some small fixes to the annotations

data/JTEI/10_2016-19/jtei-10-dumont-source.xml

@@ -47,19 +47,6 @@
           humanities and social sciences, open to quality periodicals looking to publish full-text
           articles online.</p>
       </projectDesc>
-      <listPrefixDef>
-        <prefixDef ident="softw" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/software-list.xml#$1">
-          <p>In the context of this project, private URIs with the prefix softw point to software
-            items in the software-list.xml file, which are encoded with <gi>item</gi> elements and
-            identified in <att>xml:id</att>.</p>
-        </prefixDef>
-        <prefixDef ident="cit" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/citation-taxonomy.xml#$1">
-          <p>In the context of this project, private URIs with the prefix cit point to
-              <gi>category</gi> elements in the citation-taxonomy.xml file.</p>
-        </prefixDef>
-      </listPrefixDef>
     </encodingDesc>
     <profileDesc>
       <langUsage>

data/JTEI/10_2016-19/jtei-10-emsley-source.xml

@@ -59,19 +59,6 @@
           humanities and social sciences, open to quality periodicals looking to publish full-text
           articles online.</p>
       </projectDesc>
-      <listPrefixDef>
-        <prefixDef ident="softw" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/software-list.xml#$1">
-          <p>In the context of this project, private URIs with the prefix softw point to software
-            items in the software-list.xml file, which are encoded with <gi>item</gi> elements and
-            identified in <att>xml:id</att>.</p>
-        </prefixDef>
-        <prefixDef ident="cit" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/citation-taxonomy.xml#$1">
-          <p>In the context of this project, private URIs with the prefix cit point to
-              <gi>category</gi> elements in the citation-taxonomy.xml file.</p>
-        </prefixDef>
-      </listPrefixDef>
     </encodingDesc>
     <profileDesc>
       <langUsage>

data/JTEI/10_2016-19/jtei-10-haaf-source.xml

@@ -224,10 +224,10 @@
                 target="http://www.deutschestextarchiv.de/doku/software#cab"/></bibl>.</note> as
           well as <ref target="http://www.deutschestextarchiv.de/dtaq/about">collaborative text
             correction and annotation</ref><note rend="inside.parenthesis">See <bibl><title
-                level="a"><ptr type="software" xml:id="R3" target="#dtaq"/><rs type="soft.name"
+                level="a"><ptr type="software" xml:id="R3" target="softw:dtaq"/><rs type="cit:soft.name"
                   ref="#R3">DTAQ: Kollaborative Qualitätssicherung im Deutschen
                 Textarchiv</rs></title> (Collaborative Quality Assurance within the DTA), accessed
-              January 28, 2017, <rs type="soft.url" ref="#R3"><ptr
+              January 28, 2017, <rs type="cit:soft.url" ref="#R3"><ptr
                   target="http://www.deutschestextarchiv.de/dtaq/about"/></rs></bibl>. On the
             process of quality assurance in the DTA, see, for example, <ref target="#haaf13"
               type="bibl">Haaf, Wiegand, and Geyken 2013</ref>.</note>) is a matter of supporting
@@ -289,7 +289,7 @@
           have been manually transcribed, annotated in TEI XML, and published via the DTA
           infrastructure. Most of these manuscripts were keyed manually by a vendor and published at
           an early stage in the web-based quality assurance platform <ptr type="software"
-            xml:id="R2" target="#dtaq"/><rs type="soft.name" ref="#R2">DTAQ</rs>. There, the
+            xml:id="R2" target="softw:dtaq"/><rs type="cit:soft.name" ref="#R2">DTAQ</rs>. There, the
           transcription as well as the annotation of each document was checked and corrected, if
           necessary; DTAQ also provided the means to add additional markup, such as the tagging of
           person names (<gi>persName</gi>), directly at page level. After the process of quality
@@ -1226,7 +1226,7 @@
           corpora. Our primary goal is to be as inclusive as possible, allowing for other projects
           to benefit from our resources (i.e., our comprehensive guidelines and documentation as
           well as the technical infrastructure that includes Schemas, ODDs, and <ptr type="software"
-            xml:id="R1" target="#xslt"/><rs type="soft.name" ref="#R1">XSLT</rs> scripts) and
+            xml:id="R1" target="softw:xslt"/><rs type="cit:soft.name" ref="#R1">XSLT</rs> scripts) and
           contribute to our corpora. We also want to ensure interoperability of all data within the
           DTA corpora. The underlying TEI format has to be continuously maintained and adapted to
           new necessities with these two premises in mind.</p>

