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505  return offset ? offset + '/' + url : url;
506}
507
508function createFuseIndex() {
509
510  // create fuse index
511  var options = {
512    keys: [
513      { name: 'title', weight: 20 },
514      { name: 'categories', weight: 15 },
515      { name: 'description', weight: 10 },
516      { name: 'contents', weight: 5 },
517    ],
518    ignoreLocation: true,
519    threshold: 0
520  };
521  var fuse = new window.Fuse([], options);
522
523  // fetch the main search.json
524  return fetch(offsetURL('search.json'))
525    .then(function(response) {
526      if (response.status == 200) {
527        return response.json().then(function(json) {
528          // index main articles
529          json.articles.forEach(function(article) {
530            fuse.add(article);
531          });
532          // download collections and index their articles
533          return Promise.all(json.collections.map(function(collection) {
534            return fetch(offsetURL(collection)).then(function(response) {
535              if (response.status === 200) {
536                return response.json().then(function(articles) {
537                  articles.forEach(function(article) {
538                    fuse.add(article);
539                  });
540                })
541              } else {
542                return Promise.reject(
543                  new Error('Unexpected status from search index request: ' +
544                            response.status)
545                );
546              }
547            });
548          })).then(function() {
549            return fuse;
550          });
551        });
552
553      } else {
554        return Promise.reject(
555          new Error('Unexpected status from search index request: ' +
556                      response.status)
557        );
558      }
559    });
560}
561
562window.document.addEventListener("DOMContentLoaded", function (event) {
563
564  // get search element (bail if we don't have one)
565  var searchEl = window.document.getElementById('distill-search');
566  if (!searchEl)
567    return;
568
569  createFuseIndex()
570    .then(function(fuse) {
571
572      // make search box visible
573      searchEl.classList.remove('hidden');
574
575      // initialize autocomplete
576      var options = {
577        autoselect: true,
578        hint: false,
579        minLength: 2,
580      };
581      window.autocomplete(searchEl, options, [{
582        source: function(query, callback) {
583          const searchOptions = {
584            isCaseSensitive: false,
585            shouldSort: true,
586            minMatchCharLength: 2,
587            limit: 10,
588          };
589          var results = fuse.search(query, searchOptions);
590          callback(results
591            .map(function(result) { return result.item; })
592          );
593        },
594        templates: {
595          suggestion: function(suggestion) {
596            var img = suggestion.preview && Object.keys(suggestion.preview).length > 0
597              ? `<img src="${offsetURL(suggestion.preview)}"</img>`
598              : '';
599            var html = `
600              <div class="search-item">
601                <h3>${suggestion.title}</h3>
602                <div class="search-item-description">
603                  ${suggestion.description || ''}
604                </div>
605                <div class="search-item-preview">
606                  ${img}
607                </div>
608              </div>
609            `;
610            return html;
611          }
612        }
613      }]).on('autocomplete:selected', function(event, suggestion) {
614        window.location.href = offsetURL(suggestion.path);
615      });
616      // remove inline display style on autocompleter (we want to
617      // manage responsive display via css)
618      $('.algolia-autocomplete').css("display", "");
619    })
620    .catch(function(error) {
621      console.log(error);
622    });
623
624});
625
626</script>
626
627
628<style type="text/css">
629
630.nav-search {
631  font-size: x-small;
632}
633
634/* Algolioa Autocomplete */
635
636.algolia-autocomplete {
637  display: inline-block;
638  margin-left: 10px;
639  vertical-align: sub;
640  background-color: white;
641  color: black;
642  padding: 6px;
643  padding-top: 8px;
644  padding-bottom: 0;
645  border-radius: 6px;
646  border: 1px #0F2E3D solid;
647  width: 180px;
648}
649
650
651@media screen and (max-width: 768px) {
652  .distill-site-nav .algolia-autocomplete {
653    display: none;
654    visibility: hidden;
655  }
656  .distill-site-nav.responsive .algolia-autocomplete {
657    display: inline-block;
658    visibility: visible;
659  }
660  .distill-site-nav.responsive .algolia-autocomplete .aa-dropdown-menu {
661    margin-left: 0;
662    width: 400px;
663    max-height: 400px;
664  }
665}
666
667.algolia-autocomplete .aa-input, .algolia-autocomplete .aa-hint {
668  width: 90%;
669  outline: none;
670  border: none;
671}
672
673.algolia-autocomplete .aa-hint {
674  color: #999;
675}
676.algolia-autocomplete .aa-dropdown-menu {
677  width: 550px;
678  max-height: 70vh;
679  overflow-x: visible;
680  overflow-y: scroll;
681  padding: 5px;
682  margin-top: 3px;
683  margin-left: -150px;
684  background-color: #fff;
685  border-radius: 5px;
686  border: 1px solid #999;
687  border-top: none;
688}
689
690.algolia-autocomplete .aa-dropdown-menu .aa-suggestion {
691  cursor: pointer;
692  padding: 5px 4px;
693  border-bottom: 1px solid #eee;
694}
695
696.algolia-autocomplete .aa-dropdown-menu .aa-suggestion:last-of-type {
697  border-bottom: none;
698  margin-bottom: 2px;
699}
700
701.algolia-autocomplete .aa-dropdown-menu .aa-suggestion .search-item {
702  overflow: hidden;
703  font-size: 0.8em;
704  line-height: 1.4em;
705}
706
707.algolia-autocomplete .aa-dropdown-menu .aa-suggestion .search-item h3 {
708  font-size: 1rem;
709  margin-block-start: 0;
710  margin-block-end: 5px;
711}
712
713.algolia-autocomplete .aa-dropdown-menu .aa-suggestion .search-item-description {
714  display: inline-block;
715  overflow: hidden;
716  height: 2.8em;
717  width: 80%;
718  margin-right: 4%;
719}
720
721.algolia-autocomplete .aa-dropdown-menu .aa-suggestion .search-item-preview {
722  display: inline-block;
723  width: 15%;
724}
725
726.algolia-autocomplete .aa-dropdown-menu .aa-suggestion .search-item-preview img {
727  height: 3em;
728  width: auto;
729  display: none;
730}
731
732.algolia-autocomplete .aa-dropdown-menu .aa-suggestion .search-item-preview img[src] {
733  display: initial;
734}
735
736.algolia-autocomplete .aa-dropdown-menu .aa-suggestion.aa-cursor {
737  background-color: #eee;
738}
739.algolia-autocomplete .aa-dropdown-menu .aa-suggestion em {
740  font-weight: bold;
741  font-style: normal;
742}
743
744</style>
745
746
747<!--/radix_placeholder_navigation_in_header-->
748  <!--radix_placeholder_distill-->
749
750<style type="text/css">
751
752body {
753  background-color: white;
754}
755
756.pandoc-table {
757  width: 100%;
758}
759
760.pandoc-table>caption {
761  margin-bottom: 10px;
762}
763
764.pandoc-table th:not([align]) {
765  text-align: left;
766}
767
768.pagedtable-footer {
769  font-size: 15px;
770}
771
772d-byline .byline {
773  grid-template-columns: 2fr 2fr;
774}
775
776d-byline .byline h3 {
777  margin-block-start: 1.5em;
778}
779
780d-byline .byline .authors-affiliations h3 {
781  margin-block-start: 0.5em;
782}
783
784.authors-affiliations .orcid-id {
785  width: 16px;
786  height:16px;
787  margin-left: 4px;
788  margin-right: 4px;
789  vertical-align: middle;
790  padding-bottom: 2px;
791}
792
793d-title .dt-tags {
794  margin-top: 1em;
795  grid-column: text;
796}
797
798.dt-tags .dt-tag {
799  text-decoration: none;
800  display: inline-block;
801  color: rgba(0,0,0,0.6);
802  padding: 0em 0.4em;
803  margin-right: 0.5em;
804  margin-bottom: 0.4em;
805  font-size: 70%;
806  border: 1px solid rgba(0,0,0,0.2);
807  border-radius: 3px;
808  text-transform: uppercase;
809  font-weight: 500;
810}
811
812d-article table.gt_table td,
813d-article table.gt_table th {
814  border-bottom: none;
815  font-size: 100%;
816}
817
818.html-widget {
819  margin-bottom: 2.0em;
820}
821
822.l-screen-inset {
823  padding-right: 16px;
824}
825
826.l-screen .caption {
827  margin-left: 10px;
828}
829
830.shaded {
831  background: rgb(247, 247, 247);
832  padding-top: 20px;
833  padding-bottom: 20px;
834  border-top: 1px solid rgba(0, 0, 0, 0.1);
835  border-bottom: 1px solid rgba(0, 0, 0, 0.1);
836}
837
838.shaded .html-widget {
839  margin-bottom: 0;
840  border: 1px solid rgba(0, 0, 0, 0.1);
841}
842
843.shaded .shaded-content {
844  background: white;
845}
846
847.text-output {
848  margin-top: 0;
