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terms.json
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terms.json
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[
{
"mixsId":"MIXS:0000092",
"structuredCommentName":"project_name",
"label":"project name",
"definition":"Name of the project within which the sequencing was organized.",
"expectedValue":"text",
"valueSyntax":"{text}",
"example":"Forest soil metagenome",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000092",
},
{
"mixsId":"MIXS:0000008",
"structuredCommentName":"experimental_factor",
"label":"experimental factor",
"definition":"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 (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.",
"expectedValue":"text or EFO and/or OBI",
"valueSyntax":"{termLabel} {[termID]}|{text}",
"example":"time series design [EFO:0001779]",
"preferredUnit":"",
"occurence":"m",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000008",
},
{
"mixsId":"MIXS:0000009",
"structuredCommentName":"lat_lon",
"label":"geographic location (latitude and longitude)",
"definition":"The geographical origin of the sample as defined by latitude and longitude. The values should be reported in decimal degrees and in WGS84 system.",
"expectedValue":"decimal degrees, limit to 8 decimal points",
"valueSyntax":"{float} {float}",
"example":"50.586825 6.408977",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000009",
},
{
"mixsId":"MIXS:0000010",
"structuredCommentName":"geo_loc_name",
"label":"geographic location (country and/or sea,region)",
"definition":"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 (http://purl.bioontology.org/ontology/GAZ).",
"expectedValue":"country or sea name (INSDC or GAZ): region(GAZ), specific location name",
"valueSyntax":"{term}: {term}, {text}",
"example":"USA: Maryland, Bethesda",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000010",
},
{
"mixsId":"MIXS:0000011",
"structuredCommentName":"collection_date",
"label":"collection date",
"definition":"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.",
"expectedValue":"date and time",
"valueSyntax":"{timestamp}",
"example":"2018-05-11T10:00:00+01:00; 2018-05-11",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000011",
},
{
"mixsId":"MIXS:0000012",
"structuredCommentName":"env_broad_scale",
"label":"broad-scale environmental context",
"definition":"In 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.",
"expectedValue":"Add terms that identify the major environment type(s) where your sample was collected. Recommend subclasses of biome [ENVO:00000428]. Multiple terms can be separated by one or more pipes e.g.: mangrove biome [ENVO:01000181]|estuarine biome [ENVO:01000020]",
"valueSyntax":"{termLabel} {[termID]}",
"example":"forest biome [ENVO:01000174]",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000012",
},
{
"mixsId":"MIXS:0000013",
"structuredCommentName":"env_local_scale",
"label":"local environmental context",
"definition":"In 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.",
"expectedValue":"Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]",
"valueSyntax":"{termLabel} {[termID]}",
"example":"litter layer [ENVO:01000338]",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000013",
},
{
"mixsId":"MIXS:0000014",
"structuredCommentName":"env_medium",
"label":"environmental medium",
" ""definition"":""Report the environmental material(s) immediately surrounding the sample or specimen at the time of sampling. We recommend using subclasses of 'environmental material' (http://purl.obolibrary.org/obo/ENVO_00010483). EnvO documentation about how to use the field: https://github.com/EnvironmentOntology/envo/wiki/Using-ENVO-with-MIxS . Terms from other OBO ontologies are permissible as long as they reference mass/volume nouns (e.g. air, water, blood) and not discrete, countable entities (e.g. a tree, a leaf, a table top). If the sample collected is a symbiont and the sequenced entity is a symbiont of that sampled symbiont, this field describes the tissue or excretion of the symbiotic host organism, not the top-level host.
