Merge branch 'master' into obo_academy_apr24

docs/organization/meetings.md

@@ -1,16 +1,16 @@
 # The Unified Phenotype Ontology (uPheno) meeting series
 
-The uPheno editors hold four regular calls at the moment (April 2024), organised by members of the Monarch Initiative and the Alliance and Genome Resources.
+The uPheno editors hold four regular calls at the moment (April 2024), organised by members of the [Monarch Initiative](https://monarchinitiative.org/) and the [Alliance of Genome Resources](https://www.alliancegenome.org/).
 If you wish to join the meeting, you can open an issue on https://github.com/obophenotype/upheno/issues with the request to be added, or send an email to [email protected].
 
 Meetings:
 
 | Meeting | Timeslot | Meeting coordinators |
 | ------- | -------- | -------------------- |
-| Phenotype editors call | Friday 8am PT, ev. 4 weeks | Sue Bello (@sbello), Ray Stefancsik (@rays22) |
-| Phenotype outreach call | Friday 8am PT, ev. 4 weeks | James McLaughlin (@jamesamcl), Arwa Ibrahim (@ar-ibrahim) |
+| Phenotype editors call ([minutes](https://docs.google.com/document/d/1WrQanAMuccS-oaoAIb9yWQAd4Rvy3R3mU01v9wHbriM/edit)) | Friday 8am PT, ev. 4 weeks | Sue Bello (@sbello), Ray Stefancsik (@rays22) |
+| Phenotype outreach call ([events](../organization/outreach.md), [minutes](https://docs.google.com/document/d/1FK_kv9s1s6xMLI-xHlJfPH4YGm85a8VylsqA3f2hRks/edit)) | Friday 8am PT, ev. 4 weeks | James McLaughlin (@jamesamcl), Arwa Ibrahim (@ar-ibrahim) |
 | HP-MP harmonisation calls | Thursday 9am PT, ev. 4 weeks | Ray Stefancsik (@rays22), Sue Bello (@sbello) |
-| OBA editors call | Friday 6:15am PT, Monthly on the third Friday | Ray Stefancsik (@rays22), Arwa Ibrahim (@ar-ibrahim) |
+| OBA editors call ([minutes](https://docs.google.com/document/d/17UOyoi_XkJTGZoctK44UtmjAlMsjzE1Cl1UhrFpPRmw/edit)) | Friday 6:15am PT, Monthly on the third Friday | Ray Stefancsik (@rays22), Arwa Ibrahim (@ar-ibrahim) |
 
 ## Meeting preparation instructions
 
@@ -21,28 +21,28 @@ Meetings:
 - The MC prepares the agenda in advance: everyone on the call is very busy and our time is precious.
 - Every agenda item has an associated ticket on GitHub, and a clear set of action items should be added in [GitHub Tasklist syntax](https://docs.github.com/en/issues/tracking-your-work-with-issues/about-task-lists) to the _first comment_ on the issue.
     - If there are issues for any subtasks (e.g. PATO or Uberon edits), the list should be edited to link these.
-    - Any items that do not have a subissue but do involve changes to patterns) should be edited to link to implementing PR.
+    - Any item that does not have a subissue but involve changes to patterns should be linked to an implementing PR.
     - It does not matter who wrote the first issue comment, the uPheno team can simply add a tasklist underneath the original comment and refine it over time.
-    - Tag all issues which need discussion with "upheno call"
+    - Tag all issues which need discussion with `editors-call`
     - It _must_ be clear from the task list what the uPheno team should be doing during the call (discuss, decide, review). For example, one item on the task list may read: "uPheno team to decide on appropriate label for template".
     - Conversely, no issue should be added to the agenda that does not have a clear set of action items associated with it _that should be addressed during the call_. These actions may include making and documenting modelling decisions.
-- Go through up to 10 issues on the [uPheno issue tracker](https://github.com/obophenotype/upheno/issues) before each meeting to determine how to progress on them, and add action items. Only if they need to be discussed, add the "upheno call" label.
+- Go through up to 10 issues on the [uPheno issue tracker](https://github.com/obophenotype/upheno/issues) before each meeting to determine how to progress on them, and add action items. Only if they need to be discussed, add the `editors-call` call" label.
 