849  line-height: 1.5em;
850}
851
852.hidden {
853  display: none !important;
854}
855
856d-article {
857  padding-top: 2.5rem;
858  padding-bottom: 30px;
859}
860
861d-appendix {
862  padding-top: 30px;
863}
864
865d-article>p>img {
866  width: 100%;
867}
868
869d-article h2 {
870  margin: 1rem 0 1.5rem 0;
871}
872
873d-article h3 {
874  margin-top: 1.5rem;
875}
876
877d-article iframe {
878  border: 1px solid rgba(0, 0, 0, 0.1);
879  margin-bottom: 2.0em;
880  width: 100%;
881}
882
883/* Tweak code blocks */
884
885d-article div.sourceCode code,
886d-article pre code {
887  font-family: Consolas, Monaco, 'Andale Mono', 'Ubuntu Mono', monospace;
888}
889
890d-article pre,
891d-article div.sourceCode,
892d-article div.sourceCode pre {
893  overflow: auto;
894}
895
896d-article div.sourceCode {
897  background-color: white;
898}
899
900d-article div.sourceCode pre {
901  padding-left: 10px;
902  font-size: 12px;
903  border-left: 2px solid rgba(0,0,0,0.1);
904}
905
906d-article pre {
907  font-size: 12px;
908  color: black;
909  background: none;
910  margin-top: 0;
911  text-align: left;
912  white-space: pre;
913  word-spacing: normal;
914  word-break: normal;
915  word-wrap: normal;
916  line-height: 1.5;
917
918  -moz-tab-size: 4;
919  -o-tab-size: 4;
920  tab-size: 4;
921
922  -webkit-hyphens: none;
923  -moz-hyphens: none;
924  -ms-hyphens: none;
925  hyphens: none;
926}
927
928d-article pre a {
929  border-bottom: none;
930}
931
932d-article pre a:hover {
933  border-bottom: none;
934  text-decoration: underline;
935}
936
937d-article details {
938  grid-column: text;
939  margin-bottom: 0.8em;
940}
941
942@media(min-width: 768px) {
943
944d-article pre,
945d-article div.sourceCode,
946d-article div.sourceCode pre {
947  overflow: visible !important;
948}
949
950d-article div.sourceCode pre {
951  padding-left: 18px;
952  font-size: 14px;
953}
954
955d-article pre {
956  font-size: 14px;
957}
958
959}
960
961figure img.external {
962  background: white;
963  border: 1px solid rgba(0, 0, 0, 0.1);
964  box-shadow: 0 1px 8px rgba(0, 0, 0, 0.1);
965  padding: 18px;
966  box-sizing: border-box;
967}
968
969/* CSS for d-contents */
970
971.d-contents {
972  grid-column: text;
973  color: rgba(0,0,0,0.8);
974  font-size: 0.9em;
975  padding-bottom: 1em;
976  margin-bottom: 1em;
977  padding-bottom: 0.5em;
978  margin-bottom: 1em;
979  padding-left: 0.25em;
980  justify-self: start;
981}
982
983@media(min-width: 1000px) {
984  .d-contents.d-contents-float {
985    height: 0;
986    grid-column-start: 1;
987    grid-column-end: 4;
988    justify-self: center;
989    padding-right: 3em;
990    padding-left: 2em;
991  }
992}
993
994.d-contents nav h3 {
995  font-size: 18px;
996  margin-top: 0;
997  margin-bottom: 1em;
998}
999
1000.d-contents li {
1001  list-style-type: none
1002}
1003
1004.d-contents nav > ul {
1005  padding-left: 0;
1006}
1007
1008.d-contents ul {
1009  padding-left: 1em
1010}
1011
1012.d-contents nav ul li {
1013  margin-top: 0.6em;
1014  margin-bottom: 0.2em;
1015}
1016
1017.d-contents nav a {
1018  font-size: 13px;
1019  border-bottom: none;
1020  text-decoration: none
1021  color: rgba(0, 0, 0, 0.8);
1022}
1023
1024.d-contents nav a:hover {
1025  text-decoration: underline solid rgba(0, 0, 0, 0.6)
1026}
1027
1028.d-contents nav > ul > li > a {
1029  font-weight: 600;
1030}
1031
1032.d-contents nav > ul > li > ul {
1033  font-weight: inherit;
1034}
1035
1036.d-contents nav > ul > li > ul > li {
1037  margin-top: 0.2em;
1038}
1039
1040
1041.d-contents nav ul {
1042  margin-top: 0;
1043  margin-bottom: 0.25em;
1044}
1045
1046.d-article-with-toc h2:nth-child(2) {
1047  margin-top: 0;
1048}
1049
1050
1051/* Figure */
1052
1053.figure {
1054  position: relative;
1055  margin-bottom: 2.5em;
1056  margin-top: 1.5em;
1057}
1058
1059.figure .caption {
1060  color: rgba(0, 0, 0, 0.6);
1061  font-size: 12px;
1062  line-height: 1.5em;
1063}
1064
1065.figure img.external {
1066  background: white;
1067  border: 1px solid rgba(0, 0, 0, 0.1);
1068  box-shadow: 0 1px 8px rgba(0, 0, 0, 0.1);
1069  padding: 18px;
1070  box-sizing: border-box;
1071}
1072
1073.figure .caption a {
1074  color: rgba(0, 0, 0, 0.6);
1075}
1076
1077.figure .caption b,
1078.figure .caption strong, {
1079  font-weight: 600;
1080  color: rgba(0, 0, 0, 1.0);
1081}
1082
1083/* Citations */
1084
1085d-article .citation {
1086  color: inherit;
1087  cursor: inherit;
1088}
1089
1090div.hanging-indent{
1091  margin-left: 1em; text-indent: -1em;
1092}
1093
1094/* Citation hover box */
1095
1096.tippy-box[data-theme~=light-border] {
1097  background-color: rgba(250, 250, 250, 0.95);
1098}
1099
1100.tippy-content > p {
1101  margin-bottom: 0;
1102  padding: 2px;
1103}
1104
1105
1106/* Tweak 1000px media break to show more text */
1107
1108@media(min-width: 1000px) {
1109  .base-grid,
1110  distill-header,
1111  d-title,
1112  d-abstract,
1113  d-article,
1114  d-appendix,
1115  distill-appendix,
1116  d-byline,
1117  d-footnote-list,
1118  d-citation-list,
1119  distill-footer {
1120    grid-template-columns: [screen-start] 1fr [page-start kicker-start] 80px [middle-start] 50px [text-start kicker-end] 65px 65px 65px 65px 65px 65px 65px 65px [text-end gutter-start] 65px [middle-end] 65px [page-end gutter-end] 1fr [screen-end];
1121    grid-column-gap: 16px;
1122  }
1123
1124  .grid {
1125    grid-column-gap: 16px;
1126  }
1127
1128  d-article {
1129    font-size: 1.06rem;
1130    line-height: 1.7em;
1131  }
1132  figure .caption, .figure .caption, figure figcaption {
1133    font-size: 13px;
1134  }
1135}
1136
1137@media(min-width: 1180px) {
1138  .base-grid,
1139  distill-header,
1140  d-title,
1141  d-abstract,
1142  d-article,
1143  d-appendix,
1144  distill-appendix,
1145  d-byline,
1146  d-footnote-list,
1147  d-citation-list,
1148  distill-footer {
1149    grid-template-columns: [screen-start] 1fr [page-start kicker-start] 60px [middle-start] 60px [text-start kicker-end] 60px 60px 60px 60px 60px 60px 60px 60px [text-end gutter-start] 60px [middle-end] 60px [page-end gutter-end] 1fr [screen-end];
1150    grid-column-gap: 32px;
1151  }
1152
1153  .grid {
1154    grid-column-gap: 32px;
1155  }
1156}
1157
1158
1159/* Get the citation styles for the appendix (not auto-injected on render since
1160   we do our own rendering of the citation appendix) */
1161
1162d-appendix .citation-appendix,
1163.d-appendix .citation-appendix {
1164  font-size: 11px;
1165  line-height: 15px;
1166  border-left: 1px solid rgba(0, 0, 0, 0.1);
1167  padding-left: 18px;
1168  border: 1px solid rgba(0,0,0,0.1);
1169  background: rgba(0, 0, 0, 0.02);
1170  padding: 10px 18px;
1171  border-radius: 3px;
1172  color: rgba(150, 150, 150, 1);
1173  overflow: hidden;
1174  margin-top: -12px;
1175  white-space: pre-wrap;
1176  word-wrap: break-word;
1177}
1178
1179/* Include appendix styles here so they can be overridden */
1180
1181d-appendix {
1182  contain: layout style;
1183  font-size: 0.8em;
1184  line-height: 1.7em;
1185  margin-top: 60px;
1186  margin-bottom: 0;
1187  border-top: 1px solid rgba(0, 0, 0, 0.1);
1188  color: rgba(0,0,0,0.5);
1189  padding-top: 60px;
1190  padding-bottom: 48px;
1191}
1192
1193d-appendix h3 {
1194  grid-column: page-start / text-start;
1195  font-size: 15px;
1196  font-weight: 500;
1197  margin-top: 1em;
1198  margin-bottom: 0;
1199  color: rgba(0,0,0,0.65);
1200}
1201
1202d-appendix h3 + * {
1203  margin-top: 1em;
1204}
1205
1206d-appendix ol {
1207  padding: 0 0 0 15px;
1208}
1209
1210@media (min-width: 768px) {
1211  d-appendix ol {
1212    padding: 0 0 0 30px;
1213    margin-left: -30px;
1214  }
1215}
1216
1217d-appendix li {
1218  margin-bottom: 1em;
1219}
1220
1221d-appendix a {
1222  color: rgba(0, 0, 0, 0.6);
1223}
1224
1225d-appendix > * {
1226  grid-column: text;
1227}
1228
1229d-appendix > d-footnote-list,
1230d-appendix > d-citation-list,
1231d-appendix > distill-appendix {
1232  grid-column: screen;
1233}
1234
1235/* Include footnote styles here so they can be overridden */
1236
1237d-footnote-list {
1238  contain: layout style;
1239}
1240
1241d-footnote-list > * {
1242  grid-column: text;
1243}
1244
1245d-footnote-list a.footnote-backlink {
1246  color: rgba(0,0,0,0.3);
1247  padding-left: 0.5em;
1248}
1249
1250
1251
1252/* Anchor.js */
1253
1254.anchorjs-link {
1255  /*transition: all .25s linear; */
1256  text-decoration: none;
1257  border-bottom: none;
1258}
1259*:hover > .anchorjs-link {
1260  margin-left: -1.125em !important;
1261  text-decoration: none;
1262  border-bottom: none;
1263}
1264
1265/* Social footer */
1266
1267.social_footer {
1268  margin-top: 30px;
1269  margin-bottom: 0;
1270  color: rgba(0,0,0,0.67);
1271}
1272
1273.disqus-comments {
1274  margin-right: 30px;
1275}
1276
1277.disqus-comment-count {
1278  border-bottom: 1px solid rgba(0, 0, 0, 0.4);
