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<extension xmlns="http://rs.gbif.org/extension/"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xmlns:dc="http://purl.org/dc/terms/"
    xsi:schemaLocation="http://rs.gbif.org/extension/ http://rs.gbif.org/schema/extension.xsd"
    dc:title="DNA derived data"
    name="dnaDerivedData"
    namespace="http://rs.gbif.org/terms/1.0/"
    rowType="http://rs.gbif.org/terms/1.0/DNADerivedData"
    dc:issued="2024-07-11"
    dc:subject=""
    dc:relation="https://w3id.org/mixs/"
    dc:description="An extension to Occurrence and Event cores to capture information relating to DNA. This extension is based on the MIxS extension for Darwin Core (underway), with additions from GGBN and MIQE standards and recommendations. This definition supports the outcomes documented in Publishing DNA-derived data through biodiversity data platforms (https://doi.org/10.35035/doc-vf1a-nr22).  This extension is subject to change, and recommended for early adopters who understand that data remapping may be required as things evolve.">
    <property group=''
        name='samp_name'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0001107'
        dc:relation=''
        dc:description='Sample Name is a name that you choose for the sample. It can have any format, but we suggest that you make it concise, unique and consistent within your lab, and as informative as possible. Every Sample Name from a single Submitter must be unique. '
        examples=''
        required='false'/>
    <property group=''
        name='occurrenceID'
        namespace='http://rs.tdwg.org/dwc/terms/'
        qualName='http://rs.tdwg.org/dwc/terms/occurrenceID'
        dc:relation='http://rs.tdwg.org/dwc/terms/index.htm#occurrenceID'
        dc:description='The identifier of the occurrence the DNA sequence relates to. If not applicable, it should be left empty.'
        examples=''
        required='false'/>
    <property group='investigation'
        name='project_name'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000092'
        dc:relation=''
        dc:description='Name of the project within which the sequencing was organized'
        examples='Forest soil metagenome'
        required='false'/>
    <property group='investigation'
        name='experimental_factor'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000008'
        dc:relation=''
        dc:description='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'
        examples='time series design [EFO:EFO_0001779]'
        required='false'/>
    <property group='investigation'
        name='samp_taxon_id'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0001320'
        dc:relation=''
        dc:description='NCBI taxon id of the sample. Maybe be a single taxon or mixed taxa sample. Use "synthetic metagenome" for mock community/positive controls, or "blank sample" for negative controls'
        examples='Gut Metagenome [NCBITaxon:749906]'
        required='false'/>
    <property group='investigation'
        name='neg_cont_type'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0001321'
        dc:relation=''
        dc:description='The substance or equipment used as a negative control in an investigation'
        examples=''
        required='false'/>
    <property group='investigation'
        name='pos_cont_type'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0001322'
        dc:relation=''
        dc:description='The substance, mixture, product, or apparatus used to verify that a process which is part of an investigation delivers a true positive'
        examples=''
        required='false'/>
    <property group='environment'
        name='env_broad_scale'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000012'
        dc:relation=''
        dc:description='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'
        examples='forest biome [ENVO:01000174]'
        required='false'/>
    <property group='environment'
        name='env_local_scale'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000013'
        dc:relation=''
        dc:description='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'
        examples='litter layer [ENVO:01000338]'
        required='false'/>
    <property group='environment'
        name='env_medium'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000014'
        dc:relation=''
        dc:description='In this field, report which environmental material or materials (pipe separated) immediately surrounded your sample or specimen prior to sampling, using one or more subclasses of ENVO’s environmental material class: http://purl.obolibrary.org/obo/ENVO_00010483. Format (one term): termLabel [termID]; Format (multiple terms): termLabel [termID]|termLabel [termID]|termLabel [termID]. Example: Annotating a fish swimming in the upper 100 m of the Atlantic Ocean, consider: ocean water [ENVO:00002151]. Example: Annotating a duck on a pond consider: pond water [ENVO:00002228]|air ENVO_00002005. If needed, request new terms on the ENVO tracker, identified here: http://www.obofoundry.org/ontology/envo.html'
        examples='soil [ENVO:00001998]'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='subspecf_gen_lin'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000020'
        dc:relation=''
        dc:description='This should provide further information about the genetic distinctness of the sequenced organism by recording additional information e.g. serovar, serotype, biotype, ecotype, or any relevant genetic typing schemes like Group I plasmid. It can also contain alternative taxonomic information. It should contain both the lineage name, and the lineage rank, i.e. biovar:abc123'
        examples='serovar:Newport'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='ploidy'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000021'
        dc:relation=''
        dc:description='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'
        examples='allopolyploidy [PATO:0001379]'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='num_replicons'
        type='integer'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000022'
        dc:relation=''
        dc:description='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'
        examples='2'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='extrachrom_elements'
        type='integer'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000023'
        dc:relation=''
        dc:description='Do plasmids exist of significant phenotypic consequence (e.g. ones that determine virulence or antibiotic resistance). Megaplasmids? Other plasmids (borrelia has 15+ plasmids)'
        examples='5'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='estimated_size'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000024'
        dc:relation=''
        dc:description='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.'
