lat lon  •  mixs:lib const meth  •  mixs:lib reads seqd  •  mixs:lib screen  •  mixs:lib size  •  mixs:lib vector  •  mixs:light intensity  •  mixs:light type  •  mixs:link addit analys  •  mixs:link class info  •  mixs:link climate info  •  mixs:liver disord  •  mixs:local class  •  mixs:local class meth  •  mixs:magnesium  •  mixs:maternal health stat  •  mixs:mean frict vel  •  mixs:mean peak frict vel  •  mixs:mechanical damage  •  mixs:medic hist perform  •  mixs:menarche  •  mixs:menopause  •  mixs:methane  •  mixs:microbial biomass  •  mixs:microbial biomass meth  •  mixs:mid  •  mixs:mineral nutr regm  •  mixs:misc param  •  mixs:n alkanes  •  mixs:nitrate  •  mixs:nitrite  •  mixs:nitro  •  mixs:non mineral nutr regm  •  mixs:nose mouth teeth throat disord  •  mixs:nose throat disord  •  mixs:nucl acid amp  •  mixs:nucl acid ext  •  mixs:num replicons  •  mixs:occup samp  •  mixs:occupant dens samp  •  mixs:org carb  •  mixs:org matter  •  mixs:org nitro  •  mixs:org particles  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:oxygen  •  mixs:part org carb  •  mixs:part org nitro  •  mixs:particle class  •  mixs:pathogenicity  •  mixs:pcr cond  •  mixs:pcr primers  •  mixs:perturbation  •  mixs:pesticide regm  •  mixs:pet farm animal  •  mixs:petroleum hydrocarb  •  mixs:ph  •  mixs:ph meth  •  mixs:ph regm  •  mixs:phaeopigments  •  mixs:phosphate  •  mixs:phosplipid fatt acid  •  mixs:photon flux  •  mixs:plant body site  •  mixs:plant product  •  mixs:ploidy  •  mixs:pollutants  •  mixs:pool dna extracts  •  mixs:porosity  •  mixs:potassium  •  mixs:pre treatment  •  mixs:pregnancy  •  mixs:pressure  •  mixs:previous land use  •  mixs:previous land use meth  •  mixs:primary prod  •  mixs:primary treatment  •  mixs:profile position  •  mixs:project name  •  mixs:propagation  •  mixs:pulmonary disord  •  mixs:radiation regm  •  mixs:rainfall regm  •  mixs:reactor type  •  mixs:redox potential  •  mixs:ref biomaterial  •  mixs:rel air humidity  •  mixs:rel to oxygen  •  mixs:resp part matter  •  mixs:salinity  •  mixs:salinity meth  •  mixs:salt regm  •  mixs:samp collect device  •  mixs:samp mat process  •  mixs:samp salinity  •  mixs:samp size  •  mixs:samp sort meth  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:season environment  •  mixs:secondary treatment  •  mixs:sediment type  •  mixs:seq meth  •  mixs:sewage type  •  mixs:sexual act  •  mixs:sieving  •  mixs:silicate  •  mixs:slope aspect  •  mixs:slope gradient  •  mixs:sludge retent time  •  mixs:smoker  •  mixs:sodium  •  mixs:soil type  •  mixs:soil type meth  •  mixs:solar irradiance  •  mixs:soluble inorg mat  •  mixs:soluble org mat  •  mixs:soluble react phosp  •  mixs:sop  •  mixs:source mat id  •  mixs:space typ state  •  mixs:special diet  •  mixs:specific host  •  mixs:standing water regm  •  mixs:store cond  •  mixs:study complt stat  •  mixs:submitted to insdc  •  mixs:subspecf gen lin  •  mixs:substructure type  •  mixs:sulfate  •  mixs:sulfide  •  mixs:surf air cont  •  mixs:surf humidity  •  mixs:surf material  •  mixs:surf moisture  •  mixs:surf moisture ph  •  mixs:surf temp  •  mixs:suspend part matter  •  mixs:suspend solids  •  mixs:target gene  •  mixs:target subfragment  •  mixs:temp  •  mixs:tertiary treatment  •  mixs:texture  •  mixs:texture meth  •  mixs:tidal stage  •  mixs:tillage  •  mixs:time last toothbrush  •  mixs:time since last wash  •  mixs:tiss cult growth med  •  mixs:tot carb  •  mixs:tot depth water col  •  mixs:tot diss nitro  •  mixs:tot inorg nitro  •  mixs:tot n meth  •  mixs:tot nitro  •  mixs:tot org c meth  •  mixs:tot org carb  •  mixs:tot part carb  •  mixs:tot phosp  •  mixs:tot phosphate  •  mixs:travel out six month  •  mixs:trophic level  •  mixs:turbidity  •  mixs:twin sibling  •  mixs:typ occupant dens  •  mixs:urine collect meth  •  mixs:url  •  mixs:urogenit disord  •  mixs:urogenit tract disor  •  mixs:ventilation rate  •  mixs:ventilation type  •  mixs:volatile org comp  •  mixs:wastewater type  •  mixs:water content  •  mixs:water content soil meth  •  mixs:water current  •  mixs:water temp regm  •  mixs:watering regm  •  mixs:weight loss 3 month  •  mixs:wind direction  •  mixs:wind speed

MIxS Environment Vocabulary

Index to MIxS Environment Vocabulary
By label: collection date  •  environment (biome)  •  environment (feature)  •  environment (material)  •  environmental package  •  geographic location (altitude/elevation)  •  geographic location (country and/or sea,region)  •  geographic location (latitude and longitude)
By concept name: mixs:alt elev  •  mixs:collection date  •  mixs:env biome  •  mixs:env feature  •  mixs:env material  •  mixs:env package  •  mixs:geo loc name  •  mixs:lat lon
Concept definitions in MIxS Environment Vocabulary
Concept Name: mixs:alt elev
Normative URI http://gensc.org/ns/mixs/alt_elev
Label geographic location (altitude/elevation)
Definition Please refer to the definitions of either altitude or elevation in the environmental packages
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:collection date
Normative URI http://gensc.org/ns/mixs/collection_date
Label collection date
Definition The time of sampling, either as an instance (single point in time) or interval. In case no exact time is available, the date/time can be right truncated i.e. all of these are valid times: 2008-01-23T19:23:10+00:00; 2008-01-23T19:23:10; 2008-01-23; 2008-01; 2008; Except: 2008-01; 2008 all are ISO8601 compliant
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:env biome
Normative URI http://gensc.org/ns/mixs/env_biome
Label environment (biome)
Definition Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate. Biome should be treated as the descriptor of the broad ecological context of a sample. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:env feature
Normative URI http://gensc.org/ns/mixs/env_feature
Label environment (feature)
Definition Environmental feature level includes geographic environmental features. Compared to biome, feature is a descriptor of the more local environment. Examples include: harbor, cliff, or lake. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:env material
Normative URI http://gensc.org/ns/mixs/env_material
Label environment (material)
Definition The environmental material level refers to the material that was displaced by the sample, or material in which a sample was embedded, prior to the sampling event. Environmental material terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v 2013-06-14) terms can be found via the link: www.environmentontology.org/Browse-EnvO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:env package
Normative URI http://gensc.org/ns/mixs/env_package
Label environmental package
Definition MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:geo loc name
Normative URI http://gensc.org/ns/mixs/geo_loc_name
Label geographic location (country and/or sea,region)
Definition The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v 1.512) (http://purl.bioontology.org/ontology/GAZ)
Defined By
  Required: No — Repeatable: No
Examples Germany:Sylt:Hausstrand
Concept Name: mixs:lat lon
Normative URI http://gensc.org/ns/mixs/lat_lon
Label geographic location (latitude and longitude)
Definition The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system.
Defined By
  Required: Yes — Repeatable: No
Examples 7.11 -110.5

MIxS Investigation Vocabulary

Concept definitions in MIxS Investigation Vocabulary
Concept Name: mixs:experimental factor
Normative URI http://gensc.org/ns/mixs/experimental_factor
Label experimental factor
Definition Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.43) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:investigation type
Normative URI http://gensc.org/ns/mixs/investigation_type
Label investigation type
Definition Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, or mimarks-specimen
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:project name
Normative URI http://gensc.org/ns/mixs/project_name
Label project name
Definition Name of the project within which the sequencing was organized
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:submitted to insdc
Normative URI http://gensc.org/ns/mixs/submitted_to_insdc
Label submitted to insdc
Definition Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases
Defined By
  Required: No — Repeatable: No

