Add codespell support with configuration and typo fixes

.codespellrc

@@ -0,0 +1,47 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+#
+# Skip generated / imported / external content:
+#   - Top-level release artifacts (derived from src/ontology/uberon-edit.obo)
+#   - subsets/, imports/, taxmods/, diffs/, languages/ (all derived)
+#   - source-ontologies/, resources/, ext-mappings/, mappings/, modules/
+#   - reports/, attic/, bulk_ntr_workflow/, experimental/
+#   - docs/resources/ (binary graffle assets)
+#   - docs/odk-workflows/ (auto-generated from odkcore -- upstream fixes only,
+#     see https://github.com/INCATools/ontology-development-kit)
+#   - src/scripts/ubermacros.el (auto-generated ~196k-line NCBITaxon index)
+#   - src/ontology/bridge/uberon-bridge-to-*.owl and cl-bridge-to-*.owl
+#     (auto-generated by SSSOM inject, see `refresh-bridges` in
+#     src/ontology/uberon.Makefile)
+#   - src/patterns/definitions.owl (generated from src/patterns/data/**/*.tsv)
+#   - LICENSE (fixed legal wording; do not rewrite even if it has typos)
+#   - .git-meta (author-workflow scratch for commit / PR message drafts)
+#   - src/ontology/uberon-edit.obo -- the ontology edit file. Its contents
+#     will be spell-checked in a separate curator-reviewed PR; skipped here
+#     so that this infrastructure PR does not conflate infrastructure setup
+#     with curator-judgement calls on ~200 biological / anatomical terms.
+skip = .git,.git-meta,.gitignore,.gitattributes,.codespellrc,LICENSE,*.pdf,*.svg,*.graffle,*.tmp*,*.LOG,attic,bulk_ntr_workflow,experimental,ext-mappings,mappings,modules,reports,resources,source-ontologies,subsets,depictions.owl,external-disjoints.owl,homology.owl,homology-relations.owl,musculoskeletal.obo,musculoskeletal.owl,project.owl,reasoner_axioms.owl,rules.owl,ssso-merged-uberon.owl,uberon-base.owl,uberon-simple-rel.obo,uberon-taxmod-amniote.obo,uberon-with-isa.obo,uberon.obo,imports,taxmods,diffs,languages,odk-workflows,ubermacros.el,uberon-edit.obo,uberon-bridge-to-*.owl,cl-bridge-to-*.owl,definitions.owl
+check-hidden = true
+# Protect:
+#   - URLs (short host substrings like bu.edu would otherwise flag "bu")
+#   - camelCase / PascalCase identifiers (Prolog vars in *.pro scripts,
+#     code identifiers)
+#   - Cross-reference values after `PREFIX:` (BAMS:MEnt, BM:Tel-OLT etc.
+#     -- external IDs must not be "corrected")
+ignore-regex = https?://\S+|\b[a-z]+[A-Z]\w*\b|\b[A-Z][a-z]+[A-Z]\w*\b|\b[A-Z]{2,}:[\w-]+
+# Domain vocabulary that codespell flags as typos but is legitimate here:
+#   Anatomical / Latin terms recurring in non-uberon-edit content
+#   (bridge/external-disjoints.obo, src/patterns/data/**/*.tsv, etc.):
+#     mater      - dura/pia/arachnoid mater (meninges)
+#     vas        - vas deferens etc.
+#     processus  - Latin "process"
+#     regio      - anatomical region (Latin)
+#     collum     - Latin "neck"
+#   Ontology terminology:
+#     disjointness - "disjointness axiom" (OWL/OBO term)
+#   Curated-data / code noise:
+#     anc          - Prolog predicate name in *.pro scripts
+#     nd           - Prolog predicate (nd/4 in src/scripts/namediff.pro) and
+#                    GO evidence code "ND" (No Data) in uberon.references
+#     heterogenous, homogenous - accepted variants
+ignore-words-list = mater,vas,processus,regio,collum,disjointness,anc,nd,heterogenous,homogenous

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [master]
+  pull_request:
+    branches: [master]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v6
+      - name: Codespell
+        uses: codespell-project/actions-codespell@8f01853be192eb0f849a5c7d721450e7a467c579  # v2.2

README-editors.txt

@@ -154,7 +154,7 @@ The editors version will most likely owl-import other ontologies. Need
 to figure this into release process.
 
