TreeOfSex.yml

# Definitions for importing CSV spreadsheets for the Tree of Sex WG

traitdb_spreadsheet_template:
  template_name: Tree of Sex
  # All taxonomy columns specified here are required
  taxonomy_columns: # keys are the local to the app.  Values are literals in the CSV
    kingdom: Kingdom # For plants or animals
    htg: Higher taxonomic group
    order: Order
    family: Family
    genus: Genus
    species: species
    species_author: species author # In template, only for plants.  Don't have a way to hide these for animals
    infraspecific: infraspecific # In template, only exists for plants.  Don't have a way to hide these for animals
  # Metadata columns are optional, could refactor into two groups
  metadata_columns:
    common_name: common name
    notes: notes, comments
    entry_name: entry name
    entry_email: entry email
    theplantlist_name: Name in ThePlantListV1.1
    theplantlist_status: ThePlantListV1.1 (1=accepted at species level,-1=recognized synonym,0=other)
    gametophytic_chromosome_number: Gametophytic chromosome number
    sporophytic_chromosome_number: Sporophytic chromosome number
    woodiness_count: Woodiness count
  trait_groups: # these define a relationship of a taxonomy to a set of traits.  They can only be applied after data is imported
    -
      name: Plants
      taxonomic_rank: kingdom
      taxon_name: Plantae
    - 
      name: Animals
      taxonomic_rank: kingdom
      taxon_name: Animal
  trait_options:
    source_prefix: "source: " # include the space after the colon
    require_source: true # source rules for formatting?
    notes_prefix: "notes: " #include the space after the colon
    value_separator: "|" # what separates multiple values in an entry
  # No trait is required.  could have a list of required traits
  categorical_trait_columns:
    -
      name: Hybrid # Denoted as hybrid based on species name; add reference to notes column if known from other data
      values: ["0","1"]
      groups: [Plants]
    -
      name: Sexual System
      values:
        - hermaphrodite
        - monoecy
        - dioecy
        - gynodioecy
        - androdioecy
        - gynomonoecy
        - andromonoecy
        - polygamodioecy
        - polygamomonoecy
        - apomictic
        - parthenogenetic
        - gonochorous
        - gonochoristic
        - other
      groups: [Plants, Animals]
    -
      name: Selfing
      values:
        - self incompatible
        - self compatible
      groups: [Plants]
    -
      name: Growth Form
      values:
        - woody
        - herb
        - shrub
        - tree
        - herbaceous vine
        - liana/woody vine
      groups: [Plants]
    -
      name: Life Form
      values:
        - annual
        - perennial
      groups: [Plants]
    -
      name: Karyotype
      values:
        - ZO
        - ZW
        - XY
        - XO
        - WO
        - homomorphic
        - complex XY
        - complex ZW
        - complex XO
      groups: [Plants, Animals]
    -
      name: Molecular basis
      values:
        - dosage
        - Y dominant
        - W dominant
      groups: [Plants, Animals]
    -
      name: Genotypic
      values:
        - male heterogametic
        - female heterogametic
        - GSD
        - polygenic
      groups: [Plants, Animals]
    -
      name: Haplodiploidy
      values: 
        - arrhenotoky
        - paternal genome elimination
        - other
      groups: [Animals]
    -
      name: Environmental
      values:
        - TSD
        - TSD Ia
        - TSD Ib
        - TSD II
        - size
        - density
        - pH
        - ESD_other
      groups: [Animals]
    -
      name: Polyfactorial
      values: ["yes", "no"]
      groups: [Animals]
    -
      name: Woodiness
      values: [W, H, variable]
      groups: [Plants]
    -
      name: Heterostyly
      values: [tristyly, distyly, homostyly, other]
      groups: [Plants]
    -
      name: Predicted ploidy
      values: ["1","2","3","4","5","6"]
      groups: [Animals]
  continuous_trait_columns:
    -
      name: Gametophytic chromosome number (minimum)
      format: integer # formats are only for display
      groups: [Plants]
    -
      name: Gametophytic chromosome number (mean)
      format: integer # formats are only for display
      groups: [Plants]
    -
      name: Sporophytic chromosome number (minimum)
      format: integer
      groups: [Plants]
    -
      name: Sporophytic chromosome number (mean)
      format: integer
      groups: [Plants]
    -
      name: Chromosome number (female) 2N
      format: integer
      groups: [Animals]
    -
      name: Chromosome number (male) 2N
      format: integer
      groups: [Animals]
    -
      name: C-value
      format: float
      groups: [Animals]