        examples='300000 bp'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='ref_biomaterial'
        type='uri'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000025'
        dc:relation=''
        dc:description='Primary publication if isolated before genome publication; otherwise, primary genome report'
        examples='doi:10.1016/j.syapm.2018.01.009'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='source_mat_id'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000026'
        dc:relation=''
        dc:description='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).'
        examples='MPI012345'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='pathogenicity'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000027'
        dc:relation=''
        dc:description='To what is the entity pathogenic'
        examples='human, animal, plant, fungi, bacteria'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='biotic_relationship'
        thesaurus='https://rs.gbif.org/vocabulary/dna/biotic_relationship.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000028'
        dc:relation=''
        dc:description='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'
        examples='free living'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='specific_host'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000029'
        dc:relation=''
        dc:description='If there is a host involved, please provide its taxid (or environmental if not actually isolated from the dead or alive host - i.e. a pathogen could be isolated from a swipe of a bench etc) and report whether it is a laboratory or natural host)'
        examples='9606'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='host_spec_range'
        type='integer'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000030'
        dc:relation=''
        dc:description='The NCBI taxonomy identifier of the specific host if it is known'
        examples='9606'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='host_disease_stat'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000031'
        dc:relation=''
        dc:description='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'
        examples='dead'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='trophic_level'
        thesaurus='https://rs.gbif.org/vocabulary/dna/trophic_level.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000032'
        dc:relation=''
        dc:description='Trophic levels are the feeding position in a food chain. Microbes can be a range of producers (e.g. chemolithotroph)'
        examples='heterotroph'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='propagation'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000033'
        dc:relation=''
        dc:description='This field is specific to different taxa. For phages: lytic/lysogenic, for plasmids: incompatibility group, for eukaryotes: sexual/asexual (Note: there is the strong opinion to name phage propagation obligately lytic or temperate, therefore we also give this choice'
        examples='lytic'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='encoded_traits'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000034'
        dc:relation=''
        dc:description='Should include key traits like antibiotic resistance or xenobiotic degradation phenotypes for plasmids, converting genes for phage'
        examples='beta-lactamase class A'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='rel_to_oxygen'
        thesaurus='https://rs.gbif.org/vocabulary/dna/rel_to_oxygen.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000015'
        dc:relation=''
        dc:description='Is this organism an aerobe, anaerobe? Please note that aerobic and anaerobic are valid descriptors for microbial environments'
        examples='aerobe'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='isol_growth_condt'
        type='uri'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000003'
        dc:relation=''
        dc:description='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'
        examples='doi: 10.1016/j.syapm.2018.01.009'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='samp_collec_device'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000002'
        dc:relation=''
        dc:description='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).'
        examples='environmental swab sampling, biopsy, niskin bottle, push core'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='samp_collec_method'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0001225'
        dc:relation=''
        dc:description='The method employed for collecting the sample'
        examples='environmental swab sampling, biopsy, niskin bottle, push core'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='samp_mat_process'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000016'
        dc:relation=''
        dc:description='Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v 2018-02-12) terms please see http://purl.bioontology.org/ontology/OBI'
        examples='filtering of seawater, storing samples in ethanol'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='size_frac'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000017'
        dc:relation=''
        dc:description='Filtering pore size used in sample preparation'
        examples='0-0.22 micrometer'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='samp_size'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000001'
        dc:relation=''
        dc:description='Amount or size of sample (volume, mass or area) that was collected'
        examples='5 liter'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='samp_vol_we_dna_ext'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000111'
        dc:relation=''
        dc:description='Volume (ml) or mass (g) of total collected sample processed for DNA extraction. Note: total sample collected should be entered under the term Sample Size (MIXS:0000001).'
