Merge branch 'master' into 2526-clean-up-review-process-docs

Author: jamesaoverton

_config.yml

@@ -414,7 +414,7 @@ ontologies:
     ontology_purl: http://purl.obolibrary.org/obo/BMONT.owl
   repository: https://github.com/SCAI-BIO/BiomarkerOntology
   title: Biomarker Ontology
-  tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue
+  tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues
 - activity_status: active
   build:
     checkout: git clone https://github.com/obophenotype/biological-spatial-ontology.git

_data/roles.yml

@@ -1,45 +1,13 @@
-- name: Code of Conduct Committee Member
-  open: true
-  description: |
-    The Code of Conduct (COC) Committee member is responsible for ensuring the OBO Code of Conduct is upheld.
-    They are, in particular, available for anyone in the community to be contacted individually or as a group.
-  commitment: 0-6 hours per month
-  requirements:
-    - being able to deal with sensitive interpersonal issues discreetly
-    - being willing to mediate between conflicting viewpoints
-    - being highly available when issues arise
-    - fully embracing the OBO Code of Conduct
-  responsibilities:
-    - Being available to receive COC-related issues via email from anyone in the community, and dealing with them discreetly (not sharing any part of the communication without permission)
-    - Developing strategies for dealing with COC-related issues according to established COC protocols
-    - Ensuring that the OBO Code of Conduct is upheld around matters directly related to the OBO Foundry
-    - (Other responsibilities are yet to be defined for this role)
-  people:
-    - github: addiehl
-      name: Alexander Diehl
-      orcid: 0000-0001-9990-8331
-      status: support
-      start: "2023-06-16"
-    - github: lschriml
-      name: Lynn Schriml
-      orcid: 0000-0001-8910-9851
-      status: support
-      start: "2023-06-16"
-    - github: matentzn
-      name: Nico Matentzoglu
-      orcid: 0000-0002-7356-1779
-      status: support
-      start: "2023-06-16"
 - name: Registry Metadata Steward
   open: false
   commitment: 2-6 hours per month
   requirements:
     - love for metadata
     - basic python
     - community mindset
-  description: You are responsible for shepherding our registry
-    metadata according to our principles and SOPs, merge changes and generally
-    protect and guard them. This involves also facilitating the implementation of QC
+  description: Responsible for shepherding our registry
+    metadata according to our principles and SOPs, merging changes and generally
+    protecting and guarding them. This also involves facilitating the implementation of QC
     checks.
   sop: /roles/metadata-steward
   responsibilities:
@@ -69,11 +37,11 @@
     - Community mindset
     - Stakeholder support
   description:
-    You will be responsible for registering new ontologies at the OBO dashboard and helping their
-    owners pass them.
+    Responsible for assinging reviewers to new ontology requests, registering new ontologies in the OBO dashboard and helping their
+    owners pass all the dashboard checks. 
   sop: /roles/nor-manager
   responsibilities:
-    - Checking OBOFoundry.github.io at least weekly for NOR related issues and pull requests.
+    - Checking OBOFoundry.github.io at least weekly for NOR-related issues and pull requests.
     - Managing the NOR Process (https://obofoundry.org/docs/SOP.html#NOR)
     - Assisting NOR submitters to understanding the NOR process and passing the NOR Dashboard
     - Assigning and reminding OBO Operations Committee Members as reviewers
@@ -97,30 +65,30 @@
     - Working knowledge of python
     - "Nice to have: knowledge of jekyll and liquid (like jinja)"
     - Should have technical background
-  description: You will be responsible for gatekeeping community changes to the website.
+  description: Responsible for gatekeeping community changes to the website.
   sop: /roles/website-coordinator
   responsibilities:
   people:
-    - github: erik-whiting
-      name: Erik Whiting
-      orcid: 0000-0003-1022-5281
-      status: lead
-      start: 2022-12
     - github: matentzn
       name: Nico Matentzoglu
       orcid: 0000-0002-7356-1779
       status: support
       start: "0000-00-00"
+    - github: jsstevenson
+      name: James Stevenson
+      orcid: 0000-0002-2568-6163
+      status: lead
+      start: "2025-00-00"
 - name: OBO Slack Community Manager
   open: false
   commitment: 1-3 hours per month
   requirements:
     - love for communication
     - passion for community building
     - community mindset
-  description: You are responsible for managing the OBO Slack community. This role includes issues like welcoming new members, deleting old ones, sending invites and directing people to the right channels.
+  description: Responsible for managing the OBO Slack community, including tasks like welcoming new members, deleting old ones, sending invites and directing people to the right channels.
   responsibilities:
-    - Adding people to the OBO slack space on request, using the 'invite members' feature
+    - Adding people to the OBO Slack space on request, using the 'invite members' feature
     - "Welcoming new members once per week in the #general channel"
     - Directing people to the appropriate channels to use for an inquiry
     - Inactivating accounts on request
@@ -135,14 +103,14 @@
   commitment: 2-4 hours per month
   requirements:
     - Should have a basic journalistic instinct, compiling the most relevant discussion points, decisions and issues for the wider community
-  description: You will be responsible for managing, compiling and disseminating the OBO Newsletter. Instructions for archiving the newsletter on the OBO Foundry's GitHub Repository can be found [here](https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/CONTRIBUTING.md#newsletter).
+  description: Responsible for managing, compiling and disseminating the OBO Newsletter. Instructions for archiving the newsletter on the OBO Foundry's GitHub Repository can be found [here](https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/CONTRIBUTING.md#newsletter).
   responsibilities:
     - Manage a Google doc with the current and previous newsletter drafts based on the newsletter skeleton
     - Add GitHub issues and/or pull requests tagged with "newsletter" to the newsletter, with one or two sentences of summary
     - Summarise key developments (ongoing and past) to the community, based on reports of the working groups to the Operations Committee meeting
     - Summarise key decisions from the OBO operations calls
     - Proactively finalise the newsletter draft for the last meeting of March, June, September and December, and requesting feedback
-    - After 10 days of requesting feedback, send the newsletter to obo-discuss mailing list
+    - Once the newsletter content has been approved, send the newsletter to the obo-discuss mailing list
   people:
     - github: LK112019
       name: Leila Kiani
@@ -154,13 +122,14 @@
   commitment: 2-10 hours per month
   requirements:
     - Basic knowledge of dashboard
-    - Social skills are a nice to have
+    - Social skills are nice to have
     - Infinite patience also helpful
-  description: Updating the OBO Dashboard once per month.
-    Fixing horrible bugs in OBO-Dashboard if they come up (should be rare).
-    Working with OBO Ops to find people for extending dashboard when new principles come along.
+  description: Keep OBO Dashboard up to date
   sop: /roles/dashboard-manager
   responsibilities:
+    - Updating the OBO Dashboard once per month.
+    - Fixing horrible bugs in OBO-Dashboard if they come up (should be rare).
+    - Working with OBO Ops to find people for extending dashboard when new principles come along.
   people:
     - github: anitacaron
       name: Anita Caron
@@ -176,16 +145,15 @@
   open: false
   commitment: 2 hours per month
   requirements:
-    - Strong python skills
-    - Some level of pro-activity helpful
-    - Experience with ODK/docker
-  description:
-    Preparing a short report about all general developments in OBO Technical
-    Working Group (TWG) for the OBO Operations team meeting. You will go
-    through pull requests and emails and summarize in bullet points and report
-    to OBO Ops.
+    - No programming ability needed, but should be able to follow technical discussions
+    - Willingness to attend TWG meetings and collect notes
+  description: Technical Working Group (TWG) representative who serves as a liaison to the OBO Foundry Operations Committee (OFOC).
   sop: /roles/twg-ops-liaison
   responsibilities:
+    - Report TWG progress at OFOC calls
+    - Serve as a first point of contact for OFOC and OBO Community for technical Q/A
+    - Mark relevant GitHub issues for discussion during OFOC call
+    - Summarise TWG activities to OBO Newsletter steward
   people:
     - github: rays22
       name: Ray Stefancsik
@@ -211,8 +179,10 @@
 - name: OMO metadata coordinator