MIxS Nucleic Acid Sequence Source Vocabulary

Concept Name: mixs:biotic relationship
Normative URI http://gensc.org/ns/mixs/biotic_relationship
Label observed biotic relationship
Definition Is it free-living or in a host and if the latter what type of relationship is observed
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:encoded traits
Normative URI http://gensc.org/ns/mixs/encoded_traits
Label encoded traits
Definition Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:estimated size
Normative URI http://gensc.org/ns/mixs/estimated_size
Label estimated Size
Definition The estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period.
Defined By
  Required: No — Repeatable: No
Examples 300000 bp
Concept Name: mixs:extrachrom elements
Normative URI http://gensc.org/ns/mixs/extrachrom_elements
Label extrachromosomal elements
Definition Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids)
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:health disease stat
Normative URI http://gensc.org/ns/mixs/health_disease_stat
Label health or disease status of specific host at time of collection
Definition Health or disease status of specific host at time of collection. This field accepts PATO (v 2013-10-28) terms, for a browser please see http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host spec range
Normative URI http://gensc.org/ns/mixs/host_spec_range
Label host specificity or range
Definition The NCBI taxonomy identifier of the specific host if it is known
Defined By
  Required: No — Repeatable: No
Examples 124
Concept Name: mixs:isol growth condt
Normative URI http://gensc.org/ns/mixs/isol_growth_condt
Label isolation and growth condition
Definition Publication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:num replicons
Normative URI http://gensc.org/ns/mixs/num_replicons
Label number of replicons
Definition Reports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:pathogenicity
Normative URI http://gensc.org/ns/mixs/pathogenicity
Label known pathogenicity
Definition To what is the entity pathogenic.
Defined By
  Required: No — Repeatable: No
Examples human, animal, plant, fungi, bacteria
Concept Name: mixs:ploidy
Normative URI http://gensc.org/ns/mixs/ploidy
Label ploidy
Definition The ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2013-10-28) please refer to http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Examples allopolyploid, polyploid
Concept Name: mixs:propagation
Normative URI http://gensc.org/ns/mixs/propagation
Label propagation
Definition This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ref biomaterial
Normative URI http://gensc.org/ns/mixs/ref_biomaterial
Label reference for biomaterial
Definition primary publication if isolated before genome publication; otherwise, primary genome report
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:rel to oxygen
Normative URI http://gensc.org/ns/mixs/rel_to_oxygen
Label relationship to oxygen
Definition Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp collect device
Normative URI http://gensc.org/ns/mixs/samp_collect_device
Label sample collection device or method
Definition The method or device employed for collecting the sample
Defined By
  Required: No — Repeatable: No
Examples biopsy, niskin bottle, push core
Concept Name: mixs:samp mat process
Normative URI http://gensc.org/ns/mixs/samp_mat_process
Label sample material processing
Definition Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2013-10-25) terms please see http://purl.bioontology.org/ontology/OBI
Defined By
  Required: No — Repeatable: No
Examples filtering of seawater, storing samples in ethanol
Concept Name: mixs:samp size
Normative URI http://gensc.org/ns/mixs/samp_size
Label sample size
Definition Amount or size of sample (volume, mass or area) that was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:source mat id
Normative URI http://gensc.org/ns/mixs/source_mat_id
Label source material identifiers
Definition A unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2)
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:specific host
Normative URI http://gensc.org/ns/mixs/specific_host
Label specific host
Definition If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host). From this we can calculate any number of groupings of hosts (e.g. animal vs plant, all fish hosts, etc)
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:subspecf gen lin
Normative URI http://gensc.org/ns/mixs/subspecf_gen_lin
Label subspecific genetic lineage
Definition This should provide further information about the genetic distinctness of this lineage by recording additional information i.e biovar, serovar, serotype, biovar, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:trophic level
Normative URI http://gensc.org/ns/mixs/trophic_level
Label trophic level
Definition Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)
Defined By
  Required: No — Repeatable: No

MIxS Sequencing

Concept definitions in MIxS Sequencing
Concept Name: mixs:adapters
Normative URI http://gensc.org/ns/mixs/adapters
Label adapters
Definition Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
Defined By
  Required: No — Repeatable: Yes
Concept Name: mixs:annot source
Normative URI http://gensc.org/ns/mixs/annot_source
Label annotation source
Definition For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
Defined By
  Required: No — Repeatable: Yes
Concept Name: mixs:assembly
Normative URI http://gensc.org/ns/mixs/assembly
Label assembly
Definition How was the assembly done (e.g. with a text based assembler like phrap or a flowgram assembler); estimated error rate associated with the finished sequences (e.g. error rate of 1 in 1000 bp); and the method of calculation
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:assembly name
Normative URI http://gensc.org/ns/mixs/assembly_name
Label assembly name
Definition Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
Defined By
  Required: No — Repeatable: No
Examples HuRef, JCVI_ISG_i3_1.0
Concept Name: mixs:chimera check
Normative URI http://gensc.org/ns/mixs/chimera_check
Label chimera check
Definition A chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:finishing strategy
Normative URI http://gensc.org/ns/mixs/finishing_strategy
Label finishing strategy
Definition Was the genome project intended to produce a complete or draft genome, Coverage, the fold coverage of the sequencing expressed as 2x, 3x, 18x etc, and how many contigs were produced for the genome
Defined By
  Required: No — Repeatable: Yes
Concept Name: mixs:lib const meth
Normative URI http://gensc.org/ns/mixs/lib_const_meth
Label library construction method
Definition Library construction method used for clone libraries
Defined By
  Required: No — Repeatable: No
Examples paired-end,single,vector
Concept Name: mixs:lib reads seqd
Normative URI http://gensc.org/ns/mixs/lib_reads_seqd
Label library reads sequenced
Definition Total number of clones sequenced from the library
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:lib screen
Normative URI http://gensc.org/ns/mixs/lib_screen
Label library screening strategy
Definition Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences
Defined By
  Required: No — Repeatable: No
Examples enriched, screened, normalized
Concept Name: mixs:lib size
Normative URI http://gensc.org/ns/mixs/lib_size
Label library size
Definition Total number of clones in the library prepared for the project
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:lib vector
Normative URI http://gensc.org/ns/mixs/lib_vector
Label library vector
Definition Cloning vector type(s) used in construction of libraries
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:mid
Normative URI http://gensc.org/ns/mixs/mid
Label multiplex identifiers
Definition Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
Defined By
  Required: No — Repeatable: Yes
Concept Name: mixs:nucl acid amp
Normative URI http://gensc.org/ns/mixs/nucl_acid_amp
Label nucleic acid amplification
Definition Link to a literature reference, electronic resource or a standard operating procedure (SOP)
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:nucl acid ext
Normative URI http://gensc.org/ns/mixs/nucl_acid_ext
Label nucleic acid extraction
Definition Link to a literature reference, electronic resource or a standard operating procedure (SOP)
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:pcr cond
Normative URI http://gensc.org/ns/mixs/pcr_cond
Label pcr conditions
Definition Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:pcr primers
Normative URI http://gensc.org/ns/mixs/pcr_primers
Label pcr primers
Definition PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase letters
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:seq meth
Normative URI http://gensc.org/ns/mixs/seq_meth
Label sequencing method
Definition Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid
Defined By
  Required: No — Repeatable: No
Examples Sanger dideoxysequencing, pyrosequencing, polony
Concept Name: mixs:seq quality check
Normative URI http://gensc.org/ns/mixs/seq_quality_check
Label sequence quality check
Definition Indicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA or DRA e.g. none or manually edited
Defined By
  Required: No — Repeatable: Yes
Concept Name: mixs:sop
Normative URI http://gensc.org/ns/mixs/sop
Label relevant standard operating procedures
Definition Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences
Defined By
  Required: No — Repeatable: Yes
Concept Name: mixs:target gene
Normative URI http://gensc.org/ns/mixs/target_gene
Label target gene
Definition Targeted gene or locus name for marker gene studies
Defined By
  Required: No — Repeatable: No
Examples 16S rRNA, 18S rRNA, nif, amoA, rpo
Concept Name: mixs:target subfragment
Normative URI http://gensc.org/ns/mixs/target_subfragment
Label target subfragment
Definition Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA
Defined By
  Required: No — Repeatable: No
Examples V6, V9, ITS
Concept Name: mixs:url
Normative URI http://gensc.org/ns/mixs/url
Label relevant electronic resources
Definition links to any additional resources
Defined By
  Required: No — Repeatable: No