 == How to deal with templates ==
-see templates/REAMDE.md
+see templates/README.md
 
 
 == Other matters ==

docs/acknowledgements.md

@@ -31,7 +31,7 @@ ELK has been created in the Knowledge Representation and Reasoning group at the
 We are also grateful to the developers of HermiT and FACT++, which are also used during development.
 
 #OWL API
-The OWL API is a Java API and reference implmentation for creating, manipulating and serialising OWL Ontologies. The current Uberon development and build infrastructure relies heavily on the OWLAPI. Many thanks to the OWLAPI developers, especially Ignazio Palmisano and Matt Horridge.
+The OWL API is a Java API and reference implementation for creating, manipulating and serialising OWL Ontologies. The current Uberon development and build infrastructure relies heavily on the OWLAPI. Many thanks to the OWLAPI developers, especially Ignazio Palmisano and Matt Horridge.
 
 In particular, we make use of an in-house library developed for the GO called [owltools](https://github.com/owlcollab/owltools), and the [ROBOT](https://robot.obolibrary.org/) ontology manipulation tool developed for the OBO Foundry. Both are built on top of the OWL API.
 

docs/onboarding.md

@@ -2,7 +2,7 @@
 
 This document is intended as a quick checklist that *existing* curators
 can follow to ensure that *new* curators are provided with the
-informations and the access that they need in order to start working
+information and the access that they need in order to start working
 with Uberon.
 
 1. Invite them to the [Anatomy and Cell

docs/uberon-editor-sop.md

@@ -162,7 +162,7 @@ Blood and lymphatic vessels are tubes that convey body fluids through the tissue
 
 However, while it is useful to have this wide range of object properties to record relations between branches, it can also lead to selecting a property that does not accurately reflect the relationship between subject and object. An example of this is the misuse of '[branching part of](http://purl.obolibrary.org/obo/RO_0002380)', which is a subclass of 'part of', but it has been used extensively for branches that are no longer part of the stem.
 
-Therefore, we need standarization for how branching relationships should be recorded in Uberon. The object property 'connecting branch of' is a subproperty of 'connected to' and should be used to describe the relation between a branching vessel and the stem vessel. Ex:
+Therefore, we need standardization for how branching relationships should be recorded in Uberon. The object property 'connecting branch of' is a subproperty of 'connected to' and should be used to describe the relation between a branching vessel and the stem vessel. Ex:
 
 ['axillary artery'](http://purl.obolibrary.org/obo/UBERON_0001394) *SubClassOf* ['connected to'](http://purl.obolibrary.org/obo/RO_0002252) some ['subclavian aretery'](http://purl.obolibrary.org/obo/UBERON_0001533)
 

reference/all-combined.md

@@ -154,8 +154,8 @@ We consider the autopod as consisting of 3 segments, divided according to the fo
 
 Note that in this document and in the ontology we currently use the unambiguous skeletal-prefixed terms, and phenoscape-preferred terms in parentheses.
 
-Hoever, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
-We accomodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
+However, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
+We accommodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
 
 This gives us a second hierarchy (also part-wise JEPD):
 
@@ -351,7 +351,7 @@ The file can be edited in a text editor (the recommended text editor
 emacs plus Phil Lord's omn-mode.el, plus ubref-helper.el). Note that
 the author should be adept in manchester notation.
 
-The prefered route is to open the articles ontology in Protege,
+The preferred route is to open the articles ontology in Protege,
 navigating to the 'individuals by type' tab (insert image here).
 
 ![Screenshot](images/udoc-in-p4.png)
@@ -361,7 +361,7 @@ markdown format. Note that hashes should be used for headings rather
 than underlines.
 
 The format used is a variant called ontology markdown. Class labels
-can be written in backtics - the derived documentation will make PURL
+can be written in backticks - the derived documentation will make PURL
 links from these (*to be implemented*).
 
 In general each article type should follow a certain template (to be
@@ -938,8 +938,8 @@ We consider the autopod as consisting of 3 segments, divided according to the fo
 
 Note that in this document and in the ontology we currently use the unambiguous skeletal-prefixed terms, and phenoscape-preferred terms in parentheses.
 
-Hoever, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
-We accomodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
+However, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
+We accommodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
 
 This gives us a second hierarchy (also part-wise JEPD):
 
@@ -1076,7 +1076,7 @@ from Rathke's pouch in tetrapods, we would say:
 
 Note that we do not need to taxonomically scope the target class.
 