data/JTEI/10_2016-19/jtei-10-homenda-source.xml

@@ -62,19 +62,6 @@
           in the humanities and social sciences, open to quality periodicals looking to publish
           full-text articles online.</p>
       </projectDesc>
-      <listPrefixDef>
-        <prefixDef ident="softw" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/software-list.xml#$1">
-          <p>In the context of this project, private URIs with the prefix softw point to software
-            items in the software-list.xml file, which are encoded with <gi>item</gi> elements and
-            identified in <att>xml:id</att>.</p>
-        </prefixDef>
-        <prefixDef ident="cit" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/citation-taxonomy.xml#$1">
-          <p>In the context of this project, private URIs with the prefix cit point to
-              <gi>category</gi> elements in the citation-taxonomy.xml file.</p>
-        </prefixDef>
-      </listPrefixDef>
     </encodingDesc>
     <profileDesc>
       <langUsage>

data/JTEI/10_2016-19/jtei-10-romary-source.xml

@@ -658,8 +658,8 @@
               available at <ptr target="https://github.com/TEIC/TEI/issues/1512"/>. In our proposal,
               the <gi>etym</gi> element has to be made recursive in order to allow the fine-grained
               representations we propose here. The corresponding ODD customization, together with
-              reference examples, is available on <ptr type="software" xml:id="R1" target="#github"
-                /><rs type="soft.name" ref="#R1">GitHub</rs>.</note> and the fact that a change
+              reference examples, is available on <ptr type="software" xml:id="R1" target="softw:github"
+                /><rs type="cit:soft.name" ref="#R1">GitHub</rs>.</note> and the fact that a change
             occurred within the contemporary lexicon (as opposed to its parent language) is
             indicated by means of <att>xml:lang</att> on the source form.<note>There may also be
               cases in which it is unknown whether a given etymological process occurred within the
@@ -780,7 +780,7 @@
               text.<note>The interested reader may ponder here the possibility to also encode
               scripts by means of the <att>notation</att> attribute instead of using a cluttering of
               language subtags on <att>xml:lang</att>. For more on this issue, see the proposal in
-              the TEI <ptr type="software" xml:id="R2" target="#github"/><rs type="soft.name"
+              the TEI <ptr type="software" xml:id="R2" target="softw:github"/><rs type="cit:soft.name"
                 ref="#R2">GitHub</rs> (<ptr target="https://github.com/TEIC/TEI/issues/1510"
               />).</note> This is why we have extended the <att>notation</att> attribute to
               <gi>orth</gi> in order to allow for better representation of both language
@@ -999,7 +999,7 @@
           <p>The <gi>date</gi><note>The element <gi>date</gi> as a child of <gi>cit</gi> is another
               example which does not adhere to the current TEI standards. We have allowed this
               within our ODD document. A feature request proposal will be made on the <ptr
-                type="software" xml:id="R3" target="#github"/><rs type="soft.name" ref="#R3"
+                type="software" xml:id="R3" target="softw:github"/><rs type="cit:soft.name" ref="#R3"
                 >GitHub</rs> page and this feature may or may not appear in future versions of the
               TEI Guidelines.</note> element is listed within each etymon block; the values of
             attributes <att>notBefore</att> and <att>notAfter</att> specify the range of time
@@ -1498,9 +1498,9 @@
           extent of knowledge that is truly necessary to create an accurate model of metaphorical
           processes. In order to do this, it is necessary to make use of one or more ontologies,
           which could be locally defined within a project, and of external linked open data sources
-          such as <ptr type="software" xml:id="R4" target="#dbpedia"/><rs type="soft.name soft.url"
+          such as <ptr type="software" xml:id="R4" target="softw:dbpedia"/><rs type="cit:soft.name soft.url"
             ref="#R4"><ref target="http://wiki.dbpedia.org/">DBpedia</ref></rs> and <ptr
-            type="software" xml:id="R5" target="#wikidata"/><rs type="soft.name soft.url" ref="#R5"
+            type="software" xml:id="R5" target="softw:wikidata"/><rs type="cit:soft.name soft.url" ref="#R5"
               ><ref target="https://www.wikidata.org/">Wikidata</ref></rs>, or some combination
           thereof. Within TEI dictionary markup, URIs for existing ontological entries can be
           referenced in the <gi>sense</gi>, <gi>usg</gi>, and <gi>ref</gi> elements as the value of
@@ -1510,8 +1510,8 @@
           reference to the source entry’s unique identifier (if such an entry exists within the
           dataset). In such cases, the etymon pointing to the source entry can be assumed to inherit
           the source’s domain and sense information, and this information can be automatically
-          extracted with a fairly simple <ptr type="software" xml:id="R6" target="#xslt"/><rs
-            type="soft.name" ref="#R6">XSLT</rs> program; thus the encoders may choose to leave some
+          extracted with a fairly simple <ptr type="software" xml:id="R6" target="softw:xslt"/><rs
+            type="cit:soft.name" ref="#R6">XSLT</rs> program; thus the encoders may choose to leave some
           or all of this information out of the etymon section. However, in the case that the
           dataset does not actually have entries for the source terms, or the encoder wants to be
           explicit in all aspects of the etymology, as mentioned above, the source domain and the
@@ -1572,7 +1572,7 @@
           URI is referenced in <gi>oRef</gi> and <gi>pRef</gi> as the value of <att>corresp</att>
             (<code>@corresp="#animal"</code>).</p>
         <p>In <gi>sense</gi>, the URI corresponding to the <ptr type="software" xml:id="R7"
-            target="#dbpedia"/><rs type="soft.name" ref="#R7">DBpedia</rs> entry for <q>horse</q> is
+            target="softw:dbpedia"/><rs type="cit:soft.name" ref="#R7">DBpedia</rs> entry for <q>horse</q> is
           the value for the attribute <att>corresp</att>. Additionally, the <tag>date
             notBefore="…"</tag> element–attribute pairing is used to specify that the term has only
           been used for the <q>horse</q> since 1517 at maximum (corresponding to the first Spanish
@@ -2502,7 +2502,7 @@
         <p>For the issues regarded as the most fundamentally important to creating a dynamic and
           sustainable model for both etymology and general lexicographic markup in TEI, we have
           submitted formal requests for changes to the TEI <ptr type="software" xml:id="R8"
-            target="#github"/><rs type="soft.name" ref="#R8">GitHub</rs>, and will continue to
+            target="softw:github"/><rs type="cit:soft.name" ref="#R8">GitHub</rs>, and will continue to
           submit change requests as needed. While this work represents a large step in the right
           direction for those looking for means of representing etymological information, there are
           still a number of unresolved issues that will need to be addressed. These remaining issues

