My greatest concern has to do with the reordering of the comment lines…

adoc/answers.adoc

@@ -232,7 +232,7 @@ endif::backend-slidy[]
 
 * OBO ontologies use numeric IDs
 * These are unreadable, so we syntactically transform labels
-* If label changes (but ID remains the same) is a problem
+* If label changes (but ID remains the same) it's a problem
 * Can use `tawny.memorize` to remember mappings
 * Which adds aliases to those now missing (with optional "deprecated" warnings)
 
@@ -368,7 +368,7 @@ endif::backend-slidy[]
 * Added in Tawny-OWL and the Music Ontology
 * We now have software that plays a tune
 * And provides OWL metadata about that tune
-* More to investigate here.
+* More to investigate here
 
 ifndef::backend-slidy[]
 [NOTE]

adoc/questions.adoc

@@ -26,7 +26,7 @@
 - What about advanced documentation for ontologies?
 - How do I collaboratively develop my ontology?
 - Can I internationalise my ontology?
-- Can I scaffolding my ontology from existing sources?
+- Can I scaffold my ontology from existing sources?
 - What happens if the labels of read ontologies change?
 - How do you convert an existing ontology to Tawny-OWL?
 - How fast is Tawny-OWL?

notes.org

@@ -227,7 +227,7 @@ And I can't do the single slide thing.
  - How do you continously integrate your ontology?
  - What about advanced documentation for ontologies?
  - Can I internationalise my ontology?
- - Can I scaffolding your ontology from existing sources?
+ - Can I scaffold my ontology from existing sources?
  - What happens if the labels of read ontologies change?
  - How do you convert an existing ontology to Tawny?
  - How fast is tawny?

src/tawny/tutorial/amino_acid_build.clj

@@ -201,7 +201,7 @@
 ;; ----
 (defmacro defaminoacids
   [& definitions]
-  `(tawny.pattern/intern-owl-entities
+  '(tawny.pattern/intern-owl-entities
     (apply amino-acids
      (tawny.util/name-tree ~definitions))))
 ;; ----
@@ -399,8 +399,8 @@
 ;; ----
 (reasoner-factory :hermit)
 
-;; => true
 (consistent?)
+;; => true
 ;; ----
 
 ;; ifndef::backend-slidy[]
@@ -420,18 +420,18 @@
 
 ;; == Reasoning
 
-;; * When reasoning, working what happened can be tough
+;; * When reasoning, working out what happened can be tough
 ;; * Especially when using a "Textual User Interface"
 ;; * But, we can count numbers
 ;; * We have reasoned many subclases of `AminoAcid`
 
 ;; [source,lisp]
 ;; ----
-;; => 20
 (count (subclasses AminoAcid))
+;; => 20
 
-;; => 451
 (count (isubclasses AminoAcid))
+;; => 451
 ;; ----
 
 ;; ifndef::backend-slidy[]
@@ -446,17 +446,17 @@
 
 ;; == Reasoning
 
-;; * While we consistent, we are not coherent
+;; * While we are consistent, we are not coherent
 ;; * In fact, we have many unsatisfiable classes
 ;; * What is happening?
 
 ;; [source,lisp]
 ;; ----
-;; => false
 (coherent?)
+;; => false
 
-;; => 242
 (count (unsatisfiable))
+;; => 242
 ;; ----
 
 ;; == Visualising
@@ -524,9 +524,9 @@
 
 ;; [source,lisp]
 ;; ----
-;; => 242
 (count
  (isubclasses SmallAminoAcid))
+;; => 242
 ;; ----
 
 ;; == As a query
@@ -536,11 +536,11 @@
 
 ;; [source,lisp]
 ;; ----
-;; => 0
 (count
  (filter
   #(not (.isDefined % aabuild))
   (isubclasses SmallAminoAcid)))
+;; => 0
 ;; ----
 
 

src/tawny/tutorial/amino_acid_pattern.clj

@@ -95,10 +95,8 @@
 ;; ObjectProperty: aa:hasSize
 ;;     Domain:
 ;;         aa:AminoAcid
-
 ;;     Range:
 ;;         aa:Size
-
 ;;     Characteristics:
 ;;         Functional
 
@@ -149,14 +147,14 @@
    :super (facet Positive Hydrophilic Polar Aliphatic Large))
 
  (defclass Asparagine
-   :super (facet Neutral Hydrophilic Polar Aliphatic Small))
+   :super (facet Neutral Hydrophilic Polar Aliphatic Small)))
 
  ;; and the rest
- )
+
 ;; ----
 
 ;; == Task {task}: Conclusions
 
 ;; * Tawny-OWL directly supports the value partition
 ;; * This integrates with facets
-;; * Together, can simply this (very common) form of ontology
+;; * Together, can simplify this (very common) form of ontology

src/tawny/tutorial/amino_acid_props.clj

@@ -148,7 +148,7 @@
 
 ;; * We can now create our amino acids using these three sizes
 ;; * We only create three amino acids here
-;; * More would be needed.
+;; * More would be needed
 
 ;; [source,lisp]
 ;; ----

src/tawny/tutorial/amino_acid_tree.clj

@@ -144,9 +144,9 @@
 
   (defclass Alanine)
   (defclass Arginine)
-  (defclass Asparagine)
+  (defclass Asparagine))
   ;; and the rest...
-  )
+
 ;; ----
 
 ;; ifndef::backend-slidy[]
@@ -183,9 +183,9 @@
 
  (defclass Alanine)
  (defclass Arginine)
- (defclass Asparagine)
+ (defclass Asparagine))
  ;; and the rest...
- )
+
 ;; ----
 
