Class: hydrocarbon resources-fluids_swabs MIGS bacteria

Combinatorial checklist Minimal Information about a Genome Sequence: cultured bacteria/archaea with environmental package hydrocarbon resources-fluids_swabs

URI: mixs.vocab:HydrocarbonResources-fluidsSwabsMIGSBacteria

Parents

• is_a: HydrocarbonResources-fluidsSwabs - hydrocarbon resources-fluids/swabs

Uses Checklist

• mixin: MIGSBacteria - Minimal Information about a Genome Sequence: cultured bacteria/archaea

Attributes

Inherited from hydrocarbon resources-fluids_swabs:

• 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
• hydrocarbon resources-fluids_swabs➞temp _1..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
• hydrocarbon resources-fluids_swabs➞hcr _1..1
  • Range: hcr_enum
• hydrocarbon resources-fluids_swabs➞hc_produced _1..1
  • Range: hc_produced_enum
• hydrocarbon resources-fluids_swabs➞basin _1..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞field _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞reservoir _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞hcr_temp _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞tvdss_of_hcr_temp _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞hcr_pressure _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞tvdss_of_hcr_press _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞lithology _0..1
  • Range: lithology_enum
• hydrocarbon resources-fluids_swabs➞depos_env _0..1
  • Range: depos_env_enum
• hydrocarbon resources-fluids_swabs➞hcr_geol_age _0..1
  • Range: hcr_geol_age_enum
• hydrocarbon resources-fluids_swabs➞hcr_fw_salinity _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞sulfate_fw _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞vfa_fw _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞prod_start_date _0..1
  • Range: Date
• hydrocarbon resources-fluids_swabs➞prod_rate _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞water_prod_rate _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞water_cut _1..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞iwf _1..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞add_recov_method _1..1
  • Range: add_recov_method_enum
• hydrocarbon resources-fluids_swabs➞iw_bt_date_well _0..1
  • Range: Date
• hydrocarbon resources-fluids_swabs➞biocide _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞biocide_admin_method _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞chem_treatment _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞chem_treat_method _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_loc_corr_rate _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_well_name _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞win _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_type _1..1
  • Range: samp_type_enum
• hydrocarbon resources-fluids_swabs➞samp_subtype _0..1
  • Range: samp_subtype_enum
• hydrocarbon resources-fluids_swabs➞samp_collect_point _1..1
  • Range: samp_collect_point_enum
• hydrocarbon resources-fluids_swabs➞pressure _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞oxy_stat_samp _0..1
  • Range: oxy_stat_samp_enum
• hydrocarbon resources-fluids_swabs➞samp_preserv _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_transport_cond _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_store_temp _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞samp_store_dur _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_store_loc _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞organism_count _0..*
  • Range: organism_count_enum
• hydrocarbon resources-fluids_swabs➞org_count_qpcr_info _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞ph _0..1
  • Range: Double
• hydrocarbon resources-fluids_swabs➞samp_salinity _1..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞salinity _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞alkalinity _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞alkalinity_method _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞sulfate _1..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞sulfide _1..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞tot_sulfur _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞nitrate _1..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞nitrite _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞ammonium _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞tot_nitro _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞diss_iron _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞sodium _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞chloride _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞potassium _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞magnesium _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞calcium _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞tot_iron _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞diss_org_carb _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞diss_inorg_carb _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞diss_inorg_phosp _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞tot_phosp _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞suspend_solids _0..*
  • Range: String
• hydrocarbon resources-fluids_swabs➞density _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞diss_carb_dioxide _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞diss_oxygen_fluid _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞vfa _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞benzene _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞toluene _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞ethylbenzene _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞xylene _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞api _1..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞tan _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞viscosity _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞pour_point _0..1
  • Range: QuantityValue
• hydrocarbon resources-fluids_swabs➞saturates_pc _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞aromatics_pc _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞resins_pc _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞asphaltenes_pc _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞misc_param _0..*
  • Range: String
• hydrocarbon resources-fluids_swabs➞additional_info _0..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_name _1..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞project_name _1..1
  • Range: String
• hydrocarbon resources-fluids_swabs➞samp_vol_we_dna_ext _0..1
  • Range: QuantityValue

Mixed in from MIGS bacteria:

• MIGS bacteria➞submitted_to_insdc _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞investigation_type _1..1
  • Range: investigation_type_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_taxon_id _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞experimental_factor _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞env_package _0..1
  • Range: env_package_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞subspecf_gen_lin _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞num_replicons _1..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞extrachrom_elements _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞estimated_size _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞ref_biomaterial _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞source_mat_id _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞pathogenicity _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞biotic_relationship _0..1
  • Range: biotic_relationship_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞specific_host _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞host_spec_range _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞health_disease_stat _0..1
  • Range: health_disease_stat_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞host_disease_stat _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞trophic_level _0..1
  • Range: trophic_level_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞encoded_traits _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞rel_to_oxygen _0..1
  • Range: rel_to_oxygen_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞isol_growth_condt _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_collec_device _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_collec_method _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_mat_process _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞samp_size _0..1
  • Range: QuantityValue

Mixed in from MIGS bacteria:

• MIGS bacteria➞nucl_acid_ext _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞nucl_acid_amp _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_size _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_reads_seqd _0..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_layout _0..1
  • Range: lib_layout_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_vector _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞lib_screen _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞adapters _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞seq_meth _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞tax_ident _0..1
  • Range: tax_ident_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_qual _1..1
  • Range: assembly_qual_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_name _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞assembly_software _1..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞annot _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞number_contig _1..1
  • Range: Integer

Mixed in from MIGS bacteria:

• MIGS bacteria➞feat_pred _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞ref_db _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞sim_search_meth _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞tax_class _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞compl_score _0..1
  • Range: compl_score_enum

Mixed in from MIGS bacteria:

• MIGS bacteria➞compl_software _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞associated resource _0..1
  • Range: String

Mixed in from MIGS bacteria:

• MIGS bacteria➞sop _0..1
  • Range: String