From fd51c1c14aa0fa42440c95a9c022c902275729c7 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 26 Aug 2026 11:06:17 -0400 Subject: [PATCH 1/5] Add GitHub Actions workflow for codespell on master --- .github/workflows/codespell.yml | 23 +++++++++++++++++++++++ 1 file changed, 23 insertions(+) create mode 100644 .github/workflows/codespell.yml diff --git a/.github/workflows/codespell.yml b/.github/workflows/codespell.yml new file mode 100644 index 000000000..9458b0c8f --- /dev/null +++ b/.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 From 1332e6653c4a00be778c75b20f2596611c34a312 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Wed, 26 Aug 2026 11:06:17 -0400 Subject: [PATCH 2/5] Add rudimentary codespell config --- .codespellrc | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 .codespellrc diff --git a/.codespellrc b/.codespellrc new file mode 100644 index 000000000..f7bb7c1f3 --- /dev/null +++ b/.codespellrc @@ -0,0 +1,6 @@ +[codespell] +# Ref: https://github.com/codespell-project/codespell#using-a-config-file +skip = .git,.gitignore,.gitattributes,*.pdf,.codespellrc +check-hidden = true +# ignore-regex = +# ignore-words-list = From 700df6085d81f3641982fb3d25012b637a970407 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 28 Aug 2026 08:40:41 -0400 Subject: [PATCH 3/5] Expand codespell config: skip derived / generated content Extend the initial rudimentary .codespellrc so the check runs cleanly against the hand-curated parts of the repo. Following review feedback on #3759 from @cmungall and @matentzn, this PR is deliberately scoped to infrastructure + typos in files that are safe to touch here; the uberon-edit.obo review and any odkcore-side fixes are deferred to separate PRs. Skip patterns: - Top-level release artifacts and derived directories (uberon.obo, uberon-base.owl, uberon-with-isa.obo, uberon-taxmod-*.obo, musculoskeletal.*, homology*, project.owl, reasoner_axioms.owl, rules.owl, ssso-merged-uberon.owl, depictions.owl, external-disjoints.owl; subsets/, imports/, taxmods/, diffs/, languages/). - source-ontologies/, resources/, ext-mappings/, mappings/, modules/ (external content); reports/, attic/, bulk_ntr_workflow/, experimental/ (archival / auto-generated / workflow scratch); docs/resources/ (binary graffle assets). - odk-workflows -- docs/odk-workflows/ is auto-generated from odkcore and any edit here would be lost on the next ODK refresh. Upstream fixes should go to https://github.com/INCATools/ontology-development-kit (per matentzn's review). - src/scripts/ubermacros.el -- ~196k-line auto-generated Emacs macros file indexing NCBITaxon species names. - uberon-bridge-to-*.owl, cl-bridge-to-*.owl (auto-generated by `refresh-bridges` via SSSOM inject). - definitions.owl (generated from src/patterns/data/**/*.tsv). - LICENSE (fixed legal wording). - .git-meta (author-workflow scratch for commit / PR message drafts). - uberon-edit.obo -- deferred to a separate curator-reviewed PR (per matentzn's review of #3759, which noted the codespell -w pass produced several biological-context false positives that need domain expertise to distinguish from genuine typos). Protections via ignore-regex: - URLs (short host substrings like bu.edu would otherwise flag "bu"). - camelCase / PascalCase identifiers (Prolog vars, code identifiers). - Cross-reference values after PREFIX: (BAMS:MEnt, BM:Tel-OLT etc.). ignore-words-list (minimal, only what still-scanned files need): - Latin / anatomical: mater, vas, processus, regio, collum. - Ontology term: disjointness (as in "disjointness axiom"). - Code / data: anc, nd (Prolog predicates + GO evidence code "ND"), heterogenous, homogenous (accepted variants). Reduces codespell hits from ~13,600 lines of noise to ~45, all of which are real typos in still-in-scope files (handled in the next commits). Co-Authored-By: Claude Code 2.1.246 / Claude Opus 4.7 (1M context) --- .codespellrc | 47 ++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 44 insertions(+), 3 deletions(-) diff --git a/.codespellrc b/.codespellrc index f7bb7c1f3..a0de985f6 100644 --- a/.codespellrc +++ b/.codespellrc @@ -1,6 +1,47 @@ [codespell] # Ref: https://github.com/codespell-project/codespell#using-a-config-file -skip = .git,.gitignore,.gitattributes,*.pdf,.codespellrc +# +# 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 -# ignore-regex = -# ignore-words-list = +# 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 From 93be763db03f6e557c23e3244c5caab475b29299 Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 28 Aug 2026 08:41:30 -0400 Subject: [PATCH 4/5] Fix ambiguous typos requiring context review Codespell flagged these with multiple possible corrections; each was reviewed in context and fixed manually. - reference/reference_0000034.md:166 "considere to be" -> "considered to be" - reference/references-edit.omn:660 same fix (mirrored file) - src/patterns/data/default/vein_and_venule_pattern.tsv:18 "A venous plexus tha connects" -> "that connects" The corresponding "tha" in the auto-generated src/patterns/definitions.owl will be corrected the next time the pattern is regenerated from the tsv. Co-Authored-By: Claude Code 2.1.246 / Claude Opus 4.7 (1M context) --- reference/reference_0000034.md | 2 +- reference/references-edit.omn | 2 +- src/patterns/data/default/vein_and_venule_pattern.tsv | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/reference/reference_0000034.md b/reference/reference_0000034.md index ebee7efe3..7db163c75 100644 --- a/reference/reference_0000034.md +++ b/reference/reference_0000034.md @@ -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 diff --git a/reference/references-edit.omn b/reference/references-edit.omn index ff20135ce..9bf9d1b1e 100644 --- a/reference/references-edit.omn +++ b/reference/references-edit.omn @@ -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 diff --git a/src/patterns/data/default/vein_and_venule_pattern.tsv b/src/patterns/data/default/vein_and_venule_pattern.tsv index c22cb302e..8a5f3f166 100644 --- a/src/patterns/data/default/vein_and_venule_pattern.tsv +++ b/src/patterns/data/default/vein_and_venule_pattern.tsv @@ -15,7 +15,7 @@ UBERON:8600068 mental vein UBERON:0001638 UBERON:0001456 A vein that is tributa UBERON:8600069 deep lingual vein FMA:50830 UBERON:0001638 UBERON:0001456 A vein that is tributary of the lingual vein and drains blood from the tongue. wikipedia:Deep_lingual_vein UBERON:0006634 UBERON:0001723 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z UBERON:8600070 dorsal lingual vein FMA:50826 UBERON:0001638 UBERON:0001456 "A vein that is tributary of the lingual vein and drains blood from the dorsum of the tongue, and the sides of the tongue." wikipedia:Dorsal_lingual_veins UBERON:0006634 UBERON:0001723 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z UBERON:8600071 sublingual vein FMA:50836 UBERON:0001638 UBERON:0001456 A vein that is tributary of the lingual vein and drains blood from the ventral (inferior) surface of the tongue and the sublingual glands. wikipedia:Sublingual_vein UBERON:0006634 UBERON:0001832 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z -UBERON:8600072 glandular venous plexus UBERON:0001593 UBERON:0002046 A venous plexus tha connects the middle and superior thyroid veins. https://www.anatomy.net/superior-thyroid-vein thiroid venous plexus doi:10.53347/rID-70578 UBERON:0007157 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z +UBERON:8600072 glandular venous plexus UBERON:0001593 UBERON:0002046 A venous plexus that connects the middle and superior thyroid veins. https://www.anatomy.net/superior-thyroid-vein thiroid venous plexus doi:10.53347/rID-70578 UBERON:0007157 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z UBERON:8600073 circumflex humeral vein UBERON:0001638 UBERON:0001467 A vein that is tributary of the axillary vein and drains blood from the region around the neck of the humerus. wikipedia:Axillary_vein UBERON:0000985 UBERON:0000976 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z UBERON:8600074 thoracoacromial vein FMA:23058 UBERON:0001638 UBERON:0001467 "A vein that is tributary of the axillary vein and drains blood from the thoracoacromial region, including the pectoral, shoulder, and clavicular regions." wikipedia:Axillary_vein thoraco-acromial vein FMA:23058 UBERON:0000985 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z UBERON:8600075 transverse cervical vein FMA:50858 UBERON:0001638 UBERON:0000974 "A vein that is tributary of the external jugular vein and drains blood from the superficial muscles of the back, mainly the trapezius muscle." wikipedia:Transverse_cervical_veins UBERON:0001101 UBERON:0002380 https://orcid.org/0000-0001-6677-8489 2024-06-06T09:53:48Z From 9e9b49c24ee43af10b7fefd2865cdef9ac81364e Mon Sep 17 00:00:00 2001 From: Yaroslav Halchenko Date: Fri, 28 Aug 2026 08:41:44 -0400 Subject: [PATCH 5/5] [DATALAD RUNCMD] Fix non-ambiguous typos via codespell -w Codespell auto-corrected 42 non-ambiguous typos (single-suggestion) across docs/, reference/, src/scripts/, src/patterns/, src/ontology/Makefile and uberon.Makefile, src/ontology/objectproperty.csv, uberon.references, README-editors.txt, and src/sparql/README.md. Common fixes: accomodate->accommodate, Hoever->However, prefered->preferred, backtics->backticks, Examplar->Exemplar, analagous->analogous, eachother-> each other, frequence->frequency, informations->information, implmentation-> implementation, standarization->standardization, and other one-offs. Co-Authored-By: Claude Code 2.1.246 / Claude Opus 4.7 (1M context) === Do not change lines below === { "chain": [], "cmd": "uvx codespell -w", "exit": 0, "extra_inputs": [], "inputs": [], "outputs": [], "pwd": "." } ^^^ Do not change lines above ^^^ --- README-editors.txt | 2 +- docs/acknowledgements.md | 2 +- docs/onboarding.md | 2 +- docs/uberon-editor-sop.md | 2 +- reference/all-combined.md | 14 +++++++------- reference/all.md | 8 ++++---- reference/reference_0000000.md | 4 ++-- reference/reference_0000019.md | 4 ++-- reference/reference_0000023.md | 2 +- reference/reference_0000034.md | 2 +- reference/reference_0000036.md | 4 ++-- reference/references-edit.omn | 16 ++++++++-------- reference/z.md | 4 ++-- src/ontology/Makefile | 2 +- src/ontology/bridge/collected-amniote-hdr.owl | 2 +- src/ontology/objectproperty.csv | 4 ++-- src/ontology/uberon.Makefile | 2 +- src/scripts/merge_species.pro | 2 +- src/scripts/taxa.py | 2 +- src/scripts/update_repo.sh | 2 +- src/sparql/README.md | 2 +- 21 files changed, 42 insertions(+), 42 deletions(-) diff --git a/README-editors.txt b/README-editors.txt index 1d28cb640..b09900f82 100644 --- a/README-editors.txt +++ b/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 == diff --git a/docs/acknowledgements.md b/docs/acknowledgements.md index 0823b14e6..bcaf420ea 100644 --- a/docs/acknowledgements.md +++ b/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. diff --git a/docs/onboarding.md b/docs/onboarding.md index 5b9c4a6f3..4275f1889 100644 --- a/docs/onboarding.md +++ b/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 diff --git a/docs/uberon-editor-sop.md b/docs/uberon-editor-sop.md index 1cd5f7a5c..d8b5b4bdd 100644 --- a/docs/uberon-editor-sop.md +++ b/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) diff --git a/reference/all-combined.md b/reference/all-combined.md index 53b157974..bdd9c9301 100644 --- a/reference/all-combined.md +++ b/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). diff --git a/reference/all.md b/reference/all.md index eab81ee96..9209ebb30 100644 --- a/reference/all.md +++ b/reference/all.md @@ -108,7 +108,7 @@ 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). In both cases, the main text should go in the dc:description tab using @@ -116,7 +116,7 @@ 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 @@ -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): diff --git a/reference/reference_0000000.md b/reference/reference_0000000.md index 70c77eb38..acf463381 100644 --- a/reference/reference_0000000.md +++ b/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 diff --git a/reference/reference_0000019.md b/reference/reference_0000019.md index 42396900d..bdd0d4b87 100644 --- a/reference/reference_0000019.md +++ b/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): diff --git a/reference/reference_0000023.md b/reference/reference_0000023.md index ec560ad61..0d3ea943f 100644 --- a/reference/reference_0000023.md +++ b/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). diff --git a/reference/reference_0000034.md b/reference/reference_0000034.md index 7db163c75..63b67d0dd 100644 --- a/reference/reference_0000034.md +++ b/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; diff --git a/reference/reference_0000036.md b/reference/reference_0000036.md index aa805fe02..47b9496b1 100644 --- a/reference/reference_0000036.md +++ b/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 diff --git a/reference/references-edit.omn b/reference/references-edit.omn index 9bf9d1b1e..768fb2e9e 100644 --- a/reference/references-edit.omn +++ b/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; @@ -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): diff --git a/reference/z.md b/reference/z.md index 6f6426c4e..d0dc7a349 100644 --- a/reference/z.md +++ b/reference/z.md @@ -685,8 +685,8 @@ 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): diff --git a/src/ontology/Makefile b/src/ontology/Makefile index 9cecd8620..aadf3c6c1 100644 --- a/src/ontology/Makefile +++ b/src/ontology/Makefile @@ -1128,7 +1128,7 @@ validate-all-tsv: $(ALL_TSV_FILES) # ---------------------------------------- # This is an experimental target people that want to use ODK Extended Prefix Map (EPM) -# can use to pull the (currently inofficial) OBO EPM into the workspace. +# can use to pull the (currently unofficial) OBO EPM into the workspace. # Users are instructed to refer to the EPM only through the variable $(EXTENDED_PREFIX_MAP) as # its location might change in a feature version of ODK. $(EXTENDED_PREFIX_MAP): /tools/obo.epm.json diff --git a/src/ontology/bridge/collected-amniote-hdr.owl b/src/ontology/bridge/collected-amniote-hdr.owl index 263fbd82f..65a095eaf 100644 --- a/src/ontology/bridge/collected-amniote-hdr.owl +++ b/src/ontology/bridge/collected-amniote-hdr.owl @@ -9,7 +9,7 @@ xmlns:terms="http://purl.org/dc/terms/"> Uberon editors - This is an ontology that collects all of the core Uberon, plus the anatomy ontologies for amniotes. This is currently limited to mammals, but ontologies for non-mammalian amniotes may be aded in the future. + This is an ontology that collects all of the core Uberon, plus the anatomy ontologies for amniotes. This is currently limited to mammals, but ontologies for non-mammalian amniotes may be added in the future. Collected anatomy ontology for amniotes Uberon ontologies with the prefix ‘collected’ are ontologies that import the core Uberon ontology together with one or more external, typically species-centric, ontologies plus bridging axioms that connect Uberon to those external ontologies. Uberon ontologies with the prefix ‘composite’ are variations of the corresponding ‘collected’ ontologies with additional reasoning performed. http://genomebiology.com/2012/13/1/R5 diff --git a/src/ontology/objectproperty.csv b/src/ontology/objectproperty.csv index 13804026b..1e36cdac1 100644 --- a/src/ontology/objectproperty.csv +++ b/src/ontology/objectproperty.csv @@ -127,7 +127,7 @@ http://purl.obolibrary.org/obo/RO_0002160,only in taxon,"x only in taxon y if an http://purl.obolibrary.org/obo/RO_0002160,only in taxon,"U only_in_taxon T: U is a feature found in only in organisms of species of taxon T. The feature cannot be found in an organism of any species outside of (not subsumed by) that taxon. Down-propagates in U hierarchy, up-propagates in T hierarchy (species taxonomy). Implies applicable_to_taxon." http://purl.obolibrary.org/obo/RO_0003000,produces,"a produces b if some process that occurs_in a has_output b, where a and b are material entities. Examples: hybridoma cell line produces monoclonal antibody reagent; chondroblast produces avascular GAG-rich matrix." http://purl.obolibrary.org/obo/RO_0002150,continuous with,X continuous_with Y if and only if X and Y share a fiat boundary. -http://purl.obolibrary.org/obo/RO_0002213,positively regulates,"Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." +http://purl.obolibrary.org/obo/RO_0002213,positively regulates,"Process(P1) positively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2." http://purl.obolibrary.org/obo/RO_0002162,in taxon,"x is in taxon y if an only if y is an organism, and the relationship between x and y is one of: part of (reflexive), developmentally preceded by, derives from, secreted by, expressed." http://purl.obolibrary.org/obo/RO_0002387,has potential to develop into,x has the potential to