mixs:air

Index to mixs:air
Concept definitions in mixs:air
Concept Name: mixs:alt
Normative URI http://gensc.org/ns/mixs/alt
Label altitude
Definition the altitude of the sample is the vertical distance between Earth's surface above sea level and the sampled position in the air
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:altitude
Normative URI http://gensc.org/ns/mixs/altitude
Label altitude
Definition the altitude of the sample is the vertical distance between Earth's surface above sea level and the sampled position in the air
Defined By
  Required: No — Repeatable: No
Examples 1 meter
Concept Name: mixs:barometric press
Normative URI http://gensc.org/ns/mixs/barometric_press
Label barometric pressure
Definition force per unit area exerted against a surface by the weight of air above that surface
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:carb dioxide
Normative URI http://gensc.org/ns/mixs/carb_dioxide
Label carbon dioxide
Definition carbon dioxide (gas) amount or concentration at the time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:carb monoxide
Normative URI http://gensc.org/ns/mixs/carb_monoxide
Label carbon monoxide
Definition carbon monoxide (gas) amount or concentration at the time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:chem administration
Normative URI http://gensc.org/ns/mixs/chem_administration
Label chemical administration
Definition list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v 111), http://purl.bioontology.org/ontology/CHEBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:elev
Normative URI http://gensc.org/ns/mixs/elev
Label elevation
Definition the elevation of the sampling site as measured by the vertical distance from mean sea level
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:humidity
Normative URI http://gensc.org/ns/mixs/humidity
Label humidity
Definition amount of water vapour in the air, at the time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:methane
Normative URI http://gensc.org/ns/mixs/methane
Label methane
Definition methane (gas) amount or concentration at the time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:misc param
Normative URI http://gensc.org/ns/mixs/misc_param
Label miscellaneous parameter
Definition any other measurement performed or parameter collected, that is not listed here
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:organism count
Normative URI http://gensc.org/ns/mixs/organism_count
Label organism count
Definition total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:oxy stat samp
Normative URI http://gensc.org/ns/mixs/oxy_stat_samp
Label oxygenation status of sample
Definition oxygenation status of sample
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:oxygen
Normative URI http://gensc.org/ns/mixs/oxygen
Label oxygen
Definition oxygen (gas) amount or concentration at the time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:perturbation
Normative URI http://gensc.org/ns/mixs/perturbation
Label perturbation
Definition type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:pollutants
Normative URI http://gensc.org/ns/mixs/pollutants
Label pollutants
Definition pollutant types and, amount or concentrations measured at the time of sampling; can report multiple pollutants by entering numeric values preceded by name of pollutant
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:resp part matter
Normative URI http://gensc.org/ns/mixs/resp_part_matter
Label respirable particulate matter
Definition concentration of substances that remain suspended in the air, and comprise mixtures of organic and inorganic substances (PM10 and PM2.5); can report multiple PM's by entering numeric values preceded by name of PM
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp salinity
Normative URI http://gensc.org/ns/mixs/samp_salinity
Label sample salinity
Definition salinity of sample, i.e. measure of total salt concentration
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store dur
Normative URI http://gensc.org/ns/mixs/samp_store_dur
Label sample storage duration
Definition duration for which sample was stored
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store loc
Normative URI http://gensc.org/ns/mixs/samp_store_loc
Label sample storage location
Definition location at which sample was stored, usually name of a specific freezer/room
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store temp
Normative URI http://gensc.org/ns/mixs/samp_store_temp
Label sample storage temperature
Definition temperature at which sample was stored, e.g. -80 degree Celsius
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp vol we dna ext
Normative URI http://gensc.org/ns/mixs/samp_vol_we_dna_ext
Label sample volume or weight for DNA extraction
Definition volume (mL) or weight (g) of sample processed for DNA extraction
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:solar irradiance
Normative URI http://gensc.org/ns/mixs/solar_irradiance
Label solar irradiance
Definition the amount of solar energy that arrives at a specific area of a surface during a specific time interval
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:temp
Normative URI http://gensc.org/ns/mixs/temp
Label temperature
Definition temperature of the sample at time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ventilation rate
Normative URI http://gensc.org/ns/mixs/ventilation_rate
Label ventilation rate
Definition ventilation rate of the system in the sampled premises
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ventilation type
Normative URI http://gensc.org/ns/mixs/ventilation_type
Label ventilation type
Definition ventilation system used in the sampled premises
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:volatile org comp
Normative URI http://gensc.org/ns/mixs/volatile_org_comp
Label volatile organic compounds
Definition concentration of carbon-based chemicals that easily evaporate at room temperature; can report multiple volatile organic compounds by entering numeric values preceded by name of compound
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:wind direction
Normative URI http://gensc.org/ns/mixs/wind_direction
Label wind direction
Definition wind direction is the direction from which a wind originates
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:wind speed
Normative URI http://gensc.org/ns/mixs/wind_speed
Label wind speed
Definition speed of wind measured at the time of sampling
Defined By
  Required: No — Repeatable: No

mixs:built environment

Concept definitions in mixs:built environment
Concept Name: mixs:abs air humidity
Normative URI http://gensc.org/ns/mixs/abs_air_humidity
Label absolute air humidity
Definition actual mass of water vapor - mh20 - present in the air water vapor mixture
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:build occup type
Normative URI http://gensc.org/ns/mixs/build_occup_type
Label building occupancy type
Definition the primary function for which a building or discrete part of a building is intended to be used
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:building setting
Normative URI http://gensc.org/ns/mixs/building_setting
Label building setting
Definition a location (geography) where a building is set
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:carb dioxide
Normative URI http://gensc.org/ns/mixs/carb_dioxide
Label carbon dioxide
Definition carbon dioxide (gas) amount or concentration at the time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:dew point
Normative URI http://gensc.org/ns/mixs/dew_point
Label dew point
Definition the temperature to which a given parcel of humid air must be cooled, at constant barometric pressure, for water vapor to condense into water.
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:filter type
Normative URI http://gensc.org/ns/mixs/filter_type
Label filter type
Definition a device which removes solid particulates or airborne molecular contaminants
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:heat cool type
Normative URI http://gensc.org/ns/mixs/heat_cool_type
Label heating and cooling system type
Definition methods of conditioning or heating a room or building
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:indoor space
Normative URI http://gensc.org/ns/mixs/indoor_space
Label indoor space
Definition a distinguishable space within a structure, the purpose for which discrete areas of a building is used
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:indoor surf
Normative URI http://gensc.org/ns/mixs/indoor_surf
Label indoor surface
Definition type of indoor surface
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:light type
Normative URI http://gensc.org/ns/mixs/light_type
Label light type
Definition application of light to achieve some practical or aesthetic effect. Lighting includes the use of both artificial light sources such as lamps and light fixtures, as well as natural illumination by capturing daylight. Can also include absence of light
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:occup samp
Normative URI http://gensc.org/ns/mixs/occup_samp
Label occupancy at sampling
Definition number of occupants present at time of sample within the given space
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:occupant dens samp
Normative URI http://gensc.org/ns/mixs/occupant_dens_samp
Label occupant density at sampling
Definition average number of occupants at time of sampling per square footage
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:organism count
Normative URI http://gensc.org/ns/mixs/organism_count
Label organism count
Definition total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:rel air humidity
Normative URI http://gensc.org/ns/mixs/rel_air_humidity
Label relative air humidity
Definition partial vapor and air pressure, density of the vapor and air, or by the actual mass of the vapor and air
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp sort meth
Normative URI http://gensc.org/ns/mixs/samp_sort_meth
Label sample size sorting method
Definition method by which samples are sorted
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:space typ state
Normative URI http://gensc.org/ns/mixs/space_typ_state
Label space typical state
Definition customary or normal state of the space
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:substructure type
Normative URI http://gensc.org/ns/mixs/substructure_type
Label substructure type
Definition the substructure or under building is that largely hidden section of the building which is built off the foundations to the ground floor level
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:surf air cont
Normative URI http://gensc.org/ns/mixs/surf_air_cont
Label surface-air contaminant
Definition contaminant identified on surface
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:surf humidity
Normative URI http://gensc.org/ns/mixs/surf_humidity
Label surface humidity
Definition surfaces: water activity as a function of air and material moisture
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:surf material
Normative URI http://gensc.org/ns/mixs/surf_material
Label surface material
Definition surface materials at the point of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:surf moisture
Normative URI http://gensc.org/ns/mixs/surf_moisture
Label surface moisture
Definition water held on a surface
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:surf moisture ph
Normative URI http://gensc.org/ns/mixs/surf_moisture_ph
Label surface moisture pH
Definition pH measurement of surface
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:surf temp
Normative URI http://gensc.org/ns/mixs/surf_temp
Label surface temperature
Definition temperature of the surface at the time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:typ occupant dens
Normative URI http://gensc.org/ns/mixs/typ_occupant_dens
Label typical occupant density
Definition customary or normal density of occupants
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ventilation type
Normative URI http://gensc.org/ns/mixs/ventilation_type
Label ventilation type
Definition ventilation system used in the sampled premises
Defined By
  Required: No — Repeatable: No

