| Index
| Item name
| Definition
| Examples
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| 1.
| MIGS Investigation
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| 1.1.
| Investigation
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| 1.1.1.
| Project name or identifier
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| 1.2.
| Submit to trace archives and 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 (Short Read Archives), ENA (European Nucleotide Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, EMBL and DDBJ
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| 1.3.
| Investigation type
| Choose from: eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome, miens-survey, miens-culture
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| 2.
| MIGS Organism
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| 2.1.
| Subspecific genetic lineage
| Information about the genetic distinctness of this lineage; i.e., biovar, serovar, serotype, biovar, or any relevant genetic typing schemes like Group I plasmid. Can also be alternative taxonomic information. Ideally, use subspecific genetic lineage information from CABRI (www.cabri.org).
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| 2.2.
| Known pathogenicity
| Those organisms to which the entity is pathogenic.
| human, animal, plant, fungi, bacteria, etc.
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| 2.3.
| Observed biotic relationship
| Free-living or in a host (with named relationship to that host)
| pathogen, commensal, symbiont, opportunist
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| 2.4.
| Specific host
| Where the organism was isolated from a living or dead host, please provide a taxid and report whether it is a lab animal.
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| 2.5.
| Host specificity or range
| List of hosts potentially usable by the organism.
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| 2.6.
| Host disease status
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| Health or disease status of the specific host at the time of collection
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| 2.7.
| Trophic level
| The position held by the organism in it's food chain.
| 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
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| 2.8.
| Propagation
| This will involve different vocabularies for different taxa
| (virus) lytic, lysogenic, temperate, obligately lytic; (plasmid) incompatibility group; (eukaryote) asexual, sexual.
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| 2.9.
| Relationship to oxygen
| Whether the organism is aerobic or anaerobic
| aerobe, anaerobe
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| 2.10.
| Encoded traits
| Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage.
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| 3.
| Organismal nucleic acid component
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| 3.1.
| Ploidy
| Ploidy level of genome for given organism or cell type
| allopolyploid, haploid, tetraploid
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| 3.2.
| Number of replicons
| Chromosome count for eukaryotes (haploid), bacteria; segments for viruses
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| 3.3.
| Extrachromosomal elements
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| 3.4.
| Estimated size
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| 4.
| Environment
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| 4.1.
| Biome
| Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate.
| desert, taiga, deciduous woodland, coral reef
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| 4.2.
| Feature
| The relevant part of the local environment
| harbour, cliff, lake
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| 4.3.
| Matter
| That which was displaced by the sample, prior to the sampling event. Environmental matter terms are generally mass nouns.
| air, soil, water
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| 5.
| Geographic location
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| 5.1.
| Country
| The geographical origin of the sample by country. Ideally, country names should be chosen from the INSDC list (http://www.insdc.org/page.php?page=country), or the GAZ ontology (http://bioportal.bioontology.org/visualize/40651)
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| 5.2.
| Sample site morphology
| State whether a point, transect or area.
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| 5.3.
| Latitude and longitude
| Provide as appropriate, given sample site morphology. Values should be reported in decimal degrees under WGS84.
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| 5.4.
| Altitude or elevation
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| 5.5.
| Depth
| Provide where appropriate. Distance from surface for samples collected underground or underwater.
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| 6.
| Sampling event
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| 6.1.
| Date
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| 6.1.1.
| Date given as YYYY-MM-DD
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| 6.2.
| Time
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| 6.2.1.
| Time, given as HH:MM in 24-hour format
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| 6.2.2.
| State whether UTC or local (give time difference from UTC for local)
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| 6.3.
| Device or method
| The apparatus or protocol employed to collect the sample (short phrase only).
| biopsy, niskin bottle, push core
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| 7.
| Sample description
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| 7.1.
| Amount or size of sample collected
| The gross sample described as appropriate (mass, volume, number, etc.)
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| 8.
| Sample processing
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| 8.1.
| Description of process
| Processing applied to the sample during or after retrieving the sample its environment. Ideally, use an ontology such as OBI (see http://bioportal.bioontology.org/visualize/40832).
| filtering of sea water, storage in ethanol
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| 9.
| Sample provenance
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| 9.1.
| isolation and growth conditions
| Publication reference in the form of a PubMed ID (pmid), digital object identifier (DOI) or URL describing the isolation and growth conditions for the organism/material.
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| 9.2.
| Reference for biomaterial
| The primary publication, if isolated before genome publication; otherwise, the primary genome report.
