Merge branch '1.0.0-rc1' into 'master'

emmo-repo · Sep 6, 2024 · 2e9932e · 2e9932e
2 parents 7a4b825 + b6089b4
commit 2e9932e
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diff --git a/.github/ABOUT.md b/.github/ABOUT.md
@@ -37,7 +37,7 @@ Directory content
 
     The format is simple - each line starts with a version
     number. Optionally it may be followed by label indicating the
-    status.  Use either "unstable" or "latest" or leave it out as
+    status.  Use either "development" or "stable" or leave it out as
     default.
 
 

diff --git a/.github/emmocheck_conf.yml b/.github/emmocheck_conf.yml
@@ -1,4 +1,7 @@
 # Configurations used when running emmocheck from the ci_emmocheck workflow
+skip:
+  - test_description
+
 test_namespace:
   exceptions:
     - manufacturing.EngineeredMaterial
@@ -21,6 +24,11 @@ test_quantity_dimension:
     - emmo.ISQDerivedQuantity
     - emmo.SIExactConstant
 
+test_class_label:
+  exceptions:
+    - pH
+    - 3DPrinting
+
 test_unit_dimension:
   exceptions:
     - emmo.MultipleUnit
@@ -40,3 +48,8 @@ test_unit_dimension:
     - emmo.SIBaseUnit
     - emmo.SIUnitSymbol
     - emmo.SIUnit
+
+test_number_of_labels:
+  exceptions:
+    - 0.1.Person  # foaf:Person
+    - 0.1.mbox  # foaf:mbox
diff --git a/.github/expected_redirections.yaml b/.github/expected_redirections.yaml
@@ -0,0 +1,98 @@
+# Input file for testing redirections
+#
+# These redirections can be tested using the redirectioncheck tool from EMMOntoPy:
+#
+#     pip install EMMOntoPy
+#     redirectioncheck expected_redirections.yaml
+#
+
+---
+redirections:
+
+  # EMMO
+  https://w3id.org/emmo#fragment:                       https://emmo-repo.github.io/emmo.ttl#fragment  # ttl file because tests are not from a browser
+
+  https://w3id.org/emmo:                                https://emmo-repo.github.io/emmo.ttl  # ttl file because tests are not from a browser
+  https://w3id.org/emmo/:                               https://emmo-repo.github.io/emmo.ttl
+  https://w3id.org/emmo/turtle:                         https://emmo-repo.github.io/emmo.ttl
+  https://w3id.org/emmo/turtle/:                        https://emmo-repo.github.io/emmo.ttl
+  https://w3id.org/emmo/inferred:                       https://emmo-repo.github.io/emmo-inferred.ttl
+  https://w3id.org/emmo/1.0.0-beta4:                    https://emmo-repo.github.io/versions/1.0.0-beta4/emmo.ttl
+  https://w3id.org/emmo/1.0.0-beta4/inferred:           https://emmo-repo.github.io/versions/1.0.0-beta4/emmo-inferred.ttl
+  https://w3id.org/emmo/1.0.0-beta5:                    https://emmo-repo.github.io/versions/1.0.0-beta5/emmo.ttl
+  https://w3id.org/emmo/1.0.0-beta5/:                   https://emmo-repo.github.io/versions/1.0.0-beta5/emmo.ttl
+  https://w3id.org/emmo/1.0.0-rc1:                      https://emmo-repo.github.io/versions/1.0.0-rc1/emmo.ttl
+  https://w3id.org/emmo/1.0.0-rc1/:                     https://emmo-repo.github.io/versions/1.0.0-rc1/emmo.ttl
+  https://w3id.org/emmo/1.0.0-rc1/turtle:               https://emmo-repo.github.io/versions/1.0.0-rc1/emmo.ttl
+  https://w3id.org/emmo/1.0.0-rc1/turtle/:              https://emmo-repo.github.io/versions/1.0.0-rc1/emmo.ttl
+
+  https://w3id.org/emmo/source:                         https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  https://w3id.org/emmo/source/:                        https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  https://w3id.org/emmo/latest:                         https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  https://w3id.org/emmo/latest/:                        https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  https://w3id.org/emmo/emmo:                           https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  https://w3id.org/emmo/emmo/:                          https://raw.githubusercontent.com/emmo-repo/EMMO/master/emmo.ttl
+  #https://w3id.org/emmo/disciplines:                    https://raw.githubusercontent.com/emmo-repo/EMMO/master/disciplines/disciplines.ttl  # not in master
+  https://w3id.org/emmo/1.0.0-beta5/mereocausality:     https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/mereocausality/mereocausality.ttl
+  https://w3id.org/emmo/1.0.0-beta5/perspectives:       https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/perspectives.ttl
+  https://w3id.org/emmo/1.0.0-beta5/multiperspective:   https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/multiperspective/multiperspective.ttl
+  https://w3id.org/emmo/1.0.0-beta5/disciplines:        https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/disciplines.ttl
+  https://w3id.org/emmo/1.0.0-beta5/disciplines/units:  https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/units/units.ttl
+  https://w3id.org/emmo/1.0.0-beta5/disciplines/units/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/units/units.ttl
+  https://w3id.org/emmo/1.0.0-beta5/disciplines/units/siunits:  https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/units/siunits.ttl
+  https://w3id.org/emmo/1.0.0-beta5/disciplines/units/siunits/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/disciplines/units/siunits.ttl
+  https://w3id.org/emmo/1.0.0-beta5/perspectives/data:  https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl
+  https://w3id.org/emmo/1.0.0-beta5/perspectives/data/: https://raw.githubusercontent.com/emmo-repo/EMMO/1.0.0-beta5/perspectives/data.ttl
+
+
+  # EMMO-LITE
+  https://w3id.org/emmo/emmo-lite:                      https://raw.githubusercontent.com/emmo-repo/EMMO-LITE/master/emmo-lite.ttl