        examples='1500 milliliter'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='source_uvig'
        thesaurus='https://rs.gbif.org/vocabulary/dna/source_uvig.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000035'
        dc:relation=''
        dc:description='Type of dataset from which the UViG was obtained'
        examples='viral fraction metagenome (virome)'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='virus_enrich_appr'
        thesaurus='https://rs.gbif.org/vocabulary/dna/virus_enrich_appr.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000036'
        dc:relation=''
        dc:description='List of approaches used to enrich the sample for viruses, if any'
        examples='filtration + FeCl Precipitation + ultracentrifugation + DNAse'
        required='false'/>
    <property group='sequencing'
        name='nucl_acid_ext'
        type='uri'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000037'
        dc:relation=''
        dc:description='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'
        examples='https://mobio.com/media/wysiwyg/pdfs/protocols/12888.pdf'
        required='false'/>
    <property group='sequencing'
        name='nucl_acid_amp'
        type='uri'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000038'
        dc:relation=''
        dc:description='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'
        examples='https://phylogenomics.me/protocols/16s-pcr-protocol/'
        required='false'/>
    <property group='sequencing'
        name='lib_size'
        type='integer'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000039'
        dc:relation=''
        dc:description='Total number of clones in the library prepared for the project'
        examples='50'
        required='false'/>
    <property group='sequencing'
        name='lib_reads_seqd'
        type='integer'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000040'
        dc:relation=''
        dc:description='Total number of clones sequenced from the library'
        examples='20'
        required='false'/>
    <property group='sequencing'
        name='lib_layout'
        thesaurus='https://rs.gbif.org/vocabulary/dna/lib_layout.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000041'
        dc:relation=''
        dc:description='Specify whether to expect single, paired, or other configuration of reads'
        examples='paired'
        required='false'/>
    <property group='sequencing'
        name='lib_vector'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000042'
        dc:relation=''
        dc:description='Cloning vector type(s) used in construction of libraries'
        examples='Bacteriophage P1'
        required='false'/>
    <property group='sequencing'
        name='lib_screen'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000043'
        dc:relation=''
        dc:description='Specific enrichment or screening methods applied before and/or after creating libraries'
        examples='enriched, screened, normalized'
        required='false'/>
    <property group='sequencing'
        name='target_gene'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000044'
        dc:relation=''
        dc:description='Targeted gene or locus name for marker gene studies'
        examples='16S rRNA, 18S rRNA, nif, amoA, rpo'
        required='false'/>
    <property group='sequencing'
        name='target_subfragment'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000045'
        dc:relation=''
        dc:description='Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA'
        examples='V6, V9, ITS'
        required='false'/>
    <property group='sequencing'
        name='pcr_primers'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000046'
        dc:relation=''
        dc:description='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'
        examples='FWD:GTGCCAGCMGCCGCGGTAA;REV:GGACTACHVGGGTWTCTAAT'
        required='false'/>
    <property group='sequencing'
        name='mid'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000047'
        dc:relation=''
        dc:description='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'
        examples='GTGAATAT'
        required='false'/>
    <property group='sequencing'
        name='adapters'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000048'
        dc:relation=''
        dc:description='Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters'
        examples='AATGATACGGCGACCACCGAGATCTACACGCT;CAAGCAGAAGACGGCATACGAGAT'
        required='false'/>
    <property group='sequencing'
        name='pcr_cond'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000049'
        dc:relation=''
        dc:description='Description of reaction conditions and components of PCR in the form of ´initial denaturation:94degC_1.5min; annealing=...´'
        examples='initial denaturation:94_3;annealing:50_1;elongation:72_1.5;final elongation:72_10;35'
        required='false'/>
    <property group='sequencing'
        name='seq_meth'
        thesaurus='https://rs.gbif.org/vocabulary/dna/seq_meth.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000050'
        dc:relation=''
        dc:description='Sequencing method used; e.g. Sanger, ABI-solid'
        examples='Illumina HiSeq 1500'
        required='false'/>
    <property group='sequencing'