1279  cursor: pointer;
1280}
1281
1282#disqus_thread {
1283  margin-top: 30px;
1284}
1285
1286.article-sharing a {
1287  border-bottom: none;
1288  margin-right: 8px;
1289}
1290
1291.article-sharing a:hover {
1292  border-bottom: none;
1293}
1294
1295.sidebar-section.subscribe {
1296  font-size: 12px;
1297  line-height: 1.6em;
1298}
1299
1300.subscribe p {
1301  margin-bottom: 0.5em;
1302}
1303
1304
1305.article-footer .subscribe {
1306  font-size: 15px;
1307  margin-top: 45px;
1308}
1309
1310
1311.sidebar-section.custom {
1312  font-size: 12px;
1313  line-height: 1.6em;
1314}
1315
1316.custom p {
1317  margin-bottom: 0.5em;
1318}
1319
1320/* Styles for listing layout (hide title) */
1321.layout-listing d-title, .layout-listing .d-title {
1322  display: none;
1323}
1324
1325/* Styles for posts lists (not auto-injected) */
1326
1327
1328.posts-with-sidebar {
1329  padding-left: 45px;
1330  padding-right: 45px;
1331}
1332
1333.posts-list .description h2,
1334.posts-list .description p {
1335  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", Arial, sans-serif;
1336}
1337
1338.posts-list .description h2 {
1339  font-weight: 700;
1340  border-bottom: none;
1341  padding-bottom: 0;
1342}
1343
1344.posts-list h2.post-tag {
1345  border-bottom: 1px solid rgba(0, 0, 0, 0.2);
1346  padding-bottom: 12px;
1347}
1348.posts-list {
1349  margin-top: 60px;
1350  margin-bottom: 24px;
1351}
1352
1353.posts-list .post-preview {
1354  text-decoration: none;
1355  overflow: hidden;
1356  display: block;
1357  border-bottom: 1px solid rgba(0, 0, 0, 0.1);
1358  padding: 24px 0;
1359}
1360
1361.post-preview-last {
1362  border-bottom: none !important;
1363}
1364
1365.posts-list .posts-list-caption {
1366  grid-column: screen;
1367  font-weight: 400;
1368}
1369
1370.posts-list .post-preview h2 {
1371  margin: 0 0 6px 0;
1372  line-height: 1.2em;
1373  font-style: normal;
1374  font-size: 24px;
1375}
1376
1377.posts-list .post-preview p {
1378  margin: 0 0 12px 0;
1379  line-height: 1.4em;
1380  font-size: 16px;
1381}
1382
1383.posts-list .post-preview .thumbnail {
1384  box-sizing: border-box;
1385  margin-bottom: 24px;
1386  position: relative;
1387  max-width: 500px;
1388}
1389.posts-list .post-preview img {
1390  width: 100%;
1391  display: block;
1392}
1393
1394.posts-list .metadata {
1395  font-size: 12px;
1396  line-height: 1.4em;
1397  margin-bottom: 18px;
1398}
1399
1400.posts-list .metadata > * {
1401  display: inline-block;
1402}
1403
1404.posts-list .metadata .publishedDate {
1405  margin-right: 2em;
1406}
1407
1408.posts-list .metadata .dt-authors {
1409  display: block;
1410  margin-top: 0.3em;
1411  margin-right: 2em;
1412}
1413
1414.posts-list .dt-tags {
1415  display: block;
1416  line-height: 1em;
1417}
1418
1419.posts-list .dt-tags .dt-tag {
1420  display: inline-block;
1421  color: rgba(0,0,0,0.6);
1422  padding: 0.3em 0.4em;
1423  margin-right: 0.2em;
1424  margin-bottom: 0.4em;
1425  font-size: 60%;
1426  border: 1px solid rgba(0,0,0,0.2);
1427  border-radius: 3px;
1428  text-transform: uppercase;
1429  font-weight: 500;
1430}
1431
1432.posts-list img {
1433  opacity: 1;
1434}
1435
1436.posts-list img[data-src] {
1437  opacity: 0;
1438}
1439
1440.posts-more {
1441  clear: both;
1442}
1443
1444
1445.posts-sidebar {
1446  font-size: 16px;
1447}
1448
1449.posts-sidebar h3 {
1450  font-size: 16px;
1451  margin-top: 0;
1452  margin-bottom: 0.5em;
1453  font-weight: 400;
1454  text-transform: uppercase;
1455}
1456
1457.sidebar-section {
1458  margin-bottom: 30px;
1459}
1460
1461.categories ul {
1462  list-style-type: none;
1463  margin: 0;
1464  padding: 0;
1465}
1466
1467.categories li {
1468  color: rgba(0, 0, 0, 0.8);
1469  margin-bottom: 0;
1470}
1471
1472.categories li>a {
1473  border-bottom: none;
1474}
1475
1476.categories li>a:hover {
1477  border-bottom: 1px solid rgba(0, 0, 0, 0.4);
1478}
1479
1480.categories .active {
1481  font-weight: 600;
1482}
1483
1484.categories .category-count {
1485  color: rgba(0, 0, 0, 0.4);
1486}
1487
1488
1489@media(min-width: 768px) {
1490  .posts-list .post-preview h2 {
1491    font-size: 26px;
1492  }
1493  .posts-list .post-preview .thumbnail {
1494    float: right;
1495    width: 30%;
1496    margin-bottom: 0;
1497  }
1498  .posts-list .post-preview .description {
1499    float: left;
1500    width: 45%;
1501  }
1502  .posts-list .post-preview .metadata {
1503    float: left;
1504    width: 20%;
1505    margin-top: 8px;
1506  }
1507  .posts-list .post-preview p {
1508    margin: 0 0 12px 0;
1509    line-height: 1.5em;
1510    font-size: 16px;
1511  }
1512  .posts-with-sidebar .posts-list {
1513    float: left;
1514    width: 75%;
1515  }
1516  .posts-with-sidebar .posts-sidebar {
1517    float: right;
1518    width: 20%;
1519    margin-top: 60px;
1520    padding-top: 24px;
1521    padding-bottom: 24px;
1522  }
1523}
1524
1525
1526/* Improve display for browsers without grid (IE/Edge <= 15) */
1527
1528.downlevel {
1529  line-height: 1.6em;
1530  font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", Arial, sans-serif;
1531  margin: 0;
1532}
1533
1534.downlevel .d-title {
1535  padding-top: 6rem;
1536  padding-bottom: 1.5rem;
1537}
1538
1539.downlevel .d-title h1 {
1540  font-size: 50px;
1541  font-weight: 700;
1542  line-height: 1.1em;
1543  margin: 0 0 0.5rem;
1544}
1545
1546.downlevel .d-title p {
1547  font-weight: 300;
1548  font-size: 1.2rem;
1549  line-height: 1.55em;
1550  margin-top: 0;
1551}
1552
1553.downlevel .d-byline {
1554  padding-top: 0.8em;
1555  padding-bottom: 0.8em;
1556  font-size: 0.8rem;
1557  line-height: 1.8em;
1558}
1559
1560.downlevel .section-separator {
1561  border: none;
1562  border-top: 1px solid rgba(0, 0, 0, 0.1);
1563}
1564
1565.downlevel .d-article {
1566  font-size: 1.06rem;
1567  line-height: 1.7em;
1568  padding-top: 1rem;
1569  padding-bottom: 2rem;
1570}
1571
1572
1573.downlevel .d-appendix {
1574  padding-left: 0;
1575  padding-right: 0;
1576  max-width: none;
1577  font-size: 0.8em;
1578  line-height: 1.7em;
1579  margin-bottom: 0;
1580  color: rgba(0,0,0,0.5);
1581  padding-top: 40px;
1582  padding-bottom: 48px;
1583}
1584
1585.downlevel .footnotes ol {
1586  padding-left: 13px;
1587}
1588
1589.downlevel .base-grid,
1590.downlevel .distill-header,
1591.downlevel .d-title,
1592.downlevel .d-abstract,
1593.downlevel .d-article,
1594.downlevel .d-appendix,
1595.downlevel .distill-appendix,
1596.downlevel .d-byline,
1597.downlevel .d-footnote-list,
1598.downlevel .d-citation-list,
1599.downlevel .distill-footer,
1600.downlevel .appendix-bottom,
1601.downlevel .posts-container {
1602  padding-left: 40px;
1603  padding-right: 40px;
1604}
1605
1606@media(min-width: 768px) {
1607  .downlevel .base-grid,
1608  .downlevel .distill-header,
1609  .downlevel .d-title,
1610  .downlevel .d-abstract,
1611  .downlevel .d-article,
1612  .downlevel .d-appendix,
1613  .downlevel .distill-appendix,
1614  .downlevel .d-byline,
1615  .downlevel .d-footnote-list,
1616  .downlevel .d-citation-list,
1617  .downlevel .distill-footer,
1618  .downlevel .appendix-bottom,
1619  .downlevel .posts-container {
1620  padding-left: 150px;
1621  padding-right: 150px;
1622  max-width: 900px;
1623}
1624}
1625
1626.downlevel pre code {
1627  display: block;
1628  border-left: 2px solid rgba(0, 0, 0, .1);
1629  padding: 0 0 0 20px;
1630  font-size: 14px;
1631}
1632
1633.downlevel code, .downlevel pre {
1634  color: black;
1635  background: none;
1636  font-family: Consolas, Monaco, 'Andale Mono', 'Ubuntu Mono', monospace;
1637  text-align: left;
1638  white-space: pre;
1639  word-spacing: normal;
1640  word-break: normal;
1641  word-wrap: normal;
1642  line-height: 1.5;
1643
1644  -moz-tab-size: 4;
1645  -o-tab-size: 4;
1646  tab-size: 4;
1647
1648  -webkit-hyphens: none;
1649  -moz-hyphens: none;
1650  -ms-hyphens: none;
1651  hyphens: none;
1652}
1653
1654.downlevel .posts-list .post-preview {
1655  color: inherit;
1656}
1657
1658
1659
1660</style>
1661
1662<script type="application/javascript">
1663
1664function is_downlevel_browser() {
1665  if (bowser.isUnsupportedBrowser({ msie: "12", msedge: "16"},
1666                                 window.navigator.userAgent)) {
1667    return true;
1668  } else {
1669    return window.load_distill_framework === undefined;
1670  }
1671}
1672
1673// show body when load is complete
1674function on_load_complete() {
1675
1676  // add anchors
1677  if (window.anchors) {
1678    window.anchors.options.placement = 'left';
1679    window.anchors.add('d-article > h2, d-article > h3, d-article > h4, d-article > h5');
1680  }
1681
1682
1683  // set body to visible
1684  document.body.style.visibility = 'visible';
1685
1686  // force redraw for leaflet widgets
1687  if (window.HTMLWidgets) {
1688    var maps = window.HTMLWidgets.findAll(".leaflet");
