Class: Human-associatedMIMARKSSpecimen

Combinatorial checklist Minimal Information about a Marker Specimen: specimen with environmental package human-associated

URI: mixs.vocab:Human-associatedMIMARKSSpecimen

Parents

• is_a: Human-associated - human-associated

Uses Mixins

• mixin: MIMARKSSpecimen - Minimal Information about a Marker Specimen: specimen

Attributes

Inherited from human-associated:

• alt _OPT
  • Description: Altitude is a term used to identify heights of objects such as airplanes, space shuttles, rockets, atmospheric balloons and heights of places such as atmospheric layers and clouds. It is used to measure the height of an object which is above the earth’s surface. In this context, the altitude measurement is the vertical distance between the earth’s surface above sea level and the sampled position in the air
  • range: QuantityValue
  • Example: 100 meter None
• amniotic_fluid_color _OPT
  • Description: Specification of the color of the amniotic fluid sample
  • range: String
  • Example: None
• blood_blood_disord _OPT
  • Description: 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, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74).
  • range: String
  • Example: None
• 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
• collection_date _OPT
  • Description: 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
  • range: Date
  • Example: 2018-05-11T10:00:00+01:00 None
• depth _OPT
  • Description: 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.
  • range: String
  • Example: None
• diet_last_six_month _OPT
  • Description: Specification of major diet changes in the last six months, if yes the change should be specified
  • range: String
  • Example: yes;vegetarian diet None
• drug_usage _OPT
  • Description: Any drug used by subject and the frequency of usage; can include multiple drugs used
  • range:
  • Example: Lipitor;2/day None
• elev _OPT
  • Description: Elevation of the sampling site is its height above a fixed reference point, most commonly the mean sea level. Elevation is mainly used when referring to points on the earth’s surface, while altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit
  • range: QuantityValue
  • Example: 100 meter None
• env_broad_scale _OPT

  • Description: In this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]

    termLabel [termID]

    termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html

  • range: String
  • Example: forest biome [ENVO:01000174] None
• env_local_scale _OPT

  • Description: In this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]

    termLabel [termID]

    termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]

    herb and fern layer [ENVO:01000337]

    litter layer [ENVO:01000338]

    understory [01000335]

    shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html

  • range: String
  • Example: litter layer [ENVO:01000338] None
• env_medium _OPT

  • Description: In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]

    termLabel [termID]

    termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]

    air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html

  • range: String
  • Example: soil [ENVO:00001998] None
• foetal_health_stat _OPT
  • Description: Specification of foetal health status, should also include abortion
  • range: String
  • Example: None
• geo_loc_name _OPT
  • Description: 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)
  • range: String
  • Example: Germany;North Rhine-Westphalia;Eifel National Park None
• gestation_state _OPT
  • Description: Specification of the gestation state
  • 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: QuantityValue
  • Example: 10 days None
• host_body_mass_index _OPT
  • Description: Body mass index, calculated as weight/(height)squared
  • range: QuantityValue
  • 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: QuantityValue
  • 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: QuantityValue
  • Example: 0.1 meter None
• host_hiv_stat _OPT
  • Description: HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO]
  • range: String
  • Example: yes;yes 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: QuantityValue
  • Example: 65 beats per minute None
• host_sex _OPT
  • Description: Physical sex of the host
  • range:
  • 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_symbiont _OPT
  • Description: The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host.
  • range: String
  • Example: flukeworms None
• host_tot_mass _OPT
  • Description: Total mass of the host at collection, the unit depends on host
  • range: QuantityValue
  • 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
• kidney_disord _OPT
  • Description: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557).
  • range: String
  • Example: None
• lat_lon _OPT
  • Description: The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system
  • range: String
  • Example: 50.586825 6.408977 None
• maternal_health_stat _OPT
  • Description: Specification of the maternal health status
  • 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
• nose_throat_disord _OPT
  • Description: History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974).
  • range: String
  • Example: 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:
  • Example: total prokaryotes;3.5e7 cells per milliliter;qPCR None
• oxy_stat_samp _OPT
  • Description: Oxygenation status of sample
  • range:
  • 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
• pet_farm_animal _OPT
  • Description: 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
  • range: String
  • Example: yes; 5 cats None
• pulmonary_disord _OPT
  • Description: History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850).
  • range: String
  • Example: 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: QuantityValue
  • 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: QuantityValue
  • 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: QuantityValue
  • Example: 1500 milliliter None
• smoker _OPT
  • Description: Specification of smoking status
  • range: String
  • Example: yes None
• study_complt_stat _OPT
  • Description: Specification of study completion status, if no the reason should be specified
  • range:
  • Example: no;non-compliance None
• temp _OPT
  • Description: Temperature of the sample at the time of sampling
  • range: QuantityValue
  • Example: 25 degree Celsius None
• travel_out_six_month _OPT
  • Description: Specification of the countries travelled in the last six months; can include multiple travels
  • range: String
  • Example: None
• twin_sibling _OPT
  • Description: Specification of twin sibling presence
  • range: String
  • Example: yes None
• urine_collect_meth _OPT
  • Description: Specification of urine collection method
  • range: String
  • Example: catheter None
• urogenit_tract_disor _OPT
  • Description: History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18).
  • range: String
  • Example: None
• weight_loss_3_month _OPT
  • Description: Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss
  • range: String
  • Example: yes;5 kilogram None

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞adapters _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞assembly_software _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞chimera_check _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞env_package _OPT
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞experimental_factor _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞investigation_type _REQ
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_layout _OPT
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_reads_seqd _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_screen _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_size _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_vector _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞mid _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞nucl_acid_amp _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞nucl_acid_ext _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞pcr_cond _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞pcr_primers _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞project_name _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞rel_to_oxygen _OPT
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_mat_process _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞samp_size _OPT
  • range: QuantityValue

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sample_collect_device _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sample_collect_method _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sample_name _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞seq_meth _REQ
  • range:

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞seq_quality_check _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞size_frac _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞sop _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞source_mat_id _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞submitted_to_insdc _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞target_gene _REQ
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞target_subfragment _OPT
  • range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞url _OPT
  • range: String