 ## Meeting execution instruction
 
 !!! note
 
-    The instructions were created for the Phenotype editors call, but the general principles hold for all calls.
+    The instructions were created for the Phenotype editors' call, but the general principles hold for all calls.
 
-- Every meeting should start with a quick (max 5 min, ideally 3 min) overview of all the goals and how they processed. The MC should mention all blockers and goals, even the ones we did not make any progress on, to keep the focus on the priorities:
+- Every meeting should start with a brief (maximum 5 minutes, ideally 3 minutes) overview of all the goals and the progress made on them. The MC should mention all blockers and goals, even the ones on which no progress was made, to keep the focus on the priorities.
     - uPheno releases
     - uPheno documentation
     - Pattern creation
     - Patternisation: The process of ensuring that phenotype ontologies are using uPheno conformant templates to define their phenotypes.
     - Harmonisation: The process of ensuring that phenotype patterns are applied consistently across ontologies.
 - For new pattern discussions:
     - Every new pattern proposal should come with a new GitHub issue, appropriately tagged.
-    - The issue text should detail the use cases for the pattern well, and these use cases should also be documented in the "description" part of the DOSDP YAML file. Uses cases should include expected classifications and why we want them (and potentially classifications to avoid).  e.g. axis-specific dimension traits should classify under more abstractly defined dimension traits which in term should classify under Morphology. Add some examples of contexts where grouping along these classifications is useful.
+    - The issue text should detail the use cases for the pattern well, and these use cases should also be documented in the "description" part of the DOSDP YAML file. Use cases should include expected classifications and why we want them (and potentially classifications to avoid). For example, axis-specific dimension traits should classify under more abstractly defined dimension traits, which in turn should classify under "morphology". Add some examples of context where grouping along these classifications is useful.
 - Agenda items may include discussion and decisions about more general modelling issues that affect more than one pattern, but these should also be documented as tickets as described above.
 
 ## After the meeting

docs/reference/data-integration.md

@@ -178,6 +178,19 @@ Note though that such methods lack the transparency of basic methods, which mean
 
     For people working on named entity recognition there is a bit of a point to be made to try and extract not only the complete phenotype expression, but actually map the individual components, like characteristics and chemicals. If you do that, you can directly construct a pre-coordinated phenotype class compatible with the uPheno framework, even if no such class currently exists. Even if it does, it would easily be recognisable as an "inferred equivalent class".
 
+#### Summary
+
+![uPheno integration](../images/phenotype-integration.png)
+
+!!! note "Figure: data integration with uPheno"
+
+    The Figure shows 4 different kinds of integration:
+
+    - A: Measurement data. A measurement in conjunction with a normal range and a mapping to a trait term is transformed to a Phenotypic abnormality term in HPO.
+    - B: Unstructured data. Free text, for example in a paper, is translated into pre-coordinated uPheno expressions
+    - C: Post-coordinated data. Mapped into uPheno expressions using design patterns.
+    - D: Related data. Mapped to phenotype terms using specific associations.
+
 ### Level 2 integration: Knowledge
 
 The real magic with respect to computational phenotype data comes through the integration of knowledge.
@@ -330,6 +343,15 @@ All of these phenotype assocations can be augmented with many others, such as ge
 
 ### Summary
 
+
+![uPheno Integration of Knowledge](../images/integration_links.png)
+
+!!! note "Figure: Integrating Knowledge in the uPheno framework."
+
+    This picture looks complicated, but it shows only a fraction of the available relationships.
+    Most of the relationships are phenotypic or core ontological, only the Hypolysinemia link to `SLC7A7` is an KG associations.
+    There are dozens of different kinds of assocations that could be added here!
+
 - We can integrate diverse phenotype data records by associating them with pre-coordinated trait and/or phenotype terms from the Unified Phenotype Ontology (uPheno).
 - There are a few different approaches we need to leverage to associate phenotype data with uPheno terms, including:
     - Using standardised logical definitions for automated classification.