Merge branch 'main' of https://github.com/DH-RSE/software-citation

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diff --git a/data/JTEI/12_2019-20/jtei-cc-ra-flanders-176-source.xml b/data/JTEI/12_2019-20/jtei-cc-ra-flanders-176-source.xml
diff --git a/data/JTEI/13_2020-22/jtei-cc-pn-kuhry-188-source.xml b/data/JTEI/13_2020-22/jtei-cc-pn-kuhry-188-source.xml
diff --git a/data/JTEI/13_2020-22/jtei-cc-ra-parisse-182-source.xml b/data/JTEI/13_2020-22/jtei-cc-ra-parisse-182-source.xml
@@ -234,16 +234,16 @@
           <p>Many software packages dedicated to editing spoken language transcription contain
             utilities that can convert many formats: for example, <ptr type="software" xml:id="R15"
               target="#exmaralda"/>
-            <rs type="soft.name" ref="#R15">EXMARaLDA</rs> ( <rs type="soft.Bib.Ref" target="#R15"
+            <rs type="soft.name" ref="#R15">EXMARaLDA</rs> ( <rs type="soft.bib.ref" ref="#R15"
                 ><ref type="bibl" target="#schmidt2004">Schmidt 2004</ref>
-            </rs>; see <rs type="soft.url" target="#R15"><ptr target="https://exmaralda.org"
+            </rs>; see <rs type="soft.url" ref="#R15"><ptr target="https://exmaralda.org"
             /></rs>), <ptr type="software" xml:id="R16" target="#anvil"/>
-            <rs type="soft.name" ref="#R16">Anvil</rs> (<rs type="soft.Bib.Ref" target="#R16">
+            <rs type="soft.name" ref="#R16">Anvil</rs> (<rs type="soft.bib.ref" ref="#R16">
               <ref type="bibl" target="#kipp2001">Kipp 2001</ref></rs>; see <rs type="soft.url"
-              target="#R16"><ptr target="https://www.anvil-software.org"/></rs>), and <ptr
+              ref="#R16"><ptr target="https://www.anvil-software.org"/></rs>), and <ptr
               type="software" xml:id="R17" target="#elan"/><rs type="soft.name" ref="#R17">ELAN</rs>
-              (<rs type="soft.bib.ref" target="#R17"><ref type="bibl" target="#wittenburg2006"
-                >Wittenburg et al. 2006</ref></rs>; see <rs type="soft.url" target="#R17">
+              (<rs type="soft.bib.ref" ref="#R17"><ref type="bibl" target="#wittenburg2006"
+                >Wittenburg et al. 2006</ref></rs>; see <rs type="soft.url" ref="#R17">
               <ptr target="https://archive.mpi.nl/tla/elan"/></rs>). However, in all cases, the
             conversions are limited to the features implemented in the tool itself—for example, with
             a limited set of metadata—and they cannot always be used to prepare data to be used by
@@ -260,9 +260,9 @@
             tools missing in the <ptr type="software" xml:id="R18" target="#teicorpo"/>
             <rs type="soft.name" ref="#R18">TEICORPO</rs> approach are <ptr type="software"
               xml:id="R19" target="#exmaralda"/><rs type="soft.name" ref="#R19">EXMARaLDA</rs> and
-              <ptr type="software" xml:id="R19" target="#folker"/>FOLKER (<rs type="soft.bib.ref"
-              target="#R19"><ref type="bibl" target="#schmidts2010">Schmidt and Schütte
-              2010</ref></rs>; see <rs type="soft.url" target="#R19"><ptr
+              <ptr type="software" xml:id="R241" target="#folker"/>FOLKER (<rs type="soft.bib.ref"
+              ref="#R19"><ref type="bibl" target="#schmidts2010">Schmidt and Schütte
+              2010</ref></rs>; see <rs type="soft.url" ref="#R241"><ptr
                 target="https://exmaralda.org/en/folker-en/"/></rs>), but this was only because the
             conversion tools from and to <ptr type="software" xml:id="R20" target="#EXMARaLDA"/><rs
               type="soft.name" ref="#R20">EXMARaLDA</rs>, <ptr type="software" xml:id="R21"
@@ -279,22 +279,22 @@
               <ptr type="software" xml:id="R25" target="#folker"/>
             <rs type="soft.name" ref="#R25">FOLKER</rs> software fit within the process chain of
               <ptr type="software" xml:id="R26" target="#teicorpo"/><rs type="soft.name"
-              target="#R26"> TEICORPO</rs>. This demonstrates the usefulness of a well-known and