        name='seq_quality_check'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000051'
        dc:relation=''
        dc:description='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'
        examples='none'
        required='false'/>
    <property group='sequencing'
        name='chimera_check'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000052'
        dc:relation=''
        dc:description='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'
        examples='uchime;v4.1;default parameters'
        required='false'/>
    <property group='sequencing'
        name='tax_ident'
        thesaurus='https://rs.gbif.org/vocabulary/dna/tax_ident.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000053'
        dc:relation=''
        dc:description='The phylogenetic marker(s) used to assign an organism name to the SAG or MAG'
        examples='other: rpoB gene'
        required='false'/>
    <property group='sequencing'
        name='assembly_qual'
        thesaurus='https://rs.gbif.org/vocabulary/dna/assembly_qual.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000056'
        dc:relation=''
        dc:description='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 &lt; 90% of the expected genome or replicon sequence, or for which no genome size could be estimated'
        examples='High-quality draft genome'
        required='false'/>
    <property group='sequencing'
        name='assembly_name'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000057'
        dc:relation=''
        dc:description='Name/version of the assembly provided by the submitter that is used in the genome browsers and in the community'
        examples='HuRef, JCVI_ISG_i3_1.0'
        required='false'/>
    <property group='sequencing'
        name='assembly_software'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000058'
        dc:relation=''
        dc:description='Tool(s) used for assembly, including version number and parameters'
        examples='metaSPAdes;3.11.0;kmer set 21,33,55,77,99,121, default parameters otherwise'
        required='false'/>
    <property group='sequencing'
        name='annot'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000059'
        dc:relation=''
        dc:description='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'
        examples='prokka'
        required='false'/>
    <property group='sequencing'
        name='number_contig'
        type='integer'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000060'
        dc:relation=''
        dc:description='Total number of contigs in the cleaned/submitted assembly that makes up a given genome, SAG, MAG, or UViG'
        examples='40'
        required='false'/>
    <property group='sequencing'
        name='feat_pred'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000061'
        dc:relation=''
        dc:description='Method used to predict UViGs features such as ORFs, integration site, etc.'
        examples='Prodigal;2.6.3;default parameters'
        required='false'/>
    <property group='sequencing'
        name='ref_db'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000062'
        dc:relation=''
        dc:description='List of database(s) used for ORF annotation, along with version number and reference to website or publication'
        examples='pVOGs;5;http://dmk-brain.ecn.uiowa.edu/pVOGs/ Grazziotin et al. 2017 doi:10.1093/nar/gkw975'
        required='false'/>
    <property group='sequencing'
        name='sim_search_meth'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000063'
        dc:relation=''
        dc:description='Tool used to compare ORFs with database, along with version and cutoffs used'
        examples='HMMER3;3.1b2;hmmsearch, cutoff of 50 on score'
        required='false'/>
    <property group='sequencing'
        name='tax_class'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000064'
        dc:relation=''
        dc:description='Method used for taxonomic classification, along with reference database used, classification rank, and thresholds used to classify new genomes'
        examples='vConTACT vContact2 (references from NCBI RefSeq v83, genus rank classification, default parameters)'
        required='false'/>
    <property group='sequencing'
        name='_16s_recover'
        type='boolean'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000065'
        dc:relation=''
        dc:description='Can a 16S gene be recovered from the submitted SAG or MAG?'
        examples='yes'
        required='false'/>
    <property group='sequencing'
        name='_16s_recover_software'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000066'
        dc:relation=''
        dc:description='Tools used for 16S rRNA gene extraction'
        examples='rambl;v2;default parameters'
        required='false'/>
    <property group='sequencing'
        name='trnas'
        type='integer'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000067'
        dc:relation=''
        dc:description='The total number of tRNAs identified from the SAG or MAG'
        examples='18'
        required='false'/>
    <property group='sequencing'
        name='trna_ext_software'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000068'
        dc:relation=''
        dc:description='Tools used for tRNA identification'
        examples='infernal;v2;default parameters'