-#### Examplar Class
+#### Exemplar Class
 
 See [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562)
 as an example (note: GCIs may not be visible in OntoBee).

reference/all.md

@@ -108,15 +108,15 @@ The file can be edited in a text editor (the recommended text editor
 emacs plus Phil Lord's omn-mode.el, plus ubref-helper.el). Note that
 the author should be adept in manchester notation.
 
-The prefered route is to open the articles ontology in Protege,
+The preferred route is to open the articles ontology in Protege,
 navigating to the 'individuals by type' tab (insert image here).
 
 In both cases, the main text should go in the dc:description tab using
 markdown format. Note that hashes should be used for headings rather
 than underlines.
 
 The format used is a variant called ontology markdown. Class labels
-can be written in backtics - the derived documentation will make PURL
+can be written in backticks - the derived documentation will make PURL
 links from these (to be implemented).
 
 In general each article type should follow a certain template (to be
@@ -774,8 +774,8 @@ We consider the autopod as consisting of 3 segments, divided according to the fo
 
 Note that in this document and in the ontology we currently use the unambiguous skeletal-prefixed terms, and phenoscape-preferred terms in parentheses.
 
-Hoever, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
-We accomodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
+However, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
+We accommodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
 
 This gives us a second hierarchy (also part-wise JEPD):
 

reference/reference_0000000.md

@@ -121,7 +121,7 @@ The file can be edited in a text editor (the recommended text editor
 emacs plus Phil Lord's omn-mode.el, plus ubref-helper.el). Note that
 the author should be adept in manchester notation.
 
-The prefered route is to open the articles ontology in Protege,
+The preferred route is to open the articles ontology in Protege,
 navigating to the 'individuals by type' tab (insert image here).
 
 ![Screenshot](images/udoc-in-p4.png)
@@ -131,7 +131,7 @@ markdown format. Note that hashes should be used for headings rather
 than underlines.
 
 The format used is a variant called ontology markdown. Class labels
-can be written in backtics - the derived documentation will make PURL
+can be written in backticks - the derived documentation will make PURL
 links from these (*to be implemented*).
 
 In general each article type should follow a certain template (to be

reference/reference_0000019.md

@@ -35,8 +35,8 @@ We consider the autopod as consisting of 3 segments, divided according to the fo
 
 Note that in this document and in the ontology we currently use the unambiguous skeletal-prefixed terms, and phenoscape-preferred terms in parentheses.
 
-Hoever, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
-We accomodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
+However, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
+We accommodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
 
 This gives us a second hierarchy (also part-wise JEPD):
 

reference/reference_0000023.md

@@ -61,7 +61,7 @@ from Rathke's pouch in tetrapods, we would say:
 
 Note that we do not need to taxonomically scope the target class.
 
-## Examplar Class
+## Exemplar Class
 
 See [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562)
 as an example (note: GCIs may not be visible in OntoBee).

reference/reference_0000034.md

@@ -57,7 +57,7 @@ Note that some subdivisions may simultaneously be considered organs
 and tube subdivisions.
 
 Note that the the same 4 terms may also be used in non-chordates for
-analagous structures. We tend to reserve these labels for vertebrates,
+analogous structures. We tend to reserve these labels for vertebrates,
 and use functional grouping classes such as `food storage organ`.
 
 There are variations and subdivisions of this scheme in vertebrates;
@@ -163,7 +163,7 @@ the genitourinary system. In vertebrates with a cloaca, we consider
 the rectum to be the terminal part of the intestine, emptying into the
 cloacal chamber.
 
-Note that in vertebrates the anus is considere to be the opening at
+Note that in vertebrates the anus is considered to be the opening at
 the end of the rectum. If the DT is considered to extend past the
 rectum and include the cloaca and the cloacal opening, then the anus
 is no longer the end of the DT. For simplicity we may consider the DT

reference/reference_0000036.md

@@ -54,7 +54,7 @@ of terms, as we have both 'gastrulation' (GO) and 'gastrula stage'
 ## Relationship types
 