1689    $.each(maps, function(i, el) {
1690      var map = this.getMap();
1691      map.invalidateSize();
1692      map.eachLayer(function(layer) {
1693        if (layer instanceof L.TileLayer)
1694          layer.redraw();
1695      });
1696    });
1697  }
1698
1699  // trigger 'shown' so htmlwidgets resize
1700  $('d-article').trigger('shown');
1701}
1702
1703function init_distill() {
1704
1705  init_common();
1706
1707  // create front matter
1708  var front_matter = $('<d-front-matter></d-front-matter>');
1709  $('#distill-front-matter').wrap(front_matter);
1710
1711  // create d-title
1712  $('.d-title').changeElementType('d-title');
1713
1714  // create d-byline
1715  var byline = $('<d-byline></d-byline>');
1716  $('.d-byline').replaceWith(byline);
1717
1718  // create d-article
1719  var article = $('<d-article></d-article>');
1720  $('.d-article').wrap(article).children().unwrap();
1721
1722  // move posts container into article
1723  $('.posts-container').appendTo($('d-article'));
1724
1725  // create d-appendix
1726  $('.d-appendix').changeElementType('d-appendix');
1727
1728  // flag indicating that we have appendix items
1729  var appendix = $('.appendix-bottom').children('h3').length > 0;
1730
1731  // replace footnotes with <d-footnote>
1732  $('.footnote-ref').each(function(i, val) {
1733    appendix = true;
1734    var href = $(this).attr('href');
1735    var id = href.replace('#', '');
1736    var fn = $('#' + id);
1737    var fn_p = $('#' + id + '>p');
1738    fn_p.find('.footnote-back').remove();
1739    var text = fn_p.html();
1740    var dtfn = $('<d-footnote></d-footnote>');
1741    dtfn.html(text);
1742    $(this).replaceWith(dtfn);
1743  });
1744  // remove footnotes
1745  $('.footnotes').remove();
1746
1747  // move refs into #references-listing
1748  $('#references-listing').replaceWith($('#refs'));
1749
1750  $('h1.appendix, h2.appendix').each(function(i, val) {
1751    $(this).changeElementType('h3');
1752  });
1753  $('h3.appendix').each(function(i, val) {
1754    var id = $(this).attr('id');
1755    $('.d-contents a[href="#' + id + '"]').parent().remove();
1756    appendix = true;
1757    $(this).nextUntil($('h1, h2, h3')).addBack().appendTo($('d-appendix'));
1758  });
1759
1760  // show d-appendix if we have appendix content
1761  $("d-appendix").css('display', appendix ? 'grid' : 'none');
1762
1763  // localize layout chunks to just output
1764  $('.layout-chunk').each(function(i, val) {
1765
1766    // capture layout
1767    var layout = $(this).attr('data-layout');
1768
1769    // apply layout to markdown level block elements
1770    var elements = $(this).children().not('details, div.sourceCode, pre, script');
1771    elements.each(function(i, el) {
1772      var layout_div = $('<div class="' + layout + '"></div>');
1773      if (layout_div.hasClass('shaded')) {
1774        var shaded_content = $('<div class="shaded-content"></div>');
1775        $(this).wrap(shaded_content);
1776        $(this).parent().wrap(layout_div);
1777      } else {
1778        $(this).wrap(layout_div);
1779      }
1780    });
1781
1782
1783    // unwrap the layout-chunk div
1784    $(this).children().unwrap();
1785  });
1786
1787  // remove code block used to force  highlighting css
1788  $('.distill-force-highlighting-css').parent().remove();
1789
1790  // remove empty line numbers inserted by pandoc when using a
1791  // custom syntax highlighting theme
1792  $('code.sourceCode a:empty').remove();
1793
1794  // load distill framework
1795  load_distill_framework();
1796
1797  // wait for window.distillRunlevel == 4 to do post processing
1798  function distill_post_process() {
1799
1800    if (!window.distillRunlevel || window.distillRunlevel < 4)
1801      return;
1802
1803    // hide author/affiliations entirely if we have no authors
1804    var front_matter = JSON.parse($("#distill-front-matter").html());
1805    var have_authors = front_matter.authors && front_matter.authors.length > 0;
1806    if (!have_authors)
1807      $('d-byline').addClass('hidden');
1808
1809    // article with toc class
1810    $('.d-contents').parent().addClass('d-article-with-toc');
1811
1812    // strip links that point to #
1813    $('.authors-affiliations').find('a[href="#"]').removeAttr('href');
1814
1815    // add orcid ids
1816    $('.authors-affiliations').find('.author').each(function(i, el) {
1817      var orcid_id = front_matter.authors[i].orcidID;
1818      if (orcid_id) {
1819        var a = $('<a></a>');
1820        a.attr('href', 'https://orcid.org/' + orcid_id);
1821        var img = $('<img></img>');
1822        img.addClass('orcid-id');
1823        img.attr('alt', 'ORCID ID');
1824        img.attr('src','data:image/png;base64,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');
1825        a.append(img);
1826        $(this).append(a);
1827      }
1828    });
1829
1830    // hide elements of author/affiliations grid that have no value
1831    function hide_byline_column(caption) {
1832      $('d-byline').find('h3:contains("' + caption + '")').parent().css('visibility', 'hidden');
1833    }
1834
1835    // affiliations
1836    var have_affiliations = false;
1837    for (var i = 0; i<front_matter.authors.length; ++i) {
1838      var author = front_matter.authors[i];
1839      if (author.affiliation !== "&nbsp;") {
1840        have_affiliations = true;
1841        break;
1842      }
1843    }
1844    if (!have_affiliations)
1845      $('d-byline').find('h3:contains("Affiliations")').css('visibility', 'hidden');
1846
1847    // published date
1848    if (!front_matter.publishedDate)
1849      hide_byline_column("Published");
1850
1851    // document object identifier
1852    var doi = $('d-byline').find('h3:contains("DOI")');
1853    var doi_p = doi.next().empty();
1854    if (!front_matter.doi) {
1855      // if we have a citation and valid citationText then link to that
1856      if ($('#citation').length > 0 && front_matter.citationText) {
1857        doi.html('Citation');
1858        $('<a href="#citation"></a>')
1859          .text(front_matter.citationText)
1860          .appendTo(doi_p);
1861      } else {
1862        hide_byline_column("DOI");
1863      }
1864    } else {
1865      $('<a></a>')
1866         .attr('href', "https://doi.org/" + front_matter.doi)
1867         .html(front_matter.doi)
1868         .appendTo(doi_p);
1869    }
1870
1871     // change plural form of authors/affiliations
1872    if (front_matter.authors.length === 1) {
1873      var grid = $('.authors-affiliations');
1874      grid.children('h3:contains("Authors")').text('Author');
1875      grid.children('h3:contains("Affiliations")').text('Affiliation');
1876    }
1877
1878    // remove d-appendix and d-footnote-list local styles
1879    $('d-appendix > style:first-child').remove();
1880    $('d-footnote-list > style:first-child').remove();
1881
1882    // move appendix-bottom entries to the bottom
1883    $('.appendix-bottom').appendTo('d-appendix').children().unwrap();
1884    $('.appendix-bottom').remove();
1885
1886    // hoverable references
1887    $('span.citation[data-cites]').each(function() {
1888      const citeChild = $(this).children()[0]
1889      // Do not process if @xyz has been used without escaping and without bibliography activated
1890      // https://github.com/rstudio/distill/issues/466
1891      if (citeChild === undefined) return true
1892
1893      if (citeChild.nodeName == "D-FOOTNOTE") {
1894        var fn = citeChild
1895        $(this).html(fn.shadowRoot.querySelector("sup"))
1896        $(this).id = fn.id
1897        fn.remove()
1898      }
1899      var refs = $(this).attr('data-cites').split(" ");
1900      var refHtml = refs.map(function(ref) {
1901        // Could use CSS.escape too here, we insure backward compatibility in navigator
1902        return "<p>" + $('div[id="ref-' + ref + '"]').html() + "</p>";
1903      }).join("\n");
1904      window.tippy(this, {
1905        allowHTML: true,
1906        content: refHtml,
1907        maxWidth: 500,
1908        interactive: true,
1909        interactiveBorder: 10,
1910        theme: 'light-border',
1911        placement: 'bottom-start'
1912      });
1913    });
1914
1915    // fix footnotes in tables (#411)
1916    // replacing broken distill.pub feature
1917    $('table d-footnote').each(function() {
1918      // we replace internal showAtNode methode which is triggered when hovering a footnote
1919      this.hoverBox.showAtNode = function(node) {
1920        // ported from https://github.com/distillpub/template/pull/105/files
1921        calcOffset = function(elem) {
1922            let x = elem.offsetLeft;
1923            let y = elem.offsetTop;
1924            // Traverse upwards until an `absolute` element is found or `elem`
1925            // becomes null.