mixs:host-associated

By label: altitude  •  chemical administration  •  elevation  •  geographic location (depth)  •  gravidity  •  host age  •  host blood pressure diastolic  •  host blood pressure systolic  •  host body habitat  •  host body product  •  host body site  •  host body temperature  •  host color  •  host common name  •  host diet  •  host disease status  •  host dry mass  •  host family relationship  •  host genotype  •  host growth conditions  •  host height  •  host infra-specific name  •  host infra-specific rank  •  host last meal  •  host length  •  host life stage  •  host phenotype  •  host sex  •  host shape  •  host subject id  •  host substrate  •  host taxid  •  host total mass  •  miscellaneous parameter  •  organism count  •  oxygenation status of sample  •  perturbation  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  temperature
By concept name: mixs:alt  •  mixs:chem administration  •  mixs:depth  •  mixs:elev  •  mixs:gravidity  •  mixs:host age  •  mixs:host blood press diast  •  mixs:host blood press syst  •  mixs:host body habitat  •  mixs:host body product  •  mixs:host body site  •  mixs:host body temp  •  mixs:host color  •  mixs:host common name  •  mixs:host diet  •  mixs:host disease stat  •  mixs:host dry mass  •  mixs:host family relationship  •  mixs:host genotype  •  mixs:host growth cond  •  mixs:host height  •  mixs:host infra specific name  •  mixs:host infra specific rank  •  mixs:host last meal  •  mixs:host length  •  mixs:host life stage  •  mixs:host phenotype  •  mixs:host sex  •  mixs:host shape  •  mixs:host subject id  •  mixs:host substrate  •  mixs:host taxid  •  mixs:host tot mass  •  mixs:misc param  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:samp salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:temp
Concept definitions in mixs:host-associated
Concept Name: mixs:alt
Normative URI http://gensc.org/ns/mixs/alt
Label altitude
Definition the altitude of the sample is the vertical distance between Earth's surface above sea level and the sampled position in the air
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:chem administration
Normative URI http://gensc.org/ns/mixs/chem_administration
Label chemical administration
Definition list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v 111), http://purl.bioontology.org/ontology/CHEBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:depth
Normative URI http://gensc.org/ns/mixs/depth
Label geographic location (depth)
Definition Depth is defined as the vertical distance below local surface, e.g. for sediment or soil samples depth is measured from sediment or soil surface, respectively. Depth can be reported as an interval for subsurface samples.
Defined By
  Required: No — Repeatable: No
Examples 10.3 m
Concept Name: mixs:elev
Normative URI http://gensc.org/ns/mixs/elev
Label elevation
Definition the elevation of the sampling site as measured by the vertical distance from mean sea level
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:gravidity
Normative URI http://gensc.org/ns/mixs/gravidity
Label gravidity
Definition whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host age
Normative URI http://gensc.org/ns/mixs/host_age
Label host age
Definition age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host blood press diast
Normative URI http://gensc.org/ns/mixs/host_blood_press_diast
Label host blood pressure diastolic
Definition resting diastolic blood pressure, measured as mm mercury
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host blood press syst
Normative URI http://gensc.org/ns/mixs/host_blood_press_syst
Label host blood pressure systolic
Definition resting systolic blood pressure, measured as mm mercury
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body habitat
Normative URI http://gensc.org/ns/mixs/host_body_habitat
Label host body habitat
Definition original body habitat where the sample was obtained from
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body product
Normative URI http://gensc.org/ns/mixs/host_body_product
Label host body product
Definition substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body site
Normative URI http://gensc.org/ns/mixs/host_body_site
Label host body site
Definition name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body temp
Normative URI http://gensc.org/ns/mixs/host_body_temp
Label host body temperature
Definition core body temperature of the host when sample was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host color
Normative URI http://gensc.org/ns/mixs/host_color
Label host color
Definition the color of host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host common name
Normative URI http://gensc.org/ns/mixs/host_common_name
Label host common name
Definition common name of the host, e.g. human
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host diet
Normative URI http://gensc.org/ns/mixs/host_diet
Label host diet
Definition type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host disease stat
Normative URI http://gensc.org/ns/mixs/host_disease_stat
Label host disease status
Definition list of diseases with which the host has been diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host dry mass
Normative URI http://gensc.org/ns/mixs/host_dry_mass
Label host dry mass
Definition measurement of dry mass
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host family relationship
Normative URI http://gensc.org/ns/mixs/host_family_relationship
Label host family relationship
Definition relationships to other hosts in the same study; can include multiple relationships
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host genotype
Normative URI http://gensc.org/ns/mixs/host_genotype
Label host genotype
Definition observed genotype
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host growth cond
Normative URI http://gensc.org/ns/mixs/host_growth_cond
Label host growth conditions
Definition literature reference giving growth conditions of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host height
Normative URI http://gensc.org/ns/mixs/host_height
Label host height
Definition the height of subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host infra specific name
Normative URI http://gensc.org/ns/mixs/host_infra_specific_name
Label host infra-specific name
Definition taxonomic information about the host below subspecies level
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host infra specific rank
Normative URI http://gensc.org/ns/mixs/host_infra_specific_rank
Label host infra-specific rank
Definition taxonomic rank information about the host below subspecies level, such as variety, form, rank etc.
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host last meal
Normative URI http://gensc.org/ns/mixs/host_last_meal
Label host last meal
Definition content of last meal and time since feeding; can include multiple values
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host length
Normative URI http://gensc.org/ns/mixs/host_length
Label host length
Definition the length of subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host life stage
Normative URI http://gensc.org/ns/mixs/host_life_stage
Label host life stage
Definition description of life stage of host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host phenotype
Normative URI http://gensc.org/ns/mixs/host_phenotype
Label host phenotype
Definition phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host sex
Normative URI http://gensc.org/ns/mixs/host_sex
Label host sex
Definition physical sex of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host shape
Normative URI http://gensc.org/ns/mixs/host_shape
Label host shape
Definition morphological shape of host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host subject id
Normative URI http://gensc.org/ns/mixs/host_subject_id
Label host subject id
Definition a unique identifier by which each subject can be referred to, de-identified, e.g. #131
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host substrate
Normative URI http://gensc.org/ns/mixs/host_substrate
Label host substrate
Definition the growth substrate of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host taxid
Normative URI http://gensc.org/ns/mixs/host_taxid
Label host taxid
Definition NCBI taxon id of the host, e.g. 9606
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host tot mass
Normative URI http://gensc.org/ns/mixs/host_tot_mass
Label host total mass
Definition total mass of the host at collection, the unit depends on host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:misc param
Normative URI http://gensc.org/ns/mixs/misc_param
Label miscellaneous parameter
Definition any other measurement performed or parameter collected, that is not listed here
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:organism count
Normative URI http://gensc.org/ns/mixs/organism_count
Label organism count
Definition total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:oxy stat samp
Normative URI http://gensc.org/ns/mixs/oxy_stat_samp
Label oxygenation status of sample
Definition oxygenation status of sample
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:perturbation
Normative URI http://gensc.org/ns/mixs/perturbation
Label perturbation
Definition type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp salinity
Normative URI http://gensc.org/ns/mixs/samp_salinity
Label sample salinity
Definition salinity of sample, i.e. measure of total salt concentration
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store dur
Normative URI http://gensc.org/ns/mixs/samp_store_dur
Label sample storage duration
Definition duration for which sample was stored
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store loc
Normative URI http://gensc.org/ns/mixs/samp_store_loc
Label sample storage location
Definition location at which sample was stored, usually name of a specific freezer/room
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store temp
Normative URI http://gensc.org/ns/mixs/samp_store_temp
Label sample storage temperature
Definition temperature at which sample was stored, e.g. -80 degree Celsius
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp vol we dna ext
Normative URI http://gensc.org/ns/mixs/samp_vol_we_dna_ext
Label sample volume or weight for DNA extraction
Definition volume (mL) or weight (g) of sample processed for DNA extraction
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:temp
Normative URI http://gensc.org/ns/mixs/temp
Label temperature
Definition temperature of the sample at time of sampling
Defined By
  Required: No — Repeatable: No

