MIGS-MIMS 07_12_10 http://gensc.org/gc_wiki/index.php/MIGS/MIMS Taken direct from the web-available version 07_12_10 on 2011-04-18 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 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 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, miens-culture [eukaryote|bacteria_archaea|plasmid|virus|organelle|metagenome|miens-survey|miens-culture] 1 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 3 project name project_name Name of the project within which the sequencing was organized {text} 1 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 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 1 eu should eukaryote ba should bacteria pl should plasmid vi should virus org should organelle me conditional metagenome http://bioportal.bioontology.org/visualize/44641 Experimental Factor Ontology http://bioportal.bioontology.org/visualize/40832 Ontology for Biomedical Investigations 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 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 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 Germany:Sylt:Hausstrand {term}:{term}:{text} 1 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome http://insdc.org/country.html INSDC country list http://bioportal.bioontology.org/visualize/40651 GAZ 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 2008-01-23T19:23:10+00:00, 2008-01-23T19:23:10, 2008-01-23, 2008-01, 2008 {timestamp} 1 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 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 desert, taiga, deciduous woodland, coral reef {term} 1 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00000428 EnvO biome 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 harbor, cliff, lake {term} 1 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00002297 EnvO environmental feature 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 air, soil, water {term} eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00010483 EnvO environmental matter migs/mims/miens extension 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 [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 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 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 biotype, biovar, ecotype, serotype, serovar, group I plasmid {text} 1 eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me na metagenome 16 ploidy 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 polyploid, allopolyploid, haploid, diploid, triploid, tetraploid {term} 1 eu shall eukaryote ba na bacteria pl na plasmid vi na virus org na organelle me na metagenome http://bioportal.bioontology.org/visualize/44601/?conceptid=PATO%3A0001374 PATO PATO:001374 ploidy 17 number of replicons num_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 for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments {integer} 1 eu shall eukaryote ba shall bacteria pl na plasmid vi conditional virus org na organelle me na metagenome 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 eu should eukaryote ba conditional bacteria pl na plasmid vi na virus org conditional organelle me na metagenome 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 bp {integer} bp 1 eu shall eukaryote ba should bacteria pl should plasmid vi should virus org should organelle me na metagenome 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 eu should eukaryote ba shall bacteria pl should plasmid vi should virus org should organelle me should metagenome 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] American Type Culture Collection (ATCC), German Collection of Microorganisms and Cell Cultures (DSMZ) {PMID|DOI|URL|text} * eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome 22 known pathogenicity pathogenicity To what is the entity pathogenic. CV human, animal, plant, fungi, bacteria {term} 1 eu conditional eukaryote ba conditional bacteria pl na plasmid vi conditional virus org na organelle me na metagenome 23 observed biotic relationship biotic_relationship Is it free-living or in a host and if the latter what type of relationship is observed enumeration free living, parasite, commensal, symbiont [free living|parasite|commensal|symbiont] 1 eu should eukaryote ba conditional bacteria pl na plasmid vi should virus org na organelle me na metagenome 24 specific host 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) host taxid, unknown, environmental 1 eu should eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org na organelle me na metagenome 25 host specificity or range host_spec_range The NCBI taxonomy identifier of the specific host if it is known NCBI taxid {integer} 1 eu should eukaryote ba should bacteria pl should plasmid vi conditional virus org na organelle me na metagenome 26 health or disease status of specific host at time of collection health_disease_stat 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 PATO {term} 1 eu should eukaryote ba conditional bacteria pl na plasmid vi conditional virus org na organelle me na metagenome http://bioportal.bioontology.org/ontologies/44601 PATO 27 trophic level trophic_level Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph) enumeration 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 [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] 1 eu conditional eukaryote ba conditional bacteria pl na plasmid vi na virus org na organelle me na metagenome 28 propagation 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 for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual) [CV] {term} 1 eu shall eukaryote ba na bacteria pl shall plasmid vi shall virus org na organelle me na metagenome 29 encoded traits encoded_traits Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage for plasmid: antibiotic resistance; for phage: converting genes {text} 1 eu na eukaryote ba should bacteria pl conditional plasmid vi conditional virus org na organelle me na metagenome 30 relationship to oxygen rel_to_oxygen Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments enumeration aerobe, anaerobe, facultative, microaerophilic, microanaerobe, obligate aerobe, obligate anaerobe [aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe] 1 eu na eukaryote ba conditional bacteria pl na plasmid vi na virus org na organelle me should metagenome 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 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me na metagenome 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 eu should eukaryote ba should bacteria pl should plasmid vi should virus org should organelle me conditional metagenome 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 eu should eukaryote ba should bacteria pl should plasmid vi should virus org should organelle me conditional metagenome http://bioportal.bioontology.org/visualize/40832 OBI 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 eu should eukaryote ba should bacteria pl should plasmid vi should virus org should organelle me conditional metagenome 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 eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome 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 eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome 37 library size lib_size Total number of clones in the library prepared for the project number of clones {integer} 1 eu na eukaryote ba na bacteria pl na plasmid vi na virus org na organelle me conditional metagenome 38 library reads sequenced lib_reads_seqd Total number of clones sequenced from the library number of reads sequenced {integer} 1 eu na eukaryote ba na bacteria pl na plasmid vi na virus org na organelle me conditional metagenome 39 library construction method lib_const_meth Library construction method used for clone libraries library construction method paired-end,single,vector {text} 1 eu na eukaryote ba na bacteria pl na plasmid vi na virus org na organelle me conditional metagenome 40 library vector lib_vector Cloning vector type(s) used in construction of libraries vector {text} 1 eu na eukaryote ba na bacteria pl na plasmid vi na virus org na organelle me conditional metagenome 41 library screening strategy lib_screen Specific enrichment or screening methods applied before and/or after creating clone libraries screening strategy name enriched, screened, normalized {text} 1 eu na eukaryote ba na bacteria pl na plasmid vi na virus org na organelle me conditional metagenome 45 multiplex identifiers mid 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 multiplex identifier sequence {dna} 1 eu na eukaryote ba na bacteria pl na plasmid vi na virus org na organelle me conditional metagenome 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 eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome 48 sequencing method seq_meth Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid Sanger dideoxysequencing, pyrosequencing, polony {text} 1 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 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 eu shall eukaryote ba shall bacteria pl shall plasmid vi shall virus org shall organelle me shall metagenome 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 eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome 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 eu shall eukaryote ba shall bacteria pl should plasmid vi should virus org should organelle me should metagenome 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 eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome 55 relevant electronic resources url URL {URL} * eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome 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} * eu conditional eukaryote ba conditional bacteria pl conditional plasmid vi conditional virus org conditional organelle me conditional metagenome