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Class: PortableMicrohaplotypeObject

Information on final results from a targeted amplicon analysis

URI: portable_microhaplotype_object:PortableMicrohaplotypeObject

classDiagram class PortableMicrohaplotypeObject click PortableMicrohaplotypeObject href "../PortableMicrohaplotypeObject" PortableMicrohaplotypeObject : experiment_infos PortableMicrohaplotypeObject --> "1..*" ExperimentInfo : experiment_infos click ExperimentInfo href "../ExperimentInfo" PortableMicrohaplotypeObject : microhaplotypes_detected PortableMicrohaplotypeObject --> "1" MicrohaplotypesDetected : microhaplotypes_detected click MicrohaplotypesDetected href "../MicrohaplotypesDetected" PortableMicrohaplotypeObject : panel_info PortableMicrohaplotypeObject --> "1" PanelInfo : panel_info click PanelInfo href "../PanelInfo" PortableMicrohaplotypeObject : pmo_name PortableMicrohaplotypeObject : postprocessing_bioinformatics_infos PortableMicrohaplotypeObject --> "0..1" BioMethod : postprocessing_bioinformatics_infos click BioMethod href "../BioMethod" PortableMicrohaplotypeObject : representative_microhaplotype_sequences PortableMicrohaplotypeObject --> "1..*" RepresentativeMicrohaplotypeSequences : representative_microhaplotype_sequences click RepresentativeMicrohaplotypeSequences href "../RepresentativeMicrohaplotypeSequences" PortableMicrohaplotypeObject : sequencing_infos PortableMicrohaplotypeObject --> "1" SequencingInfo : sequencing_infos click SequencingInfo href "../SequencingInfo" PortableMicrohaplotypeObject : specimen_infos PortableMicrohaplotypeObject --> "1..*" SpecimenInfo : specimen_infos click SpecimenInfo href "../SpecimenInfo" PortableMicrohaplotypeObject : taramp_bioinformatics_infos PortableMicrohaplotypeObject --> "1" TarAmpBioinformaticsInfo : taramp_bioinformatics_infos click TarAmpBioinformaticsInfo href "../TarAmpBioinformaticsInfo" PortableMicrohaplotypeObject : target_demultiplexed_experiment_samples PortableMicrohaplotypeObject --> "0..1" DemultiplexedExperimentSamples : target_demultiplexed_experiment_samples click DemultiplexedExperimentSamples href "../DemultiplexedExperimentSamples"

Slots

Name Cardinality and Range Description Inheritance
pmo_name 1
String		 a name for this PMO, can be a concatenation of names if combined more than on... direct
experiment_infos 1..*
ExperimentInfo		 a list of experiments of all the seq/amp of samples within this project direct
specimen_infos 1..*
SpecimenInfo		 a list of SpecimenInfo of all the samples within this project direct
sequencing_infos 1
SequencingInfo		 the sequencing info for this project direct
panel_info 1
PanelInfo		 the info on the targeted sequencing panel used for this project direct
representative_microhaplotype_sequences 1..*
RepresentativeMicrohaplotypeSequences		 a list of the representative sequences for the results for this project direct
microhaplotypes_detected 1
MicrohaplotypesDetected		 the microhaplotypes detected in this projects direct
target_demultiplexed_experiment_samples 0..1
DemultiplexedExperimentSamples		 the raw demultiplex target counts for each sample direct
taramp_bioinformatics_infos 1
TarAmpBioinformaticsInfo		 the bioinformatics pipeline/methods used to generated the amplicon analysis f... direct
postprocessing_bioinformatics_infos 0..1
BioMethod		 any additional methods that were applied to the processing of this file/analy... direct

Identifier and Mapping Information

Schema Source

  • from schema: https://plasmogenepi.github.io/portable-microhaplotype-object

Mappings

Mapping Type Mapped Value
self portable_microhaplotype_object:PortableMicrohaplotypeObject
native portable_microhaplotype_object:PortableMicrohaplotypeObject