"","
"expectedValue":"The material displaced by the entity at time of sampling. Recommend subclasses of environmental material [ENVO:00010483].",
"valueSyntax":"{termLabel} {[termID]}",
"example":"intestine environment [ENVO:2100002]",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000014",
},
{
"mixsId":"MIXS:0000020",
"structuredCommentName":"subspecf_gen_lin",
"label":"subspecific genetic lineage",
"definition":"Information about the genetic distinctness of the sequenced organism below the subspecies level, e.g., serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. Subspecies should not be recorded in this term, but in the NCBI taxonomy. Supply both the lineage name and the lineage rank separated by a colon, e.g., biovar:abc123.",
"expectedValue":"genetic lineage below lowest rank of NCBI taxonomy, which is subspecies, e.g. serovar, biotype, ecotype, variety, cultivar",
"valueSyntax":"{rank name}:{text}",
"example":"serovar:Newport",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000020",
},
{
"mixsId":"MIXS:0000021",
"structuredCommentName":"ploidy",
"label":"ploidy",
"definition":"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 (v 2018-03-27) please refer to http://purl.bioontology.org/ontology/PATO",
"expectedValue":"PATO",
"valueSyntax":"{termLabel} {[termID]}",
"example":"allopolyploidy [PATO:0001379]",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000021",
},
{
"mixsId":"MIXS:0000022",
"structuredCommentName":"num_replicons",
"label":"number of replicons",
"definition":"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",
"expectedValue":"for eukaryotes and bacteria: chromosomes (haploid count); for viruses: segments",
"valueSyntax":"{integer}",
"example":"2",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000022",
},
{
"mixsId":"MIXS:0000023",
"structuredCommentName":"extrachrom_elements",
"label":"extrachromosomal elements",
"definition":"Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids)",
"expectedValue":"number of extrachromosmal elements",
"valueSyntax":"{integer}",
"example":"5",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000023",
},
{
"mixsId":"MIXS:0000024",
"structuredCommentName":"estimated_size",
"label":"estimated size",
"definition":"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.",
"expectedValue":"number of base pairs",
"valueSyntax":"{integer} bp",
"example":"300000 bp",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000024",
},
{
"mixsId":"MIXS:0000025",
"structuredCommentName":"ref_biomaterial",
"label":"reference for biomaterial",
"definition":"Primary publication if isolated before genome publication; otherwise, primary genome report.",
"expectedValue":"PMID, DOI or URL",
"valueSyntax":"{PMID}|{DOI}|{URL}",
"example":"doi:10.1016/j.syapm.2018.01.009",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000025",
},
{
"mixsId":"MIXS:0000026",
"structuredCommentName":"source_mat_id",
"label":"source material identifiers",
"definition":"A 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).",
"expectedValue":"for cultures of microorganisms: identifiers for two culture collections; for other material a unique arbitrary identifer",
"valueSyntax":"{text}",
"example":"MPI012345",
"preferredUnit":"",
"occurence":"m",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000026",
},
{
"mixsId":"MIXS:0000027",
"structuredCommentName":"pathogenicity",
"label":"known pathogenicity",
"definition":"To what is the entity pathogenic",
"expectedValue":"CV",
"valueSyntax":"{term}",
"example":"human, animal, plant, fungi, bacteria",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000027",
},
{
"mixsId":"MIXS:0000028",
"structuredCommentName":"biotic_relationship",
"label":"observed biotic relationship",
"definition":"Description 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",
"expectedValue":"enumeration",
"valueSyntax":"[free living|parasite|commensal|symbiont]",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000028",
},
{
"mixsId":"MIXS:0000029",
"structuredCommentName":"specific_host",
"label":"host scientific name",
"definition":"Report the host's taxonomic name and/or NCBI taxonomy ID.",
"expectedValue":"host scientific name, taxonomy ID",
"valueSyntax":"{text}|{NCBI taxid}",
"example":"Homo sapiens and/or 9606",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000029",
},
{
"mixsId":"MIXS:0000030",
"structuredCommentName":"host_spec_range",
"label":"host specificity or range",
"definition":"The range and diversity of host species that an organism is capable of infecting, defined by NCBI taxonomy identifier.",
"expectedValue":"NCBI taxid",
"valueSyntax":"{integer}",
"example":"",
"preferredUnit":"",
"occurence":"m",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000030",
},
{
"mixsId":"MIXS:0000031",
"structuredCommentName":"host_disease_stat",
"label":"host disease status",
