MIxS Sample

http://gensc.org/ns/mixs/terms/Sample

Under Development

MIxS sample based terms extending a classic Darwin Core Occurrence.

Keywords: dwc:Occurrence

Link: http://www.gensc.org/gc_wiki/index.php/MIxS


Properties



Sample

submitted_to_insdc
Depending on the study (large-scale e.g. done with next generation sequencing technology, or small-scale) sequences have to be submitted to SRA (Sequence Read Archive), DRA (DDBJ Read Archive) or via the classical Webin/Sequin systems to Genbank, ENA and DDBJ
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/submitted_to_insdc
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type boolean
Requiredtrue
investigation_type
Nucleic Acid Sequence Report is the root element of all MIGS/MIMS compliant reports as standardized by Genomic Standards Consortium. This field is either eukaryote,bacteria,virus,plasmid,organelle, metagenome, mimarks-survey or mimarks-culture
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/investigation_type
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type MIxS Investigation Type vocabulary
Requiredtrue
project_name
Name of the project within which the sequencing was organized
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/project_name
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
experimental_factor
Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. This field accepts ontology terms from Experimental Factor Ontology (EFO) and/or Ontology for Biomedical Investigations (OBI). For a browser of EFO (v132) terms, please see http://bioportal.bioontology.org/visualize/44641; for a browser of OBI (v1.0) terms please see http://bioportal.bioontology.org/visualize/40832
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/experimental_factor
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
env_biome
In environmental biome level are the major classes of ecologically similar communities of plants, animals, and other organisms. Biomes are defined based on factors such as plant structures, leaf types, plant spacing, and other factors like climate. Examples include: desert, taiga, deciduous woodland, or coral reef. EnvO (v1.53) terms listed under environmental biome can be found from the link: http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00000428
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/env_biome
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredtrue
env_feature
Environmental feature level includes geographic environmental features. Examples include: harbor, cliff, or lake. EnvO (v1.53) terms listed under environmental feature can be found from the link: http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00002297
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/env_feature
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredtrue
env_material
The environmental material level refers to the matter that was displaced by the sample, prior to the sampling event. Environmental matter terms are generally mass nouns. Examples include: air, soil, or water. EnvO (v1.53) terms listed under environmental matter can be found from the link: http://bioportal.bioontology.org/visualize/44405/?conceptid=ENVO%3A00010483
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/env_material
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredtrue
env_package
MIGS/MIMS/MIMARKS extension for reporting of measurements and observations obtained from one or more of the environments where the sample was obtained. All environmental packages listed here are further defined in separate subtables. By giving the name of the environmental package, a selection of fields can be made from the subtables and can be reported
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/env_package
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type MIxS Environmental Package vocabulary
Requiredtrue
samp_collect_device
The method or deviced employed for collecting the sample
Examples: biopsy, niskin bottle, push core
Qualified Namehttp://gensc.org/ns/mixs/terms/samp_collect_device
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
samp_mat_process
Any processing applied to the sample during or after retrieving the sample from environment. This field accepts OBI, for a browser of OBI (v1.0) terms please see http://bioportal.bioontology.org/visualize/40832
Examples: filtering of seawater, storing samples in ethanol
Qualified Namehttp://gensc.org/ns/mixs/terms/samp_mat_process
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
samp_size
Amount or size of sample (volume, mass or area) that was collected
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/samp_size
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
nucl_acid_ext
Link to a literature reference, electronic resource or a standard operating procedure (SOP)
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/nucl_acid_ext
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
nucl_acid_amp
Link to a literature reference, electronic resource or a standard operating procedure (SOP)
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/nucl_acid_amp
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
lib_size
Total number of clones in the library prepared for the project
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/lib_size
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type integer
Requiredfalse
lib_reads_seqd
Total number of clones sequenced from the library
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/lib_reads_seqd
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type integer
Requiredfalse
lib_const_meth
Library construction method used for clone libraries
Examples: paired-end,single,vector
Qualified Namehttp://gensc.org/ns/mixs/terms/lib_const_meth
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
lib_vector
Cloning vector type(s) used in construction of libraries
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/lib_vector
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
lib_screen
Specific enrichment or screening methods applied before and/or after creating clone libraries in order to select a specific group of sequences
Examples: enriched, screened, normalized
Qualified Namehttp://gensc.org/ns/mixs/terms/lib_screen
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
target_gene
Targeted gene or locus name for marker gene studies
Examples: 16S rRNA, 18S rRNA, nif, amoA, rpo
Qualified Namehttp://gensc.org/ns/mixs/terms/target_gene
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
target_subfragment
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
Qualified Namehttp://gensc.org/ns/mixs/terms/target_subfragment
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
pcr_primers
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:
Qualified Namehttp://gensc.org/ns/mixs/terms/pcr_primers
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
mid
Molecular barcodes, called Multiplex Identifiers (MIDs), that are used to specifically tag unique samples in a sequencing run. Sequence should be reported in uppercase letters
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/mid
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
adapters
Adapters provide priming sequences for both amplification and sequencing of the sample-library fragments. Both adapters should be reported; in uppercase letters
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/adapters
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
pcr_cond
Description of reaction conditions and components for PCR in the form of 'initial denaturation:94degC_1.5min; annealing=...'
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/pcr_cond
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
seq_meth
Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid
Examples: Sanger dideoxysequencing, pyrosequencing, polony
Qualified Namehttp://gensc.org/ns/mixs/terms/seq_meth
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredtrue
seq_quality_check
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 or DRA
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/seq_quality_check
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
annot_source
For cases where annotation was provided by a community jamboree or model organism database rather than by a specific submitter
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/annot_source
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse
sop
Standard operating procedures used in assembly and/or annotation of genomes, metagenomes or environmental sequences
Examples:
Qualified Namehttp://gensc.org/ns/mixs/terms/sop
Namespacehttp://gensc.org/ns/mixs/terms/
GroupSample
Data Type string
Requiredfalse