1926            while (elem = elem.offsetParent && elem.style.position != 'absolute') {
1927                x += elem.offsetLeft;
1928                y += elem.offsetTop;
1929            }
1930
1931            return { left: x, top: y };
1932        }
1933        // https://developer.mozilla.org/en-US/docs/Web/API/HTMLElement/offsetTop
1934        const bbox = node.getBoundingClientRect();
1935        const offset = calcOffset(node);
1936        this.show([offset.left + bbox.width, offset.top + bbox.height]);
1937      }
1938    })
1939
1940    // clear polling timer
1941    clearInterval(tid);
1942
1943    // show body now that everything is ready
1944    on_load_complete();
1945  }
1946
1947  var tid = setInterval(distill_post_process, 50);
1948  distill_post_process();
1949
1950}
1951
1952function init_downlevel() {
1953
1954  init_common();
1955
1956   // insert hr after d-title
1957  $('.d-title').after($('<hr class="section-separator"/>'));
1958
1959  // check if we have authors
1960  var front_matter = JSON.parse($("#distill-front-matter").html());
1961  var have_authors = front_matter.authors && front_matter.authors.length > 0;
1962
1963  // manage byline/border
1964  if (!have_authors)
1965    $('.d-byline').remove();
1966  $('.d-byline').after($('<hr class="section-separator"/>'));
1967  $('.d-byline a').remove();
1968
1969  // remove toc
1970  $('.d-contents').remove();
1971
1972  // move appendix elements
1973  $('h1.appendix, h2.appendix').each(function(i, val) {
1974    $(this).changeElementType('h3');
1975  });
1976  $('h3.appendix').each(function(i, val) {
1977    $(this).nextUntil($('h1, h2, h3')).addBack().appendTo($('.d-appendix'));
1978  });
1979
1980
1981  // inject headers into references and footnotes
1982  var refs_header = $('<h3></h3>');
1983  refs_header.text('References');
1984  $('#refs').prepend(refs_header);
1985
1986  var footnotes_header = $('<h3></h3');
1987  footnotes_header.text('Footnotes');
1988  $('.footnotes').children('hr').first().replaceWith(footnotes_header);
1989
1990  // move appendix-bottom entries to the bottom
1991  $('.appendix-bottom').appendTo('.d-appendix').children().unwrap();
1992  $('.appendix-bottom').remove();
1993
1994  // remove appendix if it's empty
1995  if ($('.d-appendix').children().length === 0)
1996    $('.d-appendix').remove();
1997
1998  // prepend separator above appendix
1999  $('.d-appendix').before($('<hr class="section-separator" style="clear: both"/>'));
2000
2001  // trim code
2002  $('pre>code').each(function(i, val) {
2003    $(this).html($.trim($(this).html()));
2004  });
2005
2006  // move posts-container right before article
2007  $('.posts-container').insertBefore($('.d-article'));
2008
2009  $('body').addClass('downlevel');
2010
2011  on_load_complete();
2012}
2013
2014
2015function init_common() {
2016
2017  // jquery plugin to change element types
2018  (function($) {
2019    $.fn.changeElementType = function(newType) {
2020      var attrs = {};
2021
2022      $.each(this[0].attributes, function(idx, attr) {
2023        attrs[attr.nodeName] = attr.nodeValue;
2024      });
2025
2026      this.replaceWith(function() {
2027        return $("<" + newType + "/>", attrs).append($(this).contents());
2028      });
2029    };
2030  })(jQuery);
2031
2032  // prevent underline for linked images
2033  $('a > img').parent().css({'border-bottom' : 'none'});
2034
2035  // mark non-body figures created by knitr chunks as 100% width
2036  $('.layout-chunk').each(function(i, val) {
2037    var figures = $(this).find('img, .html-widget');
2038    // ignore leaflet img layers (#106)
2039    figures = figures.filter(':not(img[class*="leaflet"])')
2040    if ($(this).attr('data-layout') !== "l-body") {
2041      figures.css('width', '100%');
2042    } else {
2043      figures.css('max-width', '100%');
2044      figures.filter("[width]").each(function(i, val) {
2045        var fig = $(this);
2046        fig.css('width', fig.attr('width') + 'px');
2047      });
2048
2049    }
2050  });
2051
2052  // auto-append index.html to post-preview links in file: protocol
2053  // and in rstudio ide preview
2054  $('.post-preview').each(function(i, val) {
2055    if (window.location.protocol === "file:")
2056      $(this).attr('href', $(this).attr('href') + "index.html");
2057  });
2058
2059  // get rid of index.html references in header
2060  if (window.location.protocol !== "file:") {
2061    $('.distill-site-header a[href]').each(function(i,val) {
2062      $(this).attr('href', $(this).attr('href').replace(/^index[.]html/, "./"));
2063    });
2064  }
2065
2066  // add class to pandoc style tables
2067  $('tr.header').parent('thead').parent('table').addClass('pandoc-table');
2068  $('.kable-table').children('table').addClass('pandoc-table');
2069
2070  // add figcaption style to table captions
2071  $('caption').parent('table').addClass("figcaption");
2072
2073  // initialize posts list
2074  if (window.init_posts_list)
2075    window.init_posts_list();
2076
2077  // implmement disqus comment link
2078  $('.disqus-comment-count').click(function() {
2079    window.headroom_prevent_pin = true;
2080    $('#disqus_thread').toggleClass('hidden');
2081    if (!$('#disqus_thread').hasClass('hidden')) {
2082      var offset = $(this).offset();
2083      $(window).resize();
2084      $('html, body').animate({
2085        scrollTop: offset.top - 35
2086      });
2087    }
2088  });
2089}
2090
2091document.addEventListener('DOMContentLoaded', function() {
2092  if (is_downlevel_browser())
2093    init_downlevel();
2094  else
2095    window.addEventListener('WebComponentsReady', init_distill);
2096});
2097
2098</script>
2098
2099
2100<style type="text/css">
2101/* base variables */
2102
2103/* Edit the CSS properties in this file to create a custom
2104   Distill theme. Only edit values in the right column
2105   for each row; values shown are the CSS defaults.
2106   To return any property to the default,
2107   you may set its value to: unset
2108   All rows must end with a semi-colon.                      */
2109
2110/* Optional: embed custom fonts here with `@import`          */
2111/* This must remain at the top of this file.                 */
2112
2113
2114
2115html {
2116  /*-- Main font sizes --*/
2117  --title-size:      50px;
2118  --body-size:       1.06rem;
2119  --code-size:       14px;
2120  --aside-size:      12px;
2121  --fig-cap-size:    13px;
2122  /*-- Main font colors --*/
2123  --title-color:     #000000;
2124  --header-color:    rgba(0, 0, 0, 0.8);
2125  --body-color:      rgba(0, 0, 0, 0.8);
2126  --aside-color:     rgba(0, 0, 0, 0.6);
2127  --fig-cap-color:   rgba(0, 0, 0, 0.6);
2128  /*-- Specify custom fonts ~~~ must be imported above   --*/
2129  --heading-font:    sans-serif;
2130  --mono-font:       monospace;
2131  --body-font:       sans-serif;
2132  --navbar-font:     sans-serif;  /* websites + blogs only */
2133}
2134
2135/*-- ARTICLE METADATA --*/
2136d-byline {
2137  --heading-size:    0.6rem;
2138  --heading-color:   rgba(0, 0, 0, 0.5);
2139  --body-size:       0.8rem;
2140  --body-color:      rgba(0, 0, 0, 0.8);
2141}
2142
2143/*-- ARTICLE TABLE OF CONTENTS --*/
2144.d-contents {
2145  --heading-size:    18px;
2146  --contents-size:   13px;
2147}
2148
2149/*-- ARTICLE APPENDIX --*/
2150d-appendix {
2151  --heading-size:    15px;
2152  --heading-color:   rgba(0, 0, 0, 0.65);
2153  --text-size:       0.8em;
2154  --text-color:      rgba(0, 0, 0, 0.5);
2155}
2156
2157/*-- WEBSITE HEADER + FOOTER --*/
2158/* These properties only apply to Distill sites and blogs  */
2159
2160.distill-site-header {
2161  --title-size:       18px;
2162  --text-color:       rgba(255, 255, 255, 0.8);
2163  --text-size:        15px;
2164  --hover-color:      white;
2165  --bkgd-color:       #0F2E3D;
2166}
2167
2168.distill-site-footer {
2169  --text-color:       rgba(255, 255, 255, 0.8);
2170  --text-size:        15px;
2171  --hover-color:      white;
2172  --bkgd-color:       #0F2E3D;
2173}
2174
2175/*-- Additional custom styles --*/
2176/* Add any additional CSS rules below                      */
2177</style>
2178<style type="text/css">/* base variables */
2179
2180/* Edit the CSS properties in this file to create a custom
2181   Distill theme. Only edit values in the right column
2182   for each row; values shown are the CSS defaults.
