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Symbiont-associated

symbiont-associated

URI: mixs.vocab:Symbiont-associated

Combinations

Slots

MIxS ID Name Multiplicity Description Pattern Info
MIXS:0000009 lat_lon 1..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 1..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 1..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 1..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 1..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 1..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:0001303 symbiont_host_role 0..1 Role of the host in the life cycle of the symbiotic organism. None .
MIXS:0000753 oxy_stat_samp 0..1 Oxygenation status of sample. None .
MIXS:0001307 type_of_symbiosis 0..1 Type of biological interaction established between the symbiotic host organism being sampled and its respective host None .
MIXS:0001300 sym_life_cycle_type 1..1 Type of life cycle of the symbiotic host species (the thing being sampled). Simple life cycles occur within a single host, complex ones within multiple different hosts over the course of their normal life cycle. None .
MIXS:0001316 route_transmission 0..1 Description of path taken by the symbiotic host organism being sampled in order to establish a symbiotic relationship with the host (with which it was observed at the time of sampling) via a mode of transmission (specified in mode_transmission). None .
MIXS:0001315 host_dependence 1..1 Type of host dependence for the symbiotic host organism to its host. None .
MIXS:0001308 host_specificity 0..1 Level of specificity of symbiont-host interaction: e.g. generalist (symbiont able to establish associations with distantly related hosts) or species-specific. None .
MIXS:0000862 host_sex 0..1 Physical sex of the host. None .
MIXS:0001312 mode_transmission 0..1 The process through which the symbiotic host organism entered the host from which it was sampled. None .
MIXS:0001313 host_cellular_loc 0..1 The localization of the symbiotic host organism within the host from which it was sampled: e.g. intracellular if the symbiotic host organism is localized within the cells or extracellular if the symbiotic host organism is localized outside of cells. 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:0001333 host_of_host_gravid 0..1 Whether or not the host of the symbiotic host organism 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:0001299 association_duration 0..1 Time spent in host of the symbiotic organism at the time of sampling; relevant scale depends on symbiotic organism and study. 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: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:0001334 host_of_host_totmass 0..1 Total mass of the host of the symbiotic host organism at collection, the unit depends on the host. None .
MIXS:0000263 host_tot_mass 0..1 Total mass of the host at collection, the unit depends on host None .
MIXS:0000109 samp_salinity 0..1 Salinity is the total concentration of all dissolved salts in a liquid or solid (in the form of an extract obtained by centrifugation) 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:0001305 host_number 0..1 Number of symbiotic host individuals pooled at the time of collection. None .
MIXS:0001306 host_of_host_taxid 0..1 NCBI taxon id of the host of the symbiotic host organism. None .
MIXS:0000250 host_taxid 0..1 NCBI taxon id of the host. None .
MIXS:0000871 host_growth_cond 0..1 Literature reference giving growth conditions of the host None .
MIXS:0001332 host_of_host_pheno 0..1 Phenotype of the host of the symbiotic host organism. For phenotypic quality ontology (PATO) terms, see http://purl.bioontology.org/ontology/pato. 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: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:0001325 host_of_host_env_loc 0..* For a symbiotic host organism the local anatomical environment within its host may have causal influences. Report the anatomical entity(s) which are in the direct environment of the symbiotic host organism being sampled and which you believe have significant causal influences on your sample or specimen. For example, if the symbiotic host organism being sampled is an intestinal worm, its local environmental context will be the term for intestine from UBERON (http://uberon.github.io/). None .
MIXS:0001326 host_of_host_env_med 0..1 Report the environmental material(s) immediately surrounding the symbiotic host organism at the time of sampling. This usually will be a tissue or substance type from the host, but may be another material if the symbiont is external to the host. We recommend using classes from the UBERON ontology, but subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483) may also be used. 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. intestines, heart).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. intestines, heart). 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:0001319 host_of_host_disease 0..* List of diseases with which the host of the symbiotic host organism has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text. 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:0000365 host_genotype 0..1 Observed genotype None .
MIXS:0000253 host_infra_specific_name 0..1 Taxonomic information about the host below subspecies level. None .
MIXS:0000254 host_infra_specific_rank 0..1 Taxonomic rank information about the host below subspecies level, such as variety, form, rank etc. None .
MIXS:0000251 host_life_stage 1..1 Description of life stage of host None .
MIXS:0001310 host_of_host_coinf 0..1 The taxonomic name of any coinfecting organism observed in a symbiotic relationship with the host of the sampled host organism. e.g. where a sample collected from a host trematode species (A) which was collected from a host_of_host fish (B) that was also infected with a nematode (C), the value here would be (C) the nematode {species name} or {common name}. Multiple co-infecting species may be added in a comma-separated list. For listing symbiotic organisms associated with the host (A) use the term Observed host symbiont. None .
MIXS:0001331 host_of_host_geno 0..1 Observed genotype of the host of the symbiotic host organism. None .
MIXS:0001329 host_of_host_infname 0..1 Taxonomic name information of the host of the symbiotic host organism below subspecies level. None .
MIXS:0001330 host_of_host_infrank 0..1 Taxonomic rank information about the host of the symbiotic host organism below subspecies level, such as variety, form, rank etc. None .
MIXS:0001324 host_of_host_name 0..1 Common name of the host of the symbiotic host organism. None .
MIXS:0001327 host_of_host_sub_id 0..1 A unique identifier by which each host of the symbiotic host organism subject can be referred to, de-identified, e.g. #H14. 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:0001317 samp_store_sol 0..1 Solution within which sample was stored, if any. None .
MIXS:0001107 sample_name 1..1 Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. 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_relationship 0..1 Relationships to other hosts in the same study; can include multiple relationships. None .
MIXS:0001328 host_of_host_fam_rel 0..* Familial relationship of the host of the symbiotic host organisms to other hosts of symbiotic host organism in the same study; can include multiple relationships. None .

Usages

Identifier and Mapping Information