emmo-repo · jesper-friis · Sep 9, 2022 · Sep 20, 2022 · Sep 22, 2022 · Sep 22, 2022
diff --git a/.github/emmocheck_conf.yml b/.github/emmocheck_conf.yml
@@ -1,7 +1,11 @@
 # Configurations used when running emmocheck from the ci_emmocheck workflow
-test_namespace:
+test_class_label:
   exceptions:
-    - manufacturing.EngineeredMaterial
+    - 3DPrinting
+
+test_number_of_labels:
+  exceptions:
+    - foaf.logo
 
 test_quantity_dimension:
   exceptions:
@@ -41,3 +45,9 @@ test_unit_dimension:
     - emmo.SIBaseUnit
     - emmo.SIUnitSymbol
     - emmo.SIUnit
+
+enable:
+  - test_physical_quantity_dimension
+
+skip:
+  - test_quantity_dimension
diff --git a/.github/pages-index.html.in b/.github/pages-index.html.in
@@ -7,28 +7,28 @@
   <meta name="author" content="Jesper Friis, SINTEF">
   <meta name="author" content="Adham Hashibon, Fraunhofer IWM">
   <meta name="author" content="Georg Schmitz, ACCESS">
-  <meta name="institution" content="European Materials &#38 Modelling Council (EMMC)">
+  <meta name="institution" content="European Materials Modelling Council (EMMC)">
   <meta name="keywords" content="EMMO, materials science, modelling, characterisation, materials, ontology">
   <meta name="dcterms.date" content="${date}">
   <link rel="stylesheet" type="text/css" href="css/style.css">
   <link rel="icon" type="image/png" href="https://avatars1.githubusercontent.com/u/51194521?s=400&u=d9e0bbceb9a6e4901077e92b2426c8bca46b1009&v=4">
-  <title>Europeean Materials &#38 Modelling Ontology</title>
+  <title>Elementary Multiperspective Material Ontology (EMMO)</title>
 </head>
 <body>
 
 <div class="header">
   <img src="https://avatars1.githubusercontent.com/u/51194521?s=400&u=d9e0bbceb9a6e4901077e92b2426c8bca46b1009&v=4" class="logo" width="64" alt="EMMO">
-  <h1 class="logo">The Europeean Materials &#38 Modelling Ontology (EMMO)</h1>
-  <img src="https://i2.wp.com/emmc.info/wp-content/uploads/2018/10/emmc_logo-low.jpg?fit=1701%2C1701&ssl=1" class="emmclogo" width="64" alt="EMMC">
+  <h1 class="logo">The Elementary Multiperspective Material Ontology (EMMO)</h1>
+  <img src="emmc.png" class="emmclogo" width="64" alt="EMMC">
 </div>
-The European Materials Modelling Ontology (EMMO) is the result of a multidisciplinary effort within the EMMC, aimed at the development of a standard representational ontology framework based on current materials modelling and characterization knowledge. Instead of starting from general upper level concepts, as done by other ontologies, the EMMO development started from the very bottom level, using the actual picture of the physical world coming from applied sciences, and in particular from physics and material sciences.
+The Elementary Multiperspective Material Ontology (EMMO) is the result of a multidisciplinary effort within the EMMC, aimed at the development of a standard representational ontology framework based on current materials modelling and characterization knowledge. Instead of starting from general upper level concepts, as done by other ontologies, the EMMO development started from the very bottom level, using the actual picture of the physical world coming from applied sciences, and in particular from physics and material sciences.
 <p>
 The EMMO has grown from the bottom (i.e. scientific application field) to the top (i.e. conceptualization), staying focused on the original scope while at the same time maintaining an approach as general as possible. The ontological framework has been built around concepts like elementary particles, wave-particle dualism, finiteness of space and time intervals coming from the perspective for experimental physics. The development of the middle and upper layers of the ontology has been functional to the respect of these low level concepts, to facilitate the understanding of the high level concepts to users with limited or no philosophical background.
 
 <h2>Links</h2>
 <ul>
   <li><a href="https://emmc.info/emmo-info/">EMMC site</a></li>
-  <li><a href="https://github.com/emmo-repo/EMMO">Github repository</a></li>
+  <li><a href="https://github.com/emmo-repo/EMMO">GitHub repository</a></li>
   <li><a href="https://github.com/emmo-repo/EMMO-python">Python API</a></li>
 </ul>
 
@@ -37,8 +37,9 @@ The EMMO has grown from the bottom (i.e. scientific application field) to the to
   <tr>
     <th></th>
     <th></th>
-    <th colspan="2">Compacted<sup><a href="#fn1" id="ref1">1</a></sup> ontology</th>
-    <th colspan="2">Inferred ontology (compacted<sup><a href="#fn1">1</a></sup>)</th>
+    <th colspan="2">Compacted ontology<sup><a href="#fn1" id="ref1">1</a></sup></th>
+    <th colspan="2">Inferred ontology<sup><a href="#fn2" id="ref2">2</a></sup></th>
+    <th colspan="2">Renamed ontology<sup><a href="#fn3" id="ref3">3</a></sup></th>
     <th colspan="2">Documentation</th>
   </tr>
   <tr>
@@ -48,17 +49,31 @@ The EMMO has grown from the bottom (i.e. scientific application field) to the to
     <th>turtle</th>
     <th>rdf/xml</th>
     <th>turtle</th>
+    <th>rdf/xml</th>
+    <th>turtle</th>
     <th>html</th>
     <th>pdf</th>
   </tr>
 ${versions}
 </table>
 
