adding content for supporting publications modeling

biolink-model.yaml

@@ -5272,6 +5272,7 @@ slots:
       - value: The administration of 50g/ml bupivacaine promoted maximum breast cancer.
 
   supporting documents:
+    deprecated: true
     is_a: association slot
     description: >-
       One or more referencable documents that report the statement expressed in an Association, or provide 
@@ -5385,12 +5386,18 @@ slots:
     range: disease or phenotypic feature
 
   publications:
-    aliases: ["supporting publications"]
+    aliases: ['supporting publications', 'supporting documents']
     singular_name: publication
     description: >-
-      One or more publications that report the statement expressed in an Association, or provide information used as 
-      evidence supporting this statement.
-    is_a: supporting documents
+      One or more publications that report the statement expressed in an 
+      Association, or provide information used as evidence supporting this statement.
+    comments: 
+      - >-
+        The notion of a ‘Publication’ is considered broadly to include any 
+        document made available for public consumption. It covers journal issues, 
+        individual articles, and books - and also things like article pre-prints, 
+        white papers, patents, drug labels, web pages, protocol documents, etc. 
+    is_a: association slot
     multivalued: true
     range: publication
 
@@ -6095,13 +6102,13 @@ classes:
   publication:
     is_a: information content entity
     description: >-
-      Any published piece of information. Can refer to a whole publication,
-      its encompassing publication (i.e. journal or book) or to a part of a
-      publication, if of significant knowledge scope (e.g. a figure, figure
-      legend, or section highlighted by NLP). The scope is intended to be
-      general and include information published on the web, as well as printed
-      materials, either directly or in one of the Publication Biolink
-      category subclasses.
+      Any ‘published’ piece of information. Publications are considered broadly 
+      to include any document or document part made available in print or on the 
+      web - which may include scientific journal issues, individual articles, and 
+      books - as well as things like pre-prints, white papers, patents, drug 
+      labels, web pages, protocol documents,  and even a part of a publication if 
+      of significant knowledge scope (e.g. a figure, figure legend, or section 
+      highlighted by NLP). 
     slots:
       - authors
       - pages
@@ -6204,6 +6211,9 @@ classes:
 
   article:
     is_a: publication
+    description: >-
+      a piece of writing on a particular topic presented as a stand-alone 
+      section of a larger publication	  
     slots:
       - published in
       - iso abbreviation
@@ -6219,12 +6229,68 @@ classes:
         description: >-
           Optional value, if used locally as a convenience, is set
           to the iso abbreviation of the 'published in' parent.
+    exact_mappings:
+      - SIO:000154
+      - fabio:article
     id_prefixes:
       # By inheritance, a DOI may be used as a publication identifier; there may be other relevant namespaces
       - PMID
     in_subset:
       - model_organism_database
 
+  journal article:
+    is_a: article
+    description: >-
+      an article, typically presenting results of research, that is published 
+      in an issue of a scientific journal.
+    exact_mappings:
+      - IAO:0000013
+      - fabio:JournalArticle
+    id_prefixes:
+     - PMID
+     - PMCID
+     - doi
+
+  patent:
+    is_a: publication
+    description: >-
+      a legal document granted by a patent issuing authority which confers upon 
+      the patenter the sole right to make, use and sell an invention for a set
+      period of time. 
+    exact_mappings:
+      - SIO:000153
+      - IAO:0000313
+      - fabio:Patent
+
+  web page:
+    is_a: publication
+    description: >-
+      a document that is published according to World Wide Web standards, which 
+      may incorporate text, graphics, sound, and/or other features.
+    exact_mappings:
+      - SIO:000302
+      - NCIT-OBO:C142749
+      - fabio:WebPage
+
+  preprint publication:
+    is_a: publication
+    description: >-
+      a document reresenting an early version of an author's original scholarly work, 
+      such as a research paper or a review, prior to formal peer review and publication 
+      in a peer-reviewed scholarly or scientific journal.
+    exact_mappings:
+      - EFO:0010558
+      - fabio:Preprint
+
+  drug label:
+    is_a: publication
+    description: >-
+      a document accompanying a drug or its container that provides written, printed or
+      graphic information abou thte drug, including drug contents, specific instructions 
+      or warnings for administration, storage and disposal instructions, etc. 
+    broad_mappings:
+      - NCIT-OBO:C41203
+
   retrieval source:
     is_a: information content entity
     description: >-