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 |
|---|---|---|
| ChromatographyConfiguration | A set of parameters that define and control the actions of a chromatography p... | yes |
| Culturing | A material processing that grows an organism under controlled conditions | yes |
| Pooling | physical combination of several instances of like material | yes |
| LibraryPreparation | yes | |
| CollectingBiosamplesFromSite | yes | |
| DataGeneration | The methods and processes used to generate omics data from a biosample or org... | no |
| MagsAnalysis | A workflow execution activity that uses computational binning tools to group ... | yes |
| ChemicalConversionProcess | A process that results in the interconversion of chemical species by a reacti... | yes |
| MetaproteomicsAnalysis | yes | |
| AnnotatingWorkflow | A WorkflowExecution whose output indicates the potential functions of genes o... | no |
| InformationObject | Any data or knowledge that reduces uncertainty or enhances understanding abou... | no |
| MetagenomeAssembly | A workflow execution activity that converts sequencing reads into an assemble... | yes |
| ReadQcAnalysis | A workflow execution activity that performs quality control on raw Illumina r... | yes |
| Instrument | A material entity that is designed to perform a function in a scientific inve... | yes |
| CalibrationInformation | A calibration object that is associated with a process | yes |
| Isolation | A material processing that separates an organism from a mixed sample by selec... | yes |
| MassSpectrometry | Spectrometry where the sample is converted into gaseous ions which are charac... | yes |
| MixingProcess | The combining of components, particles or layers into a more homogeneous stat... | yes |
| Biosample | Biological source material which can be characterized by an experiment | yes |
| OrganismSample | A material sample in which all cells are expected to share the same genome | yes |
| Organism | A material entity that is a living or once-living individual | yes |
| NcbiTaxon | A taxonomy term from NCBI Taxonomy | yes |
| NamedThing | a databased entity or concept/class | no |
| ReadBasedTaxonomyAnalysis | A workflow execution activity that performs taxonomy classification using seq... | yes |
| DissolvingProcess | A mixing step where a soluble component is mixed with a liquid component | yes |
| Extraction | A material separation in which a desired component of an input material is se... | yes |
| OrthologyGroup | A set of genes or gene products in which all members are orthologous | no |
| StorageProcess | A planned process with the objective to preserve and protect material entitie... | yes |
| Configuration | A set of parameters that define the actions of a process and is shared among ... | no |
| Manifest | A qualified collection of DataObjects that can be analyzed together in the sa... | yes |
| PlannedProcess | A named thing that is executed according to a plan | no |
| Site | no | |
| MetatranscriptomeExpressionAnalysis | A workflow process that provides expression values and read counts for gene f... | yes |
| FieldResearchSite | A site, outside of a laboratory, from which biosamples may be collected | yes |
| ProcessedSample | yes | |
| ChromatographicSeparationProcess | The process of using a selective partitioning of the analyte or interferent b... | yes |
| MetatranscriptomeAssembly | yes | |
| FiltrationProcess | The process of segregation of phases; e | yes |
| MaterialEntity | A named thing that occupies space and has mass | no |
| SubSamplingProcess | Separating a sample aliquot from the starting material for downstream activit... | yes |
| Pathway | A pathway is a sequence of steps/reactions carried out by an organism or comm... | no |
| Study | A study summarizes the overall goal of a research initiative and outlines the... | yes |
| OntologyClass | A representation of class defined in an external ontology | yes |
| WorkflowExecution | Represents an instance of an execution of a particular workflow | no |
| DataObject | An object that primarily consists of symbols that represent information | yes |
| MetabolomicsAnalysis | yes | |
| MetagenomeSequencing | Initial sequencing activity that precedes any analysis | yes |
| MetatranscriptomeAnnotation | yes | |
| DataEmitterProcess | A process that generates data objects as output | no |
| NucleotideSequencing | A DataGeneration in which the sequence of DNA or RNA molecules is generated | yes |
| MassSpectrometryConfiguration | A set of parameters that define and control the actions of a mass spectrometr... | yes |
| Sample | A sample is a material entity that can be characterized by an experiment | no |
| NomAnalysis | yes | |
| ProtocolExecution | A PlannedProces that has PlannedProcess parts | yes |
| MaterialProcessing | A process that takes one or more samples as inputs and generates one or more ... | no |
| EnvironmentalMaterialTerm | no | |
| MetagenomeAnnotation | A workflow execution activity that provides functional and structural annotat... | yes |
| GeneProduct | A molecule encoded by a gene that has an evolved function | no |
| ChemicalEntity | An atom or molecule that can be represented with a chemical formula | no |
| FunctionalAnnotationTerm | Abstract grouping class for any term/descriptor that can be applied to a func... | no |
Properties
-
Range: Uriorcurie
-
Required: True
-
Regex pattern:
^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$
Examples
| Value |
|---|
| nmdc:mgmag-00-x012.1_7_c1 |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
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
alias: id
domain_of:
- NamedThing
range: uriorcurie
required: true
pattern: ^[a-zA-Z0-9][a-zA-Z0-9_\.]+:[a-zA-Z0-9_][a-zA-Z0-9_\-\/\.,]*$