-<sup id="fn1"><a href="#ref1" title="Jump back to footnote 1.">1</a>.
-  With "compacted ontology", we here mean that all
-  the top and middle level modules are joint together into a single
-  file with no imports.
-</sup>
+
+<p><small>
+<br>
+  <sup id="fn1"><a href="#ref1" title="Jump back to footnote 1.">1.</a></sup>
+  In the <b>compacted ontology</b>, all modules has been squashed together into a single file
+  with no imports.  <code>rdfs:isDefinedBy</code> annotations referring to the original module IRI
+  have been added.
+<br>
+  <sup id="fn2"><a href="#ref2" title="Jump back to footnote 2.">2.</a></sup>
+  <b>Inferred ontologies</b> are reasoned and compacted.
+<br>
+  <sup id="fn3"><a href="#ref3" title="Jump back to footnote 3.">3.</a></sup>
+  In a <b>renamed ontology</b> has the numerical ID part of the IRIs been
+  replaced with human readable prefLabel's.
+  The original IRI is available via a <code>skos:exactMatch</code> annotation.
+  The renamed ontologies are also compacted and inferred.
+</small></p>
 
 </body>
 </html>
diff --git a/.github/scripts/makeindex.sh b/.github/scripts/makeindex.sh
@@ -38,27 +38,33 @@ done
 
 # Parse versions.sh and save html table rows in tmpfile
 tdlink() {
-    echo "    <td><a href=\"$1\" target=\"_blank\">$2</a></td>"
+    href=$1
+    cell=$2
+    checkfile=$3
+    #echo "*** checkfile=$checkfile" >&2
+    if [ -z "$checkfile" -o -f "$checkfile" ]; then
+        echo "    <td><a href=\"$href\" target=\"_blank\">$cell</a></td>"
+    else
+        echo "    <td><a href=\"$href\" target=\"_blank\"></a></td>"
+    fi
 }
 rm -rf "$tmpfile"
 while read version name; do
     [ -z "$name" ] && name=$version
     iri=$emmo_url/$version
     d=$pages_url/versions/$version
-    inferred=$pages_url/versions/$version/emmo-inferred.owl
-    inferred_iri=$iri/emmo-inferred
-    html=$pages_url/versions/$version/emmo.html
-    pdf=$pages_url/versions/$version/emmo.pdf
+    l=$pagesdir/versions/$version
     echo "  <tr>" >> "$tmpfile"
     echo "    <td>$name</td>" >> "$tmpfile"
-    tdlink $iri $iri >> "$tmpfile"
-    tdlink $d/emmo.owl $version >> "$tmpfile"
-    tdlink $d/emmo.ttl $version >> "$tmpfile"
-    #tdlink $inferred $inferred_iri >> "$tmpfile"
-    tdlink $inferred $version >> "$tmpfile"
-    tdlink $d/emmo-inferred.ttl $version >> "$tmpfile"
-    tdlink $html $version >> "$tmpfile"
-    tdlink $pdf $version >> "$tmpfile"
+    tdlink $iri                 $iri                          >> "$tmpfile"
+    tdlink $d/emmo.owl          $version $l/emmo.owl          >> "$tmpfile"
+    tdlink $d/emmo.ttl          $version $l/emmo.ttl          >> "$tmpfile"
+    tdlink $d/emmo-inferred.owl $version $l/emmo-inferred.owl >> "$tmpfile"
+    tdlink $d/emmo-inferred.ttl $version $l/emmo-inferred.ttl >> "$tmpfile"
+    tdlink $d/emmo-renamed.owl  $version $l/emmo-renamed.owl  >> "$tmpfile"
+    tdlink $d/emmo-renamed.ttl  $version $l/emmo-renamed.ttl  >> "$tmpfile"
+    tdlink $d/emmo.html         $version $l/emmo.html         >> "$tmpfile"
+    tdlink $d/emmo.pdf          $version $l/emmo.pdf          >> "$tmpfile"
     echo "  </tr>" >> "$tmpfile"
 done < "$versionsfile"
 

diff --git a/.github/scripts/makeversions.sh b/.github/scripts/makeversions.sh
@@ -1,12 +1,16 @@
 #!/bin/sh
 