2183   To return any property to the default,
2184   you may set its value to: unset
2185   All rows must end with a semi-colon.                      */
2186
2187/* Optional: embed custom fonts here with `@import`          */
2188/* This must remain at the top of this file.                 */
2189@import url('https://fonts.googleapis.com/css?family=Lato:400,400i,700&display=swap');
2190@import url('https://fonts.googleapis.com/css2?family=Merriweather');
2191@import url('https://fonts.googleapis.com/css2?family=Lora');
2192@import url('https://fonts.googleapis.com/css2?family=Play');
2193@import url('https://fonts.googleapis.com/css2?family=PT+Sans');
2194@import url('https://fonts.googleapis.com/css2?family=Roboto+Condensed');
2195@import url('https://fonts.googleapis.com/css2?family=Nunito');
2196
2197html {
2198  /*-- Main font sizes --*/
2199  --title-size:      32px;
2200  --body-size:       1.06rem;
2201  --code-size:       14px;
2202  --aside-size:      13px;
2203  --fig-cap-size:    13px;
2204  /*-- Main font colors --*/
2205  --title-color:     #000000;
2206  --header-color:    rgba(0, 0, 0, 0.8);
2207  --body-color:      rgba(0, 0, 0, 0.8);
2208  --aside-color:     rgba(0, 0, 0, 0.6);
2209  --fig-cap-color:   rgba(0, 0, 0, 0.6);
2210  /*-- Specify custom fonts ~~~ must be imported above   --*/
2211  --heading-font:   'Merriweather', serif;
2212  --mono-font:       monospace;
2213  --body-font:       'Nunito', sans-serif;
2214  --navbar-font:     'Play', sans-serif;  /* websites + blogs only */
2215}
2216
2217/*-- ARTICLE METADATA --*/
2218d-byline {
2219  --heading-size:    0.6rem;
2220  --heading-color:   rgba(0, 0, 0, 0.5);
2221  --body-size:       0.9rem;
2222  --body-color:      rgba(0, 0, 0, 0.8);
2223  --font-weight:     400;
2224}
2225
2226/*-- ARTICLE TABLE OF CONTENTS --*/
2227.d-contents {
2228  --heading-size:    18px;
2229  --contents-size:   14px;
2230}
2231
2232/*-- ARTICLE APPENDIX --*/
2233d-appendix {
2234  --heading-size:    15px;
2235  --heading-color:   rgba(0, 0, 0, 0.8);
2236  --text-size:       0.9em;
2237  --text-color:      rgba(0, 0, 0, 0.8);
2238}
2239
2240/*-- WEBSITE HEADER + FOOTER --*/
2241/* These properties only apply to Distill sites and blogs  */
2242
2243.distill-site-footer {
2244  --text-color:       #431c5d;
2245  --text-size:        15px;
2246  --hover-color:      #e05915;
2247  --bkgd-color:       #bccbde;
2248}
2249
2250.distill-site-header {
2251  --hover-color:      #e05915;
2252  --bkgd-color:       #bccbde;
2253}
2254
2255.distill-site-header .title{
2256  color:#431c5d;
2257  font-family: 'Merriweather';
2258  font-size: 24px;
2259  font-style: normal;
2260  letter-spacing: 1.3px;
2261  font-weight: 200;
2262}
2263
2264.distill-site-header .logo img{
2265  max-height: 35px;
2266  margin-bottom: -10px;
2267  padding-top: 3px;
2268}
2269
2270html, body, p {
2271  font-family: 'Nunito', sans-serif;
2272  font-weight: 200;
2273  line-height: 1.4; 
2274  font-size: 0.95em;
2275  letter-spacing: 0.2px;
2276  color: #383838;
2277  font-style: normal;
2278}
2279
2280.distill-site-nav {
2281  color: #431c5d;
2282  font-family: 'Lato', sans-serif;
2283  font-size: 16px;
2284}
2285
2286.distill-site-nav a:hover {
2287  color: #e05915;
2288}
2289
2290.distill-site-nav a {
2291  color:#431c5d;
2292  text-decoration: none;
2293}
2294
2295
2296.posts-list .metadata .publishedDate {
2297    color: #e05915;
2298}
2299
2300 .posts-list .post-preview h2,
2301 .posts-list .description h2 {
2302  font-family: 'Merriweather';
2303  line-height: 1.3; 
2304  font-size: 1.1em;
2305  font-style: bold;
2306  letter-spacing: 1.3px;
2307  font-weight: 600;
2308}
2309
2310h2, h1, d-title h2, d-title h1, title {
2311  font-family: 'Merriweather';
2312  line-height: 1.3; 
2313  font-size: 1.0em;
2314  font-style: normal;
2315  letter-spacing: 1.3px;
2316  font-weight: 600;
2317}
2318
2319code, code.r{
2320  font-family: 'Consolas', "Roboto Mono", "Ubuntu Mono", monospace;
2321  color: #431c5d;
2322  line-height: 1.2; 
2323  font-weight: 400;
2324  font-size: 1em;
2325  padding: 1px 0px;
2326}
2327
2328d-article div.sourceCode code, 
2329d-article pre code{
2330  font-family: 'Consolas', "Roboto Mono", "Ubuntu Mono", monospace;
2331  line-height: 1.2; 
2332  font-weight: 400;
2333  font-size: 1.1em;
2334}
2335
2336d-article div.sourceCode pre {
2337  border: 1px solid rgba(0,0,0,0.1);
2338  background: rgba(0, 0, 0, 0.02);
2339  padding: 10px 18px;
2340  border-radius: 3px;
2341}
2342
2343d-article a {
2344    border-bottom: 1px solid rgba(67, 28, 93, 0.4);
2345    text-decoration: none;
2346}
2347
2348.posts-list .dt-tags .dt-tag, .dt-tags .dt-tag {
2349  padding-top: 0.1em;
2350  padding-right: 0.3em;
2351  padding-bottom: 0.2em;
2352  padding-left: 0.3em;
2353  border-radius: 5px;
2354  font-size: 85%;
2355  text-transform: lowercase;
2356  background-color: #e6e9f0;
2357  font-weight: 300;
2358}
2359
2360element, d-article details{
2361	font-size: 14px;
2362	color: #e05915;
2363}
2364
2365td {  /* Table  */
2366  font-size: 14px;
2367  font-family: "Roboto Condensed", "Nunito", sans-serif;
2368}
2369
2370th {  /* Table Header */
2371  font-size: 14px;
2372  font-weight: bold;
2373  font-family: "Roboto Condensed", "Nunito", sans-serif;
2374}
2375
2376div.datatables {
2377 height: auto !important;
2378}
2379
2380table.dataTable tbody th, 
2381table.dataTable tbody td { 
2382  padding-top: 2px;
2383	padding-bottom: 2px;
2384	padding-left: 5px;
2385	font-size: 14px; 
2386	line-height: 1.3em;
2387}
2388
2389.dataTables_wrapper .dataTables_length, 
2390.dataTables_wrapper .dataTables_filter, 
2391.dataTables_wrapper .dataTables_info, 
2392.dataTables_wrapper .dataTables_processing, 
2393.dataTables_wrapper .dataTables_paginate {
2394	color: #333;
2395	font-size: 14px;
2396}</style>
2397<style type="text/css">
2398/* base style */
2399
2400/* FONT FAMILIES */
2401
2402:root {
2403  --heading-default: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", Arial, sans-serif;
2404  --mono-default: Consolas, Monaco, 'Andale Mono', 'Ubuntu Mono', monospace;
2405  --body-default: -apple-system, BlinkMacSystemFont, "Segoe UI", Roboto, Oxygen, Ubuntu, Cantarell, "Fira Sans", "Droid Sans", "Helvetica Neue", Arial, sans-serif;
2406}
2407
2408body,
2409.posts-list .post-preview p,
2410.posts-list .description p {
2411  font-family: var(--body-font), var(--body-default);
2412}
2413
2414h1, h2, h3, h4, h5, h6,
2415.posts-list .post-preview h2,
2416.posts-list .description h2 {
2417  font-family: var(--heading-font), var(--heading-default);
2418}
2419
2420d-article div.sourceCode code,
2421d-article pre code {
2422  font-family: var(--mono-font), var(--mono-default);
2423}
2424
2425
2426/*-- TITLE --*/
2427d-title h1,
2428.posts-list > h1 {
2429  color: var(--title-color, black);
2430}
2431
2432d-title h1 {
2433  font-size: var(--title-size, 50px);
2434}
2435
2436/*-- HEADERS --*/
2437d-article h1,
2438d-article h2,
2439d-article h3,
2440d-article h4,
2441d-article h5,
2442d-article h6 {
2443  color: var(--header-color, rgba(0, 0, 0, 0.8));
2444}
2445
2446/*-- BODY --*/
2447d-article > p,  /* only text inside of <p> tags */
2448d-article > ul, /* lists */
2449d-article > ol {
2450  color: var(--body-color, rgba(0, 0, 0, 0.8));
2451  font-size: var(--body-size, 1.06rem);
2452}
2453
2454
2455/*-- CODE --*/
2456d-article div.sourceCode code,
2457d-article pre code {
2458  font-size: var(--code-size, 14px);
2459}
2460
2461/*-- ASIDE --*/
2462d-article aside {
2463  font-size: var(--aside-size, 12px);
2464  color: var(--aside-color, rgba(0, 0, 0, 0.6));
2465}
2466
2467/*-- FIGURE CAPTIONS --*/
2468figure .caption,
2469figure figcaption,
2470.figure .caption {
2471  font-size: var(--fig-cap-size, 13px);
2472  color: var(--fig-cap-color, rgba(0, 0, 0, 0.6));
2473}
2474
2475/*-- METADATA --*/
2476d-byline h3 {
2477  font-size: var(--heading-size, 0.6rem);
2478  color: var(--heading-color, rgba(0, 0, 0, 0.5));
2479}
2480
2481d-byline {
2482  font-size: var(--body-size, 0.8rem);
2483  color: var(--body-color, rgba(0, 0, 0, 0.8));
2484}
2485
2486d-byline a,
2487d-article d-byline a {
2488  color: var(--body-color, rgba(0, 0, 0, 0.8));
2489}
2490
2491/*-- TABLE OF CONTENTS --*/
2492.d-contents nav h3 {
2493  font-size: var(--heading-size, 18px);
2494}
2495
2496.d-contents nav a {
2497  font-size: var(--contents-size, 13px);
2498}
2499
2500/*-- APPENDIX --*/
2501d-appendix h3 {
2502  font-size: var(--heading-size, 15px);
2503  color: var(--heading-color, rgba(0, 0, 0, 0.65));
2504}
2505
2506d-appendix {
2507  font-size: var(--text-size, 0.8em);
2508  color: var(--text-color, rgba(0, 0, 0, 0.5));
2509}
2510
2511d-appendix d-footnote-list a.footnote-backlink {
2512  color: var(--text-color, rgba(0, 0, 0, 0.5));
2513}
2514
2515/*-- WEBSITE HEADER + FOOTER --*/
2516.distill-site-header .title {
2517  font-size: var(--title-size, 18px);
2518  font-family: var(--navbar-font), var(--heading-default);
2519}
2520
2521.distill-site-header a,
2522.nav-dropdown .nav-dropbtn {
2523  font-family: var(--navbar-font), var(--heading-default);
2524}
2525
2526.nav-dropdown .nav-dropbtn {
2527  color: var(--text-color, rgba(255, 255, 255, 0.8));
2528  font-size: var(--text-size, 15px);
2529}
2530
2531.distill-site-header a:hover,
2532.nav-dropdown:hover .nav-dropbtn {
2533  color: var(--hover-color, white);
2534}
2535
2536.distill-site-header {
2537  font-size: var(--text-size, 15px);
2538  color: var(--text-color, rgba(255, 255, 255, 0.8));
2539  background-color: var(--bkgd-color, #0F2E3D);
2540}
2541
2542.distill-site-footer {
2543  font-size: var(--text-size, 15px);
2544  color: var(--text-color, rgba(255, 255, 255, 0.8));
2545  background-color: var(--bkgd-color, #0F2E3D);
2546}
2547
2548.distill-site-footer a:hover {
2549  color: var(--hover-color, white);
2550}</style>
2551<!--/radix_placeholder_distill-->
2552  
2552<script src="../../site_libs/htmlwidgets-1.5.3/htmlwidgets.js"></script>
2552
2553  
2553<script src="../../site_libs/jquery-1.12.4/jquery.min.js"></script>
2553
2554  <link href="../../site_libs/datatables-css-0.0.0/datatables-crosstalk.css" rel="stylesheet" />
2555  
2555<script src="../../site_libs/datatables-binding-0.17/datatables.js"></script>
2555
2556  <link href="../../site_libs/dt-core-1.10.20/css/jquery.dataTables.min.css" rel="stylesheet" />
2557  <link href="../../site_libs/dt-core-1.10.20/css/jquery.dataTables.extra.css" rel="stylesheet" />
2558  
2558<script src="../../site_libs/dt-core-1.10.20/js/jquery.dataTables.min.js"></script>
2558
2559  <link href="../../site_libs/crosstalk-1.1.0.1/css/crosstalk.css" rel="stylesheet" />
2560  
2560<script src="../../site_libs/crosstalk-1.1.0.1/js/crosstalk.min.js"></script>
2560
2561  
2561<script src="../../site_libs/jszip-1.10.20/jszip.min.js"></script>
2561
