PPOD.yaml

# PPOD LinkML schema for UC Davis Food Systems Lab information

id: https://github.com/PPODschema/PPOD_FSL
name: PPOD_FSL
version: v0.9.8
license: https://creativecommons.org/publicdomain/zero/1.0/
prefixes:
  linkml: https://w3id.org/linkml/
  foaf: http://xmlns.com/foaf/0.1/
  skos: http://www.w3.org/2004/02/skos/core#
  dcterms: http://purl.org/dc/terms/
  org: http://www.w3.org/ns/org#
  core: http://vivoweb.org/ontology/core#
  obo: http://purl.obolibrary.org/obo/
  sds: http://www.sdsconsortium.org/schemas/sds-okn.owl#
  fsl: https://raw.githubusercontent.com/adhollander/FSLschemas/main/sustsource.owl#
  fsls: https://raw.githubusercontent.com/adhollander/FSLschemas/main/fsisupp.owl#
  fsli: https://raw.githubusercontent.com/adhollander/FSLschemas/main/sustsourceindiv.rdf#
  fslp: https://raw.githubusercontent.com/adhollander/FSLschemas/main/CA_PPODterms.ttl#
  FRAPO: http://purl.org/cerif/frapo/
  poder: http://poderopedia.com/vocab/
  dbpo: http://dbpedia.org/ontology/
  wgs84: http://www.w3.org/2003/01/geo/wgs84_pos#
  frbrer: http://iflastandards.info/ns/fr/frbr/frbrer/
  dg: https://w3id.org/dingo#
  rdfs: http://www.w3.org/2000/01/rdf-schema#
  schema: http://schema.org/
  agrovoc: http://aims.fao.org/aos/agrovoc/
  sio: http://semanticscience.org/resource/
  opengis: http://www.opengis.net/ont/geosparql#

imports: 
  - linkml:types
  - vocabs
default_range: string


classes:
  Container:
    class_uri: fsls:Container
    description: A class holding a list of entities in the system
    tree_root: true
    slots:
      - id
      - organizations
      - projects
      - programs
      - persons
      - guidelinemandates 
      - datasets 
      - roles 
      - tools 
      - infrastructures

    # attributes:
    #   organizations:
    #     slot_uri: fsls:organizations
    #     multivalued: true
    #     inlined_as_list: true
    #     range: Organization
    #   projects:
    #     slot_uri: fsls:projects
    #     multivalued: true
    #     inlined_as_list: true
    #     range: Project
    #   programs:
    #     slot_uri: fsls:programs
    #     multivalued: true
    #     inlined_as_list: true
    #     range: Program
    #   persons:
    #     slot_uri: fsls:persons
    #     multivalued: true
    #     inlined_as_list: true
    #     range: Person
    #   guidelinemandates:
    #     slot_uri: fsls:guidelinemandates
    #     multivalued: true
    #     inlined_as_list: true
    #     range: GuidelineMandate
    #   datasets:
    #     slot_uri: fsls:datasets
    #     multivalued: true
    #     inlined_as_list: true
    #     range: Dataset
    #   roles:
    #     slot_uri: fsls:roles
    #     multivalued: true
    #     inlined_as_list: true
    #     range: Role
    #   tools: 
    #     slot_uri: fsls:tools
    #     multivalued: true
    #     inlined_as_list: true
    #     range: Tool
      
  Organization:
    class_uri: foaf:Organization
    description: A class corresponding to social instititutions such as companies, societies etc.
    slots:
      - title
      - id
      - label
      - alias
      - is_part_of
      - is_member_of
      - in_county
      - in_ecoregion
      - associated_geography
      - has_organization_type
      - has_partner
      - is_funded_by
      - has_organization_activity
      - related_sustainability_issue
      - has_url
      - contact
      - taxa
      - cwhr_land_cover
      - commodity
      - ecological_process
      - gm_name
      - use_case
      - creator_of 
      - created_by 
      - implements
      - mandates 
      - is_bound_by 
      - has_funding_vehicle 
      - is_certified_by
      - enforces

