In module level, fixed reference ids and extra captions; In Enhanced,…

… brought protocol IRIs back, figure 2 back, and reformatted appendix; In Standard, fixed reference ids and protocol IRIs, added figure 2 back

vocab_files/methods_by_module/floristics/collection.ttl

@@ -15,7 +15,7 @@ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
     <h3>Contents</h3> 
   <ol>
     <li><a href="#module-overview">Module Overview</a></li>
-    <li><a href="#introduction">Introduction and Background</a></li>
+    <li><a href="#introduction-and-background">Introduction and Background</a></li>
     <li>
       <a href="#key-definitions-and-terminology"
         >Key Definitions and Terminology</a
@@ -310,9 +310,6 @@ CO<sub>2</sub> from pre-industrial levels. <em>Nature</em>
     <h2 id="key-definitions-and-terminology">Key Definitions and
 Terminology</h2>
 <table>
-<caption><p><span class="anchor" id="figure-2"></span>Figure 2.
-Plant specimen voucher placed in a newspaper sheet in a field
-press.</p></caption>
 <colgroup>
 <col style="width: 19%"/>
 <col style="width: 80%"/>
@@ -945,7 +942,7 @@ vouchers of all species to support the species list recorded. Plant
 specimen vouchers ensure correct species identification, provide a
 taxonomic reference and ensure the repeatability of studies. Plant
 specimen vouchers are collected and preserved appropriately in the field
-using a plant press (see Table 1), and later identified by taxonomic
+using a plant press (see <a href="#key-definitions-and-terminology">Table 1</a>), and later identified by taxonomic
 experts (Heard and Channon 1997; Culley 2013; Sparrow <em>et al.</em>
 2020).</p>
 <p>A plant specimen voucher consists of a pressed and dried specimen of

vocab_files/methods_by_module/floristics/enhanced-protocol/enhanced-protocol.ttl

@@ -153,7 +153,7 @@ based on morphology. Try to minimise the number of individual specimens
 needed to represent each species by maximising the number of plant
 components (e.g. flowers, fruit, leaves) on each specimen
 collected.</p></li>
-<li><p>If also undertaking the Plant Tissue Vouchering Module, collect
+<li><p>If also undertaking the <a href="https://linked.data.gov.au/def/nrm/1f2ac884-2177-403a-a6c3-27e109b1fc95">Plant Tissue Vouchering Module</a>, collect
 young, actively growing material if available. Although it is inevitable
 that during some surveys only sterile or vegetative material will be
 available, such material should still be collected. The quantity of leaf
@@ -684,7 +684,7 @@ botanists)</p></li>
 </ul>"""^^rdf:HTML ;
     tern:instructions """<h3 id="instructions-and-procedures">Instructions and Procedures</h3>
 <ol type="1">
-<li><p>Ensure the Plot Selection and Layout Module has been completed to
+<li><p>Ensure the <a href="https://linked.data.gov.au/def/nrm/d15d05db-5007-411e-b257-105ef4f76821">Plot Selection and Layout Module</a> has been completed to
 mark out the plot boundary and define the current plot and visit in the
 Monitor app.</p></li>
 <li><p>Search the entire plot for each flora species present. Search
@@ -695,7 +695,7 @@ storing them in a day press. Take enough material for an A3 size
 herbarium sheet (<a href="#figure-1">Figure 1A</a>). If the species is small, a whole plant
 specimen/s including basal material and roots should be collected
 (<a href="#figure-1">Figure 1B</a> and <a href="#figure-1">Figure 1C</a>). Collect extra material for plant tissue
-vouchers if required (see the Plant Tissue Vouchering Module).</p></li>
+vouchers if required (see the <a href="https://linked.data.gov.au/def/nrm/1f2ac884-2177-403a-a6c3-27e109b1fc95">Plant Tissue Vouchering Module</a>).</p></li>
 <li><p>Return to the field vehicle or a designated area with the
 equipment required to process the specimens. If you have collected an
 epiphyte, mistletoe or parasite, process the host species first so that
@@ -714,7 +714,6 @@ at the same time as the Floristics Module, and if you’re doing the
 enhanced or standard protocol. This will enable a button to open a popup
 of the Plant Tissue Vouchering Module.</p></li>
 </ol>
-</ul>
 <table>
 <colgroup>
 <col style="width: 51%"/>
@@ -733,7 +732,7 @@ from a large species. An envelop is used to store material that has come loose (
 </tr>
 </tbody>
 </table>
-<ol start="2" type="1">
+<ol start="8" type="1">
 <li><p>For each specimen, assign a <em>field name</em>. Assign a
 definitive species name if you are confident of the identification. If
 not, assign a descriptive name (e.g. yellow daisy flower) that can be
@@ -756,11 +755,10 @@ attributes relevant the specimen (<a href="#appendix-3">Appendix 3</a>).</p></li
 an individual from within the plot by selecting the <em>camera</em>
 button. This can be a useful reference for unfamiliar species for the
 remainder of the survey. Use a photo reference scale in each photo (see
-Appendix 4). Record a <em>comment</em> (optional) of the photo if
+<a href="#appendix-4">Appendix 4</a>). Record a <em>comment</em> (optional) of the photo if
 required. Take multiple photos if required.</p></li>
 <li><p>If collecting plant tissue vouchers, select the <em>plant tissue
-voucher</em> button to open a popup of the Plant Tissue Vouchering
-Module. Once the associated plant tissue voucher barcode label is
+voucher</em> button to open a popup of the <a href="https://linked.data.gov.au/def/nrm/1f2ac884-2177-403a-a6c3-27e109b1fc95">Plant Tissue Vouchering Module</a>. Once the associated plant tissue voucher barcode label is
 scanned into the app, return to the Enhanced protocol in the Floristics
 Module.</p></li>
 <li><p>Select the <em>save species record</em> button to save the
@@ -781,6 +779,8 @@ press using a permanent marker on the top sheet of cardboard with the
 <li><p>Inspect the field press every 2–3 days during the field survey
     and replace newspaper when necessary.</p>
     <p><img id="figure-2" alt="figure_2" height="400" src="https://w3id.org/tern/static/dawe-rlp/latest/floristic/Figure_2.jpg" width="600"/></p></li>
-</ol>"""^^rdf:HTML ;
+</ol>
+<p><span class="anchor"></span>Figure 2. Plant
+specimen voucher placed in a newspaper sheet in a field press.</p>"""^^rdf:HTML ;
 .
 