LinkML Source

Direct

name: PortableMicrohaplotypeObject
description: Information on final results from a targeted amplicon analysis
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  pmo_name:
    name: pmo_name
    description: a name for this PMO, can be a concatenation of names if combined
      more than one PMO
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: true
    domain_of:
    - PortableMicrohaplotypeObject
    range: string
    required: true
  experiment_infos:
    name: experiment_infos
    description: a list of experiments of all the seq/amp of samples within this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: ExperimentInfo
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  specimen_infos:
    name: specimen_infos
    description: a list of SpecimenInfo of all the samples within this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: SpecimenInfo
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  sequencing_infos:
    name: sequencing_infos
    description: the sequencing info for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: SequencingInfo
    required: true
    inlined: true
    inlined_as_list: true
  panel_info:
    name: panel_info
    description: the info on the targeted sequencing panel used for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: PanelInfo
    required: true
  representative_microhaplotype_sequences:
    name: representative_microhaplotype_sequences
    description: a list of the representative sequences for the results for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: RepresentativeMicrohaplotypeSequences
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  microhaplotypes_detected:
    name: microhaplotypes_detected
    description: the microhaplotypes detected in this projects
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: MicrohaplotypesDetected
    required: true
  target_demultiplexed_experiment_samples:
    name: target_demultiplexed_experiment_samples
    description: the raw demultiplex target counts for each sample
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: DemultiplexedExperimentSamples
    required: false
    inlined: true
    inlined_as_list: true
  taramp_bioinformatics_infos:
    name: taramp_bioinformatics_infos
    description: the bioinformatics pipeline/methods used to generated the amplicon
      analysis for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: TarAmpBioinformaticsInfo
    required: true
    inlined: true
    inlined_as_list: true
  postprocessing_bioinformatics_infos:
    name: postprocessing_bioinformatics_infos
    description: any additional methods that were applied to the processing of this
      file/analysis, this can be filtering, adding info etc
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    domain_of:
    - PortableMicrohaplotypeObject
    range: BioMethod
    required: false
    inlined: true
    inlined_as_list: true
tree_root: true

Induced

name: PortableMicrohaplotypeObject
description: Information on final results from a targeted amplicon analysis
from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
attributes:
  pmo_name:
    name: pmo_name
    description: a name for this PMO, can be a concatenation of names if combined
      more than one PMO
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    identifier: true
    alias: pmo_name
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: string
    required: true
  experiment_infos:
    name: experiment_infos
    description: a list of experiments of all the seq/amp of samples within this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: experiment_infos
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: ExperimentInfo
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  specimen_infos:
    name: specimen_infos
    description: a list of SpecimenInfo of all the samples within this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: specimen_infos
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: SpecimenInfo
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  sequencing_infos:
    name: sequencing_infos
    description: the sequencing info for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: sequencing_infos
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: SequencingInfo
    required: true
    inlined: true
    inlined_as_list: true
  panel_info:
    name: panel_info
    description: the info on the targeted sequencing panel used for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: panel_info
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: PanelInfo
    required: true
  representative_microhaplotype_sequences:
    name: representative_microhaplotype_sequences
    description: a list of the representative sequences for the results for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: representative_microhaplotype_sequences
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: RepresentativeMicrohaplotypeSequences
    required: true
    multivalued: true
    inlined: true
    inlined_as_list: true
  microhaplotypes_detected:
    name: microhaplotypes_detected
    description: the microhaplotypes detected in this projects
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: microhaplotypes_detected
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: MicrohaplotypesDetected
    required: true
  target_demultiplexed_experiment_samples:
    name: target_demultiplexed_experiment_samples
    description: the raw demultiplex target counts for each sample
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: target_demultiplexed_experiment_samples
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: DemultiplexedExperimentSamples
    required: false
    inlined: true
    inlined_as_list: true
  taramp_bioinformatics_infos:
    name: taramp_bioinformatics_infos
    description: the bioinformatics pipeline/methods used to generated the amplicon
      analysis for this project
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: taramp_bioinformatics_infos
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: TarAmpBioinformaticsInfo
    required: true
    inlined: true
    inlined_as_list: true
  postprocessing_bioinformatics_infos:
    name: postprocessing_bioinformatics_infos
    description: any additional methods that were applied to the processing of this
      file/analysis, this can be filtering, adding info etc
    from_schema: https://plasmogenepi.github.io/portable-microhaplotype-object
    rank: 1000
    alias: postprocessing_bioinformatics_infos
    owner: PortableMicrohaplotypeObject
    domain_of:
    - PortableMicrohaplotypeObject
    range: BioMethod
    required: false
    inlined: true
    inlined_as_list: true
tree_root: true