Merge branch 'master' into nataled-patch-26

docs/EditorialWG.md

@@ -3,28 +3,25 @@ layout: doc
 title: Editorial Working Group
 ---
 
-The primary task of the Editorial WG is to facilitate the review of candidate OBO Foundry ontologies. This task includes developing the principles against which ontologies are reviewed, developing the review process itself, conducting the reviews, and setting policies governing the process.
+The primary tasks of the Editorial WG are to develop and maintain OBO Foundry principles and to facilitate the review of candidate OBO Foundry ontologies. This task includes developing the principles against which ontologies are reviewed, developing the review process itself, conducting the reviews, and setting policies governing the process.
 
 ## Scope
 
-The OBO Foundry Editorial WG will:
+The OBO Foundry Editorial WG is responsible for:
 
-- create guidelines for ontology review process (how we do reviews, operationally)
-- create policies for ontology review criteria (what aspects of an ontology and which ontologies we should review)
-- manage the ontology review process
+- Principles: drafting text, and creating the workflow and guidelines for the principles development process
+- Ontologies: reviewing, and creating the workflow and guidelines for the ontology review process
+- Policies: crafting the policies for the above
 
-Current activities are focused on creating guidelines for reviews. Once those guidelines are in place, the working group will shift its focus to carrying out the review process, with an aim of reducing the backlog of ontologies awaiting review.
+## Guidelines and policies
 
-## Draft guidelines and policies
+#### Ontologies Review
 
-### Ontology Review
+- [Ontologies review workflow](/docs/OntologiesReviewWorkflow.html)
 
-- [Ontology review process guidelines](/docs/ReviewProcessGuidelines.html)
-- [Ontology review criteria policies](/docs/ReviewCriteriaPolicies.html)
+#### Principles Review
 
-### Principles Review
-
-[Principles review workflow](/docs/PrinciplesReviewWorkflow.html)
+- [Principles review workflow](/docs/PrinciplesReviewWorkflow.html)
 
 ## Contact Us
 

docs/OntologiesReviewWorkflow.md

@@ -0,0 +1,54 @@
+---
+layout: doc
+title: Ontology Review Process
+---
+
+This page deals with the process, policies, and guidelines for manually reviewing newly-submitted ontologies, with particular focus on operational aspects such as:
+
+- which ontologies are reviewed, and in what order?
+- how are reviewers chosen?
+- what is the workflow for conducting a review?
+- what are the criteria used?
+
+Newly-submitted ontologies are reviewed manually after passing the automated evaluation. Though the automated evaluation checks for adherence to [OBO Foundry principles](http://www.obofoundry.org/principles/fp-000-summary.html), it cannot capture certain nuances outlined in the principles nor evaluate ontology quality. The purpose of the manual review is to check the ontology for issues that the NOR Dashboard does not cover.
+
+# Steps prior to manual review
+
+Once an ontology is submitted to the OBO Foundry, it is added to the New Ontology Dashboard for automated evaluation. The steps involved in ontology submission and subsequent dashboard evaluation are described in detail in this [FAQ answer](http://obofoundry.org/faq/how-do-i-register-my-ontology.html) and links therein.
+
+# Review priority
+
+All submitted ontologies will be manually reviewed based on the order in which the ontology becomes compliant with the automated evaluation (that is, when the [New Ontology Request (NOR) Dashboard](http://obofoundry.org/obo-nor.github.io/dashboard/index.html) status is 'pass').
+
+# Choosing reviewers
+
+Reviewers are chosen on a rotating basis from the members of the [OBO Foundry Operations Committee](http://obofoundry.org/docs/Membership.html).
+
+# Ontology review workflow
+
+The manual process begins once a reviewer is assigned. The reviewer will assess key aspects of the ontology (see below) and report the findings both to the submitter (via the issue tracker ticket used for submission) and to the OBO Operations Committee. The latter will discuss the findings and make a recommendation for acceptance, revision, or rejection.
+
+# Manual review criteria
+
+For the list below, yes/no questions include the expected answers in square brackets after the question. Criteria for review minimally include:
+
+1. Ontology scope
+   - Do the terms fall within the ontology's stated target domain of knowledge? [yes]
+   - Was the ontology developed for a very specific purpose or community?
+2. Terms with the new ontology prefix
+   - Do the terms follow the OBO identifier scheme? [yes]
+   - Are there terms with the same <i>meaning</i> available in another OBO Foundry ontology? [no]
+   - Is there another OBO Foundry ontology whose scope covers any of the new terms? [no]
+3. Correct use of imported terms
+   - If the ontology reuses terms from other OBO ontologies, are they used accurately? [yes] 
+   - Are imported terms in appropriate hierarchies, and do they preserve the term's upper-level alignment? [yes]
+   - Are any additional axioms used for these terms correct in both a technical (e.g. passes reasoning) and substantive sense? [yes]
+4. Basic review of axiomatic patterns
+   - Are axioms generally stated simply or are they highly complex? (Highly complex axioms will require extra scrutiny.)
+   - Are existential restrictions used correctly? [yes] (Typical mistakes include “R some (A and B and C)” to mean “(R some A and R some B and R some C)”).
+5. Appropriate use of object properties - 
+   - Are object properties used in a manner consistent with their definitions, domain, and range? [yes] (Examples of incorrect usage include those based on some interpretation of the label of the object property but not actually fitting the property definition or domain and range.)
+6. Responsiveness to suggested changes - 
+   - Have the developers been willing to fix any identified issues during the review? [yes]
+
+

