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 --> "1" GeneProduct : best_protein
click GeneProduct href "../GeneProduct"
ProteinQuantification : peptide_sequence_count
ProteinQuantification : protein_spectral_count
ProteinQuantification : protein_sum_masic_abundance
Slots
Name | Cardinality and Range | Description | Inheritance |
---|---|---|---|
all_proteins | 0..* 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 |
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
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
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
multivalued: true
alias: all_proteins
owner: ProteinQuantification
domain_of:
- PeptideQuantification
- ProteinQuantification
range: GeneProduct
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