vocab_files/methods_by_module/floristics/standard-protocol/standard-protocol.ttl

@@ -76,7 +76,7 @@ species, so always check with your local authority.</p></li>
 </ul>"""^^rdf:HTML ;
     rdfs:isDefinedBy <https://linked.data.gov.au/def/nrm> ;
     skos:note """
-    <h3 id="additional-guidelines-1">Additional guidelines</h3>
+    <h3 id="additional-guidelines">Additional guidelines</h3>
 <h4 class="unnumbered" id="survey-timing-1">Survey timing</h4>
 <ul>
 <li><p>The Floristics Module is best undertaken during the main plant
@@ -208,7 +208,7 @@ based on morphology. Try to minimise the number of individual specimens
 needed to represent each species by maximising the number of plant
 components (e.g. flowers, fruit, leaves) on each specimen
 collected.</p></li>
-<li><p>If also undertaking the Plant Tissue Vouchering Module, collect
+<li><p>If also undertaking the <a href="https://linked.data.gov.au/def/nrm/1f2ac884-2177-403a-a6c3-27e109b1fc95">Plant Tissue Vouchering Module</a>, collect
 young, actively growing material if available. Although it is inevitable
 that during some surveys only sterile or vegetative material will be
 available, such material should still be collected. The quantity of leaf
@@ -683,7 +683,7 @@ scale card, coin, pen).</td>
 </tbody>
 </table>"""^^rdf:HTML ;
     tern:equipment """
-  <h3 id="equipment-1">Equipment</h3>
+  <h3 id="equipment">Equipment</h3>
 <ul>
 <li><p>Mobile device (tablet/phone) with the Monitor app
 pre-loaded</p></li>
@@ -717,23 +717,23 @@ botanists)</p></li>
 <li><p>Field herbarium dryer (working in the tropics).</p></li>
 </ul>"""^^rdf:HTML ;
     tern:instructions """
-   <h3 id="instructions-and-procedures-1">Instructions and Procedures</h3>
+   <h3 id="instructions-and-procedures">Instructions and Procedures</h3>
 <ol type="1">
-<li><p>Ensure the Plot Selection and Layout Module has been completed to
+<li><p>Ensure the <a href="https://linked.data.gov.au/def/nrm/d15d05db-5007-411e-b257-105ef4f76821">Plot Selection and Layout Module</a> has been completed to
 mark out the plot boundary and define the current plot and visit in the
 Monitor app.</p></li>
 </ol>
-<ol start="14" type="1">
+<ol start="2" type="1">
 <li><p>Search the entire plot for each flora species present. Search
 between 30 and 90 minutes or more depending on the diversity and density
 of the vegetation and surveyor experience.</p></li>
 <li><p>Collect specimens for new, unknown, important, contentious and
-threatened species (see Table 1) present within the plot, storing them
+threatened species (see Key definitions and terminology in <a href="https://linked.data.gov.au/def/nrm/2b5c2281-e0f4-4ef5-8ae0-8ae745af9a7e">Floristics</a>) present within the plot, storing them
 in a day press. Take enough material to cover an A3 size herbarium sheet
 (<a href="#figure-1">Figure 1A</a>). If the species is small, a whole plant specimen/s including
 basal material and roots should be collected (<a href="#figure-1">Figure 1B</a> and <a href="#figure-1">Figure 1C</a>).