        required='false'/>
    <property group='sequencing'
        name='compl_score'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000069'
        dc:relation=''
        dc:description='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: &gt;90%, Medium Quality Draft: &gt;50%, and Low Quality Draft: &lt; 50% should have the indicated completeness scores'
        examples='med;60%'
        required='false'/>
    <property group='sequencing'
        name='compl_software'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000070'
        dc:relation=''
        dc:description='Tools used for completion estimate, i.e. checkm, anvi´o, busco'
        examples='checkm'
        required='false'/>
    <property group='sequencing'
        name='compl_appr'
        thesaurus='https://rs.gbif.org/vocabulary/dna/compl_appr.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000071'
        dc:relation=''
        dc:description='The approach used to determine the completeness of a given SAG or MAG, 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'
        examples='other: UViG length compared to the average length of reference genomes from the P22virus genus (NCBI RefSeq v83)'
        required='false'/>
    <property group='sequencing'
        name='contam_score'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000072'
        dc:relation=''
        dc:description='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: &lt; 5%, Medium Quality Draft: &lt; 10%, Low Quality Draft: &lt; 10%. Contamination must be below 5% for a SAG or MAG to be deposited into any of the public databases'
        examples='1%'
        required='false'/>
    <property group='sequencing'
        name='contam_screen_input'
        thesaurus='https://rs.gbif.org/vocabulary/dna/contam_screen_input.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000005'
        dc:relation=''
        dc:description='The type of sequence data used as input'
        examples='contigs'
        required='false'/>
    <property group='sequencing'
        name='contam_screen_param'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000073'
        dc:relation=''
        dc:description='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'
        examples='kmer'
        required='false'/>
    <property group='sequencing'
        name='decontam_software'
        thesaurus='https://rs.gbif.org/vocabulary/dna/decontam_software.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000074'
        dc:relation=''
        dc:description='Tool(s) used in contamination screening'
        examples='anvi´o'
        required='false'/>
    <property group='sequencing'
        name='sort_tech'
        thesaurus='https://rs.gbif.org/vocabulary/dna/sort_tech.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000075'
        dc:relation=''
        dc:description='Method used to sort/isolate cells or particles of interest'
        examples='optical manipulation'
        required='false'/>
    <property group='sequencing'
        name='single_cell_lysis_appr'
        thesaurus='https://rs.gbif.org/vocabulary/dna/single_cell_lysis_appr.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000076'
        dc:relation=''
        dc:description='Method used to free DNA from interior of the cell(s) or particle(s)'
        examples='enzymatic'
        required='false'/>
    <property group='sequencing'
        name='single_cell_lysis_prot'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000054'
        dc:relation=''
        dc:description='Name of the kit or standard protocol used for cell(s) or particle(s) lysis'
        examples='ambion single cell lysis kit'
        required='false'/>
    <property group='sequencing'
        name='wga_amp_appr'
        thesaurus='https://rs.gbif.org/vocabulary/dna/wga_amp_appr.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000055'
        dc:relation=''
        dc:description='Method used to amplify genomic DNA in preparation for sequencing'
        examples='mda based'
        required='false'/>
    <property group='sequencing'
        name='wga_amp_kit'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000006'
        dc:relation=''
        dc:description='Kit used to amplify genomic DNA in preparation for sequencing'
        examples='qiagen repli-g'
        required='false'/>
    <property group='sequencing'
        name='bin_param'
        thesaurus='https://rs.gbif.org/vocabulary/dna/bin_param.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000077'
        dc:relation=''
        dc:description='The parameters that have been applied during the extraction of genomes from metagenomic datasets'
        examples='coverage and kmer'
        required='false'/>
    <property group='sequencing'
        name='bin_software'
        thesaurus='https://rs.gbif.org/vocabulary/dna/bin_software.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000078'
        dc:relation=''
        dc:description='Tool(s) used for the extraction of genomes from metagenomic datasets'
        examples='concoct and maxbin'
        required='false'/>
    <property group='sequencing'
        name='reassembly_bin'
        type='boolean'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000079'
        dc:relation=''
        dc:description='Has an assembly been performed on a genome bin extracted from a metagenomic assembly?'
