Class: host-associated MIMARKS specimen

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

URI: mixs.vocab:Host-associatedMIMARKSSpecimen

Parents

• is_a: Host-associated - host-associated

Uses Checklist

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

Attributes

Inherited from host-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
• host-associated➞depth _0..1
  • Range: QuantityValue
• host-associated➞alt _0..1
  • Range: QuantityValue
• host-associated➞elev _0..1
  • Range: QuantityValue
• host-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
• host-associated➞ances_data _0..1
  • Range: String
• host-associated➞biol_stat _0..1
  • Range: biol_stat_enum
• host-associated➞genetic_mod _0..1
  • Range: String
• host-associated➞host_common_name _0..1
  • Range: String
• host-associated➞samp_capt_status _0..1
  • Range: samp_capt_status_enum
• host-associated➞samp_dis_stage _0..1
  • Range: samp_dis_stage_enum
• host-associated➞host_taxid _0..1
  • Range: String
• host-associated➞host_subject_id _0..1
  • Range: String
• host-associated➞host_age _0..1
  • Range: QuantityValue
• host-associated➞host_life_stage _0..1
  • Range: String
• host-associated➞host_sex _0..1
  • Range: host_sex_enum
• host-associated➞chem_administration _0..*
  • Range: String
• host-associated➞host_body_habitat _0..1
  • Range: String
• host-associated➞host_body_site _0..1
  • Range: String
• host-associated➞host_body_product _0..1
  • Range: String
• host-associated➞host_tot_mass _0..1
  • Range: QuantityValue
• host-associated➞host_height _0..1
  • Range: QuantityValue
• host-associated➞host_length _0..1
  • Range: QuantityValue
• host-associated➞host_diet _0..*
  • Range: String
• host-associated➞host_last_meal _0..*
  • Range: String
• host-associated➞host_growth_cond _0..1
  • Range: String
• host-associated➞host_substrate _0..1
  • Range: String
• host-associated➞host_family_relation _0..*
  • Range: String
• host-associated➞host_infra_spec_name _0..1
  • Range: String
• host-associated➞host_infra_spec_rank _0..1
  • Range: String
• host-associated➞host_subspecf_genlin _0..*
  • Range: String
• host-associated➞host_genotype _0..1
  • Range: String
• host-associated➞host_phenotype _0..1
  • Range: String
• host-associated➞host_body_temp _0..1
  • Range: QuantityValue
• host-associated➞host_dry_mass _0..1
  • Range: QuantityValue
• host-associated➞blood_press_diast _0..1
  • Range: QuantityValue
• host-associated➞blood_press_syst _0..1
  • Range: QuantityValue
• host-associated➞host_color _0..1
  • Range: String
• host-associated➞host_shape _0..1
  • Range: String
• host-associated➞gravidity _0..1
  • Range: String
• host-associated➞perturbation _0..*
  • Range: String
• host-associated➞samp_salinity _0..1
  • Range: QuantityValue
• host-associated➞salinity _0..1
  • Range: QuantityValue
• host-associated➞oxy_stat_samp _0..1
  • Range: oxy_stat_samp_enum
• host-associated➞organism_count _0..*
  • Range: organism_count_enum
• host-associated➞samp_store_temp _0..1
  • Range: QuantityValue
• host-associated➞samp_store_dur _0..1
  • Range: String
• host-associated➞samp_store_loc _0..1
  • Range: String
• host-associated➞host_symbiont _0..*
  • Range: String
• host-associated➞misc_param _0..*
  • Range: String
• host-associated➞samp_name _1..1
  • Range: String
• host-associated➞project_name _1..1
  • Range: String
• host-associated➞host_disease_stat _0..1
  • Range: String
• host-associated➞samp_vol_we_dna_ext _0..1
  • Range: QuantityValue

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞size_frac _0..1
  • Range: String

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_size _0..1
  • Range: Integer

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_reads_seqd _0..1
  • Range: Integer

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_layout _0..1
  • Range: lib_layout_enum

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_vector _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞lib_screen _0..1
  • Range: String

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞mid _0..1
  • Range: String

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞adapters _0..1
  • Range: String

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

• MIMARKS specimen➞assembly_software _0..1
  • Range: String

Mixed in from MIMARKS specimen:

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

Mixed in from MIMARKS specimen:

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