ABCDEFGHIJKLMNOPRSTUVWX
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# creator_id: "https://orcid.org/0000-0003-1336-5554", "https://orcid.org/0000-0001-9625-1899", "https://orcid.org/0000-0002-6601-2165", "https://orcid.org/0000-0003-1144-0290", "https://orcid.org/0000-0002-8083-6048", "https://orcid.org/0000-0003-3770-3714", "https://orcid.org/0000-0002-4366-3088", "https://orcid.org/0000-0002-4236-0384", "https://orcid.org/0000-0001-8815-0078", "https://orcid.org/0000-0002-2996-719X", "https://orcid.org/0000-0001-9401-8460", "https://orcid.org/0000-0003-1691-239X", "https://orcid.org/0000-0001-6215-3617", "https://orcid.org/0000-0002-3237-4547", "https://orcid.org/0000-0001-7087-2646"
# curie_map: dwc: "http://rs.tdwg.org/dwc/terms/", skos: "http://www.w3.org/2004/02/skos/core, MIXS: "https://w3id.org/gensc.org/terms/MIXS_"
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subject_idsubject_labelsubject_definition
subject_valueSyntax
subject_categorypredicate_id
predicate_label
syntax_predicate_id
syntax_predicate_label
object_idobject_labelobject_definitionobject_valueSyntax
object_category
match_typecreator_idsubject_sourcesubject_source_versionobject_source
object_source_version
mapping_date
dwc:samplingProtocol covers both of the concepts samp_collect_device and samp_collect_process. Both of these terms list both, the names of (or links to) methods, or devices (either in the definition or in the examples). Taking the definition and the examples into account these could be skos:exactMatch, focusing only on the definition, skos:broadMatch would be appropriate.
syntax_comment
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MIXS:0000004submitted_to_insdcDepending 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 Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ. Although this field is mandatory, it is meant as a self-test field, therefore it is not necessary to include this field in contextual data submitted to databases{boolean}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
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MIXS:0000007investigation_typeNucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome,mimarks-survey, mimarks-specimen, metatranscriptome, single amplified genome, metagenome-assembled genome, or uncultivated viral genome
[eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|metatranscriptome|mimarks-survey|mimarks-specimen|misag|mimag|miuvig]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
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MIXS:0000092project_nameName of the project within which the sequencing was organized{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
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MIXS:0000008experimental_factorExperimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v 2.95) terms, please see http://purl.bioontology.org/ontology/EFO; for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI{termLabel} {[termID]}|{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
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dwc:verbatimCoordinatesVerbatim Coordinates
The verbatim original spatial coordinates of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem.
verbatimhttp://purl.org/dc/terms/Locationskos:broadMatchbroad match toskos:relatedMatchrelated match toMIXS:0000009lat_lonThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system{float} {float}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/verbatimCoordinateshttp://rs.tdwg.org/dwc/terms/version/verbatimCoordinates-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
The Coordinate Reference System "epsg:4326" must be provided explicitly in dwc:verbatimSRS in order for the mapping to be complete.
The DwC term expects a verbatim input (so anything really), whereas MIxS expects decimal degrees input as {float} {float}
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dwc:decimalLatitudeDecimal Latitude
The geographic latitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are north of the Equator, negative values are south of it. Legal values lie between -90 and 90, inclusive.
 http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toMIXS:0000009lat_lonThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system{float} {float}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/decimalLatitudehttp://rs.tdwg.org/dwc/terms/version/decimalLatitude-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-03-30The DwC term only refers to half of the MIxS term
The DwC term expects decimal degrees, and so does MIxS - however, MIxS expects two input values, while DwC only expects one
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dwc:decimalLongitudeDecimal Longitude
The geographic longitude (in decimal degrees, using the spatial reference system given in geodeticDatum) of the geographic center of a Location. Positive values are east of the Greenwich Meridian, negative values are west of it. Legal values lie between -180 and 180, inclusive.
 http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toMIXS:0000009lat_lonThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system{float} {float}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/decimalLongitudehttp://rs.tdwg.org/dwc/terms/version/decimalLongitude-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-03-30The DwC term only refers to half of the MIxS term
The DwC term expects decimal degrees, and so does MIxS - however, MIxS expects two input values, while DwC only expects one
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dwc:verbatimLatitudeVerbatim Latitude
The verbatim original latitude of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem.