  Project:
    class_uri: foaf:Project
    description: A class representing a project or collective endeavour of some kind
    is_a: ProjectProgram
    slots:
      - title # changed from "project" in script
      - id
      - label
      - alias 
      - is_part_of 
      - project_type
      - occurs_in 
      - lead_organization 
      - funding_organization
      - has_funding_vehicle 
      - lead_individual 
      - partner_organization 
      - located_in 
      - in_county 
      - in_ecoregion 
      - in_watershed 
      - related_sustainability_issue 
      - project_details
      - has_indicator 
      - input_of 
      - output_of 
      - has_strategy 
      - has_url 
      - taxa 
      - cwhr_land_cover 
      - ecological_process
      - start_year
      - end_year 
      - is_funded_by 
      - latitude 
      - longitude 
      - fsl_doc 
      - use_case
      - is_contained_in
      - contains
      - intersects
      - creator_of 

  Program: 
    class_uri: core:Program
    description: A plan of action to accomplish a specified end, usually taken as an initiative by an organization
    is_a: ProjectProgram
    slots:
      - title
      - id
      - label
      - alias
      - program_type
      - lead_organization
      - partner_organization
      - related_sustainability_issue
      - lead_individual
      - gm_name
      - in_county
      - in_ecoregion
      - has_url
      - taxa
      - use_case

  Person:
    class_uri: foaf:Person
    description: A class representing a person
    slots:
      - label
      - id 
      - full_name
      - last_name
      - first_name
      - email 
      - phone 
      - related_sustainability_issue
      - note 
      - use_case

  GuidelineMandate: 
    class_uri: sds:BestPracticesAndMandates
    description: A class representing a mandate or a guideline such as specific regulations or certification standards
    slots:
      - title
      - id
      - label
      - alias
      - related_sustainability_issue
      - guideline_or_mandate_type
      - has_date 
      - government_level
      - in_county
      - in_ecoregion
      - has_url
      - taxa
      - cwhr_land_cover
      - ecological_process
      - use_case
      - authorizes
      - binds 
      - mandates

  Dataset:
    class_uri: core:Dataset
    description: A named collection of data, usually containing only one type of data
    slots:
      - title
      - id
      - label
      - created_by
      - related_sustainability_issue
      - mandated_by
      - has_url
      - use_case

  Role:
    class_uri: obo:BFO_0000023
    description: A function or position of an entity with respect to another entity, for instance a person within an organization
    slots:
      - label
      - id
      - has_participant
      - role_of
      - involved_in
      - title
      - position_type
      - start_year
      - end_year
      - has_role
    slot_usage:
      title:
        required: false

  Tool: 
    class_uri: sds:Tool
    description: A physical implement, procedure, software, or method used to analyse or take a closer look at something 
    slots:
      - title
      - id 
      - label
      - alias 
      - created_by
      - related_sustainability_issue
      - has_url
      - has_input 
      - has_output
      - references

  Infrastructure:
#    class_uri: agrovoc:c_26790
    class_uri: fsls:infrastructure
    description: The basic facilities, equipment, or underlying framework that are necessary for a system or organization to function.
    slots:
      - title
      - id
      - label
      - alias
      - infrastructure_type
      - is_part_of_infrastructure
      - organization_owner
      - organization_manager
      - organization_user
      - involved_in
#      - in_project
#      - in_program
      - has_capacity
      - in_county
      - in_ecoregion
      - issue_addressed_on_purpose
      - other_issues_affected
      - associated_geography
      - upstream_infrastructure
      - downstream_infrastructure
      - adjacent_infrastructure
      - intersecting_infrastructure
      - has_url
      - taxa
      - cwhr_land_cover
  ProjectProgram:
    description: An abstract class that is the union of the project and program classes.
    abstract: true
      
slots:
  organizations:
    slot_uri: fsls:organizations
    description: a list of URIs of the organizations in this database
    multivalued: true
    inlined_as_list: true
    range: Organization
  projects:
    slot_uri: fsls:projects
    description: a list of URIs of the projects in this database
    multivalued: true
    inlined_as_list: true
    range: Project
  programs:
    slot_uri: fsls:programs
    description: a list of URIs of the programs in this database
    multivalued: true
    inlined_as_list: true
    range: Program
  persons:
    slot_uri: fsls:persons
    description: a list of URIs of the people in this database
    multivalued: true
    inlined_as_list: true
    range: Person
  guidelinemandates:
    slot_uri: fsls:guidelinemandates
    description: a list of URIs of the guidelines/mandates in this database
    multivalued: true
    inlined_as_list: true
    range: GuidelineMandate
  datasets:
    slot_uri: fsls:datasets
    description: a list of URIs of the datasets in this database
    multivalued: true
    inlined_as_list: true
    range: Dataset
  roles:
    slot_uri: fsls:roles
    description: a list of URIs of the roles in this database
    multivalued: true
    inlined_as_list: true
    range: Role
  tools: 
    slot_uri: fsls:tools
    description: a list of URIs of the tools in this database
    multivalued: true
    inlined_as_list: true
    range: Tool
  infrastructures:
    slot_uri: fsls:infrastructure
    description: a list of URIs of the infrastructure elements in this database
    multivalued: true
    inlined_as_list: true
    range: Infrastructure


