Table 1 MIxS symbiont-associated environmental package representative terms, along with requirement status, description and MIXS IDs.
MIxS Package | Metadata category | Package item | Req | Definition | MIXS ID |
|---|---|---|---|---|---|
Symbiont-associated | Symbiont specific descriptors | host dependence | M | Type of host dependence for the symbiotic host organism to its host. | 0001315 |
type of symbiosis | C | Type of biological interaction established between the symbiotic host organism being sampled and its respective host. | 0001307 | ||
symbiotic host organism life cycle type | M | 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. | 0001300 | ||
host life stage | M | Description of life stage of host. | 0000251 | ||
mode of transmission | C | The process through which the symbiotic host organism entered the host from which it was sampled. | 0001312 | ||
route of transmission | O | 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). | 0001316 | ||
host number individual | O | Number of symbiotic host individuals pooled at the time of collection. | 0001305 | ||
Symbiont – host relationship descriptors | observed host symbionts | O | The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. For cases when the specific host of the sample is a symbiont this field should refer to other organisms it is associated with: e.g.: hyperparasite species X (parasite of the parasite). | 0001309 | |
host specificity | C | Level of specificity of symbiont-host interaction: e.g. generalist (symbiont able to establish associations with distantly related hosts) or species-specific. | 0001308 | ||
host of the symbiont role | C | Role of the host in the life cycle of the symbiotic organism. | 0001303 | ||
host cellular location | C | 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. | 0001313 | ||
duration of association with the host | O | Time spent in host of the symbiotic organism at the time of sampling; relevant scale depends on symbiotic organism and study. | 0001299 | ||
observed coinfecting organisms in host of host | O | 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 coinfecting species may be added in a comma-separated list. For listing symbiotic organisms associated with the host (A) use the term Observed host symbiont. | 0001310 | ||
Host of the symbiont descriptors | host of the symbiotic host common name | O | Common name of the host of the symbiotic host organism. | 0001324 | |
host of the symbiotic host local environmental context | O | 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/). | 0001325 | ||
host of the symbiotic host environmental medium | O | 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). | 0001326 | ||
host of the symbiotic host taxon id | O | NCBI taxon id of the host of the symbiotic host organism. | 0001306 | ||
host of the symbiotic host subject id | O | A unique identifier by which each host of the symbiotic host organism subject can be referred to, de-identified, e.g. #H14. | 0001327 | ||
Core | Relationship to other samplesa | C | indicates the direct relationship with another sample from the same Bioproject. Accepted terms are: ‘technical replicate of’, ‘after’, ‘before’, ‘next to’, ‘within’, and ‘contains’. Can be repeated to reveal relationship to many samples. | TBD | |
Biotic relationship | C | Description of relationship(s) between the subject organism and other organism(s) it is associated with. E.g., parasite on species X; mutualist with species Y. The target organism is the subject of the relationship, and the other organism(s) is the object. | 0000028 | ||
Otherb | Observed host symbionts | O | The taxonomic name of the organism(s) found living in mutualistic, commensalistic, or parasitic symbiosis with the specific host. | 0001309 |
