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Host-associated

host-associated

URI: mixs.vocab:Host-associated

Combinations

Slots

MIxS ID Name Multiplicity Description Pattern Info
MIXS:0000009 lat_lon 0..1 The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system None .
MIXS:0000018 depth 0..1 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. None .
MIXS:0000094 alt 0..1 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 None .
MIXS:0000093 elev 0..1 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. None .
MIXS:0000113 temp 0..1 Temperature of the sample at the time of sampling. None .
MIXS:0000010 geo_loc_name 0..1 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) None .
MIXS:0000011 collection_date 0..1 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 None .
MIXS:0000012 env_broad_scale 0..1 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 None .
MIXS:0000013 env_local_scale 0..1 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. None .
MIXS:0000014 env_medium 0..1 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). None .
MIXS:0000860 samp_capt_status 0..1 Reason for the sample None .
MIXS:0000753 oxy_stat_samp 0..1 Oxygenation status of sample. None .
MIXS:0000249 samp_dis_stage 0..1 Stage of the disease at the time of sample collection, e.g. inoculation, penetration, infection, growth and reproduction, dissemination of pathogen. None .
MIXS:0000862 host_sex 0..1 Physical sex of the host. None .
MIXS:0000858 biol_stat 0..1 The level of genome modification. None .
MIXS:0000875 gravidity 0..1 Whether or not subject is gravid, and if yes date due or date post-conception, specifying which is used None .
MIXS:0000116 samp_store_dur 0..1 Duration for which the sample was stored None .
MIXS:0000258 blood_press_diast 0..1 Resting diastolic blood pressure, measured as mm mercury None .
MIXS:0000259 blood_press_syst 0..1 Resting systolic blood pressure, measured as mm mercury None .
MIXS:0000255 host_age 0..1 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 None .
MIXS:0000274 host_body_temp 0..1 Core body temperature of the host when sample was collected None .
MIXS:0000257 host_dry_mass 0..1 Measurement of dry mass None .
MIXS:0000264 host_height 0..1 The height of subject None .
MIXS:0000256 host_length 0..1 The length of subject None .
MIXS:0000263 host_tot_mass 0..1 Total mass of the host at collection, the unit depends on host None .
MIXS:0000183 salinity 0..1 The total concentration of all dissolved salts in a liquid or solid 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. None .
MIXS:0000110 samp_store_temp 0..1 Temperature at which sample was stored, e.g. -80 degree Celsius None .
MIXS:0000250 host_taxid 0..1 NCBI taxon id of the host. None .
MIXS:0000859 genetic_mod 0..1 Genetic modifications of the genome of an organism, which may occur naturally by spontaneous mutation, or be introduced by some experimental means, e.g. specification of a transgene or the gene knocked-out or details of transient transfection. None .
MIXS:0000871 host_growth_cond 0..1 Literature reference giving growth conditions of the host None .
MIXS:0001318 host_subspecf_genlin 0..* Information about the genetic distinctness of the host organism below the subspecies level e.g., serovar, serotype, biotype, ecotype, variety, cultivar, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123. None .
MIXS:0000868 host_body_product 0..1 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. None .
MIXS:0000867 host_body_site 0..1 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 None .
MIXS:0000874 host_phenotype 0..1 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. None .
MIXS:0000751 chem_administration 0..* 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 None .
MIXS:0000247 ances_data 0..1 Information about either pedigree or other ancestral information description (e.g. parental variety in case of mutant or selection), e.g. A/3*B (meaning [(A x B) x B] x B) None .
MIXS:0000866 host_body_habitat 0..1 Original body habitat where the sample was obtained from None .
MIXS:0000260 host_color 0..1 The color of host None .
MIXS:0000248 host_common_name 0..1 Common name of the host. None .
MIXS:0000869 host_diet 0..* Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types None .
MIXS:0000365 host_genotype 0..1 Observed genotype None .
MIXS:0000251 host_life_stage 0..1 Description of life stage of host None .
MIXS:0000261 host_shape 0..1 Morphological shape of host None .
MIXS:0000861 host_subject_id 0..1 A unique identifier by which each subject can be referred to, de-identified. None .
MIXS:0000252 host_substrate 0..1 The growth substrate of the host. None .
MIXS:0001298 host_symbiont 0..* The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. None .
MIXS:0000755 samp_store_loc 0..1 Location at which sample was stored, usually name of a specific freezer/room None .
MIXS:0000870 host_last_meal 0..* Content of last meal and time since feeding; can include multiple values None .
MIXS:0000752 misc_param 0..* Any other measurement performed or parameter collected, that is not listed here None .
MIXS:0000103 organism_count 0..* 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). None .
MIXS:0000754 perturbation 0..* 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 None .
MIXS:0000872 host_family_relation 0..* Familial relationships to other hosts in the same study; can include multiple relationships None .

Usages

Identifier and Mapping Information