mixs:human-associated

By label: IHMC ethnicity  •  IHMC medication code  •  amniotic fluid/color  •  amniotic fluid/foetal health status  •  amniotic fluid/gestation state  •  amniotic fluid/maternal health status  •  blood/blood disorder  •  chemical administration  •  drug usage  •  host HIV status  •  host age  •  host body product  •  host body site  •  host body temperature  •  host body-mass index  •  host diet  •  host disease status  •  host family relationship  •  host genotype  •  host height  •  host last meal  •  host occupation  •  host phenotype  •  host pulse  •  host sex  •  host subject id  •  host total mass  •  lung/nose-throat disorder  •  lung/pulmonary disorder  •  major diet change in last six months  •  medical history performed  •  miscellaneous parameter  •  organism count  •  oxygenation status of sample  •  perturbation  •  presence of pets or farm animals  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  smoker  •  study completion status  •  temperature  •  travel outside the country in last six months  •  twin sibling presence  •  urine/collection method  •  urine/kidney disorder  •  urine/urogenital tract disorder  •  weight loss in last three months
By concept name: mixs:amniotic fluid color  •  mixs:blood blood disord  •  mixs:chem administration  •  mixs:diet last six month  •  mixs:drug usage  •  mixs:foetal health stat  •  mixs:gestation state  •  mixs:host age  •  mixs:host body mass index  •  mixs:host body product  •  mixs:host body site  •  mixs:host body temp  •  mixs:host diet  •  mixs:host disease stat  •  mixs:host family relationship  •  mixs:host genotype  •  mixs:host height  •  mixs:host hiv stat  •  mixs:host last meal  •  mixs:host occupation  •  mixs:host phenotype  •  mixs:host pulse  •  mixs:host sex  •  mixs:host subject id  •  mixs:host tot mass  •  mixs:ihmc ethnicity  •  mixs:ihmc medication code  •  mixs:kidney disord  •  mixs:maternal health stat  •  mixs:medic hist perform  •  mixs:misc param  •  mixs:nose throat disord  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:pet farm animal  •  mixs:pulmonary disord  •  mixs:samp salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:smoker  •  mixs:study complt stat  •  mixs:temp  •  mixs:travel out six month  •  mixs:twin sibling  •  mixs:urine collect meth  •  mixs:urogenit tract disor  •  mixs:weight loss 3 month
Concept definitions in mixs:human-associated
Concept Name: mixs:amniotic fluid color
Normative URI http://gensc.org/ns/mixs/amniotic_fluid_color
Label amniotic fluid/color
Definition specification of the color of the amniotic fluid sample
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:blood blood disord
Normative URI http://gensc.org/ns/mixs/blood_blood_disord
Label blood/blood disorder
Definition history of blood disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:chem administration
Normative URI http://gensc.org/ns/mixs/chem_administration
Label chemical administration
Definition list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v 111), http://purl.bioontology.org/ontology/CHEBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:diet last six month
Normative URI http://gensc.org/ns/mixs/diet_last_six_month
Label major diet change in last six months
Definition specification of major diet changes in the last six months, if yes the change should be specified
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:drug usage
Normative URI http://gensc.org/ns/mixs/drug_usage
Label drug usage
Definition any drug used by subject and the frequency of usage; can include multiple drugs used
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:foetal health stat
Normative URI http://gensc.org/ns/mixs/foetal_health_stat
Label amniotic fluid/foetal health status
Definition specification of foetal health status, should also include abortion
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:gestation state
Normative URI http://gensc.org/ns/mixs/gestation_state
Label amniotic fluid/gestation state
Definition specification of the gestation state
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host age
Normative URI http://gensc.org/ns/mixs/host_age
Label host age
Definition age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body mass index
Normative URI http://gensc.org/ns/mixs/host_body_mass_index
Label host body-mass index
Definition body mass index, calculated as weight/(height)squared
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body product
Normative URI http://gensc.org/ns/mixs/host_body_product
Label host body product
Definition substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body site
Normative URI http://gensc.org/ns/mixs/host_body_site
Label host body site
Definition name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body temp
Normative URI http://gensc.org/ns/mixs/host_body_temp
Label host body temperature
Definition core body temperature of the host when sample was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host diet
Normative URI http://gensc.org/ns/mixs/host_diet
Label host diet
Definition type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host disease stat
Normative URI http://gensc.org/ns/mixs/host_disease_stat
Label host disease status
Definition list of diseases with which the host has been diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host family relationship
Normative URI http://gensc.org/ns/mixs/host_family_relationship
Label host family relationship
Definition relationships to other hosts in the same study; can include multiple relationships
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host genotype
Normative URI http://gensc.org/ns/mixs/host_genotype
Label host genotype
Definition observed genotype
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host height
Normative URI http://gensc.org/ns/mixs/host_height
Label host height
Definition the height of subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host hiv stat
Normative URI http://gensc.org/ns/mixs/host_hiv_stat
Label host HIV status
Definition HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO]
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host last meal
Normative URI http://gensc.org/ns/mixs/host_last_meal
Label host last meal
Definition content of last meal and time since feeding; can include multiple values
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host occupation
Normative URI http://gensc.org/ns/mixs/host_occupation
Label host occupation
Definition most frequent job performed by subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host phenotype
Normative URI http://gensc.org/ns/mixs/host_phenotype
Label host phenotype
Definition phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host pulse
Normative URI http://gensc.org/ns/mixs/host_pulse
Label host pulse
Definition resting pulse, measured as beats per minute
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host sex
Normative URI http://gensc.org/ns/mixs/host_sex
Label host sex
Definition physical sex of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host subject id
Normative URI http://gensc.org/ns/mixs/host_subject_id
Label host subject id
Definition a unique identifier by which each subject can be referred to, de-identified, e.g. #131
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host tot mass
Normative URI http://gensc.org/ns/mixs/host_tot_mass
Label host total mass
Definition total mass of the host at collection, the unit depends on host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc ethnicity
Normative URI http://gensc.org/ns/mixs/ihmc_ethnicity
Label IHMC ethnicity
Definition ethnicity of the subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc medication code
Normative URI http://gensc.org/ns/mixs/ihmc_medication_code
Label IHMC medication code
Definition can include multiple medication codes
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:kidney disord
Normative URI http://gensc.org/ns/mixs/kidney_disord
Label urine/kidney disorder
Definition history of kidney disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:maternal health stat
Normative URI http://gensc.org/ns/mixs/maternal_health_stat
Label amniotic fluid/maternal health status
Definition specification of the maternal health status
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:medic hist perform
Normative URI http://gensc.org/ns/mixs/medic_hist_perform
Label medical history performed
Definition whether full medical history was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:misc param
Normative URI http://gensc.org/ns/mixs/misc_param
Label miscellaneous parameter
Definition any other measurement performed or parameter collected, that is not listed here
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:nose throat disord
Normative URI http://gensc.org/ns/mixs/nose_throat_disord
Label lung/nose-throat disorder
Definition history of nose-throat disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:organism count
Normative URI http://gensc.org/ns/mixs/organism_count
Label organism count
Definition total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:oxy stat samp
Normative URI http://gensc.org/ns/mixs/oxy_stat_samp
Label oxygenation status of sample
Definition oxygenation status of sample
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:perturbation
Normative URI http://gensc.org/ns/mixs/perturbation
Label perturbation
Definition type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:pet farm animal
Normative URI http://gensc.org/ns/mixs/pet_farm_animal
Label presence of pets or farm animals
Definition specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:pulmonary disord
Normative URI http://gensc.org/ns/mixs/pulmonary_disord
Label lung/pulmonary disorder
Definition history of pulmonary disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp salinity
Normative URI http://gensc.org/ns/mixs/samp_salinity
Label sample salinity
Definition salinity of sample, i.e. measure of total salt concentration
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store dur
Normative URI http://gensc.org/ns/mixs/samp_store_dur
Label sample storage duration
Definition duration for which sample was stored
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store loc
Normative URI http://gensc.org/ns/mixs/samp_store_loc
Label sample storage location
Definition location at which sample was stored, usually name of a specific freezer/room
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store temp
Normative URI http://gensc.org/ns/mixs/samp_store_temp
Label sample storage temperature
Definition temperature at which sample was stored, e.g. -80 degree Celsius
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp vol we dna ext
Normative URI http://gensc.org/ns/mixs/samp_vol_we_dna_ext
Label sample volume or weight for DNA extraction
Definition volume (mL) or weight (g) of sample processed for DNA extraction
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:smoker
Normative URI http://gensc.org/ns/mixs/smoker
Label smoker
Definition specification of smoking status
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:study complt stat
Normative URI http://gensc.org/ns/mixs/study_complt_stat
Label study completion status
Definition specification of study completion status, if no the reason should be specified
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:temp
Normative URI http://gensc.org/ns/mixs/temp
Label temperature
Definition temperature of the sample at time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:travel out six month
Normative URI http://gensc.org/ns/mixs/travel_out_six_month
Label travel outside the country in last six months
Definition specification of the countries travelled in the last six months; can include multiple travels
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:twin sibling
Normative URI http://gensc.org/ns/mixs/twin_sibling
Label twin sibling presence
Definition specification of twin sibling presence
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:urine collect meth
Normative URI http://gensc.org/ns/mixs/urine_collect_meth
Label urine/collection method
Definition specification of urine collection method
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:urogenit tract disor
Normative URI http://gensc.org/ns/mixs/urogenit_tract_disor
Label urine/urogenital tract disorder
Definition history of urogenitaltract disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:weight loss 3 month
Normative URI http://gensc.org/ns/mixs/weight_loss_3_month
Label weight loss in last three months
Definition specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss
Defined By
  Required: No — Repeatable: No