 We use a variety of relationship types for connecting stages to
-eachother, and for connecting stages to structures. These relations
+each other, and for connecting stages to structures. These relations
 are based on work by Fabian Neuhaus and David Osumi-Sutherland and
 will be described in more detail in a subsequent publication. A brief
 overview is provided here.
@@ -118,7 +118,7 @@ In order of preferences, stage ontologies should:
  * use identifiers that are conformant to OBO guidelines
  * isa-complete
  * uses isa vs part_of in the correct way
- * be openly released at a reasonable frequence, and be resposibe to reasonable requests
+ * be openly released at a reasonable frequency, and be resposibe to reasonable requests
  * uses intermediate subdivisions where appropriate (ie isn't a flat list)
  * uses preceded_by relationships to create a temporal ordering - this should be a total order on the leaf nodes
  * use standard naming conventions

reference/references-edit.omn

@@ -288,7 +288,7 @@ The file can be edited in a text editor (the recommended text editor
 emacs plus Phil Lord's omn-mode.el, plus ubref-helper.el). Note that
 the author should be adept in manchester notation.
 
-The prefered route is to open the articles ontology in Protege,
+The preferred route is to open the articles ontology in Protege,
 navigating to the 'individuals by type' tab (insert image here).
 
 ![Screenshot](images/udoc-in-p4.png)
@@ -298,7 +298,7 @@ markdown format. Note that hashes should be used for headings rather
 than underlines.
 
 The format used is a variant called ontology markdown. Class labels
-can be written in backtics - the derived documentation will make PURL
+can be written in backticks - the derived documentation will make PURL
 links from these (*to be implemented*).
 
 In general each article type should follow a certain template (to be
@@ -551,7 +551,7 @@ Note that some subdivisions may simultaneously be considered organs
 and tube subdivisions.
 
 Note that the the same 4 terms may also be used in non-chordates for
-analagous structures. We tend to reserve these labels for vertebrates,
+analogous structures. We tend to reserve these labels for vertebrates,
 and use functional grouping classes such as `food storage organ`.
 
 There are variations and subdivisions of this scheme in vertebrates;
@@ -657,7 +657,7 @@ the genitourinary system. In vertebrates with a cloaca, we consider
 the rectum to be the terminal part of the intestine, emptying into the
 cloacal chamber.
 
-Note that in vertebrates the anus is considere to be the opening at
+Note that in vertebrates the anus is considered to be the opening at
 the end of the rectum. If the DT is considered to extend past the
 rectum and include the cloaca and the cloacal opening, then the anus
 is no longer the end of the DT. For simplicity we may consider the DT
@@ -880,7 +880,7 @@ of terms, as we have both 'gastrulation' (GO) and 'gastrula stage'
 ## Relationship types
 
 We use a variety of relationship types for connecting stages to
-eachother, and for connecting stages to structures. These relations
+each other, and for connecting stages to structures. These relations
 are based on work by Fabian Neuhaus and David Osumi-Sutherland and
 will be described in more detail in a subsequent publication. A brief
 overview is provided here.
@@ -944,7 +944,7 @@ In order of preferences, stage ontologies should:
  * use identifiers that are conformant to OBO guidelines
  * isa-complete
  * uses isa vs part_of in the correct way
- * be openly released at a reasonable frequence, and be resposibe to reasonable requests
+ * be openly released at a reasonable frequency, and be resposibe to reasonable requests
  * uses intermediate subdivisions where appropriate (ie isn't a flat list)
  * uses preceded_by relationships to create a temporal ordering - this should be a total order on the leaf nodes
  * use standard naming conventions
@@ -1239,7 +1239,7 @@ from Rathke's pouch in tetrapods, we would say:
 
 Note that we do not need to taxonomically scope the target class.
 
-## Examplar Class
+## Exemplar Class
 
 See [thymus primordium](http://purl.obolibrary.org/obo/UBERON_0005562)
 as an example (note: GCIs may not be visible in OntoBee).
@@ -1289,8 +1289,8 @@ We consider the autopod as consisting of 3 segments, divided according to the fo
 
 Note that in this document and in the ontology we currently use the unambiguous skeletal-prefixed terms, and phenoscape-preferred terms in parentheses.
 
-Hoever, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
-We accomodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
+However, it is also possible to first group the acropodium and metapodium - confusingly, this is sometimes called the acropodium (e.g. Wagner and Chin 2001).
+We accommodate this group, and introduce a new label 'digitopodium' (Ibrahim and Sereno) to group the proximal-most two elements
 
 This gives us a second hierarchy (also part-wise JEPD):