  title:
    required: false
    description:
      name of the entity
    slot_uri: dcterms:title
  id:
    description: Canonical identifier for the entity
    identifier: true
    slot_uri: schema:identifier
    range: uriorcurie
  label:
    required: true
    description: a captioning label for the entity
    slot_uri: rdfs:label
  alias:
    description:
      alternative name for the entity
    slot_uri: skos:altLabel
    multivalued: true
  is_part_of:
    description:
      entity is part of the related entity
    slot_uri: dcterms:isPartOf
#    range: Organization   # also applies to infrastructure, but how is LinkML with multiple ranges these days?
    multivalued: true
  is_member_of:
    description:
      is a member of the related entity
    slot_uri: org:memberOf 
    range: Organization
    multivalued: true
  in_county:
    description:
      entity is in the named county 
    slot_uri: fsls:inCounty
    range: County
    multivalued: true
  in_ecoregion:
    description:
      entity is in the named ecoregion 
    slot_uri: fsls:inEcoregion
    multivalued: true  
  associated_geography:
    description:
      entity has the associated geography
    slot_uri: fsls:assocGeo
    multivalued: true
  has_organization_type:
    description:
      the type of the organization
    slot_uri: org:classification
    multivalued: true
    range: OrganizationType
  has_partner:
    description:  
      partner of the organization
    slot_uri: core:hasCollaborator
    multivalued: true
    range: Organization
  is_funded_by:
    description: the entity providing funding
    slot_uri: FRAPO:isFundedBy 
    multivalued: true
    any_of:
      - range: Organization
      - range: Program
      - range: Project
  has_organization_activity:
    description: the activity carried out by the organization
    slot_uri: obo:RO_0000056   # this is what I have in the python script but maybe we want something else?
    multivalued: true
    range: OrganizationActivity
  related_sustainability_issue:
    description: a sustainability issue of interest to the entity
    slot_uri: fsls:FSI_000239
    multivalued: true
    #any_of:  # per Unions as ranges in the experimental features of the spec
     # - range: IntegratedIssue
      #- range: ComponentIssue
    range: Issue
  has_url: 
    description: URL of the entity 
    slot_uri: poder:hasURL
    multivalued: true
    range: uriorcurie
  contact: 
    description: contact information for the entity
    slot_uri: core:contactInformation 
    multivalued: false 
  taxa: 
    description: taxa of interest to the entity
    slot_uri: fsls:taxa
    multivalued: true
  cwhr_land_cover:
    description: land cover classification according to the California Wildlife Habitat Relationships classification system
    slot_uri: fsls:habitatType
    multivalued: true
    range: CWHRHabitatType
  commodity:
    description: commodity of interest to the entity
    slot_uri: fsls:commodity
    multivalued: true
    range: CommodityType
  ecological_process:
    description: ecological process of interest to the entity
    slot_uri: fsls:ecologicalProcess
    multivalued: true
  gm_name:
    description: name of guideline or mandate related to the entity
    slot_uri: fsls:GM_Name
    multivalued: true
    range: GuidelineMandate 
  mandated_by:
    description: name of guideline or mandate that requires creation of the entity
    slot_uri: fsls:mandatedBy
    multivalued: true
    range: GuidelineMandate 
  use_case: 
    description: use case the entity participates in
    slot_uri: fsls:usecase
    multivalued: true
    range: UseCases
  project_type:
    description: category describing the project
    slot_uri: fsls:projType
    multivalued: true
    range: ProjectType 
  occurs_in: 
    description: activity takes place in related entity
    slot_uri: obo:BFO_0000066
    multivalued: true
    range: uriorcurie
  lead_organization:
    description: organization leading the project
    slot_uri: fsls:leadOrg
    multivalued: true
    range: Organization
  funding_organization:
    description: entity that provides funding for the activity
    slot_uri: core:fundingAgentFor
    multivalued: true
    range: Organization 
  has_funding_vehicle:
    description: program or activity under which funding for the effort is provided
    slot_uri: core:hasFundingVehicle
    multivalued: true
  lead_individual:
    description: person who is the project lead
    slot_uri: fsls:leadIndividual
    multivalued: false
  partner_organization:
    description: an organization that is affiliated with this activity
    slot_uri: core:affiliatedOrganization
    range: Organization
    multivalued: true
  located_in: 