 Collect extra material if required for plant tissue vouchers (see the
-Plant Tissue Vouchering Module).</p></li>
+<a href="https://linked.data.gov.au/def/nrm/1f2ac884-2177-403a-a6c3-27e109b1fc95">Plant Tissue Vouchering Module</a>).</p></li>
 <li><p>While searching the plot, select the Floristics Module and then
 the Standard protocol in the Monitor app to record and photograph flora
 species that do not require a plant specimen voucher as they are
@@ -765,9 +765,9 @@ is optional to take a <em>flower photo</em>, <em>bud photo</em>,
 <em>fruit photo</em>, <em>seed photo</em>, <em>stem photo, bark photo,
 roots photo</em>, or <em>other photo</em>. Use a photo reference scale
 in each photo. Record a <em>comment</em> (optional) of each photo if
-required. Example plant photo vouchers are provided in Appendix 4.
+required. Example plant photo vouchers are provided in <a href="#appendix-4">Appendix 4</a>.
 Instructions and guidelines for taking plant photo vouchers are provided
-in Appendix 5.</p></li>
+in <a href="#appendix-5">Appendix 5</a>.</p></li>
 <li><p>Select the <em>save species record</em> button to save the
 current species record.</p></li>
 <li><p>Select the <em>add another species</em> button to begin recording
@@ -805,12 +805,11 @@ apply to the species (<a href="#appendix-2">Appendix 2</a>).</p></li>
 attributes relevant to the specimen (<a href="#appendix-3">Appendix 3</a>).</p></li>
 <li><p>If required, take a <em>photo</em> (optional) of the specimen or
 an individual from within the plot by selecting the <em>camera</em>
-button. Use a photo reference scale in each photo (see Appendix 4).
+button. Use a photo reference scale in each photo (see <a href="#appendix-4">Appendix 4</a>).
 Record a <em>comment</em> (optional) of the photo if required. Take
 multiple photos if required.</p></li>
 <li><p>If collecting plant tissue vouchers, select the <em>plant tissue
-voucher</em> button to open a popup of the Plant Tissue Vouchering
-Module. Once the associated plant tissue voucher barcode label is
+voucher</em> button to open a popup of the <a href="https://linked.data.gov.au/def/nrm/1f2ac884-2177-403a-a6c3-27e109b1fc95">Plant Tissue Vouchering Module</a>. Once the associated plant tissue voucher barcode label is
 scanned into the app, return to the Standard protocol in the Floristics
 Module.</p></li>
 <li><p>Select the <em>save species record</em> button to save the
@@ -832,6 +831,9 @@ press using a permanent marker on the top sheet of cardboard with the
 <em>plot number</em> and <em>date</em>.</p></li>
 <li><p>Inspect the field press every 2–3 days during the field survey
 and replace newspaper when necessary.</p></li>
+<p><img id="figure-2" alt="figure_2" height="400" src="https://w3id.org/tern/static/dawe-rlp/latest/floristic/Figure_2.jpg" width="600"/></p></li>
+<p><span class="anchor"></span>Figure 2. Plant
+specimen voucher placed in a newspaper sheet in a field press.</p>
 </ol>
 """^^rdf:HTML ;
 .