Class: omics processing

The methods and processes used to generate omics data from a biosample or organism.

URI: nmdc:OmicsProcessing

Parents

• is_a: BiosampleProcessing - A process that takes one or more biosamples as inputs and generates one or as outputs. Examples of outputs include samples cultivated from another sample or data objects created by instruments runs.

Referenced by Class

• Database omics processing set _0..* OmicsProcessing

Attributes

Own

• add_date _0..1

  • Description: The date on which the information was added to the database.

  • Range: String

• mod_date _0..1

  • Description: The last date on which the database information was modified.

  • Range: String

• has input _0..*

  • Description: An input to a process.

  • Range: NamedThing

• has output _0..*

  • Description: An output biosample to a processing step

  • Range: NamedThing

• instrument_name _0..1

  • Description: The name of the instrument that was used for processing the sample.

  • Range: String

• ncbi_project_name _0..1

  • Range: String

• omics type _0..1

  • Description: The type of omics data

  • Range: ControlledTermValue

  • Example: metatranscriptome None

  • Example: metagenome None

• part of _0..*

  • Description: Links a resource to another resource that either logically or physically includes it.

  • Range: NamedThing

• principal investigator _0..1

  • Description: Principal Investigator who led the study and/or generated the dataset.

  • Range: PersonValue

• processing_institution _0..1

  • Description: The organization that processed the sample.

  • Range: String

• type _0..1

  • Description: An optional string that specifies the type object. This is used to allow for searches for different kinds of objects.

  • Range: String

  • Example: nmdc:Biosample None

  • Example: nmdc:Study None

• GOLD sequencing project identifiers _0..*

  • Description: identifiers for corresponding sequencing project in GOLD

  • Range: ExternalIdentifier

  • Example: https://identifiers.org/gold:Gp0108335 None

• INSDC experiment identifiers _0..*

  • Range: ExternalIdentifier

• samp_vol_we_dna_ext _0..1

  • Description: Volume (ml), weight (g) of processed sample, or surface area swabbed from sample for DNA extraction

  • Range: QuantityValue

• nucl_acid_ext _0..1

  • 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

  • Range: TextValue

  • in subsets: (sequencing)

• nucl_acid_amp _0..1

  • 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

  • Range: TextValue

  • in subsets: (sequencing)

• target_gene _0..1

  • Description: Targeted gene or locus name for marker gene studies

  • Range: TextValue

  • in subsets: (sequencing)

• target_subfragment _0..1

  • Description: Name of subfragment of a gene or locus. Important to e.g. identify special regions on marker genes like V6 on 16S rRNA

  • Range: TextValue

  • in subsets: (sequencing)

• pcr_primers _0..1

  • 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

  • Range: TextValue

  • in subsets: (sequencing)

• pcr_cond _0..1

  • Description: Description of reaction conditions and components of PCR in the form of ‘initial denaturation:94degC_1.5min; annealing=…’

  • Range: TextValue

  • in subsets: (sequencing)

• seq_meth _0..1

  • Description: Sequencing method used; e.g. Sanger, pyrosequencing, ABI-solid

  • Range: TextValue

  • in subsets: (sequencing)

• seq_quality_check _0..1

  • 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

  • Range: TextValue

  • in subsets: (sequencing)

• chimera_check _0..1

  • 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

  • Range: TextValue

  • in subsets: (sequencing)

• omics processing➞has input _1..*

  • Description: An input to a process.

  • Range: Biosample

Inherited from biosample processing:

• id _1..1

  • Description: A unique identifier for a thing. Must be either a CURIE shorthand for a URI or a complete URI

  • Range: String

• name _0..1

  • Description: A human readable label for an entity

  • Range: String

• description _0..1

  • Description: a human-readable description of a thing

  • Range: String

• alternative identifiers _0..*

  • Description: A list of alternative identifiers for the entity.

  • Range: String

Other properties

Aliases:		omics assay
		sequencing project
		experiment
Alt Descriptions:		An experiment contains information about a sequencing experiment including library and instrument details. (embl.ena)
Comments:		The IDs for objects coming from GOLD will have prefixes gold:GpNNNN
In Subsets:		sample subset
Broad Mappings:		OBI:0000070
		ISA:Assay