Class: Analyte

name: Analyte
description: Table containing analyte information
from_schema: https://w3id.org/madanucd/gregor_linkml
slots:
- analyte_id
- participant_id
- analyte_type
- analyte_processing_details
- primary_biosample
- primary_biosample_id
- primary_biosample_details
- tissue_affected_status
- age_at_collection
- participant_drugs_intake
- participant_special_diet
- hours_since_last_meal
- passage_number
- time_to_freeze
- sample_transformation_detail
- quality_issues

name: Analyte
description: Table containing analyte information
from_schema: https://w3id.org/madanucd/gregor_linkml
attributes:
  analyte_id:
    name: analyte_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: analyte_id
    owner: Analyte
    domain_of:
    - Analyte
    - Experiment_dna_short_read
    - Experiment_rna_short_read
    - Experiment_nanopore
    - Experiment_pac_bio
    - Experiment_atac_short_read
    range: string
    required: true
  participant_id:
    name: participant_id
    description: ''
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: participant_id
    owner: Analyte
    domain_of:
    - Participant
    - Phenotype
    - Genetic_findings
    - Analyte
    - Experiment
    - Aligned
    range: string
    required: true
  analyte_type:
    name: analyte_type
    description: analyte derived from the primary_biosample. The actual thing you're
      sticking into a machine to analyze/sequence
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: analyte_type
    owner: Analyte
    domain_of:
    - Analyte
    range: Analyte_typeEnum
    required: true
  analyte_processing_details:
    name: analyte_processing_details
    description: details about how the analyte or original biosample was extracted
      or processed
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: analyte_processing_details
    owner: Analyte
    domain_of:
    - Analyte
    range: string
  primary_biosample:
    name: primary_biosample
    description: Tissue type of biosample taken from the participant that the analyte
      was extracted or processed from (for unknown can use tissue - UBERON:0000479),
      e.g. skin, liver, brain
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: primary_biosample
    owner: Analyte
    domain_of:
    - Analyte
    range: Primary_biosampleEnum
    required: true
  primary_biosample_id:
    name: primary_biosample_id
    description: Optional ID for the biosample; allows for linking of multiple analytes
      extracted or processed from the same biosample
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: primary_biosample_id
    owner: Analyte
    domain_of:
    - Analyte
    range: string
  primary_biosample_details:
    name: primary_biosample_details
    description: Free text to capture information not in structured fields
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: primary_biosample_details
    owner: Analyte
    domain_of:
    - Analyte
    range: string
  tissue_affected_status:
    name: tissue_affected_status
    description: If applicable to disease (suspected mosaic), is the tissue from an
      affected source or an unaffected source?
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: tissue_affected_status
    owner: Analyte
    domain_of:
    - Analyte
    range: Tissue_affected_statusEnum
  age_at_collection:
    name: age_at_collection
    description: age or participant in years at biosample collection
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: age_at_collection
    owner: Analyte
    domain_of:
    - Analyte
    range: float
  participant_drugs_intake:
    name: participant_drugs_intake
    description: The list of drugs patient is on, at the time of sample collection.
      This information is helpful during analysis of metabolomics and immune asssays.
      Free Text
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: participant_drugs_intake
    owner: Analyte
    domain_of:
    - Analyte
    range: string
  participant_special_diet:
    name: participant_special_diet
    description: If the patient was fasting, when the sample was collected. this is
      relevant when analyzing metabolomics data. Free Text
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: participant_special_diet
    owner: Analyte
    domain_of:
    - Analyte
    range: string
  hours_since_last_meal:
    name: hours_since_last_meal
    description: his is relevant when analyzing metabolomics data
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: hours_since_last_meal
    owner: Analyte
    domain_of:
    - Analyte
    range: float
  passage_number:
    name: passage_number
    description: passage_number is relevant for fibroblast cultures and possibly iPSC.
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: passage_number
    owner: Analyte
    domain_of:
    - Analyte
    range: integer
  time_to_freeze:
    name: time_to_freeze
    description: time (in hours) from collection to freezing the sample. delayed freeze
      turns out to be useful / important info for PaxGene blood (for RNA isolation).
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: time_to_freeze
    owner: Analyte
    domain_of:
    - Analyte
    range: float
  sample_transformation_detail:
    name: sample_transformation_detail
    description: details regarding sample transformation
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: sample_transformation_detail
    owner: Analyte
    domain_of:
    - Analyte
    range: string
  quality_issues:
    name: quality_issues
    description: describe if there are any QC issues that would be important to note
    from_schema: https://w3id.org/madanucd/gregor_linkml
    rank: 1000
    alias: quality_issues
    owner: Analyte
    domain_of:
    - Analyte
    - Aligned_dna_short_read
    - Aligned_rna_short_read
    - Aligned_nanopore
    range: string