"definition":"List of diseases with which the host has been diagnosed; can include multiple diagnoses. The value of the field depends on host; for humans the terms should be chosen from the DO (Human Disease Ontology) at https://www.disease-ontology.org, non-human host diseases are free text",
"expectedValue":"disease name or Disease Ontology term",
"valueSyntax":"{termLabel} {[termID]}|{text}",
"example":"rabies [DOID:11260]",
"preferredUnit":"",
"occurence":"m",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000031",
},
{
"mixsId":"MIXS:0000032",
"structuredCommentName":"trophic_level",
"label":"trophic level",
"definition":"Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)",
"expectedValue":"enumeration",
"valueSyntax":"[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]",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000032",
},
{
"mixsId":"MIXS:0000033",
"structuredCommentName":"propagation",
"label":"propagation",
"definition":"The type of reproduction from the parent stock. Values for this field is specific to different taxa. For phage or virus: lytic/lysogenic/temperate/obligately lytic. For plasmids: incompatibility group. For eukaryotes: sexual/asexual. ",
"expectedValue":"for virus: lytic, lysogenic, temperate, obligately lytic; for plasmid: incompatibility group; for eukaryote: asexual, sexual; other more specific values (e.g., incompatibility group) are allowed",
"valueSyntax":"{text}",
"example":"lytic",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000033",
},
{
"mixsId":"MIXS:0000034",
"structuredCommentName":"encoded_traits",
"label":"encoded traits",
"definition":"Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage",
"expectedValue":"for plasmid: antibiotic resistance; for phage: converting genes",
"valueSyntax":"{text}",
"example":"beta-lactamase class A",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000034",
},
{
"mixsId":"MIXS:0000015",
"structuredCommentName":"rel_to_oxygen",
"label":"relationship to oxygen",
"definition":"Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments",
"expectedValue":"enumeration",
"valueSyntax":"[aerobe|anaerobe|facultative|microaerophilic|microanaerobe|obligate aerobe|obligate anaerobe]",
"example":"aerobe",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000015",
},
{
"mixsId":"MIXS:0000003",
"structuredCommentName":"isol_growth_condt",
"label":"isolation and growth condition",
"definition":"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",
"expectedValue":"PMID,DOI or URL",
"valueSyntax":"{PMID|DOI|URL}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000003",
},
{
"mixsId":"MIXS:0000002",
"structuredCommentName":"samp_collect_device",
"label":"sample collection device",
"definition":"The device used to collect an environmental sample. This field accepts terms listed under environmental sampling device (http://purl.obolibrary.org/obo/ENVO). This field also accepts terms listed under specimen collection device (http://purl.obolibrary.org/obo/GENEPIO_0002094).",
"expectedValue":"device name",
"valueSyntax":"{termLabel} {[termID]}|{text}",
"example":"swab, biopsy, niskin bottle, push core, drag swab [GENEPIO:0002713]",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000002",
},
{
"mixsId":"MIXS:0000016",
"structuredCommentName":"samp_mat_process",
"label":"sample material processing",
"definition":"A brief description of any processing applied to the sample during or after retrieving the sample from environment, or a link to the relevant protocol(s) performed.",
"expectedValue":"text or OBI",
"valueSyntax":"{text|term}",
"example":"filtering of seawater, storing samples in ethanol",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000016",
},
{
"mixsId":"MIXS:0000017",
"structuredCommentName":"size_frac",
"label":"size fraction selected",
"definition":"Filtering pore size used in sample preparation",
"expectedValue":"filter size value range",
"valueSyntax":"{float}-{float} {unit}",
"example":"0-0.22 micrometer",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000017",
},
{
"mixsId":"MIXS:0000001",
"structuredCommentName":"samp_size",
"label":"amount or size of sample collected",
"definition":"The total amount or size (volume (ml), mass (g) or area (m2) ) of sample collected.",
"expectedValue":"measurement value",
"valueSyntax":"{float} {unit}",
"example":"5 liters",
"preferredUnit":"liter, gram, cm^2",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000001",
},
{
"mixsId":"MIXS:0000035",
"structuredCommentName":"source_uvig",
"label":"source of UViGs",
"definition":"Type of dataset from which the UViG was obtained",
"expectedValue":"enumeration",
"valueSyntax":"[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]",
"example":"viral fraction metagenome (virome)",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000035",
},
{
"mixsId":"MIXS:0000036",
"structuredCommentName":"virus_enrich_appr",
"label":"virus enrichment approach",
"definition":"List of approaches used to enrich the sample for viruses, if any",
"expectedValue":"enumeration",
"valueSyntax":"[filtration|ultrafiltration|centrifugation|ultracentrifugation|PEG Precipitation|FeCl Precipitation|CsCl density gradient|DNAse|RNAse|targeted sequence capture|other|none]",
"example":"filtration + FeCl Precipitation + ultracentrifugation + DNAse",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000036",
},
{
"mixsId":"MIXS:0000037",
"structuredCommentName":"nucl_acid_ext",
"label":"nucleic acid extraction",
"definition":"A 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.",
"expectedValue":"PMID, DOI or URL",
"valueSyntax":"{PMID}|{DOI}|{URL}",
"example":"https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000037",
},
{
"mixsId":"MIXS:0000038",
"structuredCommentName":"nucl_acid_amp",
"label":"nucleic acid amplification",
"definition":"A 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",
"expectedValue":"reference to amplification method; clean-up method",
"valueSyntax":"{PMID|DOI|URL}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000038",
},
{
"mixsId":"MIXS:0000039",
"structuredCommentName":"lib_size",
"label":"library size",
"definition":"Total number of clones in the library prepared for the project",
"expectedValue":"number of clones",
"valueSyntax":"{integer}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000039",
},
{
"mixsId":"MIXS:0000040",
"structuredCommentName":"lib_reads_seqd",
"label":"library reads sequenced",
"definition":"Total number of clones sequenced from the library",
"expectedValue":"number of reads sequenced",
"valueSyntax":"{integer}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000040",
},
{
"mixsId":"MIXS:0000041",
"structuredCommentName":"lib_layout",
"label":"library layout",
"definition":"Specify whether to expect single, paired, or other configuration of reads",
"expectedValue":"enumeration",
"valueSyntax":"[paired|single|vector|other]",
"example":"paired",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000041",
},
{
"mixsId":"MIXS:0000042",
"structuredCommentName":"lib_vector",
"label":"library vector",
"definition":"Cloning vector type(s) used in construction of libraries",
"expectedValue":"vector",
"valueSyntax":"{text}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000042",
},
{
"mixsId":"MIXS:0000043",
"structuredCommentName":"lib_screen",
"label":"library screening strategy",
"definition":"Specific enrichment or screening methods applied before and/or after creating libraries",
"expectedValue":"screening strategy name",
"valueSyntax":"{text}",
"example":"enriched, screened, normalized",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000043",
},
{
"mixsId":"MIXS:0000044",
"structuredCommentName":"target_gene",
"label":"target gene",
"definition":"Targeted gene or locus name for marker gene studies",
"expectedValue":"gene name",
"valueSyntax":"{text}",
"example":"16S rRNA, 18S rRNA, nif, amoA, rpo",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000044",
},
{
"mixsId":"MIXS:0000045",
"structuredCommentName":"target_subfragment",
"label":"target subfragment",
"definition":"Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA",
"expectedValue":"gene fragment name",
"valueSyntax":"{text}",
"example":"V6, V9, ITS",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000045",
},
{
"mixsId":"MIXS:0000046",
"structuredCommentName":"pcr_primers",
"label":"pcr primers",
"definition":"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",
"expectedValue":"FWD:{dna} REV:{dna}",
"valueSyntax":"0",
"example":"FWD: forward primer sequence REV:reverse primer sequence",
"preferredUnit":"",
"occurence":"m",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000046",
},
{
"mixsId":"MIXS:0000047",
"structuredCommentName":"mid",
"label":"multiplex identifiers",
"definition":"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",
"expectedValue":"multiplex identifier sequence",
"valueSyntax":"{dna}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000047",
},
{
"mixsId":"MIXS:0000048",
"structuredCommentName":"adapters",
"label":"adapters",
"definition":"Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters",
"expectedValue":"adapter A and B sequence",
"valueSyntax":"{dna},{dna}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000048",
},
{
"mixsId":"MIXS:0000049",
"structuredCommentName":"pcr_cond",
"label":"pcr conditions",
"definition":"Description of reaction conditions and components of PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'",
"expectedValue":"initial denaturation:degrees_minutes; annealing:degrees_minutes; elongation: degrees_minutes; final elongation:degrees_minutes; total cycles",
"valueSyntax":"initial denaturation:degrees_minutes; annealing:degrees_minutes; elongation: degrees_minutes; final elongation:degrees_minutes; total cycles",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000049",
},
{
"mixsId":"MIXS:0000050",
"structuredCommentName":"seq_meth",
"label":"sequencing method",
