fix: ensure yaml examples are valid and conform to format expectations (#2812)

Author: jsstevenson

principles/fp-009-users.md

@@ -20,7 +20,7 @@ scientific area and does so in a usable and sustainable fashion.
 It is important to be able to illustrate usage outside of the immediate circle of ontology developers and stakeholders. Demonstrations of usage MUST be publicly available. Preferred indicators of usage are those that directly demonstrate such, including:
 
 - Use of the target ontology's term IRIs in an external ontology. Indicators of this type MUST include one or more IRIs for a term _within the external ontology_ that uses a term from the target ontology.
-  
+
 - Documentation of requests from multiple users. Indicators of this type MUST link to specific requests in the issue tracker, OR link to an issue tracker search (for example, showing new term requests), OR link to an email thread or other mechanism _if publicly viewable_.
 
 - Publications showing the ontology being used in research by external users. Indicators of this type MUST provide citation details for the publications (link to PubMed or full text) and MUST include a sentence demonstrating the use (preferably taken from the title, abstract, or full text of the cited reference). Note that if citing full text that is behind a paywall, it may be necessary to provide a PDF for the paper.
@@ -42,7 +42,7 @@ Other indicators are currently possible as well:
   within some community (mere mention of the existence is not enough
   to warrant inclusion).
 
-Note that the ontology can still be listed on the OBO Foundry website while publicising your resource in appropriate channels and searching for users with needs you can meet. 
+Note that the ontology can still be listed on the OBO Foundry website while publicising your resource in appropriate channels and searching for users with needs you can meet.
 
 ## Implementation
 
@@ -51,58 +51,58 @@ use within your ontology [metadata file](https://github.com/OBOFoundry/OBOFoundr
 
 ```yaml
 usages:
-- user: http://www.informatics.jax.org/disease (link to group)
-  description: MGI disease model annotations use DO (description of group)
+- description: MGI disease model annotations use DO (description of group)
   examples:
-   - url: http://www.informatics.jax.org/disease/DOID:4123 (link to specific example)
-     description: Human genes and mouse homology associated with nail diseases (description of specific example)
+    - description: Human genes and mouse homology associated with nail diseases (description of specific example)
+      url: "http://www.informatics.jax.org/disease/DOID:4123"  # link to specific example)
+  user: "http://www.informatics.jax.org/disease"  # link to group
 ```
 
-You may have multiple examples for each user, and mulitple users under the `usages` tag.
+You may have multiple examples for each user, and multiple users under the `usages` tag.
 
 ## Examples
 
 Use of PSI-MOD term IRI (in the form of a CURIE) in the PR ontology:
 ```yaml
-- user: http://purl.obolibrary.org/obo/pr
-  description: Protein Ontology
+- description: Protein Ontology
   examples:
-   - url: https://proconsortium.org/app/export/obo/PR:000027653/
-     description: OBO Format stanza showing use of PSI-MOD term in logical definition
+    - description: OBO Format stanza showing use of PSI-MOD term in logical definition
+      url: "https://proconsortium.org/app/export/obo/PR:000027653/"
+  user: "http://purl.obolibrary.org/obo/pr"
 ```
 Term requests to PR from multiple users:
 ```yaml
-- user: (multiple)
-  description: Term requests made via the Protein Ontology GitHub tracker
+- description: Term requests made via the Protein Ontology GitHub tracker
   examples:
-   - url: https://github.com/PROconsortium/PRoteinOntology/issues?q=is%3Aissue+label%3A%22Term+Request%22
-     description: List of issues tagged with 'Term Request' to PRO
+    - description: "List of issues tagged with 'Term Request' to PRO"
+      url: "https://github.com/PROconsortium/PRoteinOntology/issues?q=is%3Aissue+label%3A%22Term+Request%22"
+  user: (multiple)
 ```
 Publication showing the Disease Ontology being used in research by external users
 ```yaml
-- user: https://pubmed.ncbi.nlm.nih.gov/36860337/
-  description: Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis
+- description: Machine learning-based prediction of candidate gene biomarkers correlated with immune infiltration in patients with idiopathic pulmonary fibrosis
   examples:
-   - url: https://pubmed.ncbi.nlm.nih.gov/36860337/
-     description: In abstract, "Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed..."
+    - description: 'In abstract, "Functional annotation, pathway enrichment, Disease Ontology and gene set enrichment analyses revealed..."'
+      url: "https://pubmed.ncbi.nlm.nih.gov/36860337/"
+  user: "https://pubmed.ncbi.nlm.nih.gov/36860337/"
 ```
 Use of terms from GO for annotation:
 ```yaml
-- user: https://www.uniprot.org
-  description: UniProt
+- description: UniProt
   examples:
-   - url: https://www.uniprot.org/uniprotkb/Q15796/entry#function
-     description: Functional annotation using GO (see subsection entitled "GO annotations")
+    - description: Functional annotation using GO (see subsection entitled "GO annotations")
+      url: "https://www.uniprot.org/uniprotkb/Q15796/entry#function"
+  user: "https://www.uniprot.org"
 ```
 OBI terms imported into external ontologies
 ```yaml
-- user: (multiple)
-  description: Ontologies using OBI terms
+- description: Ontologies using OBI terms
   examples:
-   - url: http://dashboard.obofoundry.org/dashboard/obi/dashboard.html
-     description: List of ontologies using at least one OBI term (See section entitled "Info: Which ontologies use it?")
-   - url: https://ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000691
-     description: List of ontologies using the term 'ABI 377 automated sequencer' (See section entitled "Ontologies that use the Class")
+    - description: 'List of ontologies using at least one OBI term (See section entitled "Info: Which ontologies use it?")'
+      url: "http://dashboard.obofoundry.org/dashboard/obi/dashboard.html"
+    - description: 'List of ontologies using the term "ABI 377 automated sequencer" (See section entitled "Ontologies that use the Class")'
+      url: "https://ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000691"
+  user: (multiple)
 ```
 
 ## Counter-Examples