+              ref="#R26"> TEICORPO</rs>. This demonstrates the usefulness of a well-known and
             efficient format such as TEI.</p>
           <p>There are, however, differences between the two projects that make them nonredundant
             but complementary, each project having specificities that can be useful or damaging
             depending on the user’s needs. One minor difference is that the <ptr type="software"
-              xml:id="R27" ref="#teicorpo"/>
-            <rs type="soft.name" target="#R27">TEICORPO</rs> project is not a functionality of an
+              xml:id="R27" target="#teicorpo"/>
+            <rs type="soft.name" ref="#R27">TEICORPO</rs> project is not a functionality of an
             editing tool, but is a standalone tool for converting data between one format and
             another. This had certain effects on the user interface and explains some of the choices
             made in the development of the two tools.</p>
           <p>There are two major differences between <ptr type="software" xml:id="R28"
               target="#teicorpo"/>
-            <rs type="soft.name" target="#R28">TEICORPO</rs> and Schmidt’s approach, which affected
+            <rs type="soft.name" ref="#R28">TEICORPO</rs> and Schmidt’s approach, which affected
             both the design of the tools and how they can be used. The first difference is that in
-            developing <ptr type="software" xml:id="R29" ref="#teicorpo"/><rs type="soft.name"
-              target="#R29">TEICORPO</rs>, it was decided that the conversion between the original
+            developing <ptr type="software" xml:id="R29" target="#teicorpo"/><rs type="soft.name"
+              ref="#R29">TEICORPO</rs>, it was decided that the conversion between the original
             formats and TEI had to be lossless (or as lossless as possible) because we wanted to
             offer a means to store the research data for long-term conservation and dissemination in
             a standard XML format instead of in proprietary formats such as those used by <ptr
@@ -1004,7 +1004,7 @@
             <rs type="soft.name" ref="#R117">TEICONVERT</rs> makes spoken language data available
             for <ptr type="software" xml:id="R118" target="#txm"/><rs type="soft.name" ref="#R118"
               >TXM</rs> (<rs type="soft.bib.ref" ref="#R118"><ref type="bibl" target="#heiden2010"
-                >Heiden 2010</ref></rs>; see <rs type="soft.turl" ref="#R118"><ptr
+                >Heiden 2010</ref></rs>; see <rs type="soft.url" ref="#R118"><ptr
                 target="http://textometrie.ens-lyon.fr"/></rs>), <ptr type="software" xml:id="R119"
               target="#letrameur"/>
             <rs type="soft.name" ref="#R119">Le Trameur</rs> (<rs type="soft.bib.ref" ref="#R119"
@@ -1149,11 +1149,13 @@
               <rs type="soft.name" ref="#R144">TEICORPO</rs> includes the ability to use any
               syntactic model. For French data, we used the PERCEO model (<ref type="bibl"
                 target="#benzitoun2012">Benzitoun, Fort, and Sagot 2012</ref>).</p>
-            <p>The command line to be used is: <code>java -cp <ptr type="software" xml:id="R208"
+            <p>The command line to be used is: <ptr type="software" xml:id="R240" target="#java"/><code>
+              <rs type="soft.name" ref="#R240">java</rs> -cp <ptr type="software" xml:id="R208"
                   target="#teicorpo"/>
                 <rs type="soft.name" ref="#R208">TEICORPO</rs>.jar fr.ortolang.<ptr type="software"
                   xml:id="R209" target="#teicorpo"/>
-                <rs type="soft.name" ref="#R209">TEICORPO</rs>.TeiTreeTagger filenames...</code>
+              <rs type="soft.name" ref="#R209">TEICORPO</rs>.<ptr type="software" xml:id="R239" target="#treetagger"/>
+             Tei <rs type="soft.name" ref="#R239">TreeTagger</rs> filenames...</code>
               with additional parameters:</p>
             <table xml:id="table2">