        examples='no'
        required='false'/>
    <property group='sequencing'
        name='mag_cov_software'
        thesaurus='https://rs.gbif.org/vocabulary/dna/mag_cov_software.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000080'
        dc:relation=''
        dc:description='Tool(s) used to determine the genome coverage if coverage is used as a binning parameter in the extraction of genomes from metagenomic datasets'
        examples='bbmap'
        required='false'/>
    <property group='sequencing'
        name='vir_ident_software'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000081'
        dc:relation=''
        dc:description='Tool(s) used for the identification of UViG as a viral genome, software or protocol name including version number, parameters, and cutoffs used'
        examples='VirSorter; 1.0.4; Virome database, category 2'
        required='false'/>
    <property group='sequencing'
        name='pred_genome_type'
        thesaurus='https://rs.gbif.org/vocabulary/dna/pred_genome_type.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000082'
        dc:relation=''
        dc:description='Type of genome predicted for the UViG'
        examples='dsDNA'
        required='false'/>
    <property group='sequencing'
        name='pred_genome_struc'
        thesaurus='https://rs.gbif.org/vocabulary/dna/pred_genome_struc.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000083'
        dc:relation=''
        dc:description='Expected structure of the viral genome'
        examples='non-segmented'
        required='false'/>
    <property group='sequencing'
        name='detec_type'
        thesaurus='https://rs.gbif.org/vocabulary/dna/detec_type.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000084'
        dc:relation=''
        dc:description='Type of UViG detection'
        examples='independent sequence (UViG)'
        required='false'/>
    <property group='sequencing'
        name='otu_class_appr'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000085'
        dc:relation=''
        dc:description='Cutoffs and approach used when clustering new UViGs in "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'
        examples='95% ANI;85% AF; greedy incremental clustering'
        required='false'/>
    <property group='sequencing'
        name='otu_seq_comp_appr'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000086'
        dc:relation=''
        dc:description='Tool and thresholds used to compare sequences when computing "species-level" OTUs'
        examples='blastn;2.6.0+;e-value cutoff: 0.001'
        required='false'/>
    <property group='sequencing'
        name='otu_db'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000087'
        dc:relation=''
        dc:description='Reference database (i.e. sequences not generated as part of the current study) used to cluster new genomes in "species-level" OTUs, if any'
        examples='NCBI Viral RefSeq;83'
        required='false'/>
    <property group='sequencing'
        name='host_pred_appr'
        thesaurus='https://rs.gbif.org/vocabulary/dna/host_pred_appr.xml'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000088'
        dc:relation=''
        dc:description='Tool or approach used for host prediction'
        examples='CRISPR spacer match'
        required='false'/>
    <property group='sequencing'
        name='host_pred_est_acc'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000089'
        dc:relation=''
        dc:description='For each tool or approach used for host prediction, estimated false discovery rates should be included, either computed de novo or from the literature'
        examples='CRISPR spacer match: 0 or 1 mismatches, estimated 8% FDR at the host genus rank (Edwards et al. 2016 doi:10.1093/femsre/fuv048)'
        required='false'/>
    <property group='sequencing'
        name='url'
        type='uri'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000091'
        dc:relation=''
        dc:description=''
        examples='http://www.earthmicrobiome.org/'
        required='false'/>
    <property group='sequencing'
        name='sop'
        type='uri'
        namespace='https://w3id.org/mixs/'
        qualName='https://w3id.org/mixs/0000090'
        dc:relation=''
        dc:description='Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences'
        examples='http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/'
        required='false'/>
    <property group='sequencing'
        name='pcr_primer_forward'
        namespace='http://rs.gbif.org/terms/'
        qualName='http://rs.gbif.org/terms/pcr_primer_forward'
        dc:relation=''
        dc:description='Forward PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. If multiple multiple forward or reverse primers are present in a single PCR reaction, there should be a full row for each of these linked to the same DWC Occurrence. The primer sequence should be reported in uppercase letters'
        examples='GGACTACHVGGGTWTCTAAT'
        required='false'/>
    <property group='sequencing'
        name='pcr_primer_reverse'
        namespace='http://rs.gbif.org/terms/'
        qualName='http://rs.gbif.org/terms/pcr_primer_reverse'
        dc:relation=''
        dc:description='Reverse PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. If multiple multiple forward or reverse primers are present in a single PCR reaction, there should be a full row for each of these linked to the same DWC Occurrence. The primer sequence should be reported in uppercase letters'
        examples='GGACTACHVGGGTWTCTAAT'
        required='false'/>
    <property group='sequencing'
        name='pcr_primer_name_forward'
        namespace='http://rs.gbif.org/terms/'
        qualName='http://rs.gbif.org/terms/pcr_primer_name_forward'
        dc:relation=''
        dc:description='Name of the forward PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. If multiple multiple forward or reverse primers are present in a single PCR reaction, there should be a full row for each of these linked to the same DWC Occurrence.'
        examples='jgLCO1490'
        required='false'/>
    <property group='sequencing'
        name='pcr_primer_name_reverse'
        namespace='http://rs.gbif.org/terms/'
        qualName='http://rs.gbif.org/terms/pcr_primer_name_reverse'
        dc:relation=''
        dc:description='Name of the reverse PCR primer that were used to amplify the sequence of the targeted gene, locus or subfragment. If multiple multiple forward or reverse primers are present in a single PCR reaction, there should be a full row for each of these linked to the same DWC Occurrence.'
