Class: PeptideQuantification (DEPRECATED)

This is used to link a metaproteomics analysis workflow to a specific peptide sequence and related information

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

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
deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
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
deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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