docs/PrinciplesReviewWorkflow.md

@@ -3,16 +3,20 @@ layout: doc
 title: Principle Review Process
 ---
 
-This page describes the process for reviewing, updating, and creating [OBO Foundry Principles](http://obofoundry.github.io/principles/fp-000-summary.html).
+This page describes the process for reviewing, updating, and creating [OBO Foundry Principles](http://obofoundry.github.io/principles/fp-000-summary.html) by the OBO Foundry Editorial Working Group (EWG).
 
-- Discuss the principle on working group call
-- Write up proposed revisions as a GitHub issue (not a pull request)
-- Inform the Editorial WG via email that the ticket needs discussion (if it doesn’t happen automatically)
-- Two-week commenting period on GitHub issue tracker
-- Make any incremental improvements on the tracker
-- When the Editorial WG agrees on a final version, discuss on an Operations Committee call or via the issue tracke
-- Make a pull request
-- Two-week commenting period on the pull request
-- Upload final changes to OBO Foundry web site for public viewing.
+For the following, steps 1-5 are internal to the EWG and steps 6-7 are internal to the OBO Operations Committee. 
+
+1. Discuss the principle during an Editorial Working Group (EWG) call.
+2. Write up proposed revisions as a [GitHub issue](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/new?assignees=nataled&labels=attn%3A+Editorial+WG&projects=&template=obo-foundry-principles.md&title=Principle+%23%3CENTER+NUMBER+HERE%3E+%22%3CENTER+NAME+HERE%3E%22) (not a pull request).
+3. Inform the Editorial WG via [email](mailto:[email protected]) that the ticket needs discussion.
+4. Allow a two-week commenting period on the GitHub issue tracker, during which members of the EWG can suggest improvements.
+5. If necessary, discuss changes made during the commenting period and finalize the text.
+6. Once the EWG agrees on a final version, a member presents the text to the OBO Foundry Operations Committee for discussion during a meeting or via the issue tracker.
+7. Once the wording is approved by OBO Operations, a member of the EWG makes a pull request reflecting the consensus of previous discussions. Note that the pull request should be marked as 'draft' if it is a new principle.
+8. For new principles or major changes to existing principles, announce the proposal on the [obo-discuss mailing list](mailto:[email protected]) and the [obo-community #general Slack channel](https://app.slack.com/client/T01BAB621JR/C01BDKWDS91) and request public feedback.
+9. Allow a two-week commenting period on the pull request.
+10. If the feedback includes major changes or objections, re-discuss during an OBO Operations call and re-do any relevant steps indicated above.
+11. At the end of the commenting period, assuming no major changes are needed, a member of the EWG will merge the pull request (removing 'draft' status if appropriate) and thereby make the changes public.
 
 The need for a new principle can arise when an existing principle tries to cover too much and requires splitting, or as new needs arise within the community.

faq/how-do-i-register-my-ontology.md

@@ -8,6 +8,6 @@ title: Submit a new ontology
 To submit a new ontology for inclusion in the OBO Foundry, you will need to:
 
 1. Review the [OBO Foundry requirements and technical details](https://obofoundry.org/docs/Policy_for_OBO_namespace_and_associated_PURL_requests.html) document for membership expectations and submission instructions.
-2. Submit your request to our GitHub tracker, using the [New Ontology Request template](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/new?assignees=&labels=new+ontology&template=new-ontology-request.md&title=). _Note: please see the [New Ontology Registration Instructions](http://obofoundry.org/docs/NewOntologyRegistrationInstructions.html) for guidance._
-3. Send an email to [obo-discuss](mailto:[email protected]) with your request to allow community feedback (you may need to [apply to join group](https://groups.google.com/forum/#!forum/obo-discuss) first.) Be sure to include the link to the issue you created in step 2.
+2. Submit your request to our GitHub tracker, using the [New Ontology Request template](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/new?assignees=&labels=new+ontology&projects=&template=new-ontology.yml&title=Request+for+new+ontology+%5BNAME%5D). _Note: please see the [New Ontology Registration Instructions](http://obofoundry.org/docs/NewOntologyRegistrationInstructions.html) for guidance._
+3. Send an email to [obo-discuss](mailto:[email protected]) with your request to allow community feedback (you may need to [apply to join the obo-discuss group](https://groups.google.com/forum/#!forum/obo-discuss) first.) Be sure to include the link to the issue you created in step 2.
 4. (_Optional_): If you would like to join the obo-community Slack, please indicate this in your email.