               <row role="label">
@@ -1329,7 +1331,10 @@
               <rs type="soft.name" ref="#R153">TreeTagger</rs> . The -model and -syntaxformat
               parameters can be used in a similar way to specify the grammatical model to be used
               and the output format. A command line example is:</p>
-            <p><code>java -cp "teicorpo.jar:directory_for_SNLP/*" fr.ortolang.teicorpo.TeiSNLP
+            <p><code><ptr type="software" xml:id="R236" target="#java"/>
+              <rs type="soft.name" ref="#R236">java</rs> -cp "<ptr type="software" xml:id="R237" target="#teicorpo"/>
+              <rs type="soft.name" ref="#R237">teicorpo</rs>.jar:directory_for_SNLP/*" fr.ortolang.<ptr type="software" xml:id="R238" target="#teicorpo"/>
+              <rs type="soft.name" ref="#R238">teicorpo</rs>.TeiSNLP
                 -syntaxformat svalue -model filename.tei_corpo.xml</code></p>
             <p>The <term>directory_for_SNLP</term> is the name of the location on a computer where
               all the <ptr type="software" xml:id="R212" target="#stanfordcorenlp"/>
@@ -1392,7 +1397,7 @@
           <p>Export can be done from TEI into a format used by textometric software (see <ptr
               target="#example_code_11" type="crossref"/>). This is the case for <ptr
               type="software" xml:id="R160" target="#txm"/><rs type="soft.name" ref="#R160">TXM</rs>,<note>
-              <p>See the Textométrie website, last updated June 29, 2020, <rs type="soft.ulr" ref="#R160"
+              <p>See the Textométrie website, last updated June 29, 2020, <rs type="soft.url" ref="#R160"
                     ><ptr target="http://textometrie.ens-lyon.fr/?lang=en"/></rs>.</p>
             </note> a textometric software application. In this case, instead of using a partition
             representation, the information from the grammatical analysis is inserted at the word
@@ -1591,7 +1596,7 @@
                 target="https://www.fon.hum.uva.nl/paul/papers/speakUnspeakPraat_glot2001.pdf"
               />.</bibl>
           </rs>
-          <ptr type="software" xml:id="R226" target="#teimata"/>
+          <ptr type="software" xml:id="R226" target="#teimeta"/>
           <rs type="soft.bib.ref" ref="#R226">
             <bibl xml:id="etienne"><rs type="soft.agent" ref="#R226"><author>Etienne,
                   Carole</author></rs>, <rs type="soft.agent" ref="#R226"><author>Loïc

diff --git a/data/JTEI/13_2020-22/jtei-cc-ra-winslow-186-source.xml b/data/JTEI/13_2020-22/jtei-cc-ra-winslow-186-source.xml
@@ -530,8 +530,8 @@
                favoring one period or type of document over another, a generic element seems both
                desirable and advisable. The proposed element, as implemented in the TEI_CEI
                   ODD,<note>See the <ref xml:id="ref13" type="bibl" target="#winslowetal2019"
-                     >CEI2TEI <ptr type="software" xml:id="GitHub" target="#GitHub"/><rs
-                        type="soft.name" ref="#GitHub">GitHub</rs> repository, accessed June 25,
+                     >CEI2TEI <ptr type="software" xml:id="R1" target="#github"/><rs
+                        type="soft.name" ref="#R1">GitHub</rs> repository, accessed June 25,
                      2021</ref>, <ptr
                      target="https://github.com/GVogeler/CEI2TEI/blob/master/tei_cei.odd"/>.</note>
                is simple (<ident>attList</ident> items suppressed for brevity: they follow the
@@ -576,8 +576,8 @@
                proposed vocabulary, provided in SKOS (Simple Knowledge Organization System) format
                (as part of the project’s <ref
                   target="https://github.com/GVogeler/CEI2TEI/blob/master/Authentication/authen.skos.ttl">
-                  <ptr type="software" xml:id="GitHub" target="#GitHub"/><rs type="soft.name"
-                     ref="#GitHub">GitHub</rs> repository</ref>,<note>Accessed July 13, 2021, <ptr
+                  <ptr type="software" xml:id="R2" target="#github"/><rs type="soft.name"
