Class: ProteinQuantification
This is used to link a metaproteomics analysis workflow to a specific protein
URI: nmdc:ProteinQuantification
classDiagram
class ProteinQuantification
click ProteinQuantification href "../ProteinQuantification"
ProteinQuantification : all_proteins
ProteinQuantification --> "*" GeneProduct : all_proteins
click GeneProduct href "../GeneProduct"
ProteinQuantification : best_protein
ProteinQuantification --> "0..1" GeneProduct : best_protein
click GeneProduct href "../GeneProduct"
ProteinQuantification : peptide_sequence_count
ProteinQuantification : protein_spectral_count
ProteinQuantification : protein_sum_masic_abundance
ProteinQuantification : type
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
all_proteins | * GeneProduct |
the grouped list of protein identifiers associated with the peptide sequences... | direct |
best_protein | 0..1 GeneProduct |
the specific protein identifier most correctly grouped to its associated pept... | direct |
peptide_sequence_count | 0..1 Integer |
count of peptide sequences grouped to the best_protein | direct |
protein_spectral_count | 0..1 Integer |
sum of filter passing MS2 spectra associated with the best protein within a g... | direct |
protein_sum_masic_abundance | 0..1 Integer |
combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... | direct |
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | direct |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:ProteinQuantification |
native | nmdc:ProteinQuantification |
LinkML Source
Direct
name: ProteinQuantification
description: This is used to link a metaproteomics analysis workflow to a specific
protein
from_schema: https://w3id.org/nmdc/nmdc
slots:
- all_proteins
- best_protein
- peptide_sequence_count
- protein_spectral_count
- protein_sum_masic_abundance
- type
slot_usage:
best_protein:
name: best_protein
description: the specific protein identifier most correctly grouped to its associated
peptide sequences
domain_of:
- PeptideQuantification
- ProteinQuantification
all_proteins:
name: all_proteins
description: the grouped list of protein identifiers associated with the peptide
sequences that were grouped to a best protein
domain_of:
- PeptideQuantification
- ProteinQuantification
class_uri: nmdc:ProteinQuantification
Induced
name: ProteinQuantification
description: This is used to link a metaproteomics analysis workflow to a specific
protein
from_schema: https://w3id.org/nmdc/nmdc
slot_usage:
best_protein:
name: best_protein
description: the specific protein identifier most correctly grouped to its associated
peptide sequences
domain_of:
- PeptideQuantification
- ProteinQuantification
all_proteins:
name: all_proteins
description: the grouped list of protein identifiers associated with the peptide
sequences that were grouped to a best protein
domain_of:
- PeptideQuantification
- ProteinQuantification
attributes:
all_proteins:
name: all_proteins
description: the grouped list of protein identifiers associated with the peptide
sequences that were grouped to a best protein
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: all_proteins
owner: ProteinQuantification
domain_of:
- PeptideQuantification
- ProteinQuantification
range: GeneProduct
multivalued: true
best_protein:
name: best_protein
description: the specific protein identifier most correctly grouped to its associated
peptide sequences
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: best_protein
owner: ProteinQuantification
domain_of:
- PeptideQuantification
- ProteinQuantification
range: GeneProduct
peptide_sequence_count:
name: peptide_sequence_count
description: count of peptide sequences grouped to the best_protein
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: peptide_sequence_count
owner: ProteinQuantification
domain_of:
- ProteinQuantification
range: integer
protein_spectral_count:
name: protein_spectral_count
description: sum of filter passing MS2 spectra associated with the best protein
within a given LC-MS/MS data file
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: protein_spectral_count
owner: ProteinQuantification
domain_of:
- ProteinQuantification
range: integer
protein_sum_masic_abundance:
name: protein_sum_masic_abundance
description: combined MS1 extracted ion chromatograms derived from MS2 spectra
associated with the best protein from a given LC-MS/MS data file using the MASIC
tool
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: protein_sum_masic_abundance
owner: ProteinQuantification
domain_of:
- ProteinQuantification
range: integer
type:
name: type
description: the class_uri of the class that has been instantiated
notes:
- replaces legacy nmdc:type slot
- makes it easier to read example data files
- required for polymorphic MongoDB collections
examples:
- value: nmdc:Biosample
- value: nmdc:Study
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- https://github.com/microbiomedata/nmdc-schema/issues/1048
- https://github.com/microbiomedata/nmdc-schema/issues/1233
- https://github.com/microbiomedata/nmdc-schema/issues/248
rank: 1000
slot_uri: rdf:type
designates_type: true
alias: type
owner: ProteinQuantification
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
class_uri: nmdc:ProteinQuantification