data/JTEI/10_2016-19/jtei-10-viglianti-source.xml

@@ -51,19 +51,6 @@
           in the humanities and social sciences, open to quality periodicals looking to publish
           full-text articles online.</p>
       </projectDesc>
-      <listPrefixDef>
-        <prefixDef ident="softw" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/software-list.xml#$1">
-          <p>In the context of this project, private URIs with the prefix softw point to software
-            items in the software-list.xml file, which are encoded with <gi>item</gi> elements and
-            identified in <att>xml:id</att>.</p>
-        </prefixDef>
-        <prefixDef ident="cit" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/citation-taxonomy.xml#$1">
-          <p>In the context of this project, private URIs with the prefix cit point to
-              <gi>category</gi> elements in the citation-taxonomy.xml file.</p>
-        </prefixDef>
-      </listPrefixDef>
     </encodingDesc>
     <profileDesc>
       <langUsage>

data/JTEI/11_2019-20/jtei-11-intro-source.xml

@@ -90,19 +90,6 @@
           humanities and social sciences, open to quality periodicals looking to publish full-text
           articles online.</p>
       </projectDesc>
-      <listPrefixDef>
-        <prefixDef ident="softw" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/software-list.xml#$1">
-          <p>In the context of this project, private URIs with the prefix softw point to software
-            items in the software-list.xml file, which are encoded with <gi>item</gi> elements and
-            identified in <att>xml:id</att>.</p>
-        </prefixDef>
-        <prefixDef ident="cit" matchPattern="([a-z]+)"
-          replacementPattern="https://raw.githubusercontent.com/DH-RSE/software-citation-jtei/main/taxonomy/citation-taxonomy.xml#$1">
-          <p>In the context of this project, private URIs with the prefix cit point to
-              <gi>category</gi> elements in the citation-taxonomy.xml file.</p>
-        </prefixDef>
-      </listPrefixDef>
     </encodingDesc>
     <profileDesc>
       <langUsage>