verbatimhttp://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:relatedMatchrelated match toMIXS:0000009lat_lonThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system{float} {float}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/verbatimLatitudehttp://rs.tdwg.org/dwc/terms/version/verbatimLatitude-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-04-07
The DwC term only refers to half of the MIxS term but allows a wider variety of input
MIxS expects two input values in decimal degrees, while DwC only expects one as verbatim (so anything really)
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dwc:verbatimLongitudeVerbatim Longitude
The verbatim original longitude of the Location. The coordinate ellipsoid, geodeticDatum, or full Spatial Reference System (SRS) for these coordinates should be stored in verbatimSRS and the coordinate system should be stored in verbatimCoordinateSystem.
verbatimhttp://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:relatedMatchrelated match toMIXS:0000009lat_lonThe geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system{float} {float}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/verbatimLongitudehttp://rs.tdwg.org/dwc/terms/version/verbatimLongitude-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-04-07
The DwC term only refers to half of the MIxS term but allows a wider variety of input
MIxS expects two input values in decimal degrees, while DwC only expects one as verbatim (so anything really)
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dwc:verbatimDepthVerbatim DepthThe original description of the depth below the local surface.verbatimhttp://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:relatedMatchrelated match toMIXS:0000018depthPlease refer to the definitions of depth in the environmental packages-MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/verbatimDepthhttp://rs.tdwg.org/dwc/terms/version/verbatimDepth-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken.
The DwC term expects a verbatim input (so anything really), while MIxS expects a {float} {unit} entry in meters
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dwc:minimumDistanceAboveSurfaceInMeters
Minimum Distance Above Surface in Meters
The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
 http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:exactMatchexact match toMIXS:0000018depthPlease refer to the definitions of depth in the environmental packages-MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/minimumDistanceAboveSurfaceInMeters
http://rs.tdwg.org/dwc/terms/version/minimumDistanceAboveSurfaceInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken.
The DwC term will expect a negative value here, while MIxS will not. Additionally, the example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.
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dwc:maximumDistanceAboveSurfaceInMeters
Maximum Distance Above Surface in Meters
The greater distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
 http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:exactMatchexact match toMIXS:0000018depthPlease refer to the definitions of depth in the environmental packages-MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/maximumDistanceAboveSurfaceInMeters
http://rs.tdwg.org/dwc/terms/version/maximumDistanceAboveSurfaceInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
In Darwin Core, according to best practices, depth is measured in water from an air-water surface, while in other media the corresponding terms are dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAboveSurfaceInMeters, where the values would be negative for depth. Thus, for a sediment at the bottom of a lake, there would be an elevation of the lake surface, the depth of the top of the sediment in the lake, and minimum and maximum distances below the sediment surface within which a sample was taken.
The DwC term will expect a negative value here, while MIxS will not. Additionally, the example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.
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dwc:minimumDepthInMetersMinimum Depth In MetersThe lesser depth of a range of depth below the local surface, in meters. http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toMIXS:0000018depthPlease refer to the definitions of depth in the environmental packages-MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/minimumDepthInMeters
http://rs.tdwg.org/dwc/terms/version/minimumDepthInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-04-12
The DwC term specifically addresses a range of depths, for which this term gives the minimum depth, whereas the MIxS term does not specify that it is about a depth range
The example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.
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dwc:maximumDepthInMetersMaximum Depth In MetersThe greater depth of a range of depth below the local surface, in meters.http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toMIXS:0000018depthPlease refer to the definitions of depth in the environmental packages-MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/maximumDepthInMeters
http://rs.tdwg.org/dwc/terms/version/maximumDepthInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-04-12
The DwC term specifically addresses a range of depths, for which this term gives the maximum depth, whereas the MIxS term does not specify that it is about a depth range
The example offered by DwC does not include the unit "meter" as part of the entry in the field, whereas the MIxS syntax would expect the unit to be added.
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dwc:minimumDistanceAboveSurfaceInMeters
Minimum Distance Above Surface in Meters
The lesser distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
 http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toaltAltitude 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{float} {unit}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/minimumDistanceAboveSurfaceInMeters
http://rs.tdwg.org/dwc/terms/version/minimumDistanceAboveSurfaceInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
A range of altitude can be captured in the combination of the terms dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAbveSurfaceInMeters. If a single value is given, the same value should be used in both DwC terms.
