trek.yaml

id: http://w3id.org/ontogpt/trek
name: trek-template
title: TReK Template
description: >-
  A template for TReK
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
  linkml: https://w3id.org/linkml/
  schema: http://schema.org/
  ENVO: http://purl.obolibrary.org/obo/ENVO_
  SWEET: http://sweetontology.net/

default_prefix: trek
default_range: string

imports:
  - linkml:types
  - core
  
classes:
  TReKAnnotations:
    tree_root: true
    is_a: NamedEntity
    attributes:
      dois:
        description: permanent identifier for the article.
        range: DOI
        annotations:
          prompt: extract the DOI related to the article.
      management_actions:
        description: A semicolon-separated list of ecosystem management actions being taken as part of the study.
        range: ManagementAction
        multivalued: true
        annotations:
          prompt: semicolon-separated list of environmental management actions analyzed
      target_species:
        description: A semicolon-separated list of focal species for the restoration project.
        multivalued: true
        range: FocalSpecies
        annotations:
          prompt: semicolon-separated list of the scientific names of species that are the focus of the restoration project
      ecosystem_types: 
        description: A semicolon-separated list of the types of ecosystem the restoration is taking place in.
        range: Ecosystem
        multivalued: true
        annotations:
          prompt: semicolon-separated list of ecosystem types
      study_sites: 
        description: A semicolon-separated list of the location(s) of the research study
        range: Site
        multivalued: true
        annotations:
          prompt: semicolon-separated list of locations, using decimal degrees, of the study sites
      degradation_types:
        range: Degradation
        description: A semicolon-separated list of the types of degradation being addressed.
        multivalued: true
        annotations:
          prompt: semicolon-separated list of the types of degradation addressed by the restoration project
  
  DOI:
    is_a: NamedEntity
  
  ManagementAction: 
    is_a: NamedEntity
    description: An ecosystem management action being taken as part of the study.
    id_prefixes:
      - ENVO
      - ENVTHES
    annotations:
      annotators: sqlite:obo:envo, bioportal:envthes
  
  FocalSpecies:
    is_a: NamedEntity
    description: A focal species in the restoration project.
    id_prefixes:
      - NCBITAXON
    annotations:
      annotators: sqlite:obo:envo, bioportal:envthes, bioportal:ncbitaxon

  Ecosystem:
    is_a: NamedEntity
    description: An ecosystem the restoration is taking place in.
    id_prefixes:
      - ENVO
      - SWEET
      - ENVTHES
    annotations:
      annotators: sqlite:obo:envo, bioportal:envthes  

  Site: 
    is_a: NamedEntity
    description: A geographic location of the research study.
    id_prefixes:
      - GAZ
      - ENVTHES
    annotations:
      annotators: sqlite:obo:envo, bioportal:gaz, bioportal:envthes
  
  Degradation:
    is_a: NamedEntity
    description: A type of ecological degradation being addressed.
    id_prefixes:
      - ENVO
      - SWEET
      - ENVTHES
    annotations:
      annotators: sqlite:obo:envo, bioportal:envthes