| Site metadata |
Collection date/time |
Restricted text, 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. ISO8601 compliant |
|
|
e.g. 2013-03-25T12:42:31+01:00 |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” |
|
|
Collected by |
Name of person or institute that collected the sample |
|
“ENA Marine Microalgae Checklist; Checklist: ERC000043” |
|
|
|
|
Geographic location |
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, or the GAZ ontology |
|
|
e.g. USA: Maryland, Bethesda; Atlantic Ocean region OR [GAZ:00051071] |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” |
|
|
Latitude |
The geographical origin of the sample as defined by latitude. The values should be reported in decimal degrees and in WGS84 system. |
|
|
e.g. -41.373744 |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” |
|
|
Longitude |
The geographical origin of the sample as defined by longitude. The values should be reported in decimal degrees and in WGS84 system. |
|
|
e.g. 146.266145 |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” |
|
|
Elevation |
Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m |
|
|
e.g. 100 m |
“GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
Altitude |
Altitude is used for points above the surface, such as an aircraft in flight or a spacecraft in orbit |
|
|
e.g. 100 m |
“GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS”, “GSC MIxS Human Associated; ENA Checklist: ERC000014” |
|
|
env_broad_scale |
Report the major environmental system the sample or specimen came from. Systems(s) identifiers should provide a coarse, general environmental context of where the sampling was done. Terms, such as anatomical sites, from OBO Library ontologies which interoperate with EnvO (e.g. [UBERON]) are accepted in this field. If more than one term applies to the field, | should be used to separate them. |
|
|
e.g. gut wall [UBERON:0000328] |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
env_local_scale |
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. Entry should be of a smaller environmental context than 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. If more than one term applies to the field, | should be used to separate them. |
|
|
e.g. if gut wall [UBERON:0000328] was used to describe the env_broad_scale one of the following subclasses should be used to describe further env_local_scale: wall of esophagus [UBERON:0001096]| wall of intestine [UBERON:0001262]| wall of stomach [UBERON:0001167]; note that further subclasses are available if applicable and better describe the sample |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
env_medium |
Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. 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). If more than one term applies to the field, | should be used to separate them. |
|
|
e.g. feces [UBERON:0001988]| excreted gas [UBERON:0034945] |
“GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
Sample size/mass |
Sample size/mass |
The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected |
|
|
e.g. H x W x L, vol., mass 2000 ml water, 1000 g soil |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
Site conditions |
Environmental temp, RH, salinity, pH |
|
|
e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 |
MSI-ECWSG (Morrison et al. (2007)) |
|
|
Material conditions |
Sample material temp, RH, salinity, pH |
|
|
e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, MSI-ECWSG (Morrison et al. (2007)), “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
Microbial ID |
Taxonomy and/or culture source, if available. Expected_value: [NCBI taxonomy ID] |
|
|
e.g. E. coli [NCBI:txid562] |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package” |
|
|
Microbial isolate |
icrobial isolate cultured?: Y/N |
|
|
|
|
|
|
Culture substrate |
This field accepts terms listed under culture medium [OBI:0000079]. If the proper descriptor is not listed please use text to describe the culture medium |
|
|
e.g. minimal defined medium [MCO:0000881] |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, MSI-ECWSG (Morrison et al. (2007)) |
|
|
chem_administration |
List of chemical compounds administered to host where sampling occurred. Can include multiple compounds separated by |. For compunds consult chemical entities of biological interest ontology (chebi) (v 163) |
|
|
e.g. tetracycline [CHEBI:27902];2023-12-11T19:41+01:00|ampicilin[CHEBI:28971];2023-12-11T19:41+01:00 |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
| Host metadata |
host_name |
Scientific name [NCBI taxonomy ID] |
e.g. Homo sapiens [NCBI:txid9606] |
“GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, MSI-ECWSG (Morrison et al. (2007)) |
|
|
|
|
host_common_name |
Common name of the host |
|
|
e.g. human, dog, cattle |
“GSC MIxS: Host-associatedMIMS” |
|
|
host_height |
Height of host |
|
|
e.g. 177 cm |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
host_tot_mass |
Total mass of host |
|
|
e.g. 77 kg OR 3568 g |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
host_body_site |
Name of body site where the sample was obtained from, such as a specific organ or tissue (tongue, lung etc…). Recomended use of FMA or UBERON ontologies. Multiple ontologies can apply, use | to separate them. Ontologies should be specific enough to discern body site and goal. |
|
|
e.g. gut [FMA:45615] OR gut wall [UBERON:0000328] |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package” |
|
|
host_body_product |
Bodily substance where the sample was obtained from. Recomended use of FMA or UBERON ontologies. Multiple ontologies can apply, use | to separate them |
|
|
e.g. feces [FMA:64183]|urine[FMA:12274] |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
host_age |
Age of host at the time of sampling; relevant scale depends on study |
|
|
e.g. year, day, hour |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
host_sex |
Gender and/or physical sex of subject/host |
|
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
|
|
host_diet |
|
|
Type of diet depending on the host, for animals omnivore, herbivore etc., for humans high-fat, meditteranean etc.; can include multiple diet types. Recommended use diet [OMIT:0005302] subclasses |
|
|
e.g. diet, high-fat [OMIT:0027565] OR diet, mediterranean [OMIT:0022848] |
|
host_subject_id |
A unique identifier by which each subject can be referred to, de-identified |
|
|
e.g. s9s8 |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
host_disease_stat |
Diagnosed diseases of host; can hold multiple values, separated by |. Recommended use of DOID ontoligies |
|
|
e.g. inflammatory bowel disease 1 [DOID:0110892]|avian influenza [DOID:4492] |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Host-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
ethnicity |
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. |
|
|
e.g. Slovene OR Turkic |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “U.s. Office of Management and Budget (OMB): About the Topic of Race” |
|
|
smoker |
Specification of smoking status |
e.g. yes |
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “GSC MIxS: Human-associatedMIMS”, “GSC MIxS: Human-gutMIMS”, “GSC MIxS: Human-oralMIMS”, “GSC MIxS: Human-skinMIMS”, “GSC MIxS: Human-vaginalMIMS” |
|
|
|
|
disorder_history |
Terms from DOID ontoligies should be used to describe disorder. Host history of pulmonary [DOID:850], nose-throat [DOID:974], blood [DOID:74], kidney [DOID:557] and urogenital tract disorders [DOID:18] . If multiple disorders apply, separate them by | |
|
e.g. lung abscess [DOID:0060317]|tonsillitis [DOID:10456]|hypochromic anemia [DOID:11759]|etc. |
|
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package”, “GSC MIxS Human Associated; ENA Checklist: ERC000014”, “U.s. Office of Management and Budget (OMB): About the Topic of Race” |
|
| Additional potential human bio/env considerations |
Ecosystem Category |
Category list |
|
|
|
JGI GOLD (“GOLD Ecosystem Classification Paths”) |
|
|
Ecosystem Type |
Type list |
|
|
|
JGI GOLD (“GOLD Ecosystem Classification Paths”) |
|
|
Ecosystem Subtype |
Subtype list |
|
|
|
JGI GOLD (“GOLD Ecosystem Classification Paths”) |
|
|
Specific Ecosystem |
Specific ecosystem list |
|
|
|
JGI GOLD (“GOLD Ecosystem Classification Paths”) |
|
|
Habitat |
Free text |
|
|
|
JGI GOLD (“GOLD Ecosystem Classification Paths”) |
|
|
Medical Record Number |
|
|
Record number (list) |
|
|
|