Not sure, MIxS expects {float} {unit}, DwC gives examples for both - {float} and {float} {unit}
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dwc:maximumDistanceAboveSurfaceInMeters
Maximum Distance Above Surface in Meters
The greater distance in a range of distance from a reference surface in the vertical direction, in meters. Use positive values for locations above the surface, negative values for locations below. If depth measures are given, the reference surface is the location given by the depth, otherwise the reference surface is the location given by the elevation.
 http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toaltAltitude 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{float} {unit}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/maximumDistanceAboveSurfaceInMeters
http://rs.tdwg.org/dwc/terms/version/maximumDistanceAboveSurfaceInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
A range of altitude can be captured in the combination of the terms dwc:minimumDistanceAboveSurfaceInMeters and dwc:maximumDistanceAbveSurfaceInMeters. If a single value is given, the same value should be used in both DwC terms.
Not sure, MIxS expects {float} {unit}, DwC gives examples for both - {float} and {float} {unit}
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dwc:verbatimElevationVerbatim Elevation
The original description of the elevation (altitude, usually above sea level) of the Location.
verbatimhttp://purl.org/dc/terms/Locationskos:exactMatchexact match toskos:relatedMatchrelated match toMIXS:0000093elevElevation 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{float} {unit}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/verbatimElevationhttp://rs.tdwg.org/dwc/terms/version/verbatimElevation-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
The DwC term expects verbatim input (so anything really), whereas MIxS expects {float} {unit} in meter
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dwc:minimumElevationInMeters
Minimum Elevation in Meters
The lower limit of the range of elevation (altitude, usually above sea level), in meters.
http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toMIXS:0000093elevElevation 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{float} {unit}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/minimumElevationInMeters
http://rs.tdwg.org/dwc/terms/version/minimumElevationInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-03-30
The DwC example does not include a unit, only a {float}, while MIxS expects the input to be {float} {unit}
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dwc:maximumElevationInMeters
Maximum Elevation in Meters
The upper limit of the range of elevation (altitude, usually above sea level), in meters.
http://purl.org/dc/terms/Locationskos:narrowMatchnarrow match toskos:narrowMatchnarrow match toMIXS:0000093elevElevation 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{float} {unit}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/maximumElevationInMeters
http://rs.tdwg.org/dwc/terms/version/maximumElevationInMeters-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-03-30
The DwC example does not include a unit, only a {float}, while MIxS expects the input to be {float} {unit}
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dwc:countryCountryThe name of the country or major administrative unit in which the Location occurs. DwC Locationskos:broadMatchbroad match toskos:relatedMatchrelated match toMIXS:0000010geo_loc_nameThe 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 (v 1.512) (http://purl.bioontology.org/ontology/GAZ){term};{term};{text}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/countryhttp://rs.tdwg.org/dwc/terms/version/country-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-01-29
the MIxS term includes both seas and countries, while DwC only refers to the country
The DwC example only expects one word, while MIxS expects two words (country or sea name + specific region name). Additionally MIxS expects terms from an ontology where appropriate, for which the input would not only be a word but a termLabel[termID] combination
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dwc:waterBodyWater BodyThe name of the water body in which the Location occurs.http://purl.org/dc/terms/Locationskos:broadMatchbroad match toskos:relatedMatchrelated match toMIXS:0000010geo_loc_nameThe 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 (v 1.512) (http://purl.bioontology.org/ontology/GAZ){term};{term};{text}MIxS coreHumanCurated
https://orcid.org/0000-0002-2996-719X
http://rs.tdwg.org/dwc/terms/waterBodyhttp://rs.tdwg.org/dwc/terms/version/waterBody-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-05-12
the MIxS term includes both seas and countries, while DwC only refers to the sea.