+                     ref="#R2">GitHub</rs> repository</ref>,<note>Accessed July 13, 2021, <ptr
                      target="https://github.com/GVogeler/CEI2TEI/blob/master/Authentication/authen.skos.ttl"
                   />.</note> at <ptr
                   target="https://github.com/GVogeler/CEI2TEI/blob/master/Authentication/authen.skos.ttl"

diff --git a/data/JTEI/14_2021-23/jtei-barabuccietal-196-source.xml b/data/JTEI/14_2021-23/jtei-barabuccietal-196-source.xml
@@ -261,11 +261,11 @@
                   text are presented in such a way that the reader is granted more informed access
                   to them.</p>
                <p>The edition will be published online using a specifically tailored version of <ptr
-                     type="software" xml:id="R29" target="#evt"/><rs type="soft.name" ref="R29"
+                     type="software" xml:id="R29" target="#evt"/><rs type="soft.name" ref="#R29"
                      >EVT</rs> (Edition Visualization Technology<note><quote source="#quote1">A
                         light-weight, open source tool specifically designed to create digital
                         editions from XML-encoded texts</quote>
-                     <rs type="soft.bib" ref="R20">(<ref type="bibl" target="#delturco2013"
+                     <rs type="soft.bib" ref="#R20">(<ref type="bibl" target="#delturco2013"
                            xml:id="quote1">Rosselli Del Turco et al. 2013</ref>)</rs>.</note>) and
                   will present, on the one hand, each witness in its continuum from facsimile to
                   multiple levels of normalization and, on the other hand, the three main witnesses
@@ -790,7 +790,7 @@
                      with no manual intervention on the resulting files.</item>
                   <item>The generated editions files will conform to the TEI subset understood by
                         <ptr type="software" xml:id="R30" target="#evt"/><rs type="soft.name"
-                        ref="R30">EVT</rs>.</item>
+                        ref="#R30">EVT</rs>.</item>
                </list>
                <p>Some of these desiderata clash with each other. For instance, the desire to
                   directly edit the XML file makes it hard and error-prone to keep in a single
@@ -855,7 +855,7 @@
                         target="#delturcond">Roberto Rosselli Del Turco (n.d.)</ref>: here two
                      levels of edition are offered, a diplomatic and a more interpretative one. The
                      user can compare the two editions visualizing them synoptically in the <ptr
-                        type="software" xml:id="R31" target="#evt"/><rs type="soft.name" ref="R31"
+                        type="software" xml:id="R31" target="#evt"/><rs type="soft.name" ref="#R31"
                         >EVT</rs> software used for the edition.</p>
                </div>
             </div>
@@ -1474,10 +1474,10 @@
                      version</biblScope>. Accessed <date>October 22, 2021</date>. <ptr
                      target="http://vbd.humnet.unipi.it/beta2/"/>.</bibl>
                <bibl xml:id="delturco2013"><ptr type="software" xml:id="R28" target="#evt"
-                        /><author><rs type="soft.agent" ref="R28">Rosselli Del Turco,
-                     Roberto</rs></author>, et al. <rs type="soft.bib" ref="R28">
+                        /><author><rs type="soft.agent" ref="#R28">Rosselli Del Turco,
+                     Roberto</rs></author>, et al. <rs type="soft.bib" ref="#R28">
                      <date>2013</date>. <title level="m">Edition Visualization Technology</title>.
-                  </rs> Accessed <date>April 19, 2021</date>.<rs type="soft.url" ref="R28"><ptr
+                  </rs> Accessed <date>April 19, 2021</date>.<rs type="soft.url" ref="#R28"><ptr
                         target="http://evt.labcd.unipi.it/"/></rs>.</bibl>
                <bibl xml:id="stella2020"><editor>Stella, Francesco</editor>, ed. <date>2020</date>.
