MIGS-ORG 07_12_10 http://gensc.org/gc_wiki/index.php/MIGS/MIMS Taken direct from the web-available version 07_12_10 on 2012-05-16 by Chris Taylor (chrisftaylor@gmail.com) investigation 1 submitted to insdc 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 boolean {boolean} 1 shall 2 investigation type 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-culture eukaryote, bacteria_archaea, plasmid, virus, organelle, metagenome,miens-survey or miens-culture [eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|miens-survey|miens-culture] 1 shall 3 project name project_name Name of the project within which the sequencing was organized {text} 1 shall 4 experimental factor 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 text or EFO and/or OBI {term|text} 1 should environment 6 geographic location (latitude and longitude) lat_lon The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system decimal degrees {float} {float} 1 shall 9 geographic location (country and/or sea,region) geo_loc_name The geographical origin of the sample as defined by the country or sea name followed by specific region name. Country or sea names should be chosen from the INSDC country list (http://insdc.org/country.html), or the GAZ ontology (v1.446) (http://bioportal.bioontology.org/visualize/40651) country or sea name (INSDC or GAZ):region(GAZ):specific location name Germany:Sylt:Hausstrand {term}:{term}:{text} 1 shall 10 collection date collection_date 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 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 date and time {timestamp} 1 shall 11 environment (biome) 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 EnvO {term} 1 shall 12 environment (feature) 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 EnvO {term} 1 shall 13 environment (material) 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 EnvO {term} 1 shall 14 environmental package env_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 CV [air|host-associated|human-associated|human-skin|human-oral|human-gut|human-vaginal|microbial mat/biofilm|misc environment|plant-associated|sediment|soil|wastewater/sludge|water] 1 shall nucleic acid sequence source 15 subspecific genetic lineage subspecf_gen_lin 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 genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype {text} 1 should 18 extrachromosomal elements extrachrom_elements Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids) number of extrachromosmal elements {integer} 1 should 19 estimated size 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. number of base pairs 300000 bp {integer} bp 1 should 20 reference for biomaterial ref_biomaterial primary publication if isolated before genome publication; otherwise, primary genome report PMID, DOI or URL {PMID|DOI|URL} 1 should 21 source material identifiers source_mat_id The name of the culture collection, holder of the voucher or an institution. Could enumerate a list of common resources, just as the American Type Culture Collection (ATCC), German Collection of Microorganisms and Cell Cultures (DSMZ) etc. Can select not deposited for cultures of microorganisms: identifiers for two culture collections; for specimens (e.g., organelles and Eukarya): voucher condition and location [CV] {PMID|DOI|URL|text} m should 31 isolation and growth condition isol_growth_condt 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 PMID,DOI or URL {PMID|DOI|URL} 1 shall 32 sample collection device or method samp_collect_device The method or deviced employed for collecting the sample type name biopsy, niskin bottle, push core {text} 1 should 33 sample material processing samp_mat_process 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 text or OBI filtering of seawater, storing samples in ethanol {text|term} 1 should 34 amount or size of sample collected samp_size Amount or size of sample (volume, mass or area) that was collected measurement value {float} {unit} 1 should sequencing 35 nucleic acid extraction nucl_acid_ext Link to a literature reference, electronic resource or a standard operating procedure (SOP) PMID, DOI or URL {PMID|DOI|URL} 1 should 36 nucleic acid amplification nucl_acid_amp Link to a literature reference, electronic resource or a standard operating procedure (SOP) reference to amplification method; clean-up method {PMID|DOI|URL} 1 should 46 adapters adapters Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters adapter A and B sequence {dna},{dna} 1 should 48 sequencing method seq_meth Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid Sanger dideoxysequencing, pyrosequencing, polony {text} 1 shall 51 assembly 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 assembly method; estimated error rate; method of calculation {text};{text};{text} 1 shall 52 assembly name assembly_name Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community name and version of assemby HuRef, JCVI_ISG_i3_1.0 {text} {text} 1 should 53 finishing strategy 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 status; coverage; number of contigs [complete|draft];{integer};{integer} 1 should 54 annotation source annot_source For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter annotation source description {text} 1 should 55 relevant electronic resources url URL {URL} m should 56 relevant standard operating procedures sop Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences reference to SOP {PMID|DOI|URL} m should