        examples='jgHCO2198'
        required='false'/>
    <property group='sequencing'
        name='pcr_primer_reference'
        namespace='http://rs.gbif.org/terms/'
        qualName='http://rs.gbif.org/terms/pcr_primer_reference'
        dc:relation=''
        dc:description='Reference for the PCR primers that were used to amplify the sequence of the targeted gene, locus or subfragment.'
        examples='https://doi.org/10.1186/1742-9994-10-34'
        required='false'/>
    <property group='sequencing'
        name='DNA_sequence'
        namespace='http://rs.gbif.org/terms/'
        qualName='http://rs.gbif.org/terms/dna_sequence'
        dc:relation=''
        dc:description='The DNA sequence'
        examples='TCTATCCTCAATTATAGGTCATAATTCACCATCAGTAGATTTAGGAATTTTCTCTATTCATATTGCAGGTGTATCATCAATTATAGGATCAATTAATTTTATTGTAACAATTTTAAATATACATACAAAAACTCATTCATTAAACTTTTTACCATTATTTTCATGATCAGTTCTAGTTACAGCAATTCTCCTTTTATTATCATTA'
        required='false'/>
    <property group='MaterialSample'
        type='decimal'
        name='concentration'
        namespace='http://data.ggbn.org/schemas/ggbn/terms/'
        qualName='http://data.ggbn.org/schemas/ggbn/terms/concentration'
        dc:relation='http://terms.tdwg.org/wiki/ggbn:concentration'
        dc:description='Concentration of DNA (weight ng/volume µl)'
        examples='67.5'
        required='false'/>
    <property group='MaterialSample'
        name='concentrationUnit'
        namespace='http://data.ggbn.org/schemas/ggbn/terms/'
        qualName='http://data.ggbn.org/schemas/ggbn/terms/concentrationUnit'
        dc:relation='http://terms.tdwg.org/wiki/ggbn:concentrationUnit'
        dc:description='Unit used for concentration measurement'
        examples='ng/µl'
        required='false'/>
    <property group='MaterialSample'
        name='methodDeterminationConcentrationAndRatios'
        namespace='http://data.ggbn.org/schemas/ggbn/terms/'
        qualName='http://data.ggbn.org/schemas/ggbn/terms/methodDeterminationConcentrationAndRatios'
        dc:relation='http://terms.tdwg.org/wiki/ggbn:methodDeterminationConcentrationAndRatios'
        dc:description='Description of method used for concentration measurement'
        examples='Nanodrop, Qubit'
        required='false'/>
    <property group='MaterialSample'
        type='decimal'
        name='ratioOfAbsorbance260_230'
        namespace='http://data.ggbn.org/schemas/ggbn/terms/'
        qualName='http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_230'
        dc:relation='http://terms.tdwg.org/wiki/ggbn:ratioOfAbsorbance260_230'
        dc:description='Ratio of absorbance at 260 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only).'
        examples='1.89'
        required='false'/>
    <property group='MaterialSample'
        type='decimal'
        name='ratioOfAbsorbance260_280'
        namespace='http://data.ggbn.org/schemas/ggbn/terms/'
        qualName='http://data.ggbn.org/schemas/ggbn/terms/ratioOfAbsorbance260_280'
        dc:relation='http://terms.tdwg.org/wiki/ggbn:ratioOfAbsorbance260_280'
        dc:description='Ratio of absorbance at 280 nm and 230 nm assessing DNA purity (mostly secondary measure, indicates mainly EDTA, carbohydrates, phenol), (DNA samples only).'
        examples='1.91'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='decimal'
        name='annealingTemp'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/annealingTemp'
        dc:relation=''
        dc:description='The reaction temperature during the annealing phase of PCR.'
        examples='60'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='annealingTempUnit'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/annealingTempUnit'
        dc:relation=''
        dc:description='Measurement unit of the reaction temperature during the annealing phase of PCR.'
        examples='Degrees celsius'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='probeReporter'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/probeReporter'
        dc:relation=''
        dc:description='Type of fluorophore (reporter) used. Probe anneals within amplified target DNA. Polymerase activity degrades the probe that has annealed to the template, and the probe releases the fluorophore from it and breaks the proximity to the quencher, thus allowing fluorescence of the fluorophore.'
