Class: human-associated MIMARKS survey

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

URI: mixs.vocab:Human-associatedMIMARKSSurvey

Parents

• is_a: Human-associated - human-associated

Uses Checklist

• mixin: MIMARKSSurvey - Minimal Information about a Marker Specimen: survey

Attributes

Inherited from human-associated:

• lat_lon _0..1
  • 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
• depth _0..1
  • 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: QuantityValue
  • Example: 10 meter None
• alt _0..1
  • 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
• elev _0..1
  • 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
• human-associated➞temp _0..1
  • Range: QuantityValue
• geo_loc_name _0..1
  • 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 (http://purl.bioontology.org/ontology/GAZ)
  • Range: String
  • Example: USA: Maryland, Bethesda None
• collection_date _0..1
  • 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; 2018-05-11 None
• env_broad_scale _0..1
  • Description: Report the major environmental system the sample or specimen came from. The system(s) identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. in the desert or a rainforest). We recommend using subclasses of EnvO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
  • Range: String
  • Example: oceanic epipelagic zone biome [ENVO:01000033] for annotating a water sample from the photic zone in middle of the Atlantic Ocean None
• env_local_scale _0..1
  • Description: Report the entity or entities which are in the sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. We recommend using EnvO terms which are of smaller spatial grain than your entry for env_broad_scale. Terms, such as anatomical sites, from other OBO Library ontologies which interoperate with EnvO (e.g. UBERON) are accepted in this field. EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS
  • Range: String
  • Example: litter layer [ENVO:01000338]; 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]. None
• env_medium _0..1
  • Description: Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top).
  • Range: String
  • Example: soil [ENVO:00001998]; 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] None
• human-associated➞host_subject_id _0..1
  • Range: String
• human-associated➞host_age _0..1
  • Range: QuantityValue
• human-associated➞host_sex _0..1
  • Range: host_sex_enum
• human-associated➞ihmc_medication_code _0..*
  • Range: Integer
• human-associated➞chem_administration _0..*
  • Range: String
• human-associated➞host_body_site _0..1
  • Range: String
• human-associated➞host_body_product _0..1
  • Range: String
• human-associated➞host_tot_mass _0..1
  • Range: QuantityValue
• human-associated➞host_height _0..1
  • Range: QuantityValue
• human-associated➞host_diet _0..*
  • Range: String
• human-associated➞host_last_meal _0..*
  • Range: String
• human-associated➞host_family_relation _0..*
  • Range: String
• human-associated➞host_genotype _0..1
  • Range: String
• human-associated➞host_phenotype _0..1
  • Range: String
• human-associated➞host_body_temp _0..1
  • Range: QuantityValue
• human-associated➞smoker _0..1
  • Range: String
• human-associated➞host_hiv_stat _0..1
  • Range: String
• human-associated➞drug_usage _0..*
  • Range: drug_usage_enum
• human-associated➞host_body_mass_index _0..1
  • Range: QuantityValue
• human-associated➞diet_last_six_month _0..1
  • Range: String
• human-associated➞weight_loss_3_month _0..1
  • Range: String
• human-associated➞ethnicity _0..*
  • Range: String
• human-associated➞host_occupation _0..1
  • Range: Integer
• human-associated➞pet_farm_animal _0..*
  • Range: String
• human-associated➞travel_out_six_month _0..*
  • Range: String
• human-associated➞twin_sibling _0..1
  • Range: String
• human-associated➞medic_hist_perform _0..1
  • Range: String
• human-associated➞study_complt_stat _0..1
  • Range: study_complt_stat_enum
• human-associated➞pulmonary_disord _0..*
  • Range: String
• human-associated➞nose_throat_disord _0..*
  • Range: String
• human-associated➞blood_blood_disord _0..*
  • Range: String
• human-associated➞host_pulse _0..1
  • Range: QuantityValue
• human-associated➞gestation_state _0..1
  • Range: String
• human-associated➞maternal_health_stat _0..1
  • Range: String
• human-associated➞foetal_health_stat _0..1
  • Range: String
• human-associated➞amniotic_fluid_color _0..1
  • Range: String
• human-associated➞kidney_disord _0..*
  • Range: String
• human-associated➞urogenit_tract_disor _0..*
  • Range: String
• human-associated➞urine_collect_meth _0..1
  • Range: String
• human-associated➞perturbation _0..*
  • Range: String
• human-associated➞samp_salinity _0..1
  • Range: QuantityValue
• human-associated➞salinity _0..1
  • Range: QuantityValue
• human-associated➞oxy_stat_samp _0..1
  • Range: oxy_stat_samp_enum
• human-associated➞organism_count _0..*
  • Range: organism_count_enum
• human-associated➞samp_store_temp _0..1
  • Range: QuantityValue
• human-associated➞samp_store_dur _0..1
  • Range: String
• human-associated➞host_symbiont _0..*
  • Range: String
• human-associated➞samp_store_loc _0..1
  • Range: String
• human-associated➞misc_param _0..*
  • Range: String
• human-associated➞samp_name _1..1
  • Range: String
• human-associated➞project_name _1..1
  • Range: String
• human-associated➞host_disease_stat _0..1
  • Range: String
• human-associated➞samp_vol_we_dna_ext _0..1
  • Range: QuantityValue

Mixed in from MIMARKS survey:

• MIMARKS survey➞submitted_to_insdc _1..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞investigation_type _1..1
  • Range: investigation_type_enum

Mixed in from MIMARKS survey:

• MIMARKS survey➞samp_taxon_id _1..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞experimental_factor _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞env_package _0..1
  • Range: env_package_enum

Mixed in from MIMARKS survey:

• MIMARKS survey➞subspecf_gen_lin _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞extrachrom_elements _0..1
  • Range: Integer

Mixed in from MIMARKS survey:

• MIMARKS survey➞source_mat_id _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞biotic_relationship _0..1
  • Range: biotic_relationship_enum

Mixed in from MIMARKS survey:

• MIMARKS survey➞trophic_level _0..1
  • Range: trophic_level_enum

Mixed in from MIMARKS survey:

• MIMARKS survey➞rel_to_oxygen _0..1
  • Range: rel_to_oxygen_enum

Mixed in from MIMARKS survey:

• MIMARKS survey➞isol_growth_condt _1..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞samp_collec_device _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞samp_collec_method _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞samp_mat_process _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞samp_size _0..1
  • Range: QuantityValue

Mixed in from MIMARKS survey:

• MIMARKS survey➞nucl_acid_ext _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞nucl_acid_amp _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞target_gene _1..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞target_subfragment _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞pcr_primers _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞pcr_cond _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞seq_meth _1..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞seq_quality_check _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞chimera_check _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞associated resource _0..1
  • Range: String

Mixed in from MIMARKS survey:

• MIMARKS survey➞sop _0..1
  • Range: String