Merge branch 'master' into hoganwr-patch-1

_includes/docs_toc.md

@@ -6,8 +6,8 @@
 
 [Editorial Working Group](/docs/EditorialWG.html)
 
-- [Review Process](/docs/ReviewProcessGuidelines.html)
-- [Review Criteria](/docs/ReviewCriteriaPolicies.html)
+- [Ontologies Review](/docs/OntologiesReviewWorkflow.html)
+- [Principles Review](/docs/PrinciplesReviewWorkflow.html)
 
 [Technical Working Group](/docs/TechnicalWG.html)
 

ontology/ontoavida.md

@@ -2,6 +2,10 @@
 layout: ontology_detail
 id: ontoavida
 title: 'OntoAvida: ontology for Avida digital evolution platform'
+browsers:
+- title: Ontoavida HTML Browser
+  label: Human-readable (HTML)
+  url: https://owl.fortunalab.org/ontoavida/
 contact:
   email: [email protected]
   github: miguelfortuna
@@ -22,12 +26,27 @@ license:
 preferredPrefix: ONTOAVIDA
 products:
 - id: ontoavida.owl
+  title: OWL
+  description: The main ontology in OWL
+  page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.owl
 - id: ontoavida.obo
+  title: OBO
+  description: Equivalent to ontoavida.owl, in obo format
+  page: https://gitlab.com/fortunalab/ontoavida/-/raw/master/ontoavida.obo
+publications:
+- id: https://doi.org/10.1038/s41597-023-02514-3
+  title: Ontology for the Avida digital evolution platform
 repository: https://gitlab.com/fortunalab/ontoavida
 tags:
 - digital evolution
 - artificial life
 tracker: https://gitlab.com/fortunalab/ontoavida/-/issues
+usages:
+- description: An R package—avidaR—uses OntoAvida to perform complex queries on an RDF database—avidaDB—containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms
+  examples:
+  - description: 'avidaR: an R library to perform complex queries on an ontology-based database of digital organisms'
+    url: http://doi.org/10.7717/peerj-cs.1568
+  user: https://cran.r-project.org/package=avidaR
 activity_status: active
 ---
-<img  src="https://fortunalab.org/images/alife_bacteria.jpg" style="padding-right:20px; padding-bottom:10px;" height="150px" align="left"/>The **Ontology for Avida ([OntoAvida](https://gitlab.com/fortunalab/ontoavida))** project aims to develop an integrated vocabulary for the description of [Avida](https://github.com/devosoft/avida), the most widely used computational approach for performing experimental evolution. The lack of a clearly defined vocabulary makes biologists feel reluctant to embrace the field of digital evolution. This unique ontology has the potential to change this picture overnight. In addition, OntoAvida will allow researchers to make inference (e.g., on phenotypic plasticity) based on certain rules and constraints, facilitate the reproducibility of the *in silico* evolution experiments reported in the [scientific literature](https://gitlab.com/fortunalab/ontoavida#references), and trace the provenance of the data stored in AvidaDB, a semantic database that stores genomes and transcriptomes of more than a million digital organisms.
+<img  src="https://fortunalab.org/images/alife_bacteria.jpg" style="padding-right:20px; padding-bottom:10px;" height="150px" align="left"/>The **Ontology for Avida ([OntoAvida](https://owl.fortunalab.org/ontoavida/))** aims to develop an integrated vocabulary for the description of [Avida](https://github.com/devosoft/avida), the most widely used computational approach for performing experimental evolution using digital organisms–self-replicating computer programs that evolve within a user-defined computational environment. The lack of a clearly defined vocabulary makes some biologists feel reluctant to embrace the field of digital evolution. This integrated framework empowers biologists by equipping them with the necessary tools to explore and analyze the field of digital evolution more effectively. By leveraging the vocabulary of Avida, researchers can gain deeper insights into the evolutionary processes and dynamics of digital organisms. In addition, OntoAvida allows researchers to make inference based on certain rules and constraints, facilitate the reproducibility of [in silico evolution experiments](https://gitlab.com/fortunalab/ontoavida#references) and trace the provenance of the data stored in avidaDB–an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms.

principles/fp-013-notification.md

@@ -20,9 +20,13 @@ and will allow updates to any dependencies (e.g., terms, annotations, ontologies
 
 Recommendations and Requirements
 -------
-Ontology owners SHOULD, in accordance with this principle, pre-announce changes to a primary group of users who actively monitor the ontology and its changes, for example, via a mailing list (ontology-specific or more general, as deemed suitable), a social media group (relevant to the ontology), or via announcements on a home page or elsewhere.
+Ontology owners SHOULD, in accordance with this principle, pre-announce changes to a primary group of users who actively monitor the ontology and its changes, for example, via a mailing list (ontology-specific or more general, as deemed suitable), a social media group (relevant to the ontology), or via announcements on a home page or elsewhere. The lead time for announcements can be determined according to release lifecycles of major ontology applications and is expected to vary by domain.
 
-The lead time for announcements can be determined according to release lifecycles of major ontology applications and is expected to vary by domain.
+The kinds of changes that might warrant a pre-announcement include (but are not limited to):
+- <i><b>Planned obsoletions.</i></b> Terms that will be made obsolete. Such announcements can provide users the opportunity to intervene if necessary.
+- <i><b>Major hierarchy rearrangements.</i></b> Moving branches from one point in the hierarchy to another, especially large branches affecting many terms or those close to the top of the hierarchy.
+
+Term additions and small hierarchy changes are not expected to need pre-announcement but doing so is not prohibited. 
 
 Implementation
 --------------