Class: PublicationReference

A reference to a publication with associated findings

URI: dismech:class/PublicationReference

 classDiagram
    class PublicationReference
    click PublicationReference href "../../classes/PublicationReference/"
      PublicationReference : findings





        PublicationReference --> "*" Finding : findings
        click Finding href "../../classes/Finding/"



      PublicationReference : found_in

      PublicationReference : reference

      PublicationReference : tags





        PublicationReference --> "*" ReferenceTagEnum : tags
        click ReferenceTagEnum href "../../enums/ReferenceTagEnum/"



      PublicationReference : title

Slots

Name	Cardinality and Range	Description	Inheritance
reference	1 PMID	The authoritative reference (publication) for this evidence item	direct
title	0..1 recommended String	Title of the referenced publication	direct
found_in	* String	Deep-research output files where this reference was cited	direct
tags	* ReferenceTagEnum	Authoritative-source tags for a reference (e	direct
findings	* Finding	Key findings or claims extracted from this source (publication or dataset)	direct

Usages

used by	used in	type	used
Disease	references	range	PublicationReference
Grouping	references	range	PublicationReference

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/monarch-initiative/dismech

Mappings

Mapping Type	Mapped Value
self	dismech:PublicationReference
native	dismech:PublicationReference

LinkML Source

Direct

name: PublicationReference
description: A reference to a publication with associated findings
from_schema: https://w3id.org/monarch-initiative/dismech
slots:
- reference
- title
- found_in
- tags
- findings
slot_usage:
  reference:
    name: reference
    identifier: true
    required: true
  title:
    name: title
    description: 'Title of the referenced publication. Recommended so that linkml-data-qc
      scores its absence, matching the `recommended: true` already carried by the
      EvidenceItem `reference_title` twin. Set here via slot_usage rather than on
      the shared `title` slot, which is also used by Dataset and TrackedIssue.'
    recommended: true

Induced

name: PublicationReference
description: A reference to a publication with associated findings
from_schema: https://w3id.org/monarch-initiative/dismech
slot_usage:
  reference:
    name: reference
    identifier: true
    required: true
  title:
    name: title
    description: 'Title of the referenced publication. Recommended so that linkml-data-qc
      scores its absence, matching the `recommended: true` already carried by the
      EvidenceItem `reference_title` twin. Set here via slot_usage rather than on
      the shared `title` slot, which is also used by Dataset and TrackedIssue.'
    recommended: true
attributes:
  reference:
    name: reference
    implements:
    - linkml:authoritative_reference
    description: The authoritative reference (publication) for this evidence item
    examples:
    - value: PMID:35533128
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    identifier: true
    alias: reference
    owner: PublicationReference
    domain_of:
    - EvidenceItem
    - PublicationReference
    - MappingConsistency
    range: PMID
    required: true
  title:
    name: title
    implements:
    - linkml:title
    description: 'Title of the referenced publication. Recommended so that linkml-data-qc
      scores its absence, matching the `recommended: true` already carried by the
      EvidenceItem `reference_title` twin. Set here via slot_usage rather than on
      the shared `title` slot, which is also used by Dataset and TrackedIssue.'
    comments:
    - 'The `linkml:title` annotation is INERT for linkml-reference-validator detection
      — lrv''s TitleURIs matches only "dcterms:title" / "dc/terms/title". Where this
      slot IS title-checked (on PublicationReference) that happens via lrv''s exact-name
      fallback FallbackSlotNames.TITLE = ("title",), not via this annotation. Kept
      because it is a reasonable semantic mapping, and noted here for the same reason
      the EvidenceItem `reference_title` comment exists: an annotation that looks
      like it enables a check, but does not, misleads readers. The title-normalization
      work that this deferral pointed at has now happened (EvidenceItem.reference_title
      carries `dcterms:title` and is checked), but this slot is still NOT retargeted:
      it is shared by PublicationReference, Dataset and TrackedIssue, so swapping
      the URI would newly expose Dataset.title and TrackedIssue.title to lrv detection.
      PublicationReference.title loses nothing by waiting — it is already checked
      via the exact-name fallback. Retarget only alongside a check of what the other
      two classes would then be asserting.'
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: title
    owner: PublicationReference
    domain_of:
    - Dataset
    - PublicationReference
    - TrackedIssue
    range: string
    recommended: true
  found_in:
    name: found_in
    description: Deep-research output files where this reference was cited
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: found_in
    owner: PublicationReference
    domain_of:
    - PublicationReference
    range: string
    multivalued: true
  tags:
    name: tags
    description: Authoritative-source tags for a reference (e.g. GeneReviews). Populated
      programmatically by scripts/tag_references.py; use `just tag-references` to
      refresh.
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: tags
    owner: PublicationReference
    domain_of:
    - PublicationReference
    range: ReferenceTagEnum
    multivalued: true
  findings:
    name: findings
    description: Key findings or claims extracted from this source (publication or
      dataset)
    from_schema: https://w3id.org/monarch-initiative/dismech
    rank: 1000
    alias: findings
    owner: PublicationReference
    domain_of:
    - Dataset
    - ExperimentalModel
    - ComputationalModel
    - PublicationReference
    range: Finding
    multivalued: true
    inlined: true
    inlined_as_list: true