MIxS terms
OWL 2 DL ontology for MIxS metadata terms from the http://gensc.org/ns/mixs/terms/ namespace; this version uses object and datatype properties instead of annotation properties where possible. Note that, because of this, when using this ontology you are restricted to using literals and non-literals in certain cases and especially you cannot use DCMI's DCSV.
adapters
Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
annotation source
For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
assembly name
Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community
HuRef, JCVI_ISG_i3_1.0
assembly
How was the assembly done (e.g. with a text based assembler like phrap or a flowgram assembler); estimated error rate associated with the finished sequences (e.g. error rate of 1 in 1000 bp); and the method of calculation
Associated References
A list (concatenated and separated) of identifiers (publication, bibliographic reference, global unique identifier, URI) of literature associated with the Occurrence.
Examples: "http://www.sciencemag.org/cgi/content/abstract/322/5899/261", "Christopher J. Conroy, Jennifer L. Neuwald. 2008. Phylogeographic study of the California vole, Microtus californicus Journal of Mammalogy, 89(3):755-767."
observed biotic relationship
Is it free-living or in a host and if the latter what type of relationship is observed
chimera check
A 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
Collection Code
The name, acronym, coden, or initialism identifying the collection or data set from which the record was derived.
Examples: "Mammals", "Hildebrandt", "eBird"
Dataset Name
The name identifying the data set from which the record was derived.
Examples: "Grinnell Resurvey Mammals", "Lacey Ctenomys Recaptures"
encoded traits
Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage
environment (biome)
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. EnvO (v1.53) terms listed under environmental biome can be found from the link: http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00000428
environment (feature)
Environmental feature level includes geographic environmental features. Examples include: harbor, cliff, or lake. EnvO (v1.53) terms listed under environmental feature can be found from the link: http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00002297
environment (material)
The environmental material level refers to the matter that was displaced by the sample, prior to 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 from the link: http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00010483
environmental package
MIGS/MIMS/MIENS 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
Environment
The category of information pertaining to environment.
estimated size
The 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.
Event
The category of information pertaining to an event (an action that occurs at a place and during a period of time).
Event 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. Recommended best practice is to use an encoding scheme, such as ISO 8601:2004(E).
Examples: "1963-03-08T14:07-0600" is 8 Mar 1963 2:07pm in the time zone six hours earlier than UTC, "2009-02-20T08:40Z" is 20 Feb 2009 8:40am UTC, "1809-02-12" is 12 Feb 1809, "1906-06" is Jun 1906, "1971" is just that year, "2007-03-01T13:00:00Z/2008-05-11T15:30:00Z" is the interval between 1 Mar 2007 1pm UTC and 11 May 2008 3:30pm UTC, "2007-11-13/15" is the interval between 13 Nov 2007 and 15 Nov 2007.
experimental factor
Experimental 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 (v132) terms, please see http://bioportal.bioontology.org/visualize/44641; for a browser of OBI (v1.0) terms please see http://bioportal.bioontology.org/visualize/40832
extrachromosomal elements
Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids)
finishing strategy
Was the genome project intended to produce a complete or draft genome, Coverage, the fold coverage of the sequencing expressed as 2x, 3x, 18x etc, and how many contigs were produced for the genome
health or disease status of specific host at time of collection
Health or disease status of specific host at time of collection. This field accepts PATO (v1.269) terms, for a browser please see http://bioportal.bioontology.org/visualize/44601
host specificity or range
The NCBI taxonomy identifier of the specific host if it is known
investigation type
Nucleic 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, miens-survey or miens-specimen
Investigation
The category of information pertaining to an investigation.
library construction method
Library construction method used for clone libraries
paired-end,single,vector
library reads sequenced
Total number of clones sequenced from the library
library screening strategy
Specific enrichment or screening methods applied before and/or after creating clone libraries
enriched, screened, normalized
library size
Total number of clones in the library prepared for the project
library vector
Cloning vector type(s) used in construction of libraries
Locality
The specific description of the place. Less specific geographic information can be provided in other geographic terms (higherGeography, continent, country, stateProvince, county, municipality, waterBody, island, islandGroup). This term may contain information modified from the original to correct perceived errors or standardize the description.
Example: "Bariloche, 25 km NNE via Ruta Nacional 40 (=Ruta 237)"
Material 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.
multiplex identifiers
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
nucleic acid amplification
Link to a literature reference, electronic resource or a standard operating procedure (SOP)
nucleic acid extraction
NucleicAcidSequenceSource
The category of information pertaining to nucleic acid sequence source.
number of replicons
Reports 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
Material Sample
A material entity that has the material sample role.
Occurrence
The category of information pertaining to evidence of an occurrence in nature, in a collection, or in a dataset (specimen, observation, etc.).
known pathogenicity
To what is the entity pathogenic.
human, animal, plant, fungi, bacteria
pcr conditions
Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
pcr primers
PCR 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 letters
ploidy
The 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 (v1.269) please refer to http://bioportal.bioontology.org/visualize/44601/?conceptid=PATO%3A0001374
allopolyploid, polyploid
propagation
This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice
reference for biomaterial
primary publication if isolated before genome publication; otherwise, primary genome report
relationship to oxygen
Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments
sample collection device or method
The method or device employed for collecting the sample
biopsy, niskin bottle, push core
sample material processing
Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v1.0) terms please see http://bioportal.bioontology.org/visualize/40832
filtering of seawater, storing samples in ethanol
amount or size of sample collected
Amount or size of sample (volume, mass or area) that was collected
Sampling Protocol
The name of, reference to, or description of the method or protocol used during an Event.
Examples: "UV light trap", "mist net", "bottom trawl", "ad hoc observation", "point count", "Penguins from space: faecal stains reveal the location of emperor penguin colonies, http://dx.doi.org/10.1111/j.1466-8238.2009.00467.x", "Takats et al. 2001. Guidelines for Nocturnal Owl Monitoring in North America. Beaverhill Bird Observatory and Bird Studies Canada, Edmonton, Alberta. 32 pp.", "http://www.bsc-eoc.org/download/Owl.pdf"
sequencing method
Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid
Sanger dideoxysequencing, pyrosequencing, polony
sequence quality check
Indicate 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
Sequencing
The category of information pertaining to sequencing.
relevant standard operating procedures
Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences
specific host
If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host). From this we can calculate any number of groupings of hosts (e.g. animal vs plant, all fish hosts, etc)
submitted to insdc
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 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
subspecific genetic lineage
This should provide further information about the genetic distinctness of this lineage by recording additional information i.e biovar, serovar, serotype, biovar, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information
target gene
Targeted gene or locus name for marker gene studies
16S rRNA, 18S rRNA, nif, amoA, rpo
target subfragment
Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA
V6, V9, ITS
trophic level
Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)
Verbatim 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.
{DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesLatLon/CoordinatesText or DataSets/DataSet/Units/Unit/Gathering/SiteCoordinateSets/SiteCoordinates/CoordinatesUTM/UTMText}
Verbatim Depth
The original description of the depth below the local surface.
Example: "100-200 m"
Verbatim Elevation
The original description of the elevation (altitude, usually above sea level) of the Location.