The DwC example only expects one sea identifier, while MIxS expects an additional word (country or sea name + specific region name). Additionally, MIxS expects terms from an ontology where appropriate, for which the input would not only be a word but a termLabel[termID] combination
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dwc:higherGeographyHigher Geography
A list (concatenated and separated) of geographic names less specific than the information captured in the locality term.
 http://purl.org/dc/terms/Locationskos:exactMatchexact match toskos:relatedMatchrelated match toMIXS:0000010geo_loc_nameThe 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 (v 1.512) (http://purl.bioontology.org/ontology/GAZ){term};{term};{text}MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/higherGeographyhttp://rs.tdwg.org/dwc/terms/version/higherGeography-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
DwC term encompasses any combination of geographic region names, while the MIxS term may either be the name of a country or a sea, followed by additional region information
DwC expects a list (of undefined length) of values separated by a vertical bar space "|", while MIxS expects two words (country or sea name + specific region name). Additionally MIxS expects terms from an ontology where appropriate, for which the input would not only be a word but a termLabel[termID] combination
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dwc:eventDateEvent Date
The date-time or interval during which an Event occurred. For occurrences, this is the date-time when the event was recorded. Not suitable for a time in a geological context.
 http://rs.tdwg.org/dwc/terms/Eventskos:narrowMatchnarrow match toskos:exactMatchexact match toMIXS:0000011collection_dateThe 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{timestamp}MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/eventDatehttp://rs.tdwg.org/dwc/terms/version/eventDate-2020-08-12
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
Events are semantically broader than sampling events (e.g. they could include observations too)
DwC requests compliance with ISO 8601-1:2019, so does MIxS
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MIXS:0000012env_broad_scaleIn this field, report which major environmental system your sample or specimen came from. The systems identified should have a coarse spatial grain, to provide the general environmental context of where the sampling was done (e.g. were you in the desert or a rainforest?). We recommend using subclasses of ENVO’s biome class: http://purl.obolibrary.org/obo/ENVO_00000428. Format (one term): termLabel [termID], Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a water sample from the photic zone in middle of the Atlantic Ocean, consider: oceanic epipelagic zone biome [ENVO:01000033]. Example: Annotating a sample from the Amazon rainforest consider: tropical moist broadleaf forest biome [ENVO:01000228]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html{termLabel} {[termID]}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
27
MIXS:0000013env_local_scaleIn this field, report the entity or entities which are in your sample or specimen’s local vicinity and which you believe have significant causal influences on your sample or specimen. Please use terms that are present in ENVO and which are of smaller spatial grain than your entry for env_broad_scale. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a pooled sample taken from various vegetation layers in a forest consider: canopy [ENVO:00000047]|herb and fern layer [ENVO:01000337]|litter layer [ENVO:01000338]|understory [01000335]|shrub layer [ENVO:01000336]. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html{termLabel} {[termID]}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
28
MIXS:0000014env_mediumIn this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html{termLabel} {[termID]}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
29
MIXS:0000019env_packageMIxS 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
[air|built environment|host-associated|human-associated|human-skin|human-oral|human-gut|human-vaginal|hydrocarbon resources-cores|hydrocarbon resources-fluids/swabs|microbial mat/biofilm|misc environment|plant-associated|sediment|soil|wastewater/sludge|water]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
30
MIXS:0000020subspecf_gen_linThis should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123{rank name}:{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
31
MIXS:0000021ploidyThe ploidy level of the genome (e.g. allopolyploid, haploid, diploid, triploid, tetraploid). It has implications for the downstream study of duplicated gene and regions of the genomes (and perhaps for difficulties in assembly). For terms, please select terms listed under class ploidy (PATO:001374) of Phenotypic Quality Ontology (PATO), and for a browser of PATO (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO{termLabel} {[termID]}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
32
MIXS:0000022num_repliconsReports the number of replicons in a nuclear genome of eukaryotes, in the genome of a bacterium or archaea or the number of segments in a segmented virus. Always applied to the haploid chromosome count of a eukaryote{integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
33
MIXS:0000023extrachrom_elementsDo plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids){integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
34
MIXS:0000024estimated_sizeThe estimated size of the genome prior to sequencing. Of particular importance in the sequencing of (eukaryotic) genome which could remain in draft form for a long or unspecified period.{integer} bpMIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
35
MIXS:0000025ref_biomaterialPrimary publication if isolated before genome publication; otherwise, primary genome report{PMID}|{DOI}|{URL}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
36
dwc:materialSampleIDMaterial Sample ID
An identifier for the MaterialSample (as opposed to a particular digital record of the material sample). In the absence of a persistent global unique identifier, construct one from a combination of identifiers in the record that will most closely make the materialSampleID globally unique.