+  #https://w3id.org/emmo/1.0.0-rc1/emmo-lite:            https://raw.githubusercontent.com/emmo-repo/EMMO-LITE/1.0.0-rc1/emmo-lite.ttl
+
+
+  # Electrochemistry
+  #https://w3id.org/emmo/domain/electrochemistry#frag:   https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.ttl#frag
+
+  #https://w3id.org/emmo/domain/electrochemistry:        https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.ttl
+  #https://w3id.org/emmo/domain/electrochemistry/:       https://emmo-repo.github.io/domain-electrochemistry/electrochemistry.ttl
+  https://w3id.org/emmo/domain/electrochemistry/source: https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry.ttl
+  https://w3id.org/emmo/domain/electrochemistry/electrochemistry: https://raw.githubusercontent.com/emmo-repo/domain-electrochemistry/master/electrochemistry.ttl
+
+
+  # Battery
+  #https://w3id.org/emmo/domain/battery#fragment:        https://emmo-repo.github.io/domain-battery/battery.ttl#fragment
+
+  #https://w3id.org/emmo/domain/battery:                 https://emmo-repo.github.io/domain-battery/battery.ttl
+  #https://w3id.org/emmo/domain/battery/:                https://emmo-repo.github.io/domain-battery/battery.ttl
+  #https://w3id.org/emmo/domain/domain-battery:          https://emmo-repo.github.io/domain-battery/battery.ttl
+  #https://w3id.org/emmo/domain/domain-battery/:         https://emmo-repo.github.io/domain-battery/battery.ttl
+  https://w3id.org/emmo/domain/domain-battery/source:   https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/domain-battery/source/:  https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/domain-battery/latest:   https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/domain-battery/latest/:  https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/domain-battery/battery:  https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/domain-battery/battery/: https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/source:          https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/source/:         https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/latest:          https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/latest/:         https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/battery:         https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+  https://w3id.org/emmo/domain/battery/battery/:        https://raw.githubusercontent.com/emmo-repo/domain-battery/master/battery.ttl
+
+
+  # Context
+  https://w3id.org/emmo/domain/domain-electrochemistry/context:       https://emmo-repo.github.io/domain-electrochemistry/context/context.json
+  https://w3id.org/emmo/domain/domain-electrochemistry/context/:      https://emmo-repo.github.io/domain-electrochemistry/context/context.json
+  #https://w3id.org/emmo/domain/domain-battery/context/abc:            https://emmo-repo.github.io/domain-battery/context/context/abc.json
+  #https://w3id.org/emmo/domain/domain-battery/context/abc/:           https://emmo-repo.github.io/domain-battery/context/context/abc.json
+
+
+  # Microstructure
+  https://w3id.org/emmo/domain/domain-microstructure/source:   https://raw.githubusercontent.com/emmo-repo/domain-microstructure/master/microstructure.ttl
+  https://w3id.org/emmo/domain/domain-microstructure:          https://emmo-repo.github.io/domain-microstructure/microstructure.ttl
+  https://w3id.org/emmo/domain/microstructure/source:          https://raw.githubusercontent.com/emmo-repo/domain-microstructure/master/microstructure.ttl
+  https://w3id.org/emmo/domain/microstructure:                 https://emmo-repo.github.io/domain-microstructure/microstructure.ttl
+
+
+  # application-battmo
+  https://w3id.org/emmo/application/battmo/source:             https://raw.githubusercontent.com/emmo-repo/application-battmo/master/battmo.ttl
diff --git a/.github/pages-index.html.in b/.github/pages-index.html.in
@@ -7,38 +7,38 @@
   <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="Elemental Multiperspective Material 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>Elemental Multiperspective Material Ontology (EMMO)</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">Elemental Multiperspective Material 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="https://raw.githubusercontent.com/emmo-repo/emmo-repo.github.io/master/emmc.png" class="emmclogo" width="64" alt="EMMC">
 </div>
-The Elemental 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.
+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-python">Python API</a></li>
+  <li><a href="https://emmc.info/emmo-info/">EMMO on old 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/EMMOntoPy">Python API</a></li>
 </ul>
 
 <h2>Releases</h2>
 <table class"reltable">
   <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">Documentation</th>
   </tr>
   <tr>
@@ -54,11 +54,15 @@ The EMMO has grown from the bottom (i.e. scientific application field) to the to
 ${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>
+<small>
+  <br>
+  <sup id="fn1"><a href="#ref1" title="Jump back to footnote 1.">1</a></sup>
+  <b>Compacted ontology</b> means that all modules have been squashed together into a single file with no imports.
+  Also, <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 ontology</b> is reasoned and compacted.
+</small>
 
 </body>
 </html>
diff --git a/.github/scripts/makeindex.sh b/.github/scripts/makeindex.sh
@@ -38,27 +38,31 @@ 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.html         $version $l/emmo.html         >> "$tmpfile"
+    tdlink $d/emmo.pdf          $version $l/emmo.pdf          >> "$tmpfile"
     echo "  </tr>" >> "$tmpfile"
 done < "$versionsfile"