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Slot: id

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

URI: nmdc:id

Applicable Classes

Name Description Modifies Slot
NamedThing a databased entity or concept/class no
NucleotideSequencing A DataGeneration in which the sequence of DNA or RNA molecules is generated. yes
MassSpectrometry Spectrometry where the sample is converted into gaseous ions which are... yes
Configuration A set of parameters that define the actions of a process and is shared among... no
MassSpectrometryConfiguration A set of parameters that define and control the actions of a mass... yes
ChromatographyConfiguration A set of parameters that define and control the actions of a chromatography process. yes
Manifest A qualified collection of DataObjects that can be analyzed together in the... yes
CalibrationInformation A calibration object that is associated with a process. yes
Pooling physical combination of several instances of like material. yes
Isolation A material processing that separates an organism from a mixed sample by... yes
Culturing A material processing that grows an organism under controlled conditions.... yes
Extraction A material separation in which a desired component of an input material is... yes
LibraryPreparation yes
CollectingBiosamplesFromSite yes
SubSamplingProcess Separating a sample aliquot from the starting material for downstream activity. yes
MixingProcess The combining of components, particles or layers into a more homogeneous state. yes
FiltrationProcess The process of segregation of phases; e.g. the separation of suspended... yes
StorageProcess A planned process with the objective to preserve and protect material... yes
ChromatographicSeparationProcess The process of using a selective partitioning of the analyte or interferent... yes
DissolvingProcess A mixing step where a soluble component is mixed with a liquid component. yes
EnvironmentalMaterialTerm no
Pathway A pathway is a sequence of steps/reactions carried out by an organism or... no
ProtocolExecution A PlannedProces that has PlannedProcess parts. Can be used to represent the... yes
MetagenomeSequencing Initial sequencing activity that precedes any analysis. This activity has... yes
ChemicalEntity An atom or molecule that can be represented with a chemical formula. Include... no
FunctionalAnnotationTerm Abstract grouping class for any term/descriptor that can be applied to a... no
OrthologyGroup A set of genes or gene products in which all members are orthologous no
OntologyClass A representation of class defined in an external ontology. yes
NcbiTaxon A taxonomy term from NCBI Taxonomy. NcbiTaxon instances are identified by... yes
MaterialEntity A named thing that occupies space and has mass. no
Instrument A material entity that is designed to perform a function in a scientific... yes
Organism A material entity that is a living or once-living individual. Organism... yes
PlannedProcess A named thing that is executed according to a plan. no
Study A study summarizes the overall goal of a research initiative and outlines... yes
InformationObject Any data or knowledge that reduces uncertainty or enhances understanding... no
DataObject An object that primarily consists of symbols that represent information. ... yes
DataEmitterProcess A process that generates data objects as output. no
DataGeneration The methods and processes used to generate omics data from a biosample or organism. no
WorkflowExecution Represents an instance of an execution of a particular workflow no
ChemicalConversionProcess A process that results in the interconversion of chemical species by a... yes
AnnotatingWorkflow A WorkflowExecution whose output indicates the potential functions of genes... no
MetagenomeAnnotation A workflow execution activity that provides functional and structural... yes
FieldResearchSite A site, outside of a laboratory, from which biosamples may be collected. yes
Sample A sample is a material entity that can be characterized by an experiment. no
Biosample Biological source material which can be characterized by an experiment. yes
MaterialProcessing A process that takes one or more samples as inputs and generates one or more... no
ProcessedSample yes
OrganismSample A material sample in which all cells are expected to share the same genome.... yes
Site no
GeneProduct A molecule encoded by a gene that has an evolved function no
MetagenomeAssembly A workflow execution activity that converts sequencing reads into an... yes
MetatranscriptomeAssembly yes
MetatranscriptomeAnnotation yes
MetatranscriptomeExpressionAnalysis A workflow process that provides expression values and read counts for gene... yes
MagsAnalysis A workflow execution activity that uses computational binning tools to group... yes
ReadQcAnalysis A workflow execution activity that performs quality control on raw Illumina... yes
ReadBasedTaxonomyAnalysis A workflow execution activity that performs taxonomy classification using... yes
MetabolomicsAnalysis yes
MetaproteomicsAnalysis yes
NomAnalysis yes

Properties

  • Range: Uriorcurie

  • Required: True

  • Regex pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$

Examples

Identifier and Mapping Information

Schema Source

Mappings

Mapping Type Mapped Value

LinkML Source

name: id
description: A unique identifier for a thing. Must be either a CURIE shorthand for
  a URI or a complete URI
notes:
- 'abstracted pattern: prefix:typecode-authshoulder-blade(.version)?(_seqsuffix)?'
- a minimum length of 3 characters is suggested for typecodes, but 1 or 2 characters
  will be accepted
- typecodes must correspond 1:1 to a class in the NMDC schema. this will be checked
  via per-class id slot usage assertions
- minting authority shoulders should probably be enumerated and checked in the pattern
examples:
- value: nmdc:mgmag-00-x012.1_7_c1
  description: https://github.com/microbiomedata/nmdc-schema/pull/499#discussion_r1018499248
from_schema: https://w3id.org/nmdc/nmdc
structured_aliases:
- literal_form: workflow_execution_id
  predicate: NARROW_SYNONYM
  contexts:
  - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
- literal_form: data_object_id
  predicate: NARROW_SYNONYM
  contexts:
  - https://bitbucket.org/berkeleylab/jgi-jat/macros/nmdc_metadata.yaml
rank: 1000
identifier: true
domain_of:
- NamedThing
range: uriorcurie
required: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$