 http://rs.tdwg.org/dwc/terms/MaterialSampleskos:exactMatchexact match toskos:exactMatchexact match toMIXS:0000026source_mat_idA unique identifier assigned to a material sample (as defined by http://rs.tdwg.org/dwc/terms/materialSampleID, and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing. The identifier can refer either to the original material collected or to any derived sub-samples. The INSDC qualifiers /specimen_voucher, /bio_material, or /culture_collection may or may not share the same value as the source_mat_id field. For instance, the /specimen_voucher qualifier and source_mat_id may both contain 'UAM:Herps:14' , referring to both the specimen voucher and sampled tissue with the same identifier. However, the /culture_collection qualifier may refer to a value from an initial culture (e.g. ATCC:11775) while source_mat_id would refer to an identifier from some derived culture from which the nucleic acids were extracted (e.g. xatc123 or ark:/2154/R2).{text}MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/materialSampleIDhttp://rs.tdwg.org/dwc/terms/version/materialSampleID-2020-10-28
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09Both expect a mix of letters, numbers, etc.
37
MIXS:0000027pathogenicityTo what is the entity pathogenic{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
38
dwc:associatedOrganismsAssociated Organisms
A list (concatenated and separated) of identifiers of other Organisms and their associations to this Organism.
 http://rs.tdwg.org/dwc/terms/Organismskos:exactMatchexact match toskos:relatedMatchrelated match toMIXS:0000028biotic_relationshipDescription 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
[free living|parasitism|commensalism|symbiotic|mutualism]
MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/associatedOrganisms
http://rs.tdwg.org/dwc/terms/version/associatedOrganisms-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
One could also capture relationships with more metadata about the assertion using the ResourceRelationship extension to Darwin Core.
DwC expects a list of terms and corresponding identifiers, while MIxS only expects a list of terms
39
MIXS:0000029specific_hostIf there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host){NCBI taxid}|{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
One could also capture relationships with more metadata about the assertion using the ResourceRelationship extension to Darwin Core.
40
MIXS:0000030host_spec_rangeThe NCBI taxonomy identifier of the specific host if it is known{integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
41
MIXS:0000031health_disease_statHealth or disease status of specific host at time of collection
[healthy|diseased|dead|disease-free|undetermined|recovering|resolving|pre-existing condition|pathological|life threatening|congenital]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
42
MIXS:0000032trophic_levelTrophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)
[autotroph|carboxydotroph|chemoautotroph|chemoheterotroph|chemolithoautotroph|chemolithotroph|chemoorganoheterotroph|chemoorganotroph|chemosynthetic|chemotroph|copiotroph|diazotroph|facultative|autotroph|heterotroph|lithoautotroph|lithoheterotroph|lithotroph|methanotroph|methylotroph|mixotroph|obligate|chemoautolithotroph|oligotroph|organoheterotroph|organotroph|photoautotroph|photoheterotroph|photolithoautotroph|photolithotroph|photosynthetic|phototroph]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
43
MIXS:0000033propagationThis field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
44
MIXS:0000034encoded_traitsShould include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
45
MIXS:0000015rel_to_oxygenIs this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments
[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
46
MIXS:0000003isol_growth_condtPublication reference in the form of pubmed ID (pmid), digital object identifier (doi) or url for isolation and growth condition specifications of the organism/material{PMID}|{DOI}|{URL}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
47
dwc:samplingProtocolSampling Protocol
The name of, reference to, or description of the method or protocol used during an Event.
 http://rs.tdwg.org/dwc/terms/Eventskos:broadMatchbroad match toskos:relatedMatchrelated match toMIXS:0000002samp_collect_deviceThe method or device employed for collecting the sample{text}MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/samplingProtocolhttp://rs.tdwg.org/dwc/terms/version/samplingProtocol-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
dwc:samplingProtocol covers both of the concepts samp_collect_device and samp_collect_process. Both of these terms list both, the names of (or links to) methods, or devices (either in the definition or in the examples). Based on the examples these could be skos:exactMatch, focusing on the definition, skos:broadMatch would be appropriate. The information that this term and the samp_mat_process capture is often captured in the method steps in the EML (metadata about the dataset, not indexed in GBIF’s case), and less in the DwC terms themselves. This influences how people will use the terms in reality.