-# Usage: makeversions.sh [-r -v]
+# Usage: makeversions.sh [-N NAME] [-V VERSION] [-r -v]
 #
 # Creates versions sub-directories in local copy of GitHub Pages.
 #
 # Options:
-#   -r  Recreate existing sub-directories and their content.
+#   -N  Recreate version with given name.
+#   -V  Recreate given version.
+#   -r  Recreate all existing sub-directories and their content.
 #   -v  Verbose.  Print commands as they are executed.
+#
+# If the `version` argument is given,
 set -e
 
 rootdir="$(git rev-parse --show-toplevel)"
@@ -19,14 +23,19 @@ tmpdir=""
 $scriptsdir/init_pages.sh
 
 # Parse options
+recreate_version=""
+recreate_name=""
 recreate=false
 verbose=false
-while getopts "rv" arg; do
+while getopts "N:V:rv" arg; do
     case $arg in
+        N)  recreate_name="$OPTARG";;
+        V)  recreate_version="$OPTARG";;
         r)  recreate=true;;
         v)  verbose=true;;
     esac
 done
+shift $(($OPTIND -1))
 
 # If verbose, print commands as they are executed
 if $verbose; then
@@ -42,14 +51,19 @@ while read version name; do
     cd "$rootdir"
     $verbose && echo
     d="$pagesdir/versions/$version"
-    if $recreate || [ ! -d "$d" ]; then
+    remake=$recreate
+    [ -n "$recreate_version" ] && [ "$recreate_version" = "$version" ] && \
+        remake=true
+    [ -n "$recreate_name" ] && [ "$recreate_name" = "$name" ] && \
+        remake=true
+    if $remake || [ ! -d "$d" ]; then
         mkdir -p "$d"
         cd "$rootdir"
         cp -f README.md LICENSE.md "$d/."
     fi
 
     # Generate single-file EMMO in turtle and owl (rfdxml) formats
-    if $recreate || [ ! -f "$d/emmo.owl" ]; then
+    if $remake || [ ! -f "$d/emmo.owl" ]; then
         echo "Generate single-file EMMO in turtle and owl (rfdxml) formats"
         if [ ! -d "$tmpdir" ]; then
             tmpdir="$(mktemp -d)"
@@ -69,32 +83,36 @@ while read version name; do
         else
             echo "missing source in EMMO $version" >&2; exit 1
         fi
-        python "$scriptsdir/ontoconvert.py" -s "$src" "$d/emmo.owl"
-        python "$scriptsdir/ontoconvert.py" -s "$src" "$d/emmo.ttl"
+        ontoconvert "$src" "$d/emmo.owl" -s -a
+        ontoconvert "$src" "$d/emmo.ttl" -s -a
     fi
 
     # Generate inferred ontology
-    if $recreate || [ ! -f "$d/emmo-inferred.owl" ]; then
+    if $remake || [ ! -f "$d/emmo-inferred.owl" ]; then
         echo "Generate inferred ontology"
-        "$scriptsdir/reason.sh" "$d/emmo.owl" "$d/emmo-inferred.owl"
-        "$scriptsdir/fixinferred.sh" "$d/emmo-inferred.owl" $version
+        ontoconvert "$d/emmo.owl" "$d/emmo-inferred.owl" \
+                    -i HermiT -b http://emmo.info/emmo-inferred
     fi
-    if $recreate || [ ! -f "$d/emmo-inferred.ttl" ]; then
-        if [ ! -d "$tmpdir" ]; then
-            tmpdir="$(mktemp -d)"
-        fi
-        python "$scriptsdir/ontoconvert.py" -s \
-               "$d/emmo-inferred.owl" "$tmpdir/emmo-inferred.ttl"
-        # Hmm, for some reason floats are written like "1.0E-09.0" - strip
-        # off the final ".0"
-        sed 's/\([0-9][eE][+-][0-9]*\)\.[0-9]*\(.*\)/\1\2/' \
-            "$tmpdir/emmo-inferred.ttl" > "$d/emmo-inferred.ttl"
+    if $remake || [ ! -f "$d/emmo-inferred.ttl" ]; then
+        ontoconvert "$d/emmo-inferred.owl" "$d/emmo-inferred.ttl"
+    fi
+
+    # Generate renamed ontology
+    if $remake || [ ! -f "$d/emmo-renamed.owl" ]; then
+        echo "Generate renamed ontology"
+        ontoconvert "$d/emmo-inferred.owl" "$d/emmo-renamed.owl" \
+                    -s -a -R -b http://emmo.info/emmo-renamed || true
+    fi
+    if $remake || [ ! -f "$d/emmo-renamed.ttl" ]; then
+        ontoconvert "$d/emmo-inferred.owl" "$d/emmo-renamed.ttl" \
+                    -s -a -R -b http://emmo.info/emmo-renamed || true
     fi
 
     # Generate documentation
-    if $recreate || [ ! -f "$d/emmo.html" ]; then
+    if $remake || [ ! -f "$d/emmo.html" ]; then
         echo "Generate documentation"
-        "$scriptsdir/makedoc.sh" "$d/emmo-inferred.owl" $version "$d"
+        "$scriptsdir/makedoc.sh" "$d/emmo-inferred.owl" $version "$d" \
+            || true
     fi
 
     # Create symlinks