"definition":"Sequencing machine used. Where possible the term should be taken from the OBI list of DNA sequencers (http://purl.obolibrary.org/obo/OBI_0400103).",
"expectedValue":"Text or OBI",
"valueSyntax":"{termLabel} {[termID]}|{text}",
"example":"454 Genome Sequencer FLX [OBI:0000702]",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000050",
},
{
"mixsId":"MIXS:0000051",
"structuredCommentName":"seq_quality_check",
"label":"sequence quality check",
"definition":"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",
"expectedValue":"none or manually edited",
"valueSyntax":"[none|manually edited]",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000051",
},
{
"mixsId":"MIXS:0000052",
"structuredCommentName":"chimera_check",
"label":"chimera check",
"definition":"Tool(s) used for chimera checking, including version number and parameters, to discover and remove chimeric sequences. A chimeric sequence is comprised of two or more phylogenetically distinct parent sequences.",
"expectedValue":"name and version of software",
"valueSyntax":"{text} {text}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000052",
},
{
"mixsId":"MIXS:0000053",
"structuredCommentName":"tax_ident",
"label":"taxonomic identity marker",
"definition":"The phylogenetic marker(s) used to assign an organism name to the SAG or MAG",
"expectedValue":"enumeration",
"valueSyntax":"[16S rRNA gene|multi-marker approach|other]",
"example":"other: rpoB gene",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000053",
},
{
"mixsId":"MIXS:0000056",
"structuredCommentName":"assembly_software",
"label":"assembly software",
"definition":"The 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",
"expectedValue":"enumeration",
"valueSyntax":"[Finished genome|High-quality draft genome|Medium-quality draft genome|Low-quality draft genome|Genome fragment(s)]",
"example":"High-quality draft genome",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000056",
},
{
"mixsId":"MIXS:0000057",
"structuredCommentName":"assembly_name",
"label":"assembly name",
"definition":"Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community",
"expectedValue":"name and version of assemby",
"valueSyntax":"{text} {text}",
"example":"HuRef, JCVI_ISG_i3_1.0",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000057",
},
{
"mixsId":"MIXS:0000058",
"structuredCommentName":"assembly_quality",
"label":"assembly quality",
"definition":"Tool(s) used for assembly, including version number and parameters",
"expectedValue":"name and version of software, parameters used",
"valueSyntax":"{software};{version};{parameters}",
"example":"metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000058",
},
{
"mixsId":"MIXS:0000059",
"structuredCommentName":"annot",
"label":"annotation",
"definition":"Tool used for annotation, or for cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter",
"expectedValue":"annotation source description",
"valueSyntax":"{text}",
"example":"",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000059",
},
{
"mixsId":"MIXS:0000060",
"structuredCommentName":"number_contig",
"label":"number of contigs",
"definition":"Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG",
"expectedValue":"value",
"valueSyntax":"{integer}",
"example":"40",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000060",
},
{
"mixsId":"MIXS:0000061",
"structuredCommentName":"feat_pred",
"label":"feature prediction",
"definition":"Method used to predict UViGs features such as ORFs, integration site, etc.",
"expectedValue":"names and versions of software(s), parameters used",
"valueSyntax":"{software};{version};{parameters}",
"example":"Prodigal;2.6.3;default parameters",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000061",
},
{
"mixsId":"MIXS:0000062",
"structuredCommentName":"ref_db",
"label":"reference database(s)",
"definition":"List of database(s) used for ORF annotation, along with version number and reference to website or publication",
"expectedValue":"names, versions, and references of databases",
"valueSyntax":"{database};{version};{reference}",
"example":"pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000062",
},
{
"mixsId":"MIXS:0000063",
"structuredCommentName":"sim_search_meth",
"label":"similarity search method",
"definition":"Tool used to compare ORFs with database, along with version and cutoffs used",
"expectedValue":"names and versions of software(s), parameters used",
"valueSyntax":"{software};{version};{parameters}",
"example":"HMMER3;3.1b2;hmmsearch, cutoff of 50 on score",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000063",
},
{
"mixsId":"MIXS:0000064",
"structuredCommentName":"tax_class",
"label":"taxonomic classification",
"definition":"Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes",
"expectedValue":"classification method, database name, and other parameters",
"valueSyntax":"{text}",
"example":"vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000064",
},
{
"mixsId":"MIXS:0000065",
