Class: human-gut MISAG

Combinatorial checklist Minimum Information About a Single Amplified Genome with environmental package human-gut

URI: mixs.vocab:Human-gutMISAG

Parents

• is_a: Human-gut - human-gut

Uses Checklist

• mixin: MISAG - Minimum Information About a Single Amplified Genome

Attributes

Inherited from human-gut:

• 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-gut➞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-gut➞gastrointest_disord _0..*
  • Range: String
• human-gut➞liver_disord _0..*
  • Range: String
• human-gut➞special_diet _0..*
  • Range: special_diet_enum
• human-gut➞host_subject_id _0..1
  • Range: String
• human-gut➞host_age _0..1
  • Range: QuantityValue
• human-gut➞host_sex _0..1
  • Range: host_sex_enum
• human-gut➞ihmc_medication_code _0..*
  • Range: Integer
• human-gut➞chem_administration _0..*
  • Range: String
• human-gut➞host_body_site _0..1
  • Range: String
• human-gut➞host_body_product _0..1
  • Range: String
• human-gut➞host_tot_mass _0..1
  • Range: QuantityValue
• human-gut➞host_height _0..1
  • Range: QuantityValue
• human-gut➞host_diet _0..*
  • Range: String
• human-gut➞host_last_meal _0..*
  • Range: String
• human-gut➞host_family_relation _0..*
  • Range: String
• human-gut➞host_genotype _0..1
  • Range: String
• human-gut➞host_phenotype _0..1
  • Range: String
• human-gut➞host_body_temp _0..1
  • Range: QuantityValue
• human-gut➞host_body_mass_index _0..1
  • Range: QuantityValue
• human-gut➞ethnicity _0..*
  • Range: String
• human-gut➞host_occupation _0..1
  • Range: Integer
• human-gut➞medic_hist_perform _0..1
  • Range: String
• human-gut➞host_pulse _0..1
  • Range: QuantityValue
• human-gut➞perturbation _0..*
  • Range: String
• human-gut➞samp_salinity _0..1
  • Range: QuantityValue
• human-gut➞salinity _0..1
  • Range: QuantityValue
• human-gut➞oxy_stat_samp _0..1
  • Range: oxy_stat_samp_enum
• human-gut➞organism_count _0..*
  • Range: organism_count_enum
• human-gut➞samp_store_temp _0..1
  • Range: QuantityValue
• human-gut➞samp_store_dur _0..1
  • Range: String
• human-gut➞host_symbiont _0..*
  • Range: String
• human-gut➞samp_store_loc _0..1
  • Range: String
• human-gut➞misc_param _0..*
  • Range: String
• human-gut➞samp_name _1..1
  • Range: String
• human-gut➞project_name _1..1
  • Range: String
• human-gut➞host_disease_stat _0..1
  • Range: String
• human-gut➞samp_vol_we_dna_ext _0..1
  • Range: QuantityValue

Mixed in from MISAG:

• MISAG➞submitted_to_insdc _1..1
  • Range: String

Mixed in from MISAG:

• MISAG➞investigation_type _1..1
  • Range: investigation_type_enum

Mixed in from MISAG:

• MISAG➞samp_taxon_id _1..1
  • Range: String

Mixed in from MISAG:

• MISAG➞experimental_factor _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞env_package _0..1
  • Range: env_package_enum

Mixed in from MISAG:

• MISAG➞ref_biomaterial _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞source_mat_id _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞rel_to_oxygen _0..1
  • Range: rel_to_oxygen_enum

Mixed in from MISAG:

• MISAG➞samp_collec_device _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞samp_collec_method _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞samp_mat_process _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞size_frac _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞samp_size _0..1
  • Range: QuantityValue

Mixed in from MISAG:

• MISAG➞nucl_acid_ext _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞nucl_acid_amp _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞lib_size _0..1
  • Range: Integer

Mixed in from MISAG:

• MISAG➞lib_reads_seqd _0..1
  • Range: Integer

Mixed in from MISAG:

• MISAG➞lib_layout _0..1
  • Range: lib_layout_enum

Mixed in from MISAG:

• MISAG➞lib_vector _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞lib_screen _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞mid _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞adapters _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞seq_meth _1..1
  • Range: String

Mixed in from MISAG:

• MISAG➞tax_ident _1..1
  • Range: tax_ident_enum

Mixed in from MISAG:

• MISAG➞assembly_qual _1..1
  • Range: assembly_qual_enum

Mixed in from MISAG:

• MISAG➞assembly_name _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞assembly_software _1..1
  • Range: String

Mixed in from MISAG:

• MISAG➞annot _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞number_contig _0..1
  • Range: Integer

Mixed in from MISAG:

• MISAG➞feat_pred _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞ref_db _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞sim_search_meth _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞tax_class _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞x_16s_recover _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞trnas _0..1
  • Range: Integer

Mixed in from MISAG:

• MISAG➞trna_ext_software _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞compl_score _1..1
  • Range: compl_score_enum

Mixed in from MISAG:

• MISAG➞compl_software _1..1
  • Range: String

Mixed in from MISAG:

• MISAG➞compl_appr _0..1
  • Range: compl_appr_enum

Mixed in from MISAG:

• MISAG➞contam_score _1..1
  • Range: String

Mixed in from MISAG:

• MISAG➞contam_screen_input _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞contam_screen_param _0..1
  • Range: contam_screen_param_enum

Mixed in from MISAG:

• MISAG➞decontam_software _0..1
  • Range: decontam_software_enum

Mixed in from MISAG:

• MISAG➞sort_tech _1..1
  • Range: sort_tech_enum

Mixed in from MISAG:

• MISAG➞single_cell_lysis_appr _1..1
  • Range: single_cell_lysis_appr_enum

Mixed in from MISAG:

• MISAG➞single_cell_lysis_prot _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞wga_amp_appr _1..1
  • Range: String

Mixed in from MISAG:

• MISAG➞wga_amp_kit _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞associated resource _0..1
  • Range: String

Mixed in from MISAG:

• MISAG➞sop _0..1
  • Range: String