Merge pull request #1256 from biolink/mbrush-supporting_pubs-patch

adding content for supporting publications modeling

biolink-model.yaml

@@ -157,6 +157,7 @@ prefixes:
   wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'
   XPO: 'http://purl.obolibrary.org/obo/XPO_'  # Xenopus Phenotype Ontology
   Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='
+  PMC: 'http://europepmc.org/articles/PMC'
 
 default_prefix: biolink
 default_range: string
@@ -5457,6 +5458,7 @@ 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 
@@ -5570,11 +5572,17 @@ slots:
     range: disease or phenotypic feature
 
   publications:
-    aliases: ["supporting publications"]
+    aliases: ['supporting publications', 'supporting documents']
     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
 
@@ -6280,13 +6288,13 @@ 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
@@ -6389,6 +6397,9 @@ 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
@@ -6404,12 +6415,68 @@ 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: >-

guidelines/README.md

@@ -11,7 +11,13 @@ Following is a primer on understanding the Biolink Model and how to work with th
 
 The guidelines are organized into five parts:
 - [Understanding the Biolink Model](understanding-the-model.md)
+- [Association Examples With qualifiers](association-examples-with-qualifiers.md)
+- [Reading a Qualifier Based Statement](reading-a-qualifier-based-statement.md)
+  - [TRAPI Query Examples](TRAPI-examples.md) 
+- [Knowledge Source Retrieval](knowledge-source-retrieval.md)
+- [Supporting Publications Guidelines](supporting-publications-guidelines.md)
 - [Curating the Biolink Model](curating-the-model.md)
 - [Using the Modeling Language](using-the-modeling-language.md)
 - [Working with the Biolink Model](working-with-the-model.md)
 - [Maintaining the Biolink Model](maintaining-the-model.md)
+- [FAQ])(faq.md)