   open: false
   description: |
-    You will be responsible for registering new ontologies at the OBO dashboard and helping their
-    owners pass them.
+    Responsible for coordinating changes to the OBO Metadata Ontology (OMO). 
+    OMO reflects OBO consensus on term and ontology metadata in OBO ontologies.
+    Changes need to be carefully reviewed and votes called if needed. No PR should be merged
+    in OMO without the consent of the OMO metadata coordinator.
   responsibilities:
   people:
     - name: Jie Zheng
@@ -228,8 +198,8 @@
 - name: OBO Tools coordinator
   open: false
   description: |
-    Coordinating and hosting OBO Tools workshops at meetings and conferences such as ICBO, and
-     making sure tools align with OBO principles and support them, etc.)
+    Coordinate and host OBO Tools workshops at meetings and conferences such as ICBO, 
+     make sure tools align with OBO principles and support them, etc.
   responsibilities:
   people:
     - name: James A. Overton
@@ -240,7 +210,7 @@
 - name: OBO Academy
   open: false
   description: |
-    Maintaining https://oboacademy.github.io/obook/ and organising OBO Tutorials.
+    Maintain https://oboacademy.github.io/obook/; organize and advertise OBO Tutorials.
   responsibilities:
   people:
     - name: Nicole Vasilevsky
@@ -258,22 +228,12 @@
       orcid: 0000-0001-5139-5557
       status: support
       start: 2021-06
-    - name: Rebecca Jackson
-      github: beckyjackson
-      orcid: 0000-0003-4871-5569
-      status: support
-      start: 2021-06
-    - name: Shawn Tan
-      github: shawntanzk
-      orcid: 0000-0001-7258-9596
-      status: support
-      start: "2022"
 - name: OBO Issue Tracker Shepherd
   open: false
   description: |
-    Assigning incoming issues at https://github.com/OBOFoundry/OBOFoundry.github.io, tagging them, chasing them
+    Keep an eye on issues in the GitHub issue tracker and help keep them prioritized appropriately
   responsibilities:
-    - "Tagging metadata related issues with 'attn: Technical Working WG' and 'metadata'."
+    - Monitor issues at https://github.com/OBOFoundry/OBOFoundry.github.io, tag them, follow up on them as needed
   people:
     - name: Nomi Harris
       github: nlharris
@@ -283,16 +243,47 @@
 - name: OBO Google Service Manager
   open: true
   description: |
-    Managing the OBO Google Drives, Calendars, Mailing list and Meeting Minutes
+    Manage the OBO Google Drives, calendars, mailing list (Google Group) and meeting minutes
   responsibilities:
     - Adding and removing people from OBO Mailing Lists
     - Adding new OBO Ops members to Google Drive and removing alumni
     - Adding important OBO events to the OBO calendar and sending out invites
     - Managing public and internal OBO Google Drives
-    - Reporting adding members to any OBO Google drive with Write or Admin rights to the OBO Operations Committee
   people:
     - github: nlharris
       name: Nomi Harris
       orcid: 0000-0001-6315-3707
       status: lead
       start: 2019-01
+- name: Code of Conduct Committee Member
+  open: true
+  description: |
+    Code of Conduct (COC) Committee members are responsible for ensuring the OBO Code of Conduct is upheld.
+    They are, in particular, available for anyone in the community to be contacted individually or as a group.
+  commitment: 0-6 hours per month
+  requirements:
+    - being able to deal with sensitive interpersonal issues discreetly
+    - being willing to mediate between conflicting viewpoints
+    - being highly available when issues arise
+    - fully embracing the OBO Code of Conduct
+  responsibilities:
+    - Being available to receive COC-related issues via email from anyone in the community, and dealing with them discreetly (not sharing any part of the communication without permission)
+    - Developing strategies for dealing with COC-related issues according to established COC protocols
+    - Ensuring that the OBO Code of Conduct is upheld around matters directly related to the OBO Foundry
+    - (Other responsibilities are yet to be defined for this role)
+  people:
+    - github: addiehl
+      name: Alexander Diehl
+      orcid: 0000-0001-9990-8331
+      status: support
+      start: "2023-06-16"
+    - github: lschriml
+      name: Lynn Schriml
+      orcid: 0000-0001-8910-9851
+      status: support
+      start: "2023-06-16"
+    - github: matentzn
+      name: Nico Matentzoglu
+      orcid: 0000-0002-7356-1779
+      status: support
+      start: "2023-06-16"