    description: area of occurrence of the activity
    slot_uri: obo:RO_0001025
    multivalued: false
  in_watershed:
    description: activity occurs in the given watershed
    slot_uri: fsls:inWatershed
    multivalued: true
  project_details:
    description: description of details of the project
    slot_uri: fsls:projDetails
    multivalued: false
  has_indicator:
    description: uses the associated environmental indicator
    slot_uri: fsls:hasIndicator
    multivalued: true
  input_of: 
    description: activity is the input_of the referred-to entity
    slot_uri: obo:RO_0002352
    multivalued: true
    range: Dataset
  output_of: 
    description: activity is the output_of the referred-to entity
    slot_uri: obo:RO_0002353
    multivalued: true
    range: Dataset
  has_strategy:
    description: activity uses the listed strategy
    slot_uri: fsls:hasStrategy
    multivalued: true
  start_year:
    description: start_year of the activity
    slot_uri: dbpo:startYear
    multivalued: false
  end_year:
    description: end_year of the activity
    slot_uri: dbpo:endYear
    multivalued: false
  latitude:
    description: latitude of the entity
    slot_uri: wgs84:lat
    multivalued: false
  longitude:
    description: longitude of the entity
    slot_uri: wgs84:long
    multivalued: false
  fsl_doc: 
    description: additional documentation describing the entity
    slot_uri: fsls:FSLdoc
    multivalued: false
    range: uriorcurie
  program_type:
    description: category describing the program
    slot_uri: fsls:progType
    multivalued: true
    range: ProgramType
  created_by:
    description: entity that created the given element
    slot_uri: frbrer:P2007
    multivalued: true
    range: Organization
  full_name:
    description: full name of the individual
    slot_uri: foaf:name 
    multivalued: false
  last_name:
    description: last name of the individual
    slot_uri: foaf:lastName
    multivalued: false
  first_name: 
    description: first name of the individual
    slot_uri: foaf:firstName
    multivalued: false
  email:
    description: email address of the individual
    slot_uri: foaf:mbox
    multivalued: true
  phone:
    description: telephone number of the individual
    slot_uri: foaf:phone
    multivalued: false
  note: 
    description: additional text information about the entity
    slot_uri: fsls:FSI_000243
    multivalued: false
  guideline_or_mandate_type:
    description: category describing the guideline or the mandate
    slot_uri: fsls:gmType
    multivalued: true
    range: GuidelineMandateType
  has_date: 
    description: date of the activity or the creation of the resource
    slot_uri: dcterms:date
    multivalued: false
    # range: linkml:Date
  government_level:
    description: level of government the activity occurs under
    slot_uri: fsls:govLevel
    multivalued: true
    range: GovernmentLevelType
  has_participant:
    description: the activity such as a role includes this person as a participant
    slot_uri: obo:RO_0000057
    multivalued: true
    range: Person 
  role_of:
    description: name of role individual takes, e.g. position title
    slot_uri: obo:RO_0000081
    multivalued: true
    any_of:
      - range: Organization
      - range: Project
  position_type:
    description: category describing the role held by the individual in the organization
    slot_uri: fsls:positionType
    multivalued: false
    range: PositionType
  involved_in:
    description: the project or program a person with a given role is involved In
    slot_uri: obo:RO_0002331
    multivalued: false
    any_of:
      - range: Project 
      - range: Program
    # range: ProjectProgram # this does not work with SHACL validation
  has_role: 
    description: name labelling the role 
    slot_uri: obo:RO_0000087
    multivalued: false
  creator_of: 
    description: "Relates a corporate body to a work of which it is responsible for the creation of the intellectual or artistic content."
    slot_uri: frbrer:P2008
    multivalued: true
#    range: GuidelineMandate # okay, this should be a superclass, probably a BFO thing.
#  was created_by: 
#    description: "Relates a work to a corporate body that is responsible for the creation of the intellectual or artistic content of the work."
#    slot_uri: frbrer:P2007
#    multivalued: true
  implements: 
    description: The relationship between the funding agency (subject) and the decision, plan, program (object) that the funding agency implements and administers.
    slot_uri: dg:implements
    multivalued: true
    range: GuidelineMandate
  mandates: 
    description: The relationship where the organization mandates a particular activity or action
    slot_uri: fsls:mandates