data/JTEI/11_2019-20/jtei-cc-ra-bermudez-sabel-137-source.xml

@@ -123,11 +123,11 @@
           ways in which the variant taxonomy may be linked to the body of the edition.</p>
         <p>Although this paper is TEI-centered, other XML technologies will be mentioned. <ptr
             type="crossref" target="#validation"/> includes a brief commentary on using <ptr
-            type="software" xml:id="R1" target="#xslt"/><rs type="soft.name" ref="#R1">XSLT</rs> to
+            type="software" xml:id="R1" target="softw:xslt"/><rs type="cit:soft.name" ref="#R1">XSLT</rs> to
           transform a TEI-conformant definition of constraints into schema rules. However, the
           greatest attention to an additional technology is in <ptr type="crossref"
             target="#analyses"/>, which discusses the use of <ptr type="software" xml:id="R2"
-            target="#xquery"/><rs type="soft.name" ref="#R2">XQuery</rs> to retrieve particular
+            target="softw:xquery"/><rs type="cit:soft.name" ref="#R2">XQuery</rs> to retrieve particular
             <foreign>loci critici</foreign> and to deploy quantitative analyses.</p>
       </div>
       <div xml:id="rationale">
@@ -225,10 +225,10 @@
             neutralized.<note>This statement is especially significant when dealing with corpora
             that have been compiled over a long period of time. As is clearly explained in the
             introduction to the Helsinki Corpus that Irma Taavitsainen and Päivi Pahta prepared for
-            the <ptr type="software" xml:id="R3" target="#cord"/><rs type="soft.name url" ref="#R3"
+            the <ptr type="software" xml:id="R3" target="softw:cord"/><rs type="cit:soft.name url" ref="#R3"
                 ><ref
                 target="http://www.helsinki.fi/varieng/CoRD/corpora/HelsinkiCorpus/meintro.html"
-                >Corpus Resource Database</ref> (CoRD)</rs> (<rs type="soft.bib" ref="#R3"><bibl
+                >Corpus Resource Database</ref> (CoRD)</rs> (<rs type="cit:soft.bib" ref="#R3"><bibl
                 xml:id="quoteref1"><title level="a">Placing the Helsinki Corpus Middle English
                   Section Introduction into Context</title>, <ptr
                   target="http://www.helsinki.fi/varieng/CoRD/corpora/HelsinkiCorpus/meintro.html"
@@ -460,12 +460,12 @@
           definition, its typed-feature modeling facilitates the creation of schema constraints. For
           instance, I process my declaration to further constrict my schema so the feature structure
           declaration and its actual application are always synchronized and up to date.<note>I use
-              <ptr type="software" xml:id="R4" target="#xslt"/><rs type="soft.name" ref="#R4"
+              <ptr type="software" xml:id="R4" target="softw:xslt"/><rs type="cit:soft.name" ref="#R4"
               >XSLT</rs> to process the feature structure declaration in order to create all
             required Schematron rules that will constrict the feature library accordingly. I am
             currently working on creating a more generic validator (see my <ref
               target="https://github.com/HelenaSabel/FS-Validator"><ptr type="software" xml:id="R5"
-                target="#github"/><rs type="soft.name" ref="#R5">Github</rs> repository</ref>, <ptr
+                target="softw:github"/><rs type="cit:soft.name" ref="#R5">Github</rs> repository</ref>, <ptr
               target="https://github.com/HelenaSabel/FS-Validator"/>).</note>
           <figure xml:id="example4">
             <egXML xmlns="http://www.tei-c.org/ns/Examples">
@@ -558,14 +558,14 @@
             2016, 12.2.3</ref>) seems to be a popular encoding technique for multi-witness editions,
           in terms of both the specific tools that have been created for this method and the number
           of projects that apply it.<note>Tools include <ptr type="software" xml:id="R6"
-              target="#versioningmachine"/><rs type="soft.name soft.url" ref="#R6"><ref
+              target="softw:versioningmachine"/><rs type="cit:soft.name soft.url" ref="#R6"><ref
                 target="http://v-machine.org/">Versioning Machine</ref></rs>, <ptr type="software"
-              xml:id="R7" target="#collatex"/><rs type="soft.name soft.url" ref="#R7"><ref
+              xml:id="R7" target="softw:collatex"/><rs type="cit:soft.name soft.url" ref="#R7"><ref
                 target="https://collatex.net/">CollateX</ref></rs> (both the <ptr type="software"
-              xml:id="R8" target="#java"/><rs type="soft.name" ref="#R8">Java</rs> and <ptr
-              type="software" xml:id="R9" target="#python"/><rs type="soft.name" ref="#R9"
-              >Python</rs> versions), and <ptr type="software" xml:id="R10" target="#juxta"/><rs
-              type="soft.name soft.url" ref="#R10"><ref target="http://www.juxtasoftware.org/"
+              xml:id="R8" target="softw:java"/><rs type="cit:soft.name" ref="#R8">Java</rs> and <ptr
+              type="software" xml:id="R9" target="softw:python"/><rs type="cit:soft.name" ref="#R9"
+              >Python</rs> versions), and <ptr type="software" xml:id="R10" target="softw:juxta"/><rs
+              type="cit:soft.name soft.url" ref="#R10"><ref target="http://www.juxtasoftware.org/"
                 >Juxta</ref></rs>. For representative projects using the parallel segmentation
             method see <ref
               target="http://scholarlyediting.org/2015/editions/lowelledition_wit-Courier.html"