docs/StandardizationGuidelines.md

@@ -5,21 +5,20 @@ title: Ontology Standardization Guidelines
 
 ### Social
 
-SOCIAL External axioms #1443 & #1991 | possible new "what to do with terms" principle (can be p14)
 
 ### Communication
 
-COMMUNICATION Ontology subsets documentation #466
-COMMUNICATION Referring to taxa not in NCBITaxon #434
-COMMUNICATION Document how to add logo #72
-COMMUNICATION Short ontology descriptions #1968
-COMMUNICATION Documentation for license #1840
+COMMUNICATION Ontology subsets documentation [#466](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/446)
+COMMUNICATION Referring to taxa not in NCBITaxon [#434](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/434)
+COMMUNICATION Document how to add logo [#72](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/72)
+COMMUNICATION Short ontology descriptions [#1968](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1968)
+COMMUNICATION Documentation for license [#1840](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1840)
 
 ### Content
 
-CONTENT Discourage BFO shadow classes #1539
+CONTENT Discourage BFO shadow classes [#1539](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1539)
 CONTENT? Ignoring NCIT (no issue, but has come up that NCIT is not well-formed enough to be a concern re: things like overlap)
-METADATA Term adoption #2330 (also #2324)
+METADATA Term adoption [#2330](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2330) and [#2324](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2324)
 
 ### Technical
 
@@ -33,16 +32,16 @@ Not yet classified:
     Every ontology MUST be coherent when classified together with RO, BFO, and COB
     Every ontology SHOULD be coherent when classified together with all its base-dependencies
 
-METADATA Versioning term identifiers #1347 /
-METADATA Linking term to discussion on tracker #1097
-METADATA Language tags #479 (also #325)
-METADATA Synonym types #2450
-METADATA Ontology root terms annotation #2149
-METADATA Publications metadata #1671
-METADATA Ontology merging #1548
-METADATA Exemplar classes #899
-METADATA Ontology metadata requirements #1365
-STANDARDIZATION? Standardized xref prefixes in ontologies #525
-Proposals here: #482 (comment)
-METADATA Modeling metaclasses #2454 (thanks @cthoyt, that's a good addition)
-METADATA Standardizing how imported ontologies are noted #424
+METADATA Versioning term identifiers [#1347](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1347)
+METADATA Linking term to discussion on tracker [#1097](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1097)
+METADATA Language tags [#479](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/479) and  [#325](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/325)
+METADATA Synonym types [#2450](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2450)
+METADATA Ontology root terms annotation [#2149](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2149)
+METADATA Publications metadata [#1671](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1671)
+METADATA Ontology merging [#1548](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1548)
+METADATA Exemplar classes [#899](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/899)
+METADATA Ontology metadata requirements [#1365](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1365)
+STANDARDIZATION? Standardized xref prefixes in ontologies [#525](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/525)
+Proposals here: [#482](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/482) (comment)
+METADATA Modeling metaclasses [#2454](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2454)
+METADATA Standardizing how imported ontologies are noted [#424](https://github.com/OBOFoundry/OBOFoundry.github.io/issues/424)

docs/roles/DashboardManager.md

@@ -4,4 +4,7 @@ permalink: /roles/dashboard-manager
 title: Dashboard Manager
 ---
 
-The Dashboard Manager has these basic duties:
+The [OBO Foundry dashboard](https://dashboard.obofoundry.org/) checks ontologies for adherence to OBO Foundry principles. The Dashboard Manager's jobs are:
+1. Update the dashboard once per month
+1. Fix important bugs in OBO-Dashboard if they come up (should be rare)
+1. Work with OBO Ops if needed to find people who can update the dashboard code when new principles are added or existing ones are changed.

ontology/bmont.md

@@ -22,6 +22,6 @@ products:
 - id: BMONT.owl
   description: Includes axioms linking to other ontologies, but no imports of those ontologies
 repository: https://github.com/SCAI-BIO/BiomarkerOntology
-tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issue
+tracker: https://github.com/SCAI-BIO/BiomarkerOntology/issues
 activity_status: active
 ---

principles/fp-001-open.md

@@ -29,7 +29,7 @@ Note: CC-BY licenses allow others to distribute, remix, tweak, and build upon th
 
 3. If an individual term is reused without change to the definition, the original term IRI should be used. If the definition of a term (either text or logical) is changed, the original term IRI should not be reused. Suggestions for changes or improvements to term definitions should be submitted to the appropriate ontology issue tracker.
 
-4. Regardless of which license an ontology uses, we strongly request and recommend that any reuse of an ontology attributes the source in accordance with scientific norms and the [OBO Citation and Attribution Policy](http://www.obofoundry.org/docs/Citation).
+4. Regardless of which license an ontology uses, we strongly request and recommend that any reuse of an ontology attributes the source in accordance with scientific norms and the [OBO Citation and Attribution Policy]({% link citation/Citation.md %}).
 
 ## Implementation
 

registry/ontologies.jsonld

@@ -549,7 +549,7 @@
             ],
             "repository": "https://github.com/SCAI-BIO/BiomarkerOntology",
             "title": "Biomarker Ontology",
-            "tracker": "https://github.com/SCAI-BIO/BiomarkerOntology/issue"
+            "tracker": "https://github.com/SCAI-BIO/BiomarkerOntology/issues"
         },
         {
             "activity_status": "active",