        examples='FAM'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='probeQuencher'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/probeQuencher'
        dc:relation=''
        dc:description='Type of quencher used. The quencher molecule quenches the fluorescence emitted by the fluorophore when excited by the cycler’s light source As long as fluorophore and the quencher are in proximity, quenching inhibits any fluorescence signals.'
        examples='NFQ-MGB'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='integer'
        name='ampliconSize'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/ampliconSize'
        dc:relation=''
        dc:description='The length of the amplicon in basepairs.'
        examples='83'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='decimal'
        name='thresholdQuantificationCycle'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/thresholdQuantificationCycle'
        dc:relation=''
        dc:description='Threshold for change in fluorescence signal between cycles'
        examples='0.3'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='integer'
        name='baselineValue'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/baselineValue'
        dc:relation=''
        dc:description='The number of cycles when fluorescence signal from the target amplification is below background fluorescence not originated from the real target amplification.'
        examples='15'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='decimal'
        name='quantificationCycle'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/quantificationCycle'
        dc:relation=''
        dc:description='The number of cycles required for the fluorescent signal to cross a given value threshold above the baseline. Quantification cycle (Cq), threshold cycle (Ct), crossing point (Cp), and take-off point (TOP) refer to the same value from the real-time instrument. Use of quantification cycle (Cq), is preferable according to the RDML (Real-Time PCR Data Markup Language) data standard (http://www.rdml.org).'
        examples='37.9450950622558'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='boolean'
        name='automaticThresholdQuantificationCycle'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/automaticThresholdQuantificationCycle'
        dc:relation=''
        dc:description='Whether the threshold was set by the instrument or manually.'
        examples='true'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='boolean'
        name='automaticBaselineValue'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/automaticBaselineValue'
        dc:relation=''
        dc:description='Whether the baseline value was set by the instrument or manually.'
        examples='true'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='boolean'
        name='contaminationAssessment'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/contaminationAssessment'
        dc:relation=''
        dc:description='Whether DNA or RNA contamination assessment was done or not.'
        examples='true'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='decimal'
        name='partitionVolume'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/partitionVolume'
        dc:relation=''
        dc:description='An accurate estimation of partition volume. The sum of the partitions multiplied by the partition volume will enable the total volume of the reaction to be calculated.'
        examples='1'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='partitionVolumeUnit'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/partitionVolumeUnit'
        dc:relation=''
        dc:description='Unit used for partition volume'
        examples='nl'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='integer'
        name='estimatedNumberOfCopies'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/estimatedNumberOfCopies'
        dc:relation=''
        dc:description='Number of target molecules per µl. Mean copies per partition (?) can be calculated using the number of partitions (n) and the estimated copy number in the total volume of all partitions (m) with a formula ?=m/n.'
        examples='10300'
        required='false'/>
    <property group='nucleic acid sequence source'
        type='decimal'
        name='amplificationReactionVolume'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/amplificationReactionVolume'
        dc:relation=''
        dc:description='PCR reaction volume'
        examples='22'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='amplificationReactionVolumeUnit'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/amplificationReactionVolumeUnit'
        dc:relation=''
        dc:description='Unit used for PCR reaction volume. Many of the instruments require preparation of a much larger initial sample volume than is actually analyzed.'
        examples='µl'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='pcr_analysis_software'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/pcr_analysis_software'
        dc:relation=''
        dc:description='The program used to analyse the d(d)PCR runs.'
        examples='BIO-RAD QuantaSoft'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='experimentalVariance'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/experimentalVariance'
        dc:relation=''
        dc:description='Multiple biological replicates are encouraged to assess total experimental variation. When single dPCR experiments are performed, a minimal estimate of variance due to counting error alone must be calculated from the binomial (or suitable equivalent) distribution.'
        examples=''
        required='false'/>
    <property group='nucleic acid sequence source'
        name='pcr_primer_lod'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/pcr_primer_lod'
        dc:relation=''
        dc:description='The assay’s ability to detect the target at low levels.'
        examples='51'
        required='false'/>
    <property group='nucleic acid sequence source'
        name='pcr_primer_loq'
        namespace='http://rs.gbif.org/terms/miqe/'
        qualName='http://rs.gbif.org/terms/miqe/pcr_primer_loq'
        dc:relation=''
        dc:description='The assay’s ability to quantify copy number at low levels.'
        examples='184'
        required='false'/>
</extension>