2562  <link href="../../site_libs/dt-ext-buttons-1.10.20/css/buttons.dataTables.min.css" rel="stylesheet" />
2563  
2563<script src="../../site_libs/dt-ext-buttons-1.10.20/js/dataTables.buttons.min.js"></script>
2563
2564  
2564<script src="../../site_libs/dt-ext-buttons-1.10.20/js/buttons.flash.min.js"></script>
2564
2565  
2565<script src="../../site_libs/dt-ext-buttons-1.10.20/js/buttons.html5.min.js"></script>
2565
2566  
2566<script src="../../site_libs/dt-ext-buttons-1.10.20/js/buttons.colVis.min.js"></script>
2566
2567  
2567<script src="../../site_libs/dt-ext-buttons-1.10.20/js/buttons.print.min.js"></script>
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2597{"title":"Tagging the Scientific Abstracts with Wikidata Items","description":"Here I am trying to build a script that process the short scientific texts (abstracts) and finds Wikidata items corresponding to the terms. An interactive and editable table is also created to allow an editor to validate the found matches and find other related items. A bit amateurish attempt by a Wikidata newbie.","authors":[{"author":"Aleksei Lutai","authorURL":"https://www.linkedin.com/in/lutaya/","affiliation":"&nbsp;","affiliationURL":"#","orcidID":"0000-0003-1341-781X"}],"publishedDate":"2021-06-16T00:00:00.000+03:00","citationText":"Lutai, 2021"}
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2626<h1>Tagging the Scientific Abstracts with Wikidata Items</h1>
2627<!--radix_placeholder_categories-->
2628<div class="dt-tags">
2629  <a class='dt-tag' href='/#category:wikidata'>wikidata</a>
2630  <a class='dt-tag' href='/#category:udpipe'>udpipe</a>
2631  <a class='dt-tag' href='/#category:api'>api</a>
2632  <a class='dt-tag' href='/#category:text_mapping'>text mapping</a>
2633  <a class='dt-tag' href='/#category:sparql'>sparql</a>
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2636<p><p>Here I am trying to build a script that process the short scientific texts (abstracts) and finds Wikidata items corresponding to the terms. An interactive and editable table is also created to allow an editor to validate the found matches and find other related items. A bit amateurish attempt by a Wikidata newbie.</p></p>
2637</div>
2638
2639<div class="d-byline">
2640  
2641  true
2642  
2643<br/>06-16-2021
2644</div>
2645
2646<div class="d-article">
2647<div class="d-contents d-contents-float">
2648<nav class="l-text toc figcaption" id="TOC">
2649<h3>Contents</h3>
2650<ul>
2651<li><a href="#size-matters">Size matters(?)</a></li>
2652<li><a href="#data">Data</a></li>
2653<li><a href="#lemmatization-and-pos-analysis-udpipe">Lemmatization and POS-analysis, udpipe</a></li>
2654<li><a href="#searching-a-term-in-wikidata">Searching a term in Wikidata</a></li>
2655<li><a href="#the-results">The results</a></li>
2656<li><a href="#case-1">Case 1</a></li>
2657<li><a href="#case-2">Case 2</a></li>
2658<li><a href="#case-3">Case 3</a></li>
2659<li><a href="#case-4">Case 4</a></li>
2660<li><a href="#case-5">Case 5</a></li>
2661<li><a href="#final-results">Final Results</a></li>
2662<li><a href="#limitations">Limitations</a></li>
2663<li><a href="#acknowledgments">Acknowledgments</a></li>
2664</ul>
2665</nav>
2666</div>
2667<p>With every day Wikidata occupies me more and more. Having played a bit with the <a href="https://dwayzer.netlify.app/posts/2021-05-27-academic-journals-through-the-lens-of-wikidata/">academic journals</a> and the <a href="https://dwayzer.netlify.app/posts/2021-05-24-riro/">institutions</a>, I started thinking how to extract the relavent Wikidata items for any text and use them for tagging.</p>
2668<p>My inner voice was like: ‘If Wikidata is an open database, there should be a lot of solutions, you just need to find a proper tutorial’. Aha, the tutorials, a little devil.</p>
2669<p>These were the options I found:</p>
2670<ul>
2671<li><p>Wikimedia community has a lot of tools, some of which are designed for tagging. One of it, <a href="https://mix-n-match.toolforge.org/#/">Mix’n’match</a> seems to be created specifically for tagging. It also provides an option to download the catalogues and dictionaries matched to Wikidata items. There could also be some other tools - <a href="https://meta.wikimedia.org/wiki/Wikipedia_Weekly_Network/Live_Wikidata_Editing">Wikipedia Weekly Network/Live Wikidata Editing</a> offers an impressive collection of video episodes that can serve a tutorial function. I have watched just few so far (will go on). But at that moment I was hoping to find a “magical” API to minimize the manual routine.</p></li>
2672<li><p><a href="https://scholia.toolforge.org/">Scholia</a> - a brilliant tool, offers <a href="https://scholia.toolforge.org/text-to-topics">Text2Topic</a> convertor, which also requires a manual input. Its open code is available at <a href="https://github.com/fnielsen/scholia/tree/master/scholia">Github</a>, but my R+/P- phenotype leaves me no chance for its adoption.</p></li>
2673<li><p>There is also an R-solution for text search in Wikidata - a new <a href="https://github.com/TS404/WikidataR">WikidataR package</a> (still in development) offers a “find item” function. It is a wrapper for <a href="https://www.mediawiki.org/wiki/API:Main_page">Wikimedia API</a> module named <a href="https://www.wikidata.org/w/api.php?action=help&amp;modules=wbsearchentities">wbsearchentities</a> that does a very generic search. Try to do query a term <a href="https://www.wikidata.org/w/api.php?action=wbsearchentities&amp;search=galaxy&amp;language=en">“galaxy”</a> and in addition to an astronomical structure, you will have the LA footbal club, military aircraft, US record label, etc, etc.</p></li>
2674<li><p>And there are many examples of <a href="https://www.wikidata.org/wiki/Wikidata:SPARQL_query_service/queries/examples#Mediawiki_API">SPARQL queries</a> for Wikidata Query Service, where I also took some ideas from.</p></li>
2675</ul>
2676<p>Finally I decided to create my own “synthetic” approach to make a search more specific and automate text tagging. In other words, another nube who pleaded ignorance for a pleasure of re-creating a bycicle. That’s one of the best privilieges the neophytes can enjoy, isn’t it?</p>
2677<h3 id="size-matters">Size matters(?)</h3>
2678<p>When it comes to scientific articles, there are many more sophisticated (and well developed) techniques for keyword extraction and topic modelling.</p>
2679<ul>
2680<li><p>the authors usually suggest the keywords (not always good ones though), which could be used for initial setting of subject area;</p></li>
2681<li><p>the indexing services (like <a href="https://pubmed.ncbi.nlm.nih.gov/">Medline</a>, <a href="https://www.semanticscholar.org/">Semantics Scholar</a>, <a href="https://www.scopus.com/">Scopus</a>) also assign the terms (not equally well for all subjects though). Some of them provide free API.</p></li>
2682<li><p>the article have references and (sometimes) the citations - they can be used to find an article’s position in the citation graph and to extract more contextual information from its closest neighbours. <
2682a href="https://opencitations.net/index/coci">COCI</a> seems to be the most practical option for this, while all the World is waiting for <a href="https://openalex.org/">OpenAlex</a> aimed for substitution of Microsoft Academic.</p></li>
2683<li><p>with Open Access development the full texts are getting more available for text data mining (TDM). If you have a facility to do ML on many millions of full-text documents, <a href="https://core.ac.uk/">CORE</a> and <a href="https://unpaywall.org/">Unpaywall</a> can provide you with the data.</p></li>
2684</ul>
2685<p>So a large-scale solution is likely to be about using ML on the abovementioned datasets for topic modelling and further fuzzy matching against <a href="https://meta.wikimedia.org/wiki/Data_dumps">Wikidata dump</a>.</p>
2686<p>This post is very much not about such scale of solution. Let’s pretend that we have just a piece of text (no references, no DOI, no keywords) and there is no budget for IT muscles (does it sound like an editorial department for many journals?).</p>
2687<h3 id="data">Data</h3>
2688<p>As a coverage of scientific terms in Wikidata <a href="https://mix-n-match.toolforge.org/#/group/science">varies between the different subjects</a>, I decided to try my solution on the abstracts from Science (AAAS, issn:1095-9203), as subject-agnostic academic journal. I utilized CrossRef API <a href="https://api.crossref.org/works?filter=issn:1095-9203,from-pub-date:2020-01,has-abstract:true&amp;sample=5&amp;select=abstract">example</a> to obtain the abstracts of 5 random articles published after Jan 2020.</p>
2689<p>You can see them in a table below.</p>
2690<div class="layout-chunk" data-layout="l-body">
2691<details>
2692<summary>Show code</summary>
2693<div class="sourceCode">
2694<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>data</span> <span class='op'>&lt;-</span> <span class='va'>dir</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/r/base/list.files.html'>list.files</a></span><span class='op'>(</span>full.names <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='va'>.</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/grep.html'>grepl</a></span><span class='op'>(</span><span class='st'>"crworks.json"</span>,<span class='va'>.</span><span class='op'>)</span><span class='op'>]</span> <span class='op'>%&gt;%</span> 
2695  <span class='fu'><a href='https://rdrr.io/pkg/jsonlite/man/fromJSON.html'>fromJSON</a></span><span class='op'>(</span>flatten <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2696  <span class='fu'>map</span><span class='op'>(</span><span class='st'>"items"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='va'>.</span><span class='op'>$</span><span class='va'>message</span> <span class='op'>%&gt;%</span>   
2697  <span class='fu'>mutate</span><span class='op'>(</span>abstract <span class='op'>=</span> <span class='fu'>str_replace_all</span><span class='op'>(</span><span class='va'>abstract</span>, <span class='st'>"&lt;.+?&gt;"</span>,<span class='st'>""</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2698  <span class='fu'>mutate</span><span class='op'>(</span>abstract <span class='op'>=</span> <span class='fu'>stringi</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/stringi/man/stri_trans_general.html'>stri_trans_general</a></span><span class='op'>(</span><span class='va'>abstract</span>, <span class='st'>'nfc; latin'</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2699  <span class='fu'>mutate</span><span class='op'>(</span>abstract <span class='op'>=</span> <span class='fu'>str_squish</span><span class='op'>(</span><span class='va'>abstract</span><span class='op'>)</span><span class='op'>)</span>
2700
