miiid_schema.yaml

---
id: https://w3id.org/FAIR-MI/miiid-schema
name: miiid-schema
title: miiid-schema
version: 0.2.0
description: |-
  Minimal Information about Intermicrobial Interaction Data schema
license: GNU GPL v3.0
see_also:
  - https://FAIR-MI.github.io/miiid-schema

prefixes:
  miiid: https://w3id.org/FAIR-MI/miiid/
  linkml: https://w3id.org/linkml/
  schema: http://schema.org/
  WIKIDATA_PROPERTY: https://www.wikidata.org/prop/
  EDAM_TOPIC: http://edamontology.org/topic_
  EDAM_DATA: http://edamontology.org/data_
  NCIT: http://purl.obolibrary.org/obo/NCIT_
  OBI: http://purl.obolibrary.org/obo/OBI_
  GENEPIO: http://purl.obolibrary.org/obo/GENEPIO_
default_prefix: miiid
default_range: string

imports:
  - linkml:types

classes:

  NamedThing:
    description: >-
      A generic grouping for any identifiable entity
    slots:
      - id
      - name
      - description
    class_uri: schema:Thing

  IntermicrobialInteraction:
    is_a: NamedThing
    description: >-
      Represents an interaction between microbial entities
    slots:
      - participants
      - tax_id
      - sequence_id
      - evidence_type
      - method_type
      - reference
      - participant_outcomes

  IntermicrobialInteractionCollection:
    tree_root: true
    description: >-
      A holder for IntermicrobialInteraction objects
    attributes:
      entries:
        range: IntermicrobialInteraction
        multivalued: true
        inlined_as_list: true
        description: >-
          An IntermicrobialInteraction object

slots:
  id:
    identifier: true
    slot_uri: schema:identifier
    range: uriorcurie
    description: A unique identifier for a thing
  name:
    slot_uri: schema:name
    description: A human-readable name for a thing
  description:
    slot_uri: schema:description
    description: A human-readable description for a thing
  participants:
    required: true
    range: string # TODO Create a dedicated Type https://linkml.io/linkml/schemas/models.html#types
    multivalued: true
    description: Names of the microbial entities, with descriptions of any genetic manipulations performed.
  tax_id:
    required: true
    range: NCBITaxId
    multivalued: true
    description: NCBI Taxonomy identifiers at the relevant taxonomic level. Novel taxa lacking identifiers are denoted by N/A.
  sequence_id:
    recommended: true
    range: SequenceId
    multivalued: true
    description: Accession to the matching sequence data (e.g., genome, marker gene sequence).
  evidence_type:
    required: true
    range: string
    description: Type of evidence used to determine the interaction using the Evidence and Conclusion Ontology.
    pattern: >-
      [^\:\n\r]+\:[^\:\n\r]+
  method_type:
    recommended: true
    range: MethodType
    multivalued: true
    description: One or several of the types of methods used to determine the interaction.
  reference:
    required: true
    exact_mappings:
      - schema:url
    description: Persistent identifier (e.g. DOI or URL) to a resource, script, or article, documenting the method.
  env_exp:
    recommended: true
    range: EnvExpId
    description: >-
      Biome term (from the Environmental Ontology) used in the experiment. Engineered ecosystems such as bioreactors, agar plates or computational models use N/A.
    pattern: >-
      [^\:\n\r]+\:[^\:\n\r]+
  participant_outcomes:
    recommended: true
    range: ParticipantOutcome
    multivalued: true
    description: Outcomes of each of the participants described in the interaction when known.


types:
  NCBITaxId:
    description: >-
      Numeric identifier following the NCBI Taxonomy schema.
    base: int
    uri: xsd:integer
    minimum_value: 2
    examples:
      - value: 1043002 # strain level: Aureobasidium pullulans EXF-150
      - value: 1236 # class level: Gammaproteobacteria
    exact_mappings:
      - WIKIDATA_PROPERTY:P685
  SequenceId:
    description: >-
      Sequence identifier to a (preferrably INSDC) database
    base: str
    uri: xsd:string
    examples:
      - value: "FJ627005.1"
      - value: "NZ_CP022412.2"
    exact_mappings:
     - EDAM_DATA:1063
  EnvExpId:
    description: >-
      Term from the Environment Ontology following by their machine-actionable identifier.
    base: str
    uri: xsd:string
    examples:
      - value: "leaf [ENVO:0025034]"

enums:
  MethodType:
    description: List of methods used to determine interactions
    permissible_values:
      simulation:
        description: Any type of biological computational model experiments
        meaning: EDAM_TOPIC:3524
        examples:
          - value: generalized Lotka-Volterra model
          - value: genome-scale metabolic model
      microscopy:
        description: Any type of imaging-related experiments
        meaning: EDAM_TOPIC:3382
        examples:
          - value: co-localization with fluorescent markers
          - value: assisted motility
      cultivation:
        description: Any laboratory procedure for growing microorganisms
        meaning: NCIT:C25300
        examples:
          - value: continuous co-culture in bioreactor
          - value: co-plating on solid media
      sample:
          description: Any type of experiments based on the analysis of a sample
          meaning: OBI:0000659
          examples:
            - value: co-occurrences drawn from analyses of abundances obtained from in situ or in vivo sampling
  ParticipantOutcome:
    description: Outcome indicating how each participant was affected
    permissible_values:
      not_affected:
        description: usually encoded with numerical 0
      positively:
        description: usually encoded with +1
      negatively:
        description: usually encoded with -1
      not_applicable:
        description: >-
          The information is inappropriate to report, this can indicate that the
          standard itself fails to model or represent the information appropriately
        meaning: GENEPIO:0001619