"structuredCommentName":"16s_recover",
"label":"16S recovered",
"definition":"Can a 16S gene be recovered from the submitted SAG or MAG?",
"expectedValue":"boolean",
"valueSyntax":"{boolean}",
"example":"yes",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000065",
},
{
"mixsId":"MIXS:0000066",
"structuredCommentName":"16s_recover_software",
"label":"16S recovery software",
"definition":"Tools used for 16S rRNA gene extraction",
"expectedValue":"names and versions of software(s), parameters used",
"valueSyntax":"{software};{version};{parameters}",
"example":"rambl;v2;default parameters",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000066",
},
{
"mixsId":"MIXS:0000067",
"structuredCommentName":"trnas",
"label":"number of standard tRNAs extracted",
"definition":"The total number of tRNAs identified from the SAG or MAG",
"expectedValue":"value from 0-21",
"valueSyntax":"{integer}",
"example":"18",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000067",
},
{
"mixsId":"MIXS:0000068",
"structuredCommentName":"trna_ext_software",
"label":"tRNA extraction software",
"definition":"Tools used for tRNA identification",
"expectedValue":"names and versions of software(s), parameters used",
"valueSyntax":"{software};{version};{parameters}",
"example":"infernal;v2;default parameters",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000068",
},
{
"mixsId":"MIXS:0000069",
"structuredCommentName":"compl_score",
"label":"completeness score",
"definition":"Completeness 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",
"expectedValue":"quality;percent completeness",
"valueSyntax":"[high|med|low];{percentage}",
"example":"med;60%",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000069",
},
{
"mixsId":"MIXS:0000070",
"structuredCommentName":"compl_software",
"label":"completeness software",
"definition":"Tools used for completion estimate, i.e. checkm, anvi'o, busco",
"expectedValue":"names and versions of software(s) used",
"valueSyntax":"{software};{version}",
"example":"checkm",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000070",
},
{
"mixsId":"MIXS:0000071",
"structuredCommentName":"compl_appr",
"label":"completeness approach",
"definition":"The approach used to determine the completeness of a given genomic assembly, 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",
"expectedValue":"text",
"valueSyntax":"[marker gene|reference based|other]",
"example":"other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000071",
},
{
"mixsId":"MIXS:0000072",
"structuredCommentName":"contam_score",
"label":"contamination score",
"definition":"The 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",
"expectedValue":"value",
"valueSyntax":"{float} percentage",
"example":"0.01",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000072",
},
{
"mixsId":"MIXS:0000005",
"structuredCommentName":"contam_screen_input",
"label":"contamination screening input",
"definition":"The type of sequence data used as input",
"expectedValue":"enumeration",
"valueSyntax":"[reads| contigs]",
"example":"contigs",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000005",
},
{
"mixsId":"MIXS:0000073",
"structuredCommentName":"contam_screen_param",
"label":"contamination screening parameters",
"definition":"Specific 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",
"expectedValue":"enumeration;value or name",
"valueSyntax":"[ref db|kmer|coverage|combination];{text|integer}",
"example":"kmer",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000073",
},
{
"mixsId":"MIXS:0000074",
"structuredCommentName":"decontam_software",
"label":"decontamination software",
"definition":"Tool(s) used in contamination screening",
"expectedValue":"enumeration",
"valueSyntax":"[checkm/refinem|anvi'o|prodege|bbtools:decontaminate.sh|acdc|combination]",
"example":"anvi'o",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000074",
},
{
"mixsId":"MIXS:0000075",
"structuredCommentName":"sort_tech",
"label":"sorting technology",
"definition":"Method used to sort/isolate cells or particles of interest",
"expectedValue":"enumeration",
"valueSyntax":"[flow cytometric cell sorting|microfluidics|lazer-tweezing|optical manipulation|micromanipulation|other]",
"example":"optical manipulation",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000075",
},
{
"mixsId":"MIXS:0000076",
"structuredCommentName":"single_cell_lysis_appr",
"label":"single cell or viral particle lysis approach",
"definition":"Method used to free DNA from interior of the cell(s) or particle(s)",
"expectedValue":"enumeration",
"valueSyntax":"[chemical|enzymatic|physical|combination]",
"example":"enzymatic",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000076",
},
{
"mixsId":"MIXS:0000054",
"structuredCommentName":"single_cell_lysis_prot",
"label":"single cell or viral particle lysis kit protocol",
"definition":"Name of the kit or standard protocol used for cell(s) or particle(s) lysis",
"expectedValue":"kit, protocol name",
