Table 1.

The core items of the MIMARKS checklists, along with the value types, descriptions and requirement status

		Report type
Item	Description	MIMARKS survey	MIMARKS specimen
Investigation
Submitted to INSDC[boolean]	Depending on the study (large-scale, e.g., done with next-generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archives), DRA (DDBJ Sequence Read Archive) or through the classical Webin/Sequin systems to GenBank, ENA and DDBJ	M	M
Investigation type[mimarks-survey or mimarks-specimen]	Nucleic Acid Sequence Report is the root element of all MIMARKS compliant reports as standardized by Genomic Standards Consortium (GSC). This field is either MIMARKS survey or MIMARKS specimen	M	M
Project name	Name of the project within which the sequencing was organized	M	M
Environment
Geographic location (latitude and longitude[float, point, transect and region])	The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system	M	M
Geographic location (depth[integer, point, interval, unit])	Please refer to the definitions of depth in the environmental packages	E	E
Geographic location (elevation of site[integer, unit]; altitude of sample[integer, unit])	Please refer to the definitions of either altitude or elevation in the environmental packages	E	E
Geographic location (country and/or sea[INSDC or GAZ]; region[GAZ])	The geographical origin of the sample as defined by the country or sea name. Country, sea or region names should be chosen from the INSDC list (http://insdc.org/country.html), or the GAZ (Gazetteer, v1.446) ontology (http://bioportal.bioontology.org/visualize/40651)	M	M
Collection date[ISO8601]	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, that is, 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 for 2008-01 and 2008, all are ISO6801 compliant	M	M
Environment (biome[EnvO])	In environmental biome level are the major classes of ecologically similar communities of plants, animals and other organisms. Biomes are defined based on factors such as plant structures, leaf types, plant spacing and other factors like climate. Examples include desert, taiga, deciduous woodland or coral reef. Environment Ontology (EnvO) (v1.53) terms listed under environmental biome can be found at http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00000428	M	M
Environment (feature[EnvO])	Environmental feature level includes geographic environmental features. Examples include harbor, cliff or lake. EnvO (v1.53) terms listed under environmental feature can be found at http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00002297	M	M
Environment (material[EnvO])	The environmental material level refers to the matter that was displaced by the sample, before the sampling event. Environmental matter terms are generally mass nouns. Examples include: air, soil or water. EnvO (v1.53) terms listed under environmental matter can be found at http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00010483	M	M
MIGS/MIMS/MIMARKS extension
Environmental package[air, host-associated, human-associated, human-skin, human-oral, human-gut, human-vaginal, microbial mat/biofilm, miscellaneous natural or artificial environment, plant-associated, sediment, soil, wastewater/sludge, water]	MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported	M	M
Nucleic acid sequence source
Isolation and growth conditions[PMID, DOI or URL]	Publication reference in the form of PubMed ID (PMID), digital object identifier (DOI) or URL for isolation and growth condition specifications of the organism/material	–	M
Sequencing
Target gene or locus (e.g., 16S rRNA, 18S rRNA, nif, amoA, rpo)	Targeted gene or locus name for marker gene study	M	M
Sequencing method (e.g., dideoxysequencing, pyrosequencing, polony)	Sequencing method used, e.g., Sanger, pyrosequencing, ABI-solid	M	M

Items for the MIMARKS specification and their mandatory (M), status for both MIMARKS-survey and MIMARKS-specimen checklists. Furthermore, “–” denotes that an item is not applicable for a given checklist. E denotes that a field has environment-specific requirements. For example, whereas “depth” is mandatory for the environments water, sediment or soil, it is optional for human-associated environments. MIMARKS-survey is applicable to contextual data for marker gene sequences, obtained directly from the environment, without culturing or identification of the organisms. MIMARKS-specimen, on the other hand, applies to the contextual data for marker gene sequences from cultured or voucher-identifiable specimens. Both MIMARKS-survey and specimen checklists can be used for any type of marker gene sequence data, ranging from 16S, 18S, 23S, 28S rRNA to COI, hence the checklists are universal for all three domains of life. Item names are followed by a short description of the value of the item in parentheses and/or value type in brackets as a superscript. Whenever applicable, value types are chosen from a controlled vocabulary (CV) or an ontology from the Open Biological and Biomedical Ontologies (OBO) foundry (http://www.obofoundry.org/). This table only presents the very core of MIMARKS checklists, that is, only mandatory items for each checklist. Supplementary Results 2 contains all MIMARKS items, the tables for environmental packages in the MIGS/MIMS/MIMARKS extension and GenBank structured comment name that should be used for submitting MIMARKS data to GenBank. In case of submitting to EBI-ENA, the full names can be used.