    multivalued: true
  is_bound_by: 
    description: The relationship where the organization is_bound_by a particular activity or action
    slot_uri: fsls:isboundby
    multivalued: true
    range: GuidelineMandate 
  is_certified_by: 
    description: The relationship where the organization is_certified_by a particular mandate or guideline
    slot_uri: fsls:iscertifiedby
    multivalued: true
    range: GuidelineMandate
  enforces: 
    description: The relationship where the organization enforces a particular mandate or guideline
    slot_uri: fsls:enforces
    multivalued: true
    range: GuidelineMandate
  authorizes: 
    description: The guideline or mandate authorizes this particular role 
    slot_uri: fsls:authorizes
    multivalued: true
    range: Role
  binds: 
    description: The guideline or mandate binds this particular role 
    slot_uri: fsls:binds
    multivalued: true
    range: Role
  references:
    description: A related resource that is referenced, cited, or otherwise pointed to by the described resource.
    slot_uri: dcterms:references
    multivalued: false
  has_input:
    description: The tool has the indicated dataset as an output to its workflow
    slot_uri: obo:RO_0002233
    multivalued: true
    range: Dataset
  has_output:
    description: The tool has the indicated dataset as an input to its workflow
    slot_uri: obo:RO_0002234
    multivalued: true
    range: Dataset
# infrastructure slots
  infrastructure_type:
    description: The category of infrastructure designated by the resources
    slot_uri: fsls:infrastructureType
    multivalued: false
    range: InfrastructureType
  is_part_of_infrastructure:
    description: Infrastructure that is part of another piece of infrastructure
    slot_uri: fsls:isPartOfInfra
    multivalued: true
    range: Infrastructure
  organization_owner:
    description: The organization that is the owner of the piece of infrastructure
    slot_uri: fsls:orgOwner
    multivalued: true
    range: Organization
  organization_manager:
    description: The organization that manages the piece of infrastructure
    slot_uri: fsls:orgManager
    multivalued: true
    range: Organization
  organization_user:
    description: The organization that uses the piece of infrastructure
    slot_uri: fsls:orgUser
    multivalued: true
    range: Organization
  issue_addressed_on_purpose:
    description: The sustainability issues that the piece of infrastructure specifically address
    slot_uri: fsls:issuesPurpose
    multivalued: true
    range: Issue
  other_issues_affected:
    description: The sustainability issues that the piece of infrastructure also affect
    slot_uri: fsls:issuesOther
    multivalued: true
    range: Issue
  in_project:
    description: The project that the piece of infrastructure is part of or was created_by
    slot_uri: fsls:inProject
    multivalued: true
    range: Project
  in_program:
    description: The program under which the piece of infrastructure falls
    slot_uri: fsls:inProgram
    multivalued: true
    range: Program
  has_capacity:
    description: The capacity of the piece of infrastructure, in units appropriate to its type (e.g. acre-feet, megawatts)
    slot_uri: fsls:hasCapacity
    multivalued: false  
  upstream_infrastructure:
    description: Infrastructure that is upstream of the piece of infrastructure of interest
    slot_uri: fsls:infrastructureUpstream
    multivalued: true
    range: Infrastructure
  downstream_infrastructure:
    description: Infrastructure that is downstream of the piece of infrastructure of interest
    slot_uri: fsls:infrastructureDownstream
    multivalued: true
    range: Infrastructure
  adjacent_infrastructure:
    description: Infrastructure that is adjacent to the piece of infrastructure of interest
    slot_uri: fsls:infrastructureAdjacent
    multivalued: true
    range: Infrastructure
  intersecting_infrastructure:
    description: Infrastructure that intersects the piece of infrastructure of interest
    slot_uri: fsls:infrastructureIntersect
    multivalued: true
    range: Infrastructure
  contains:
    description: A contains B iff the spatial region occupied by A has the spatial region occupied by B as a part, and B is not part of A. 
    slot_uri: sio:SIO_000202
    multivalued: true
  is_contained_in:
    description: A is contained in B iff the spatial region occupied by A is part of the spatial region occupied by B and A is not part of B. 
    slot_uri: sio:SIO_000128 
    multivalued: true
  intersects:
    description: Represents spatial relations in which two geometries (or the places they represent) have at least one point in common.
    slot_uri: opengis:sfIntersects
    multivalued: true