DwC expects the name of, reference to, or description (which could also include a URI, IRI, etc.), while MIxS only expects a label
48
dwc:samplingProtocolSampling Protocol
The name of, reference to, or description of the method or protocol used during an Event.
 http://rs.tdwg.org/dwc/terms/Eventskos:narrowMatchnarrow match toskos:relatedMatchrelated match toMIXS:0000016samp_mat_processAny processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI{text}|{termLabel} {[termID]}MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/samplingProtocolhttp://rs.tdwg.org/dwc/terms/version/samplingProtocol-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
dwc:samplingProtocol covers both of the concepts samp_collect_device and samp_collect_process. The object is narrower as it specifies that it has to be “after the sample was taken” vs anytime; and the “The name of, reference to, or description of the method [...]” vs a specific ontology term. The information that this term and samp_collect_device capture is often captured in the method steps in the EML (metadata about the dataset, not indexed in GBIF’s case), and less in the DwC terms themselves. This influences how people will use the terms in reality.
DwC expects the name of, reference to, or description (which could also include a URI, IRI, etc.), while MIxS expects terms from an ontology where appropriate, for which the input would not only be a word but a termLabel[termID] combination
49
MIXS:0000017size_fracFiltering pore size used in sample preparation{float}-{float} {unit}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
50
dwc:sampleSizeValueSample Size Value
A numeric value for a measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.
 http://rs.tdwg.org/dwc/terms/Eventskos:broadMatchbroad match toskos:relatedMatchrelated match toMIXS:0000001samp_sizeAmount or size of sample (volume, mass or area) that was collected{float} {unit}MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/sampleSizeValuehttp://rs.tdwg.org/dwc/terms/version/sampleSizeValue-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
dwc:sampleSizeValue requires the units of the measure to be given in dwc:sampleSizeUnit.
MIxS expects {float} {unit}, while DwC only expects {float}
51
dwc:sampleSizeUnitSample Size Unit
The unit of measurement of the size (time duration, length, area, or volume) of a sample in a sampling event.
 http://rs.tdwg.org/dwc/terms/Eventskos:broadMatchbroad match toskos:relatedMatchrelated match toMIXS:0000001samp_sizeAmount or size of sample (volume, mass or area) that was collected{float} {unit}MIxS coreHumanCurated
https://orcid.org/0000-0003-1144-0290
http://rs.tdwg.org/dwc/terms/sampleSizeUnithttp://rs.tdwg.org/dwc/terms/version/sampleSizeUnit-2017-10-06
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
52021-02-09
dwc:sampleSizeUnit must accompany the measure given in dwc:sampleSizeValue.
MIxS expects {float} {unit}, while DwC only expects {unit}
52
MIXS:0000035source_uvigType of dataset from which the UViG was obtained
[metagenome (not viral targeted)|viral fraction metagenome (virome)|sequence-targeted metagenome|metatranscriptome (not viral targeted)|viral fraction RNA metagenome (RNA virome)|sequence-targeted RNA metagenome|microbial single amplified genome (SAG)|viral single amplified genome (vSAG)|isolate microbial genome|other]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
53
MIXS:0000036virus_enrich_apprList of approaches used to enrich the sample for viruses, if any
[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
54
MIXS:0000037nucl_acid_extA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the material separation to recover the nucleic acid fraction from a sample{PMID}|{DOI}|{URL}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
55
MIXS:0000038nucl_acid_ampA link to a literature reference, electronic resource or a standard operating procedure (SOP), that describes the enzymatic amplification (PCR, TMA, NASBA) of specific nucleic acids{PMID}|{DOI}|{URL}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
56
MIXS:0000039lib_sizeTotal number of clones in the library prepared for the project{integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
57
MIXS:0000040lib_reads_seqdTotal number of clones sequenced from the library{integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
58
MIXS:0000041lib_layoutSpecify whether to expect single, paired, or other configuration of reads[paired|single|vector|other]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
59
MIXS:0000042lib_vectorCloning vector type(s) used in construction of libraries{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
60
MIXS:0000043lib_screenSpecific enrichment or screening methods applied before and/or after creating libraries{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
61
MIXS:0000044target_geneTargeted gene or locus name for marker gene studies{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
62
MIXS:0000045target_subfragmentName of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
63