                      <title level="m">Corpus Rhythmorum Musicum.</title> Last modified <date>July

diff --git a/data/JTEI/14_2021-23/jtei-cc-pn-erjavec-195-source.xml b/data/JTEI/14_2021-23/jtei-cc-pn-erjavec-195-source.xml
@@ -326,9 +326,9 @@
           <head>Presentation of Parla-CLARIN</head>
           <p>Like the TEI Guidelines, the Parla-CLARIN recommendations are available on <ref
               target="https://github.com/clarin-eric/parla-clarin/"><ptr type="software" xml:id="R1"
-                target="#GitHub"/><rs type="soft.name" ref="#R1">GitHub</rs></ref>, as a
+                target="#github"/><rs type="soft.name" ref="#R1">GitHub</rs></ref>, as a
               project<note>Tomaž Erjavec and Andrej Pančur, Parla-CLARIN project <ptr
-                type="software" xml:id="R2" target="#GitHub"/><rs type="soft.name" ref="#R2"
+                type="software" xml:id="R2" target="#github"/><rs type="soft.name" ref="#R2"
                 >GitHub</rs> site, last updated March 17, 2021, <ptr type="software" xml:id="R9"
                 target="#parlaclarinscripts"/><rs type="soft.url" ref="#R9"><ptr
                   target="https://github.com/clarin-eric/parla-clarin/"/></rs>.</note> of the CLARIN
@@ -581,7 +581,7 @@
           and into developing the <ptr type="software" xml:id="R12" target="#parlaclarinscripts"
             /><rs type="soft.name" ref="#R12">conversion from Akoma Ntoso to Parla-CLARIN</rs>. We
           have not included examples of the encoding, as these are readily available on the <ptr
-            type="software" xml:id="R3" target="#GitHub"/><rs type="soft.name" ref="#R3">GitHub</rs>
+            type="software" xml:id="R3" target="#github"/><rs type="soft.name" ref="#R3">GitHub</rs>
           documentation page of the project, and large Parla-CLARIN encoded corpora are openly
           available.</p>
         <p>Apart from the siParl 2.0 corpus mentioned above (<ptr type="crossref"
@@ -632,7 +632,7 @@
           specification from the default ones in the TEI Guidelines to ones taken or adapted from
           the collected parliamentary corpora.</p>
         <p>Second, as we have already done for ParlaMint, we plan to add to the <ptr type="software"
-            xml:id="R4" target="#GitHub"/><rs type="soft.name" ref="#R4">GitHub</rs> Parla-CLARIN
+            xml:id="R4" target="#github"/><rs type="soft.name" ref="#R4">GitHub</rs> Parla-CLARIN
           project more down-conversion scripts with which we would increase the usability of the
           Parla-CLARIN corpora. As mentioned, work also needs to be done to develop a conversion to
           RDF.</p>
@@ -803,7 +803,8 @@
           <bibl xml:id="kilgarriff14"><author>Kilgarriff, Adam</author>, <author>Vít Baisa</author>,
               <author>Jan Bušta</author>, <author>Miloš Jakubíček</author>, <author>Vojtěch
               Kovář</author>, <author>Jan Michelfeit</author>, <author>Pavel Rychlý</author>, and
-              <author>Vít Suchomel</author>. <rs type="soft.bib.ref" ref="ewfew"><date>2014</date>.
+              <author>Vít Suchomel</author>. <ptr type="software" xml:id="R30"
+                target="#sketchengine"/><rs type="soft.name soft.bib.ref" ref="#R30"><date>2014</date>.
                 <title level="a">The Sketch Engine: Ten Years On.</title></rs>
             <title level="j">Lexicography: Journal of ASIALEX</title>
             <biblScope unit="volume">1</biblScope> (<biblScope unit="issue">1</biblScope>):

diff --git a/data/JTEI/8_2014-15/jtei-8-boschetti-source.xml b/data/JTEI/8_2014-15/jtei-8-boschetti-source.xml
@@ -240,7 +240,7 @@
             </list>. The continuous integration and release are supported by open source Integrated
             Development Environments (IDEs) like <ptr type="software" xml:id="R10" target="#eclipse"/>
             <rs type="soft.name" ref="#R10">Eclipse</rs> or <ptr type="software" xml:id="R11"
-              target="netbeans"/><rs type="soft.name" ref="#R11"> NetBeans</rs> and by a software
+              target="#netbeans"/> <rs type="soft.name" ref="#R11">NetBeans</rs> and by a software
             configuration management tool such as <ptr type="software" xml:id="R13" target="#svn"/>
             <rs type="soft.name" ref="#R13">SVN</rs> or <ptr type="software" xml:id="R12"
               target="#git"/>
@@ -722,7 +722,7 @@
               Environment: Metadata, Vocabularies and Techniques in the Digital Humanities</title>,
             article no. 11. <pubPlace>New York</pubPlace>: <publisher>ACM</publisher>. doi:<idno
               type="doi">10.1145/2517978.2517990</idno>.</bibl>
-          <ptr type="software" xml:id="R39" target="g2a"/>
+          <ptr type="software" xml:id="R39" target="#g2a"/>
           <rs type="soft.ref.bib" ref="#R39">
             <bibl xml:id="bozzi13"><author><rs type="soft.agent" ref="#R39">Bozzi,
                 Andrea</rs></author>. <date>2013</date>. <title level="a">G2A: A Web Application to