Human-associated
human-associated
URI: mixs.vocab:Human-associated
Combinations
- Human-associated
- Human-associatedMIGSEukaryote [ MIGS eukaryote]
- Human-associatedMIGSBacteria [ MIGS bacteria]
- Human-associatedMIGSPlant [ MIGS plant]
- Human-associatedMIGSVirus [ MIGS virus]
- Human-associatedMIGSOrg [ MIGS org]
- Human-associatedMIMS [ MIMS]
- Human-associatedMIMARKSSpecimen [ MIMARKS specimen]
- Human-associatedMIMARKSSurvey [ MIMARKS survey]
- Human-associatedMISAG [ MISAG]
- Human-associatedMIMAG [ MIMAG]
- Human-associatedMIUVIG [ MIUVIG]
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:0000753 | oxy_stat_samp | 0..1 | Oxygenation status of sample. | None | . |
| MIXS:0000899 | urine_collect_meth | 0..1 | Specification of urine collection method | None | . |
| MIXS:0000862 | host_sex | 0..1 | Physical sex of the host. | None | . |
| MIXS:0000897 | medic_hist_perform | 0..1 | Whether full medical history was collected | None | . |
| MIXS:0000262 | smoker | 0..1 | Specification of smoking status | None | . |
| MIXS:0000326 | twin_sibling | 0..1 | Specification of twin sibling presence | None | . |
| MIXS:0000898 | study_complt_stat | 0..1 | Specification of study completion status, if no the reason should be specified | None | . |
| MIXS:0000265 | host_hiv_stat | 0..1 | HIV status of subject, if yes HAART initiation status should also be indicated as [YES or NO] | None | . |
| MIXS:0000295 | weight_loss_3_month | 0..1 | Specification of weight loss in the last three months, if yes should be further specified to include amount of weight loss | None | . |
| MIXS:0000266 | diet_last_six_month | 0..1 | Specification of major diet changes in the last six months, if yes the change should be specified | None | . |
| MIXS:0000267 | pet_farm_animal | 0..* | Specification of presence of pets or farm animals in the environment of subject, if yes the animals should be specified; can include multiple animals present | None | . |
| MIXS:0000116 | samp_store_dur | 0..1 | Duration for which the sample was stored | 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:0000317 | host_body_mass_index | 0..1 | Body mass index, calculated as weight/(height)squared | None | . |
| MIXS:0000274 | host_body_temp | 0..1 | Core body temperature of the host when sample was collected | None | . |
| MIXS:0000264 | host_height | 0..1 | The height of subject | None | . |
| MIXS:0000333 | host_pulse | 0..1 | Resting pulse, measured as beats per minute | 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:0000896 | host_occupation | 0..1 | Most frequent job performed by subject | None | . |
| MIXS:0000884 | ihmc_medication_code | 0..* | Can include multiple medication codes | 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:0000276 | amniotic_fluid_color | 0..1 | Specification of the color of the amniotic fluid sample | None | . |
| MIXS:0000271 | blood_blood_disord | 0..* | History of blood disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, hematopoietic system disease (https://disease-ontology.org/?id=DOID:74). | None | . |
| MIXS:0000895 | ethnicity | 0..* | A category of people who identify with each other, usually on the basis of presumed similarities such as a common language, ancestry, history, society, culture, nation or social treatment within their residing area. https://en.wikipedia.org/wiki/List_of_contemporary_ethnic_groups | None | . |
| MIXS:0000275 | foetal_health_stat | 0..1 | Specification of foetal health status, should also include abortion | None | . |
| MIXS:0000272 | gestation_state | 0..1 | Specification of the gestation state | 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:0000861 | host_subject_id | 0..1 | A unique identifier by which each subject can be referred to, de-identified. | 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:0000277 | kidney_disord | 0..* | History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557). | None | . |
| MIXS:0000273 | maternal_health_stat | 0..1 | Specification of the maternal health status | None | . |
| MIXS:0000270 | nose_throat_disord | 0..* | History of nose-throat disorders; can include multiple disorders, The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850), upper respiratory tract disease (https://disease-ontology.org/?id=DOID:974). | None | . |
| MIXS:0000269 | pulmonary_disord | 0..* | History of pulmonary disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, lung disease (https://disease-ontology.org/?id=DOID:850). | None | . |
| MIXS:0000755 | samp_store_loc | 0..1 | Location at which sample was stored, usually name of a specific freezer/room | None | . |
| MIXS:0000268 | travel_out_six_month | 0..* | Specification of the countries travelled in the last six months; can include multiple travels | None | . |
| MIXS:0000278 | urogenit_tract_disor | 0..* | History of urogenital tract disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, urinary system disease (https://disease-ontology.org/?id=DOID:18). | 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:0000894 | drug_usage | 0..* | Any drug used by subject and the frequency of usage; can include multiple drugs used | 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 | . |