srp_templates.yaml

id: http://w3id.org/linkml/examples/srpanalyics
name: srpanalytics
prefixes:
   linkml: https://w3id.org/linkml
   coderdata: https://w3id.org/linkml/examples/srpanalytics
   schema: http://schema.org/
imports:
   - linkml:types
default_range: string
default_prefix: srpanalytics

slots:
  chemical.id:
    description: Chemical identifier as prescribed by the Tanguay lab, maps to value in mapping file. 
    identifier: true
    slot_uri: schema:identifier
  bottle.id:
    description: Identifier for bottle.
    identifier: true
    slot_uri: schema:identifier
  conc:
    description: concentration of the measurement. units are always in uM
    range: numeric
  plate.id:
    description: Identifier for zebrafish plate
  well:
    description: Idnetifier for well on plate. Are we sure this is a string?
  date:
    description: Date collected written as YYYYMMDD.
    range: numeric
classes:
  morphology:
    description: Morphology data from the Tanguay LIMS
    slots:
      - chemical.id
      - bottle.id
      - conc
      - well
      - date
      - endpoint
      - value
    attributes:
     endpoint:
       description: Name of specific endpoint
       range: zebrafish_morphology
     value:
       description: Numeric representing whether or not a zebrafish was observed in this well with the endpoint.
       range: numeric
  behavior:
    slots:
      - chemical.id
      - bottle.id
      - conc
      - well
      - date
    attributes:
     endpoint:
       description: Name of time point from t0 to t67, each representing 6 second time points
     value:
       description: Numeric or NA vaule representing the behavior measurement at this time point
       range: linkml:Any
  zebrafishMapping:
    description: Mapping file for the zebrafish data
    slots:
      - bottle.id
      - chemical.id
      - casrn
    attributes:
      chemical.name:
        description:
      casrn:
        description: CAS Number
  fses:
    description: FSES data exported from the Anderson lab
    attributes:
       SampleNumber:
         description:
       date_sampled:
         description:
       sample_matrix:
         description:
       technology:
         description:
       Sample_ID:
         description:
         range: numeric
       zf_lims_id:
         description: Should match to bottle.id slot above
       cas_number:
         description: Important- this is the CAS identifier of the chemical measured
         range: string
       ClientName:
         description: Name of client supplying sample 
       SampleName:
         description: Name of sample
       LocationLat:
         description: Latitude of sample collection site. Can be numeric or missing
         range: linkml:Any
       LocationLon:
         description: Logitude of sample collection sate. Can be numeric or missing
         range: linkml:Any
       LocationName:
         description: Name of location
       AlternateName:
         description: Alternate name of location
       LocationAlternateDescription:
         description: Alternate location description
       Chemical_ID:
         description: Chemical identifier if present
         range: numeric
       measurement_value:
         description: concentration of chemical in passive sampling device. Numeric or 'BDL' if below detected level.
         range: numeric
       measurement_value_qualifier:
         description: flag required to determine if value is valid- J, Null, Or NA
         range:
            measurementQualifier
       measurement_value_unit:
         description: unit of measurement value
       measurement_value_molar:
         description: measurement value in moles
         range: numeric
       measurement_value_molar_unit:
         description: unit of molar measurement value
       environmental_concentration:
         description: concentration of chemical in environemnet
         range: numeric
       environmental_concentration_qualifier:
         description: qualifier determining if the concentration is good
       environmental_concentration_unit:
          description: unit of concentration value  
       environmental_concentration_molar:
         description: measurement value in moles
         range: numeric
       environmental_concentration_molar_unit:
         description: unit of molar measurement value       
       parentSampleNumber:
         description: ??
       childSampleNumber:
         description: ??
       projectName:
         description: Name of project to be displayed on portal
       date_sample_start:
         description: Date that sample was collected
       projectLink:
         description: URL to projet information for portal
  
enums:
  measurementQualifer:
    permissible_values:
      J:
        description:
      U:
        description:
      NULL:
        description:
      JB:
        description:
  zebrafish_morphology:
    permissible_values:
      MO24:
        description:
      DP24:
        description:
      SM24:
        description:
      NC24:
        description:
      MORT:
        description:
      YSE_:
        description:
      AXIS:
        description:
      EYE_:
        description:
      SNOU:
        description:
      JAW_:
        description:
      OTIC:
        description:
      PE__:
        description:
      BRAI:
        description:
      SOMI:
        description:
      PFIN:
        description:
      CFIN:
        description:
      PIG_:
        description:
      CIRC:
        description:
      TRUN:
        description:
      SWIM:
        description:
      NC__:
        description:
      TR__:
        description:
      DNC_:
        description: