| metadata | definition | reference of definition[<url_to_definition>] | expected unit of measurement | example | sources( where this or similar matadata field is mentioned) | ||
|---|---|---|---|---|---|---|---|
| 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 | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024” | |||
| 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] | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024” | ||||
| 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. 54.400939 | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024” | ||||
| 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. -1.340951 | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024” | ||||
| Elevation | Elevation is mainly used when referring to points on the earth’s surface. Origin elevation in m | e.g. 100 m | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| 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: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS”, “ENA Marine Microalgae Checklist; Checklist: ERC000043”, “ENA Tara Oceans; Checklist: ERC000030”, “GSC MIxS Water; ENA Checklist: ERC000024” | ||||
| 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. Recommended use of EnvO s biome class: [ENVO_00000428]. If more than one term applies to the field, | should be used to separate them.; note here, that multiple subclasses of biome [ENVO_00000428] can apply here. | E.g. terrestrial biome [ENVO:00000446] OR subtropical biome [ENVO:01001832] OR tropical biome [ENVO:01001830] OR etc. ; note here, that most of ontology classes found under biome have further subclasses that may apply, if they can better describe the broad environmental context of the sample, use | to separate them | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| 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. If more than one term applies to the field, | should be used to separate them. | e.g. if tropical biome [ENVO:01001830] was used in env_broad_scale, env_local_scale should be one of the following subclasses : tropical savanna biome [ENVO:01000188]|tropical shrubland biome [ENVO:01000214]|tropical woodland biome [ENVO:01000220]; note here, that some ontologies listed here under other subclasses of biome [ENVO_00000428], have further subclasses that can be used, if they better describe the local environment of the sample. | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| env_medium | Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. Recommended use of EnvO’s subclasses of environmental material [ENVO:00010483]. 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. arable soil [ENVO:00005742]|bare soil [ENVO:01001616]|bulk soil [ENVO:00005802]; note here, that these are only examples, there is a variety of different ontology classes that can apply here | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| 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 | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| Site conditions | Environmental temp, RH, salinity, pH | e.g. 25 degree Celsius, 25 practical salinity unit, pH 7.2 | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS”, 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 | MSI-ECWSG (Morrison et al. (2007)), “ENA Tara Oceans; Checklist: ERC000030” | ||||
| Microbial ID | Taxonomy and/or culture source, if available. Expected_value: [NCBI taxonomy ID] | e.g. E. coli [NCBI:txid562] | “ENA Marine Microalgae Checklist; Checklist: ERC000043” | ||||
| Microbial isolate | Microbial 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] | MSI-ECWSG (Morrison et al. (2007)) | ||||
| chem_administration | List of chemical compounds administered to host or on site where sampling occurred. Can include multiple compounds separated by |. For compounds consult chemical entities of biological interest ontology (chebi) (v 163) | E.g. agar [CHEBI:2509];2018-05-11T20:00Z|castor oil [CHEBI:140618];2023-12-07T17:00+02:00 | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| Host metadata | Host name OR host_taxid | Scientific name [NCBI taxonomy ID] | e.g. *Arabidopsis thaliana * [NCBI:txid3702] | MSI-ECWSG (Morrison et al. (2007)) | |||
| host_common_name | Common name of the host | e.g. thale cress | “GSC MIxS: Host-associatedMIMS” | ||||
| host_height OR host_length | Height of host or length of host | e.g. 177 cm | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| host_tot_mass | Total mass of host | e.g. 77 kg OR 3568 g | “GSC MIxS: Plant-associatedMIMS”, “GSC MIxS: Host-associatedMIMS” | ||||
| plant_struc | Name of plant structure the sample was obtained from, such as a specific organ or tissue (epidermis, etc…). Recommended use of plant anatomical entity [PO:0025131] subclasses | e.g. root system ground meristem [PO:0025596]; note here that multiple ontology classes and subclasses may apply here, use | to separate them | “MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package” | ||||
| host_age | 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 | e.g. year, day, hour | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| plant_sex | Sex of the reproductive parts on the whole plant | e.g. pistillate, staminate, monoecieous, hermaphrodite | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| host_disease_stat | Diagnosed diseases of host; can hold multiple values, separated by |. Non-human host diseases should be deposited as free text | e.g. powdery mildew, late blight, citrus canker etc. | “GSC MIxS: Plant-associatedMIMS” | ||||
| host_symbiont | Name the organism found living in a symbiotic, commensalistic, mutualistic relationship with the host. Expected values: Scientific or common name of species | e.g. Rhizobium tropici | “GSC MIxS: AgricultureMIMS”, “GSC MIxS: Symbiont-associatedMIMS”, “GSC MIxS: Plant-associatedMIMS” | ||||
| Additional potential plant-associated 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”) |
“ENA Marine Microalgae Checklist; Checklist: ERC000043.” https://www.ebi.ac.uk/ena/browser/view/ERC000043.
“ENA Tara Oceans; Checklist: ERC000030.” https://www.ebi.ac.uk/ena/browser/view/ERC000030.
“GOLD Ecosystem Classification Paths.” https://gold.jgi.doe.gov/ecosystem_classification.
“GSC MIxS Water; ENA Checklist: ERC000024.” https://www.ebi.ac.uk/ena/browser/view/ERC000024.
“GSC MIxS: AgricultureMIMS.” https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/.
“GSC MIxS: Host-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/.
“GSC MIxS: Plant-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/.
“GSC MIxS: Symbiont-associatedMIMS.” https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/.
“MIMS: Metagenome/Environmental, Human-Associated; Version 6.0 Package.” https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/.
Morrison, Norman, Daniel Bearden, Jacob G. Bundy, Timothy Collette, Fraser Currie, Matthew Davey, Migdalia Dominguez, et al. 2007. “Standard Reporting Requirements for Biological Samples in Metabolomics Experiments: Environmental Context.” Metabolomics 3 (2): 203–10. https://doi.org/10.1007/s11306-007-0067-1.