MIXS:0000046pcr_primersPCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment. This field should contain all the primers used for a single PCR reaction if multiple forward or reverse primers are present in a single PCR reaction. The primer sequence should be reported in uppercase lettersFWD:{dna};REV:{dna}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
64
MIXS:0000047midMolecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters{dna}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
65
MIXS:0000048adaptersAdapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters{dna};{dna}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
66
MIXS:0000049pcr_condDescription of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
initial denaturation:degrees_minutes;annealing:degrees_minutes;elongation:degrees_minutes;final elongation:degrees_minutes;total cycles
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
67
MIXS:0000050seq_methSequencing method used; e.g. Sanger, pyrosequencing, ABI-solid
[MinION|GridION|PromethION|454 GS|454 GS 20|454 GS FLX|454 GS FLX+|454 GS FLX Titanium|454 GS Junior|Illumina Genome Analyzer|Illumina Genome Analyzer II|Illumina Genome Analyzer IIx|Illumina HiSeq 4000|Illumina HiSeq 3000|Illumina HiSeq 2500|Illumina HiSeq 2000|Illumina HiSeq 1500|Illumina HiSeq 1000|Illumina HiScanSQ|Illumina MiSeq|Illumina HiSeq X Five|Illumina HiSeq X Ten|Illumina NextSeq 500|Illumina NextSeq 550|AB SOLiD System|AB SOLiD System 2.0|AB SOLiD System 3.0|AB SOLiD 3 Plus System|AB SOLiD 4 System|AB SOLiD 4hq System|AB SOLiD PI System|AB 5500 Genetic Analyzer|AB 5500xl Genetic Analyzer|AB 5500xl-W Genetic Analysis System|Ion Torrent PGM|Ion Torrent Proton|Ion Torrent S5|Ion Torrent S5 XL|PacBio RS|PacBio RS II|Sequel|AB 3730xL Genetic Analyzer|AB 3730 Genetic Analyzer|AB 3500xL Genetic Analyzer|AB 3500 Genetic Analyzer|AB 3130xL Genetic Analyzer|AB 3130 Genetic Analyzer|AB 310 Genetic Analyzer|BGISEQ-500]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
68
MIXS:0000051seq_quality_checkIndicate if the sequence has been called by automatic systems (none) or undergone a manual editing procedure (e.g. by inspecting the raw data or chromatograms). Applied only for sequences that are not submitted to SRA,ENA or DRA[none|manually edited]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
69
MIXS:0000052chimera_checkA chimeric sequence, or chimera for short, is a sequence comprised of two or more phylogenetically distinct parent sequences. Chimeras are usually PCR artifacts thought to occur when a prematurely terminated amplicon reanneals to a foreign DNA strand and is copied to completion in the following PCR cycles. The point at which the chimeric sequence changes from one parent to the next is called the breakpoint or conversion point{software};{version};{parameters}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
70
MIXS:0000053tax_identThe phylogenetic marker(s) used to assign an organism name to the SAG or MAG[16S rRNA gene|multi-marker approach|other]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
71
MIXS:0000056assembly_qualThe assembly quality category is based on sets of criteria outlined for each assembly quality category. For MISAG/MIMAG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities with a consensus error rate equivalent to Q50 or better. High Quality Draft:Multiple fragments where gaps span repetitive regions. Presence of the 23S, 16S and 5S rRNA genes and at least 18 tRNAs. Medium Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Low Quality Draft:Many fragments with little to no review of assembly other than reporting of standard assembly statistics. Assembly statistics include, but are not limited to total assembly size, number of contigs, contig N50/L50, and maximum contig length. For MIUVIG; Finished: Single, validated, contiguous sequence per replicon without gaps or ambiguities, with extensive manual review and editing to annotate putative gene functions and transcriptional units. High-quality draft genome: One or multiple fragments, totaling ≥ 90% of the expected genome or replicon sequence or predicted complete. Genome fragment(s): One or multiple fragments, totalling < 90% of the expected genome or replicon sequence, or for which no genome size could be estimated
[Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality draft genome|Genome fragment(s)]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
72
MIXS:0000057assembly_nameName/version of the assembly provided by the submitter that is used in the genome browsers and in the community{text} {text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
73
MIXS:0000058assembly_softwareTool(s) used for assembly, including version number and parameters{software};{version};{parameters}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
74
MIXS:0000059annotTool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
75
MIXS:0000060number_contigTotal number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG{integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
76
MIXS:0000061feat_predMethod used to predict UViGs features such as ORFs, integration site, etc.{software};{version};{parameters}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