mixs:human-gut

By label: IHMC ethnicity  •  IHMC medication code  •  chemical administration  •  gastrointestinal tract disorder  •  host age  •  host body product  •  host body site  •  host body temperature  •  host body-mass index  •  host diet  •  host disease status  •  host family relationship  •  host genotype  •  host height  •  host last meal  •  host occupation  •  host phenotype  •  host pulse  •  host sex  •  host subject id  •  host total mass  •  liver disorder  •  medical history performed  •  miscellaneous parameter  •  organism count  •  oxygenation status of sample  •  perturbation  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  special diet  •  temperature
By concept name: mixs:chem administration  •  mixs:gastrointest disord  •  mixs:host age  •  mixs:host body mass index  •  mixs:host body product  •  mixs:host body site  •  mixs:host body temp  •  mixs:host diet  •  mixs:host disease stat  •  mixs:host family relationship  •  mixs:host genotype  •  mixs:host height  •  mixs:host last meal  •  mixs:host occupation  •  mixs:host phenotype  •  mixs:host pulse  •  mixs:host sex  •  mixs:host subject id  •  mixs:host tot mass  •  mixs:ihmc ethnicity  •  mixs:ihmc medication code  •  mixs:liver disord  •  mixs:medic hist perform  •  mixs:misc param  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:samp salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:special diet  •  mixs:temp
Concept definitions in mixs:human-gut
Concept Name: mixs:chem administration
Normative URI http://gensc.org/ns/mixs/chem_administration
Label chemical administration
Definition list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v 111), http://purl.bioontology.org/ontology/CHEBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:gastrointest disord
Normative URI http://gensc.org/ns/mixs/gastrointest_disord
Label gastrointestinal tract disorder
Definition history of gastrointestinal tract disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host age
Normative URI http://gensc.org/ns/mixs/host_age
Label host age
Definition age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body mass index
Normative URI http://gensc.org/ns/mixs/host_body_mass_index
Label host body-mass index
Definition body mass index, calculated as weight/(height)squared
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body product
Normative URI http://gensc.org/ns/mixs/host_body_product
Label host body product
Definition substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body site
Normative URI http://gensc.org/ns/mixs/host_body_site
Label host body site
Definition name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body temp
Normative URI http://gensc.org/ns/mixs/host_body_temp
Label host body temperature
Definition core body temperature of the host when sample was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host diet
Normative URI http://gensc.org/ns/mixs/host_diet
Label host diet
Definition type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host disease stat
Normative URI http://gensc.org/ns/mixs/host_disease_stat
Label host disease status
Definition list of diseases with which the host has been diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host family relationship
Normative URI http://gensc.org/ns/mixs/host_family_relationship
Label host family relationship
Definition relationships to other hosts in the same study; can include multiple relationships
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host genotype
Normative URI http://gensc.org/ns/mixs/host_genotype
Label host genotype
Definition observed genotype
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host height
Normative URI http://gensc.org/ns/mixs/host_height
Label host height
Definition the height of subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host last meal
Normative URI http://gensc.org/ns/mixs/host_last_meal
Label host last meal
Definition content of last meal and time since feeding; can include multiple values
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host occupation
Normative URI http://gensc.org/ns/mixs/host_occupation
Label host occupation
Definition most frequent job performed by subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host phenotype
Normative URI http://gensc.org/ns/mixs/host_phenotype
Label host phenotype
Definition phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host pulse
Normative URI http://gensc.org/ns/mixs/host_pulse
Label host pulse
Definition resting pulse, measured as beats per minute
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host sex
Normative URI http://gensc.org/ns/mixs/host_sex
Label host sex
Definition physical sex of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host subject id
Normative URI http://gensc.org/ns/mixs/host_subject_id
Label host subject id
Definition a unique identifier by which each subject can be referred to, de-identified, e.g. #131
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host tot mass
Normative URI http://gensc.org/ns/mixs/host_tot_mass
Label host total mass
Definition total mass of the host at collection, the unit depends on host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc ethnicity
Normative URI http://gensc.org/ns/mixs/ihmc_ethnicity
Label IHMC ethnicity
Definition ethnicity of the subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc medication code
Normative URI http://gensc.org/ns/mixs/ihmc_medication_code
Label IHMC medication code
Definition can include multiple medication codes
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:liver disord
Normative URI http://gensc.org/ns/mixs/liver_disord
Label liver disorder
Definition history of liver disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:medic hist perform
Normative URI http://gensc.org/ns/mixs/medic_hist_perform
Label medical history performed
Definition whether full medical history was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:misc param
Normative URI http://gensc.org/ns/mixs/misc_param
Label miscellaneous parameter
Definition any other measurement performed or parameter collected, that is not listed here
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:organism count
Normative URI http://gensc.org/ns/mixs/organism_count
Label organism count
Definition total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:oxy stat samp
Normative URI http://gensc.org/ns/mixs/oxy_stat_samp
Label oxygenation status of sample
Definition oxygenation status of sample
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:perturbation
Normative URI http://gensc.org/ns/mixs/perturbation
Label perturbation
Definition type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp salinity
Normative URI http://gensc.org/ns/mixs/samp_salinity
Label sample salinity
Definition salinity of sample, i.e. measure of total salt concentration
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store dur
Normative URI http://gensc.org/ns/mixs/samp_store_dur
Label sample storage duration
Definition duration for which sample was stored
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store loc
Normative URI http://gensc.org/ns/mixs/samp_store_loc
Label sample storage location
Definition location at which sample was stored, usually name of a specific freezer/room
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store temp
Normative URI http://gensc.org/ns/mixs/samp_store_temp
Label sample storage temperature
Definition temperature at which sample was stored, e.g. -80 degree Celsius
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp vol we dna ext
Normative URI http://gensc.org/ns/mixs/samp_vol_we_dna_ext
Label sample volume or weight for DNA extraction
Definition volume (mL) or weight (g) of sample processed for DNA extraction
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:special diet
Normative URI http://gensc.org/ns/mixs/special_diet
Label special diet
Definition specification of special diet; can include multiple special diets
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:temp
Normative URI http://gensc.org/ns/mixs/temp
Label temperature
Definition temperature of the sample at time of sampling
Defined By
  Required: No — Repeatable: No