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| 9.3.
| Source material identifiers
| The name of the culture collection, the holder of the voucher or an institution. Could enumerate a list of common resources, as done by the American Type Culture Collection (ATCC), German Collection of Microorganisms and Cell Cultures (DSMZ), etc. Can state 'not deposited'. Ideally use an ontology such as OBI where appropriate; for a browser of OBI terms please see http://bioportal.bioontology.org/visualize/40547
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| 10.
| Study design
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| 10.1.
| Design description
| Provide a short phrase at most. Ideally, use an ontology such as OBI (see http://bioportal.bioontology.org/visualize/40832).
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| 10.2.
| Factors
| Use only where appropriate for a given study design. A factor is a parameter that is deliberately varied to study its influence on the outcome, in contrast to confounders, or covariates such as temperature, pH or humidity. Ideally use an ontology such as OBI (see http://bioportal.bioontology.org/visualize/40832).
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| 11.
| Nucleic acid sequencing
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| 11.1.
| Nucleic acid preparation
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| 11.1.1.
| Extraction method
| Link to a literature reference, electronic resource or a standard operating procedure (SOP) through a DOI, PMID or URL.
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| 11.1.2.
| Amplification method
| Link to a literature reference, electronic resource or a standard operating procedure (SOP) through a DOI, PMID or URL.
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| 11.1.3.
| Cleanup
| Link to a literature reference, electronic resource or a standard operating procedure (SOP) through a DOI, PMID or URL.
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| 11.2.
| Library construction
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| 11.2.1.
| Library size
| The total number of clones in the library prepared for the project.
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| 11.2.2.
| Library reads sequenced
| The total number of clones sequenced.
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| 11.2.3.
| Library vector
| The cloning vector types used to construct the library.
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| 11.2.4.
| Library screening strategy
| Specific enrichment or screening methods applied before and/or after creating clone libraries.
| enriched, screened, normalized
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| 11.3.
| PCR amplification
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| 11.3.1.
| Target gene
| Targeted gene or locus name for marker gene studies.
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| 11.3.2.
| Target subfragment
| Name of subfragment of a gene or locus. It is important, for example, to identify special regions on marker genes like V6 on 16S rRNA.
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| 11.3.3.
| PCR primers
| PCR primers, barcodes and adaptors that were used to amplify the sequence of the targeted gene or locus. If multiple forward or reverse primers are present in a single PCR reaction, describe all the primers used. Primer sequence should be reported in uppercase, except barcode or adaptor sequence, which should be in lowercase.
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| 11.3.4.
| Multiplex identifiers
| Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag samples in a sequencing run. Their sequence should be reported in uppercase.
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| 11.3.5.
| PCR conditions
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| 11.3.5.1.
| Denaturation
| Provide time and temperature for this step.
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| 11.3.5.2.
| Annealing
| Provide time and temperature for this step.
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| 11.3.5.3.
| Elongation
| Provide time and temperature for this step.
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| 11.3.5.4.
| Final elongation
| Provide time and temperature for this step.
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| 11.4.
| Sequencing
|
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| 11.4.1.
| Sequencing method
| The type of sequencing used.
| dideoxysequencing, pyrosequencing, polony
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| 11.4.2.
| Sequence quality check
| Indicate if the sequence has been called automatically or has undergone a manual editing procedure (e.g., by inspecting the raw data or chromatograms). Applies only to sequences that are not submitted to SRA,ENA or DRA.
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| 12.
| Nucleic acid sequencing data processing
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| 12.1.
| Chimera check
| State whether the data have been checked for chimeric sequence, and how.
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| 12.2.
| Assembly
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| 12.2.1.
| Assembly method
| How was the assembly done (e.g. with a text based assembler like phrap or a flowgram assembler).
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| 12.2.2.
| Estimated error rate
| The estimated error rate associated with the finished sequences (e.g., error rate of 1 in 1000 bp).
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| 12.2.3.
| Method of calculation of error rate
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| 12.3.
| Finishing strategy
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| 12.3.1.
| Status
| Was the genome project intended to produce a complete or draft genome.
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| 12.3.2.
| Coverage
| The fold coverage of the sequencing expressed as 2x, 3x, 18x etc.
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| 12.3.3.
| Number of contigs
| Number of contigs produced for the genome.
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| 12.4.
| Additional information
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| 12.4.1.
| Relevant Standard Operating Procedures (SOPs)
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| 12.4.2.
| Relevant electronic resources
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