77
MIXS:0000062ref_dbList of database(s) used for ORF annotation, along with version number and reference to website or publication{database};{version};{reference}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
78
MIXS:0000063sim_search_methTool used to compare ORFs with database, along with version and cutoffs used{software};{version};{parameters}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
79
MIXS:0000064tax_classMethod used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
80
MIXS:000006516s_recoverCan a 16S gene be recovered from the submitted SAG or MAG?{boolean}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
81
MIXS:000006616s_recover_softwareTools used for 16S rRNA gene extraction{software};{version};{parameters}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
82
MIXS:0000067trnasThe total number of tRNAs identified from the SAG or MAG{integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
83
MIXS:0000068trna_ext_softwareTools used for tRNA identification{software};{version};{parameters}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
84
MIXS:0000069compl_scoreCompleteness score is typically based on either the fraction of markers found as compared to a database or the percent of a genome found as compared to a closely related reference genome. High Quality Draft: >90%, Medium Quality Draft: >50%, and Low Quality Draft: < 50% should have the indicated completeness scores[high|med|low];{percentage}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
85
MIXS:0000070compl_softwareTools used for completion estimate, i.e. checkm, anvi'o, busco{software};{version}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
86
MIXS:0000071compl_apprThe approach used to determine the completeness of a given SAG or MAG, which would typically make use of a set of conserved marker genes or a closely related reference genome. For UViG completeness, include reference genome or group used, and contig feature suggesting a complete genome[marker gene|reference based|other]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
87
MIXS:0000072contam_scoreThe contamination score is based on the fraction of single-copy genes that are observed more than once in a query genome. The following scores are acceptable for; High Quality Draft: < 5%, Medium Quality Draft: < 10%, Low Quality Draft: < 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases{float} percentageMIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
88
MIXS:0000005contam_screen_inputThe type of sequence data used as input[reads| contigs]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
89
MIXS:0000073contam_screen_paramSpecific parameters used in the decontamination sofware, such as reference database, coverage, and kmers. Combinations of these parameters may also be used, i.e. kmer and coverage, or reference database and kmer[ref db|kmer|coverage|combination];{text|integer}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
90
MIXS:0000074decontam_softwareTool(s) used in contamination screening
[checkm/refinem|anvi'o|prodege|bbtools:decontaminate.sh|acdc|combination]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
91
MIXS:0000075sort_techMethod used to sort/isolate cells or particles of interest
[flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|micromanipulation|other]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
92
MIXS:0000076single_cell_lysis_apprMethod used to free DNA from interior of the cell(s) or particle(s)[chemical|enzymatic|physical|combination]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
93
MIXS:0000054single_cell_lysis_protName of the kit or standard protocol used for cell(s) or particle(s) lysis{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
94
MIXS:0000055wga_amp_apprMethod used to amplify genomic DNA in preparation for sequencing[pcr based|mda based]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
95
MIXS:0000006wga_amp_kitKit used to amplify genomic DNA in preparation for sequencing{text}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
96
MIXS:0000077bin_paramThe parameters that have been applied during the extraction of genomes from metagenomic datasets
[homology search|kmer|coverage|codon usage|combination]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
97
MIXS:0000078bin_softwareTool(s) used for the extraction of genomes from metagenomic datasets
[metabat|maxbin|concoct|groupm|esom|metawatt|combination|other]
MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
98
MIXS:0000079reassembly_binHas an assembly been performed on a genome bin extracted from a metagenomic assembly?{boolean}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
99
MIXS:0000080mag_cov_softwareTool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets[bwa|bbmap|bowtie|other]MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5
100
MIXS:0000081vir_ident_softwareTool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used{software};{version};{parameters}MIxS core
https://github.com/GenomicsStandardsConsortium/mixs-legacy/blob/master/mixs5/mixs_v5.xlsx
5