mixs:human-oral

By label: IHMC ethnicity  •  IHMC medication code  •  chemical administration  •  host age  •  host body product  •  host body site  •  host body temperature  •  host body-mass index  •  host diet  •  host disease status  •  host family relationship  •  host genotype  •  host height  •  host last meal  •  host occupation  •  host phenotype  •  host pulse  •  host sex  •  host subject id  •  host total mass  •  medical history performed  •  miscellaneous parameter  •  nose/mouth/teeth/throat disorder  •  organism count  •  oxygenation status of sample  •  perturbation  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  temperature  •  time since last toothbrushing
By concept name: mixs:chem administration  •  mixs:host age  •  mixs:host body mass index  •  mixs:host body product  •  mixs:host body site  •  mixs:host body temp  •  mixs:host diet  •  mixs:host disease stat  •  mixs:host family relationship  •  mixs:host genotype  •  mixs:host height  •  mixs:host last meal  •  mixs:host occupation  •  mixs:host phenotype  •  mixs:host pulse  •  mixs:host sex  •  mixs:host subject id  •  mixs:host tot mass  •  mixs:ihmc ethnicity  •  mixs:ihmc medication code  •  mixs:medic hist perform  •  mixs:misc param  •  mixs:nose mouth teeth throat disord  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:samp salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:temp  •  mixs:time last toothbrush
Concept definitions in mixs:human-oral
Concept Name: mixs:chem administration
Normative URI http://gensc.org/ns/mixs/chem_administration
Label chemical administration
Definition list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v 111), http://purl.bioontology.org/ontology/CHEBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host age
Normative URI http://gensc.org/ns/mixs/host_age
Label host age
Definition age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body mass index
Normative URI http://gensc.org/ns/mixs/host_body_mass_index
Label host body-mass index
Definition body mass index, calculated as weight/(height)squared
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body product
Normative URI http://gensc.org/ns/mixs/host_body_product
Label host body product
Definition substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body site
Normative URI http://gensc.org/ns/mixs/host_body_site
Label host body site
Definition name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body temp
Normative URI http://gensc.org/ns/mixs/host_body_temp
Label host body temperature
Definition core body temperature of the host when sample was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host diet
Normative URI http://gensc.org/ns/mixs/host_diet
Label host diet
Definition type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host disease stat
Normative URI http://gensc.org/ns/mixs/host_disease_stat
Label host disease status
Definition list of diseases with which the host has been diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host family relationship
Normative URI http://gensc.org/ns/mixs/host_family_relationship
Label host family relationship
Definition relationships to other hosts in the same study; can include multiple relationships
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host genotype
Normative URI http://gensc.org/ns/mixs/host_genotype
Label host genotype
Definition observed genotype
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host height
Normative URI http://gensc.org/ns/mixs/host_height
Label host height
Definition the height of subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host last meal
Normative URI http://gensc.org/ns/mixs/host_last_meal
Label host last meal
Definition content of last meal and time since feeding; can include multiple values
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host occupation
Normative URI http://gensc.org/ns/mixs/host_occupation
Label host occupation
Definition most frequent job performed by subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host phenotype
Normative URI http://gensc.org/ns/mixs/host_phenotype
Label host phenotype
Definition phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host pulse
Normative URI http://gensc.org/ns/mixs/host_pulse
Label host pulse
Definition resting pulse, measured as beats per minute
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host sex
Normative URI http://gensc.org/ns/mixs/host_sex
Label host sex
Definition physical sex of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host subject id
Normative URI http://gensc.org/ns/mixs/host_subject_id
Label host subject id
Definition a unique identifier by which each subject can be referred to, de-identified, e.g. #131
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host tot mass
Normative URI http://gensc.org/ns/mixs/host_tot_mass
Label host total mass
Definition total mass of the host at collection, the unit depends on host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc ethnicity
Normative URI http://gensc.org/ns/mixs/ihmc_ethnicity
Label IHMC ethnicity
Definition ethnicity of the subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc medication code
Normative URI http://gensc.org/ns/mixs/ihmc_medication_code
Label IHMC medication code
Definition can include multiple medication codes
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:medic hist perform
Normative URI http://gensc.org/ns/mixs/medic_hist_perform
Label medical history performed
Definition whether full medical history was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:misc param
Normative URI http://gensc.org/ns/mixs/misc_param
Label miscellaneous parameter
Definition any other measurement performed or parameter collected, that is not listed here
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:nose mouth teeth throat disord
Normative URI http://gensc.org/ns/mixs/nose_mouth_teeth_throat_disord
Label nose/mouth/teeth/throat disorder
Definition history of nose/mouth/teeth/throat disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:organism count
Normative URI http://gensc.org/ns/mixs/organism_count
Label organism count
Definition total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:oxy stat samp
Normative URI http://gensc.org/ns/mixs/oxy_stat_samp
Label oxygenation status of sample
Definition oxygenation status of sample
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:perturbation
Normative URI http://gensc.org/ns/mixs/perturbation
Label perturbation
Definition type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp salinity
Normative URI http://gensc.org/ns/mixs/samp_salinity
Label sample salinity
Definition salinity of sample, i.e. measure of total salt concentration
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store dur
Normative URI http://gensc.org/ns/mixs/samp_store_dur
Label sample storage duration
Definition duration for which sample was stored
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store loc
Normative URI http://gensc.org/ns/mixs/samp_store_loc
Label sample storage location
Definition location at which sample was stored, usually name of a specific freezer/room
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store temp
Normative URI http://gensc.org/ns/mixs/samp_store_temp
Label sample storage temperature
Definition temperature at which sample was stored, e.g. -80 degree Celsius
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp vol we dna ext
Normative URI http://gensc.org/ns/mixs/samp_vol_we_dna_ext
Label sample volume or weight for DNA extraction
Definition volume (mL) or weight (g) of sample processed for DNA extraction
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:temp
Normative URI http://gensc.org/ns/mixs/temp
Label temperature
Definition temperature of the sample at time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:time last toothbrush
Normative URI http://gensc.org/ns/mixs/time_last_toothbrush
Label time since last toothbrushing
Definition specification of the time since last toothbrushing
Defined By
  Required: No — Repeatable: No

mixs:human-skin

By label: IHMC ethnicity  •  IHMC medication code  •  chemical administration  •  dermatology disorder  •  dominant hand  •  host age  •  host body product  •  host body site  •  host body temperature  •  host body-mass index  •  host diet  •  host disease status  •  host family relationship  •  host genotype  •  host height  •  host last meal  •  host occupation  •  host phenotype  •  host pulse  •  host sex  •  host subject id  •  host total mass  •  medical history performed  •  miscellaneous parameter  •  organism count  •  oxygenation status of sample  •  perturbation  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  temperature  •  time since last wash
By concept name: mixs:chem administration  •  mixs:dermatology disord  •  mixs:dominant hand  •  mixs:host age  •  mixs:host body mass index  •  mixs:host body product  •  mixs:host body site  •  mixs:host body temp  •  mixs:host diet  •  mixs:host disease stat  •  mixs:host family relationship  •  mixs:host genotype  •  mixs:host height  •  mixs:host last meal  •  mixs:host occupation  •  mixs:host phenotype  •  mixs:host pulse  •  mixs:host sex  •  mixs:host subject id  •  mixs:host tot mass  •  mixs:ihmc ethnicity  •  mixs:ihmc medication code  •  mixs:medic hist perform  •  mixs:misc param  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:samp salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:temp  •  mixs:time since last wash
Concept definitions in mixs:human-skin
Concept Name: mixs:chem administration
Normative URI http://gensc.org/ns/mixs/chem_administration
Label chemical administration
Definition list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v 111), http://purl.bioontology.org/ontology/CHEBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:dermatology disord
Normative URI http://gensc.org/ns/mixs/dermatology_disord
Label dermatology disorder
Definition history of dermatology disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:dominant hand
Normative URI http://gensc.org/ns/mixs/dominant_hand
Label dominant hand
Definition dominant hand of the subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host age
Normative URI http://gensc.org/ns/mixs/host_age
Label host age
Definition age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body mass index
Normative URI http://gensc.org/ns/mixs/host_body_mass_index
Label host body-mass index
Definition body mass index, calculated as weight/(height)squared
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body product
Normative URI http://gensc.org/ns/mixs/host_body_product
Label host body product
Definition substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body site
Normative URI http://gensc.org/ns/mixs/host_body_site
Label host body site
Definition name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body temp
Normative URI http://gensc.org/ns/mixs/host_body_temp
Label host body temperature
Definition core body temperature of the host when sample was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host diet
Normative URI http://gensc.org/ns/mixs/host_diet
Label host diet
Definition type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host disease stat
Normative URI http://gensc.org/ns/mixs/host_disease_stat
Label host disease status
Definition list of diseases with which the host has been diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host family relationship
Normative URI http://gensc.org/ns/mixs/host_family_relationship
Label host family relationship
Definition relationships to other hosts in the same study; can include multiple relationships
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host genotype
Normative URI http://gensc.org/ns/mixs/host_genotype
Label host genotype
Definition observed genotype
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host height
Normative URI http://gensc.org/ns/mixs/host_height
Label host height
Definition the height of subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host last meal
Normative URI http://gensc.org/ns/mixs/host_last_meal
Label host last meal
Definition content of last meal and time since feeding; can include multiple values
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host occupation
Normative URI http://gensc.org/ns/mixs/host_occupation
Label host occupation
Definition most frequent job performed by subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host phenotype
Normative URI http://gensc.org/ns/mixs/host_phenotype
Label host phenotype
Definition phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host pulse
Normative URI http://gensc.org/ns/mixs/host_pulse
Label host pulse
Definition resting pulse, measured as beats per minute
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host sex
Normative URI http://gensc.org/ns/mixs/host_sex
Label host sex
Definition physical sex of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host subject id
Normative URI http://gensc.org/ns/mixs/host_subject_id
Label host subject id
Definition a unique identifier by which each subject can be referred to, de-identified, e.g. #131
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host tot mass
Normative URI http://gensc.org/ns/mixs/host_tot_mass
Label host total mass
Definition total mass of the host at collection, the unit depends on host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc ethnicity
Normative URI http://gensc.org/ns/mixs/ihmc_ethnicity
Label IHMC ethnicity
Definition ethnicity of the subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc medication code
Normative URI http://gensc.org/ns/mixs/ihmc_medication_code
Label IHMC medication code
Definition can include multiple medication codes
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:medic hist perform
Normative URI http://gensc.org/ns/mixs/medic_hist_perform
Label medical history performed
Definition whether full medical history was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:misc param
Normative URI http://gensc.org/ns/mixs/misc_param
Label miscellaneous parameter
Definition any other measurement performed or parameter collected, that is not listed here
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:organism count
Normative URI http://gensc.org/ns/mixs/organism_count
Label organism count
Definition total count of any organism per gram or volume of sample, should include name of organism followed by count; can include multiple organism counts
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:oxy stat samp
Normative URI http://gensc.org/ns/mixs/oxy_stat_samp
Label oxygenation status of sample
Definition oxygenation status of sample
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:perturbation
Normative URI http://gensc.org/ns/mixs/perturbation
Label perturbation
Definition type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with time that perturbation occurred; can include multiple perturbation types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp salinity
Normative URI http://gensc.org/ns/mixs/samp_salinity
Label sample salinity
Definition salinity of sample, i.e. measure of total salt concentration
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store dur
Normative URI http://gensc.org/ns/mixs/samp_store_dur
Label sample storage duration
Definition duration for which sample was stored
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store loc
Normative URI http://gensc.org/ns/mixs/samp_store_loc
Label sample storage location
Definition location at which sample was stored, usually name of a specific freezer/room
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp store temp
Normative URI http://gensc.org/ns/mixs/samp_store_temp
Label sample storage temperature
Definition temperature at which sample was stored, e.g. -80 degree Celsius
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:samp vol we dna ext
Normative URI http://gensc.org/ns/mixs/samp_vol_we_dna_ext
Label sample volume or weight for DNA extraction
Definition volume (mL) or weight (g) of sample processed for DNA extraction
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:temp
Normative URI http://gensc.org/ns/mixs/temp
Label temperature
Definition temperature of the sample at time of sampling
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:time since last wash
Normative URI http://gensc.org/ns/mixs/time_since_last_wash
Label time since last wash
Definition specification of the time since last wash
Defined By
  Required: No — Repeatable: No