 ;; ifndef::backend-slidy[]

src/tawny/tutorial/autosave.clj

@@ -95,9 +95,9 @@
   "Autosave the current ontology everytime any change happens."
   ([o filename format]
    (let [listener (proxy [org.semanticweb.owlapi.model.OWLOntologyChangeListener]
-               []
-             (ontologiesChanged[l]
-               (o/save-ontology o filename format)))]
+                   []
+                   (ontologiesChanged[l]
+                     (o/save-ontology o filename format)))]
      (reset! auto-save-listener listener)
      (.addOntologyChangeListener
       (o/owl-ontology-manager) listener)

src/tawny/tutorial/core.clj

@@ -6,9 +6,9 @@
     amino-acid-tree amino-acid-props
     amino-acid-pattern whats-in-a-name
     use-abc read-abc amino-acid-build
-    autosave amino-acid-sio]
-   )
-  )
+    autosave amino-acid-sio]))
+
+
 
 (defonce output-file-path "./output/")
 

src/tawny/tutorial/features.clj

@@ -358,7 +358,7 @@
 ;; == Broadcasting
 
 ;; * Tawny-OWL does something similar
-;; * `owl-some` expand to *two* existential restrictions
+;; * `owl-some` expands to *two* existential restrictions
 
 ;; [source,lisp]
 ;; ----
@@ -411,7 +411,6 @@
 ;; [source,omn]
 ;; ----
 ;; Class: o:D
-
 ;;     SubClassOf:
 ;;         o:r some o:A,
 ;;         o:r some o:B,
@@ -500,13 +499,13 @@
 (defclass F
    :equivalent (owl-some r (owl-or A B)))
 
-;; #{}
 (subclasses F)
+;; #{}
 
 (reasoner-factory :hermit)
 
-;; #{C D E}
 (isubclasses F)
+;; #{C D E}
 ;; ----
 
 ;; ifndef::backend-slidy[]
@@ -565,7 +564,7 @@
 
 ;; * Editing
 ;; ** IDEs: Eclipse, IntelliJ, Netbeans
-;; ** Power Editors: Emacs, Vim, Sublime
+;; ** Power Editors: Emacs, Vim, Sublime, Cursive (via IntelliJ)
 ;; ** Web Editors: Catnip, GorrilaRepl
 ;; ** Novel: LightTable
 

src/tawny/tutorial/read_abc.clj

@@ -7,9 +7,9 @@
 
 ;; * We showed that we can import existing Tawny-OWL ontologies
 ;; * By using and importing the relevant namespace
-;; * In order for this to work, we need the Tawny-OWL source code
-;; * What if we do not have it?
-;; * Or worse, what if it does not exist?
+;; * In order for this to work, we need the ontologies defined using Tawny-OWL
+;; * What if they aren't?
+;; * What if all we have are ontologies defined in other languages?
 ;; * Tawny-OWL supports this
 
 ;; ifndef::backend-slidy[]
@@ -33,7 +33,7 @@
 
 ;; * As usual, we declare the namespace
 ;; * It is different
-;; * `Require` the `tawny.owl` and `tawny.read`
+;; * `require` the `tawny.owl` and `tawny.read`
 ;; * Have access to the symbols but do not import them into the local
 ;; namespace
 ;; * Ensures that the namespace has nothing else in it

src/tawny/tutorial/whats_in_a_name.clj

@@ -130,9 +130,9 @@
 ;; ----
 (defontology o)
 
-;; => #<OWLClassImpl <8d9d3120-d374-4ffb-99d8-ffd93a7d5fdd#o#A>>
 (defclass A
   :ontology o)
+;; => #<OWLClassImpl <8d9d3120-d374-4ffb-99d8-ffd93a7d5fdd#o#A>>
 ;; ----
 
 ;; * Generates a random UUID
@@ -172,9 +172,9 @@
 (defontology i
    :iri "http://www.w3id.org/ontolink/example/i")
 
-;; => #<OWLClassImpl <http://www.w3id.org/ontolink/example/i#B>>
 (defclass B
   :ontology i)
+;; => #<OWLClassImpl <http://www.w3id.org/ontolink/example/i#B>>
 ;; ----
 
 ;; == Symbols and IRIs
@@ -194,9 +194,9 @@
                        "#"
                        (s/reverse name)))))
 
-;; => #<OWLClassImpl <http://www.w3id.org/ontolink/example/r#EDC>>
 (defclass CDE
   :ontology r)
+;; => #<OWLClassImpl <http://www.w3id.org/ontolink/example/r#EDC>>
 ;; ----
 
 ;; ifndef::backend-slidy[]
@@ -254,17 +254,17 @@
 
 ;; [source,lisp]
 ;; ----
-;; => #<OWLClassImpl <http://purl.obolibrary.org/obo/EXAM_000003>>
 (defclass F
   :ontology obo)
+;; => #<OWLClassImpl <http://purl.obolibrary.org/obo/EXAM_000003>>
 
-;; => #<OWLClassImpl <http://purl.obolibrary.org/obo/EXAM_000002>>
 (defclass G
   :ontology obo)
+;; => #<OWLClassImpl <http://purl.obolibrary.org/obo/EXAM_000002>>
 
-;; => #<OWLObjectPropertyImpl <http://purl.obolibrary.org/obo/EXAM_000001>>
 (defoproperty ro
   :ontology obo)
+;; => #<OWLObjectPropertyImpl <http://purl.obolibrary.org/obo/EXAM_000001>>
 ;; ----
 
 ;; ifndef::backend-slidy[]