Class: ProteinQuantification (DEPRECATED)

This is used to link a metaproteomics analysis workflow to a specific protein

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 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
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
deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
from_schema: https://w3id.org/nmdc/nmdc
slots:
- all_proteins
- best_protein
- peptide_sequence_count
- protein_spectral_count
- protein_sum_masic_abundance
- type
class_uri: nmdc:ProteinQuantification

Induced

name: ProteinQuantification
description: This is used to link a metaproteomics analysis workflow to a specific
  protein
deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
from_schema: https://w3id.org/nmdc/nmdc
attributes:
  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: ProteinQuantification
    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: ProteinQuantification
    domain_of:
    - PeptideQuantification
    - ProteinQuantification
    range: GeneProduct
  peptide_sequence_count:
    name: peptide_sequence_count
    description: count of peptide sequences grouped to the best_protein
    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_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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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
    deprecated: not used. 2024-11 https://github.com/microbiomedata/nmdc-schema/issues/2250
    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