develop into y iff x develops into y or if x is capable of developing into y http://purl.obolibrary.org/obo/RO_0002387,has potential to develop into,x has the potential to develop into y iff x develops into y or if x is capable of developing into y @@ -165,7 +165,7 @@ http://purl.obolibrary.org/obo/BSPO_0000096,anterior to,"x anterior to y iff x i http://purl.obolibrary.org/obo/BSPO_0000096,anterior_to,"x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer" http://purl.obolibrary.org/obo/BSPO_0000096,anterior to,"x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer" http://purl.obolibrary.org/obo/uberon/core#proximally_connected_to,proximally connected to,x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. -http://purl.obolibrary.org/obo/RO_0002212,negatively regulates,"Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." +http://purl.obolibrary.org/obo/RO_0002212,negatively regulates,"Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 decreases the the frequency of initiation of P2 or the magnitude or rate of output of P2." http://purl.obolibrary.org/obo/BSPO_0000107,deep_to,"Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines." http://purl.obolibrary.org/obo/BSPO_0000107,deep to,"Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines." http://purl.obolibrary.org/obo/BSPO_0001107,immediately_deep_to,This relation holds when both the deep_to and ajdacent_to relationship similarly hold. diff --git a/src/ontology/uberon.Makefile b/src/ontology/uberon.Makefile index 1ccb118ad..09e9299d7 100644 --- a/src/ontology/uberon.Makefile +++ b/src/ontology/uberon.Makefile @@ -1643,7 +1643,7 @@ docs/releases.md: uberon-odk.yaml # if http://purl.obolibrary.org/obo/mondo/releases/2021-01-01/mondo.owl exists, include it in overview. # Use Github or obo purls (include switch that we can conficgue with ODK) -### Removing uberon_2 contraints +### Removing uberon_2 constraints ### refer to https://github.com/obophenotype/uberon/discussions/2158 remove_uberon_two_constraints: $(ROBOT) query -i $(SRC) --update ../sparql/delete_uberon_two_constraints.ru convert -f obo -o $(SRC) diff --git a/src/scripts/merge_species.pro b/src/scripts/merge_species.pro index 105e78617..52124160a 100644 --- a/src/scripts/merge_species.pro +++ b/src/scripts/merge_species.pro @@ -198,7 +198,7 @@ add_default_parent(X) :- add_default_parent(X) :- class_categ(X,Z,C), !, - debug(merge,' assering default: ~w in ~w [~w]',[X,Z,C]), + debug(merge,' asserting default: ~w in ~w [~w]',[X,Z,C]), assert(ontol_db:subclass(X,Z)). add_default_parent(X) :- !, diff --git a/src/scripts/taxa.py b/src/scripts/taxa.py index 9a9b9ba1d..ec22ece49 100644 --- a/src/scripts/taxa.py +++ b/src/scripts/taxa.py @@ -4,7 +4,7 @@ # # Uberon bridging and compositing processes require a bit of information # about the taxa that are involved. To make it easier to manage those -# informations, they are centralised in the config/taxa.yaml file. +# information, they are centralised in the config/taxa.yaml file. # # The main contents of the config/taxa.yaml file is a list of taxa, # where each taxon is represented by a structure that should look like diff --git a/src/scripts/update_repo.sh b/src/scripts/update_repo.sh index 0b9fde207..4acc1c71c 100644 --- a/src/scripts/update_repo.sh +++ b/src/scripts/update_repo.sh @@ -1,5 +1,5 @@ echo "This (experimental) update script will create a new repo according to your config file. It will:" -echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries wont be touched) and docker wrapper (run.sh)." +echo "(1) overwrite your repositories Makefile, ODK sparql queries (your custom queries won't be touched) and docker wrapper (run.sh)." echo "(2) and add missing files, if any." set -e diff --git a/src/sparql/README.md b/src/sparql/README.md index d36af6d7f..69fdf542f 100644 --- a/src/sparql/README.md +++ b/src/sparql/README.md @@ -2,7 +2,7 @@ [SPARQL](https://www.w3.org/TR/rdf-sparql-query/) is a W3C standard query language for RDF. This directory contains useful SPARQL queries -for perfoming over the ontology. +for performing over the ontology. SPARQL can be executed on a triplestore or directly on any OWL file. The queries here are all executed on either uberon-edit.obo or