Class: PeptideQuantification
This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information
URI: nmdc:PeptideQuantification
classDiagram
class PeptideQuantification
click PeptideQuantification href "../PeptideQuantification"
PeptideQuantification : all_proteins
PeptideQuantification --> "*" GeneProduct : all_proteins
click GeneProduct href "../GeneProduct"
PeptideQuantification : best_protein
PeptideQuantification --> "0..1" GeneProduct : best_protein
click GeneProduct href "../GeneProduct"
PeptideQuantification : min_q_value
PeptideQuantification : peptide_sequence
PeptideQuantification : peptide_spectral_count
PeptideQuantification : peptide_sum_masic_abundance
PeptideQuantification : type
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
type | 1 Uriorcurie |
the class_uri of the class that has been instantiated | direct |
all_proteins | * GeneProduct |
the list of protein identifiers that are associated with the peptide sequence | direct |
best_protein | 0..1 GeneProduct |
the specific protein identifier most correctly associated with the peptide se... | direct |
min_q_value | 0..1 Float |
smallest Q-Value associated with the peptide sequence as provided by MSGFPlus... | direct |
peptide_sequence | 0..1 String |
direct | |
peptide_spectral_count | 0..1 Integer |
sum of filter passing MS2 spectra associated with the peptide sequence within... | direct |
peptide_sum_masic_abundance | 0..1 Integer |
combined MS1 extracted ion chromatograms derived from MS2 spectra associated ... | direct |
Usages
used by | used in | type | used |
---|---|---|---|
MetaproteomicsAnalysis | has_peptide_quantifications | range | PeptideQuantification |
Identifier and Mapping Information
Schema Source
- from schema: https://w3id.org/nmdc/nmdc
Mappings
Mapping Type | Mapped Value |
---|---|
self | nmdc:PeptideQuantification |
native | nmdc:PeptideQuantification |
LinkML Source
Direct
name: PeptideQuantification
description: This is used to link a metaproteomics analysis workflow to a specific
peptide sequence and related information
from_schema: https://w3id.org/nmdc/nmdc
slots:
- type
- all_proteins
- best_protein
- min_q_value
- peptide_sequence
- peptide_spectral_count
- peptide_sum_masic_abundance
class_uri: nmdc:PeptideQuantification
Induced
name: PeptideQuantification
description: This is used to link a metaproteomics analysis workflow to a specific
peptide sequence and related information
from_schema: https://w3id.org/nmdc/nmdc
attributes:
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: PeptideQuantification
domain_of:
- EukEval
- FunctionalAnnotationAggMember
- MobilePhaseSegment
- PortionOfSubstance
- MagBin
- MetaboliteIdentification
- PeptideQuantification
- ProteinQuantification
- GenomeFeature
- FunctionalAnnotation
- AttributeValue
- NamedThing
- FailureCategorization
- Protocol
- CreditAssociation
- Doi
range: uriorcurie
required: true
all_proteins:
name: all_proteins
description: the list of protein identifiers that are associated with the peptide
sequence
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: all_proteins
owner: PeptideQuantification
domain_of:
- PeptideQuantification
- ProteinQuantification
range: GeneProduct
multivalued: true
best_protein:
name: best_protein
description: the specific protein identifier most correctly associated with the
peptide sequence
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: best_protein
owner: PeptideQuantification
domain_of:
- PeptideQuantification
- ProteinQuantification
range: GeneProduct
min_q_value:
name: min_q_value
description: smallest Q-Value associated with the peptide sequence as provided
by MSGFPlus tool
from_schema: https://w3id.org/nmdc/nmdc
see_also:
- OBI:0001442
rank: 1000
alias: min_q_value
owner: PeptideQuantification
domain_of:
- PeptideQuantification
range: float
peptide_sequence:
name: peptide_sequence
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: peptide_sequence
owner: PeptideQuantification
domain_of:
- PeptideQuantification
range: string
peptide_spectral_count:
name: peptide_spectral_count
description: sum of filter passing MS2 spectra associated with the peptide sequence
within a given LC-MS/MS data file
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: peptide_spectral_count
owner: PeptideQuantification
domain_of:
- PeptideQuantification
range: integer
peptide_sum_masic_abundance:
name: peptide_sum_masic_abundance
description: combined MS1 extracted ion chromatograms derived from MS2 spectra
associated with the peptide sequence from a given LC-MS/MS data file using the
MASIC tool
from_schema: https://w3id.org/nmdc/nmdc
rank: 1000
alias: peptide_sum_masic_abundance
owner: PeptideQuantification
domain_of:
- PeptideQuantification
range: integer
class_uri: nmdc:PeptideQuantification