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Class: Human-gut

human-gut

URI: mixs.vocab:Human-gut

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Attributes

Own

  • chem_administration OPT
    • Description: 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 163), http://purl.bioontology.org/ontology/chebi
    • range: String
    • Example: agar [CHEBI:2509];2018-05-11T20:00Z None
  • gastrointest_disord OPT
    • Description: History of gastrointestinal tract disorders; can include multiple disorders. History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, gastrointestinal system disease (https://disease-ontology.org/?id=DOID:77).
    • range: String
    • Example: None
  • host_age OPT
    • Description: 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
    • range: String
    • Example: 10 days None
  • host_body_mass_index OPT
    • Description: Body mass index, calculated as weight/(height)squared
    • range: String
    • Example: 22 kilogram per square meter None
  • host_body_product OPT
    • Description: Substance produced by the body, e.g. Stool, mucus, where the sample was obtained from. For foundational model of anatomy ontology (fma) or Uber-anatomy ontology (UBERON) terms, please see https://www.ebi.ac.uk/ols/ontologies/fma or https://www.ebi.ac.uk/ols/ontologies/uberon
    • range: String
    • Example: Portion of mucus [fma66938] None
  • host_body_site OPT
    • Description: 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 4.11.0) or Uber-anatomy ontology (UBERON) (v releases/2014-06-15) terms, please see http://purl.bioontology.org/ontology/FMA or http://purl.bioontology.org/ontology/UBERON
    • range: String
    • Example: gill [UBERON:0002535] None
  • host_body_temp OPT
    • Description: Core body temperature of the host when sample was collected
    • range: String
    • Example: 15 degree Celsius None
  • host_diet OPT
    • Description: Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types
    • range: String
    • Example: herbivore None
  • host_disease_stat OPT
    • Description: 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 the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text
    • range: String
    • Example: rabies [DOID:11260] None
  • host_family_relationship OPT
    • Description: Relationships to other hosts in the same study; can include multiple relationships
    • range: String
    • Example: offspring;Mussel25 None
  • host_genotype OPT
    • Description: Observed genotype
    • range: String
    • Example: C57BL/6 None
  • host_height OPT
    • Description: The height of subject
    • range: String
    • Example: 0.1 meter None
  • host_last_meal OPT
    • Description: Content of last meal and time since feeding; can include multiple values
    • range: String
    • Example: corn feed;P2H None
  • host_occupation OPT
    • Description: Most frequent job performed by subject
    • range: String
    • Example: veterinary None
  • host_phenotype OPT
    • Description: Phenotype of human or other host. For phenotypic quality ontology (pato) (v 2018-03-27) terms, please see http://purl.bioontology.org/ontology/pato. For Human Phenotype Ontology (HP) (v 2018-06-13) please see http://purl.bioontology.org/ontology/HP
    • range: String
    • Example: elongated [PATO:0001154] None
  • host_pulse OPT
    • Description: Resting pulse, measured as beats per minute
    • range: String
    • Example: 65 beats per minute None
  • host_sex OPT
    • Description: Physical sex of the host
    • range: String
    • Example: female None
  • host_subject_id OPT
    • Description: A unique identifier by which each subject can be referred to, de-identified, e.g. #131
    • range: String
    • Example: MPI123 None
  • host_tot_mass OPT
    • Description: Total mass of the host at collection, the unit depends on host
    • range: String
    • Example: 2500 gram None
  • ihmc_ethnicity OPT
    • Description: Ethnicity of the subject
    • range: String
    • Example: caucasian None
  • ihmc_medication_code OPT
    • Description: Can include multiple medication codes
    • range: String
    • Example: 810 None
  • liver_disord OPT
    • Description: History of liver disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, liver disease (https://disease-ontology.org/?id=DOID:409).
    • range: String
    • Example: None
  • medic_hist_perform OPT
    • Description: Whether full medical history was collected
    • range: String
    • Example: TRUE None
  • misc_param OPT
    • Description: Any other measurement performed or parameter collected, that is not listed here
    • range: String
    • Example: Bicarbonate ion concentration;2075 micromole per kilogram None
  • organism_count OPT
    • Description: Total cell count of any organism (or group of organisms) per gram, volume or area of sample, should include name of organism followed by count. The method that was used for the enumeration (e.g. qPCR, atp, mpn, etc.) Should also be provided. (example: total prokaryotes; 3.5e7 cells per ml; qpcr)
    • range: String
    • Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None
  • oxy_stat_samp OPT
    • Description: Oxygenation status of sample
    • range: String
    • Example: aerobic None
  • perturbation OPT
    • Description: Type of perturbation, e.g. chemical administration, physical disturbance, etc., coupled with perturbation regimen including how many times the perturbation was repeated, how long each perturbation lasted, and the start and end time of the entire perturbation period; can include multiple perturbation types
    • range: String
    • Example: antibiotic addition;R2/2018-05-11T14:30Z/2018-05-11T19:30Z/P1H30M None
  • samp_salinity OPT
    • Description: Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) sample. While salinity can be measured by a complete chemical analysis, this method is difficult and time consuming. More often, it is instead derived from the conductivity measurement. This is known as practical salinity. These derivations compare the specific conductance of the sample to a salinity standard such as seawater
    • range: String
    • Example: 1 milligram per liter None
  • samp_store_dur OPT
    • Description: Duration for which the sample was stored
    • range: String
    • Example: P1Y6M None
  • samp_store_loc OPT
    • Description: Location at which sample was stored, usually name of a specific freezer/room
    • range: String
    • Example: Freezer no:5 None
  • samp_store_temp OPT
    • Description: Temperature at which sample was stored, e.g. -80 degree Celsius
    • range: String
    • Example: -80 degree Celsius None
  • samp_vol_we_dna_ext OPT
    • Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction
    • range: String
    • Example: 1500 milliliter None
  • special_diet OPT
    • Description: Specification of special diet; can include multiple special diets
    • range: String
    • Example: other:vegan None
  • temp OPT
    • Description: Temperature of the sample at the time of sampling
    • range: String
    • Example: 25 degree Celsius None