"valueSyntax":"{text}",
"example":"ambion single cell lysis kit",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000054",
},
{
"mixsId":"MIXS:0000055",
"structuredCommentName":"wga_amp_appr",
"label":"WGA amplification approach",
"definition":"Method used to amplify genomic DNA in preparation for sequencing",
"expectedValue":"enumeration",
"valueSyntax":"[pcr based|mda based]",
"example":"mda based",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000055",
},
{
"mixsId":"MIXS:0000006",
"structuredCommentName":"wga_amp_kit",
"label":"WGA amplification kit",
"definition":"Kit used to amplify genomic DNA in preparation for sequencing",
"expectedValue":"kit name",
"valueSyntax":"{text}",
"example":"qiagen repli-g",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000006",
},
{
"mixsId":"MIXS:0000077",
"structuredCommentName":"bin_param",
"label":"binning parameters",
"definition":"The parameters that have been applied during the extraction of genomes from metagenomic datasets",
"expectedValue":"enumeration",
"valueSyntax":"[homology search|kmer|coverage|codon usage|combination]",
"example":"coverage and kmer",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000077",
},
{
"mixsId":"MIXS:0000078",
"structuredCommentName":"bin_software",
"label":"binning software",
"definition":"Tool(s) used for the extraction of genomes from metagenomic datasets, where possible include a product ID (PID) of the tool(s) used.",
"expectedValue":"names and versions of software(s) used",
"valueSyntax":"{software};{version}{PID}",
"example":"MetaCluster-TA (RRID:SCR_004599), MaxBin (biotools:maxbin)",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000078",
},
{
"mixsId":"MIXS:0000079",
"structuredCommentName":"reassembly_bin",
"label":"reassembly post binning",
"definition":"Has an assembly been performed on a genome bin extracted from a metagenomic assembly?",
"expectedValue":"boolean",
"valueSyntax":"{boolean}",
"example":"no",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000079",
},
{
"mixsId":"MIXS:0000080",
"structuredCommentName":"mag_cov_software",
"label":"MAG coverage software",
"definition":"Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets",
"expectedValue":"enumeration",
"valueSyntax":"[bwa|bbmap|bowtie|other]",
"example":"bbmap",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000080",
},
{
"mixsId":"MIXS:0000081",
"structuredCommentName":"vir_ident_software",
"label":"viral identification software",
"definition":"Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used",
"expectedValue":"software name, version and relevant parameters",
"valueSyntax":"{software};{version};{parameters}",
"example":"VirSorter; 1.0.4; Virome database, category 2",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000081",
},
{
"mixsId":"MIXS:0000082",
"structuredCommentName":"pred_genome_type",
"label":"predicted genome type",
"definition":"Type of genome predicted for the UViG",
"expectedValue":"enumeration",
"valueSyntax":"[DNA|dsDNA|ssDNA|RNA|dsRNA|ssRNA|ssRNA (+)|ssRNA (-)|mixed|uncharacterized]",
"example":"dsDNA",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000082",
},
{
"mixsId":"MIXS:0000083",
"structuredCommentName":"pred_genome_struc",
"label":"predicted genome structure",
"definition":"Expected structure of the viral genome",
"expectedValue":"enumeration",
"valueSyntax":"[segmented|non-segmented|undetermined]",
"example":"non-segmented",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000083",
},
{
"mixsId":"MIXS:0000084",
"structuredCommentName":"detec_type",
"label":"detection type",
"definition":"Type of UViG detection",
"expectedValue":"enumeration",
"valueSyntax":"[independent sequence (UViG)|provirus (UpViG)]",
"example":"independent sequence (UViG)",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000084",
},
{
"mixsId":"MIXS:0000085",
"structuredCommentName":"otu_class_appr",
"label":"OTU classification approach",
"definition":"Cutoffs and approach used when clustering “species-level” OTUs. Note that results from standard 95% ANI / 85% AF clustering should be provided alongside OTUS defined from another set of thresholds, even if the latter are the ones primarily used during the analysis",
"expectedValue":"cutoffs and method used",
"valueSyntax":"{ANI cutoff};{AF cutoff};{clustering method}",
"example":"95% ANI;85% AF; greedy incremental clustering",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000085",
},
{
"mixsId":"MIXS:0000086",
"structuredCommentName":"otu_seq_comp_appr",
"label":"OTU sequence comparison approach",
"definition":"Tool and thresholds used to compare sequences when computing "species-level" OTUs",
"expectedValue":"software name, version and relevant parameters",
"valueSyntax":"{software};{version};{parameters}",
"example":"blastn;2.6.0+;e-value cutoff: 0.001",
"preferredUnit":"",
"occurence":"1",
"url":"https://genomicsstandardsconsortium.github.io/mixs/0000086",
},
{
"mixsId":"MIXS:0000087",