mixs:human-vaginal

By label: HRT  •  IHMC ethnicity  •  IHMC medication code  •  birth control  •  chemical administration  •  douche  •  gynecological disorder  •  host age  •  host body product  •  host body site  •  host body temperature  •  host body-mass index  •  host diet  •  host disease status  •  host family relationship  •  host genotype  •  host height  •  host last meal  •  host occupation  •  host phenotype  •  host pulse  •  host sex  •  host subject id  •  host total mass  •  hysterectomy  •  medical history performed  •  menarche  •  menopause  •  miscellaneous parameter  •  organism count  •  oxygenation status of sample  •  perturbation  •  pregnancy  •  sample salinity  •  sample storage duration  •  sample storage location  •  sample storage temperature  •  sample volume or weight for DNA extraction  •  sexual activity  •  temperature  •  urogenital disorder
By concept name: mixs:birth control  •  mixs:chem administration  •  mixs:douche  •  mixs:gynecologic disord  •  mixs:host age  •  mixs:host body mass index  •  mixs:host body product  •  mixs:host body site  •  mixs:host body temp  •  mixs:host diet  •  mixs:host disease stat  •  mixs:host family relationship  •  mixs:host genotype  •  mixs:host height  •  mixs:host last meal  •  mixs:host occupation  •  mixs:host phenotype  •  mixs:host pulse  •  mixs:host sex  •  mixs:host subject id  •  mixs:host tot mass  •  mixs:hrt  •  mixs:hysterectomy  •  mixs:ihmc ethnicity  •  mixs:ihmc medication code  •  mixs:medic hist perform  •  mixs:menarche  •  mixs:menopause  •  mixs:misc param  •  mixs:organism count  •  mixs:oxy stat samp  •  mixs:perturbation  •  mixs:pregnancy  •  mixs:samp salinity  •  mixs:samp store dur  •  mixs:samp store loc  •  mixs:samp store temp  •  mixs:samp vol we dna ext  •  mixs:sexual act  •  mixs:temp  •  mixs:urogenit disord
Concept definitions in mixs:human-vaginal
Concept Name: mixs:birth control
Normative URI http://gensc.org/ns/mixs/birth_control
Label birth control
Definition specification of birth control medication used
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:chem administration
Normative URI http://gensc.org/ns/mixs/chem_administration
Label chemical administration
Definition list of chemical compounds administered to the host or site where sampling occurred, and when (e.g. antibiotics, N fertilizer, air filter); can include multiple compounds. For Chemical Entities of Biological Interest ontology (CHEBI) (v 111), http://purl.bioontology.org/ontology/CHEBI
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:douche
Normative URI http://gensc.org/ns/mixs/douche
Label douche
Definition date of most recent douche
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:gynecologic disord
Normative URI http://gensc.org/ns/mixs/gynecologic_disord
Label gynecological disorder
Definition history of gynecological disorders; can include multiple disorders
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host age
Normative URI http://gensc.org/ns/mixs/host_age
Label host age
Definition age of host at the time of sampling; relevant scale depends on species and study, e.g. could be seconds for amoebae or centuries for trees
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body mass index
Normative URI http://gensc.org/ns/mixs/host_body_mass_index
Label host body-mass index
Definition body mass index, calculated as weight/(height)squared
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body product
Normative URI http://gensc.org/ns/mixs/host_body_product
Label host body product
Definition substance produced by the body, e.g. stool, mucus, where the sample was obtained from. For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body site
Normative URI http://gensc.org/ns/mixs/host_body_site
Label host body site
Definition name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc...). For Foundational Model of Anatomy Ontology (FMA) (v 3.1) terms, please see http://purl.bioontology.org/ontology/FMA
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host body temp
Normative URI http://gensc.org/ns/mixs/host_body_temp
Label host body temperature
Definition core body temperature of the host when sample was collected
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host diet
Normative URI http://gensc.org/ns/mixs/host_diet
Label host diet
Definition type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host disease stat
Normative URI http://gensc.org/ns/mixs/host_disease_stat
Label host disease status
Definition list of diseases with which the host has been diagnosed; can include multiple diagnoses. the value of the field depends on host; for humans the terms should be chosen from DO (Disease Ontology) at http://www.disease-ontology.org, other hosts are free text
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host family relationship
Normative URI http://gensc.org/ns/mixs/host_family_relationship
Label host family relationship
Definition relationships to other hosts in the same study; can include multiple relationships
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host genotype
Normative URI http://gensc.org/ns/mixs/host_genotype
Label host genotype
Definition observed genotype
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host height
Normative URI http://gensc.org/ns/mixs/host_height
Label host height
Definition the height of subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host last meal
Normative URI http://gensc.org/ns/mixs/host_last_meal
Label host last meal
Definition content of last meal and time since feeding; can include multiple values
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host occupation
Normative URI http://gensc.org/ns/mixs/host_occupation
Label host occupation
Definition most frequent job performed by subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host phenotype
Normative URI http://gensc.org/ns/mixs/host_phenotype
Label host phenotype
Definition phenotype of host. For Phenotypic quality Ontology (PATO) (v 2013-10-28) terms, please see http://purl.bioontology.org/ontology/PATO
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host pulse
Normative URI http://gensc.org/ns/mixs/host_pulse
Label host pulse
Definition resting pulse, measured as beats per minute
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host sex
Normative URI http://gensc.org/ns/mixs/host_sex
Label host sex
Definition physical sex of the host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host subject id
Normative URI http://gensc.org/ns/mixs/host_subject_id
Label host subject id
Definition a unique identifier by which each subject can be referred to, de-identified, e.g. #131
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:host tot mass
Normative URI http://gensc.org/ns/mixs/host_tot_mass
Label host total mass
Definition total mass of the host at collection, the unit depends on host
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:hrt
Normative URI http://gensc.org/ns/mixs/hrt
Label HRT
Definition whether subject had hormone replacement theraphy, and if yes start date
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:hysterectomy
Normative URI http://gensc.org/ns/mixs/hysterectomy
Label hysterectomy
Definition specification of whether hysterectomy was performed
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc ethnicity
Normative URI http://gensc.org/ns/mixs/ihmc_ethnicity
Label IHMC ethnicity
Definition ethnicity of the subject
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:ihmc medication code
Normative URI http://gensc.org/ns/mixs/ihmc_medication_code
Label IHMC medication code
Definition can include multiple medication codes
Defined By
  Required: No — Repeatable: No
Concept Name: mixs:medic hist perform