2701<span class='va'>data</span> <span class='op'>%&gt;%</span> 
2702  <span class='co'>#mutate(abstract - substr(abstract, 1,250)) %&gt;% </span>
2703  <span class='co'>
2703#summarize(abstracts = paste(abstract, collapse  = " ...")) %&gt;% </span>
2704  <span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>dom <span class='op'>=</span> <span class='st'>"tip"</span>, pageLength <span class='op'>=</span> <span class='fl'>1</span> <span class='op'>)</span><span class='op'>)</span>
2705</code></pre>
2706</div>
2707</details>
2708<div id="htmlwidget-c8cb1a1347fcc8a0ab8d" style="width:100%;height:auto;" class="datatables html-widget"></div>
2709<script type="application/json" data-for="htmlwidget-c8cb1a1347fcc8a0ab8d">{"x":{"filter":"none","data":[["The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.","Freshwater fish represent one-fourth of the world’s vertebrates and provide irreplaceable goods and services but are increasingly affected by human activities. A new index, Cumulative 
2709Change in Biodiversity Facets, revealed marked changes in biodiversity in &amp;gt;50% of the world’s rivers covering &amp;gt;40% of the world’s continental surface and &amp;gt;37% of the world’s river length, whereas &amp;lt;14% of the world’s surface and river length remain least impacted. Present-day rivers are more similar to each other and have more fish species with more diverse morphologies and longer evolutionary legacies. In temperate rivers, where the impact has been greatest, biodiversity changes were primarily due to river fragmentation and introduction of non-native species.","The surface of neutron-rich heavy nuclei, with a neutron skin created by excess neutrons, provides an important terrestrial model system to study dilute neutron-rich matter. By using quasi-free a cluster–knockout reactions, we obtained direct experimental evidence for the formation of a clusters at the surface of neutron-rich tin isotopes. The observed monotonous decrease of the reaction cross sections with increasing mass number, in excellent agreement with the theoretical prediction, implies a tight interplay between a-cluster formation and the neutron skin. This result, in turn, calls for a revision of the correlation between the neutron-skin thickness and the density dependence of the symmetry energy, which is essential for understanding neutron stars. Our result also provides a natural explanation for the origin of a particles in a decay.","Ecological resilience is the magnitude of the largest perturbation from which a system can still recover to its original state. However, a transition into another state may often be invoked by a series of minor synergistic perturbations rather than a single big one. We show how resilience can be estimated in terms of average life expectancy, accounting for this natural regime of variability. We use time series to fit a model that captures the stochastic as well as the deterministic components. The model is then used to estimate the mean exit time from the basin of attraction. This approach offers a fresh angle to anticipating the chance of a critical transition at a time when high-resolution time series are becoming increasingly available.","Cosmological models predict that galaxies forming in the early Universe experience a chaotic phase of gas accretion and star formation, followed by gas ejection due to feedback processes. Galaxy bulges may assemble later via mergers or internal evolution. Here we present submillimeter observations (with spatial resolution of 700 parsecs) of ALESS 073.1, a starburst galaxy at redshift z≃5 when the Universe was 1.2 billion years old. This galaxy’s cold gas forms a regularly rotating disk with negligible noncircular motions. The galaxy rotation curve requires the presence of a central bulge in addition to a star-forming disk. We conclude that massive bulges and regularly rotating disks can form more rapidly in the early Universe than predicted by models of galaxy formation."]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>abstract<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":1,"dom":"tip","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"order":[],"orderClasses":false,"lengthMenu":[1,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>
2709
2710</div>
2711<p>Our next step would be to extract from the abstracts the words and their combinations that can be a scientific term and have an item in Wikidata. I am not a linguist, but from what I read it seemed to me that there is a consensus that most terms are nouns - as a sole word (galaxy), or in a combination (coronavirus disease), or preceded with the adjective (clinical trial).</p>
2712<h3 id="lemmatization-and-pos-analysis-udpipe">Lemmatization and POS-analysis, udpipe</h3>
2713<p>The package <a href="https://bnosac.github.io/udpipe/en/index.html">udpipe</a> offers a set of functions for Tokenization, Parts-of-Speech (POS) tagging, Lemmatization, Dependency Parsing, etc.</p>
2714<p>The process I am using below is described <a href="https://bnosac.github.io/udpipe/docs/doc7.html">here</a> with few exceptions:</p>
2715<ul>
2716<li><p>udpipe tokenizer splits the words by hyphens (no chance for SARS-CoV-2), so I tokenized the abstracts with regular expression.</p></li>
2717<li><p>in POS-analysis udpipe tags the pronouns as nouns (N) and the numericals as adjectives (A). Therefore, I removed them (“which” or “37” are unlikely to be a sensible terms) at some level. This does not affect the numbers in cov-2 or covid-19, as the hyphens are not cleaved.</p></li>
2718</ul>
2719<p>More details are in the code below.</p>
2720<div class="layout-chunk" data-layout="l-body">
2721<details>
2722<summary>Show code</summary>
2723<div class="sourceCode">
2724<pre class="sourceCode r"><code class="sourceCode r"><span class='co'># to avoid running the chunks I saved the results on hard disk </span>
2725<span class='va'>file_d_terms</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>dir</span>, <span class='st'>"data_terms.RDS"</span><span class='op'>)</span>
2726
2727<span class='kw'>if</span><span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/files.html'>file.exists</a></span><span class='op'>(</span><span class='va'>file_d_terms</span><span class='op'>)</span><span class='op'>)</span><span class='op'>{</span>
2728  <span class='co'># for the first run, model_dir is not used</span>
2729  <span class='co'># the library is getting downloaded from www (default)</span>
2730  <span class='va'>udmodel</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/udpipe/man/udpipe_download_model.html'>udpipe_download_model</a></span><span class='op'>(</span>
2731    model_dir <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>onedrive</span>, <span class='st'>"/Wikidata/Science/"</span><span class='op'>)</span>, 
2732    language <span class='op'>=</span> <span class='st'>"english"</span>, 
2733    overwrite <span class='op'>=</span> <span class='cn'>FALSE</span>
2734    <span class='op'>)</span>
2735  <span class='va'>udmodel</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/pkg/udpipe/man/udpipe_load_model.html'>udpipe_load_model</a></span><span class='op'>(</span>file <span class='op'>=</span> <span class='va'>udmodel</span><span class='op'>$</span><span class='va'>file_model</span><span class='op'>)</span>
2736  
2737  <span class='co'># udpipe breaks by hyphens, so I use str_extract_all with a regex expr.</span>
2738  <span class='va'>datax</span> <span class='op'>&lt;-</span> <span class='va'>data</span><span class='op'>$</span><span class='va'>abstract</span> <span class='op'>%&gt;%</span> 
2739    <span class='fu'>map</span><span class='op'>(</span><span class='op'>~</span><span class='fu'>str_extract_all</span><span class='op'>(</span><span class='va'>.x</span>,<span class='st'>"[[:alnum:]\\-]+"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2740          <span class='fu'>map_chr</span><span class='op'>(</span><span class='op'>~</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>.x</span>, collapse <span class='op'>=</span> <span class='st'>"\n"</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2741    <span class='fu'><a href='https://rdrr.io/r/stats/setNames.html'>setNames</a></span><span class='op'>(</span><span class='va'>LETTERS</span><span class='op'>[</span><span class='fl'>1</span><span class='op'>:</span><span class='fl'>5</span><span class='op'>]</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
2742    <span class='fu'>map</span><span class='op'>(</span><span class='op'>~</span><span class='fu'><a href='https://rdrr.io/pkg/udpipe/man/udpipe_annotate.html'>udpipe_annotate</a></span><span class='op'>(</span>object <span class='op'>=</span> <span class='va'>udmodel</span>, x <span class='op'>=</span> <span class='va'>.x</span>, 
2743                         tokenizer <span class='op'>=</span> <span class='st'>"vertical"</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
2744          <span class='fu'><a href='https://rdrr.io/r/base/as.data.frame.html'>as.data.frame</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2745          <span class='fu'>mutate</span><span class='op'>(</span>phrase_tag <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/udpipe/man/as_phrasemachine.html'>as_phrasemachine</a></span><span class='op'>(</span><span class='va'>upos</span>, type <span class='op'>=</span> <span class='st'>"upos"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2746          <span class='fu'>mutate</span><span class='op'>(</span>lemma <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/chartr.html'>tolower</a></span><span class='op'>(</span><span class='va'>lemma</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> 
2747     
2748  <span class='va'>data_terms</span> <span class='op'>&lt;-</span> <span class='va'>datax</span> <span class='op'>%&gt;%</span>
2749    <span class='co'># udpipe tags pronouns (PRON) similar as nouns (N)</span>
2750    <span class='co'># I remove the pronons before keywords_phrases</span>
2751    <span class='fu'>map</span><span class='op'>(</span><span class='op'>~</span><span class='va'>.x</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>upos</span><span class='op'>!=</span><span class='st'>"PRON"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
2752    <span class='co'># udpipe tags numericals (NUM) similar as adjectives (A)</span>
2753    <span class='co'># I remove the numericals before keywords_phrases</span>
2754    <span class='fu'>map</span><span class='op'>(</span><span class='op'>~</span><span class='va'>.x</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>upos</span><span class='op'>!=</span><span class='st'>"NUM"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
2755    <span class='fu'>map</span><span class='op'>(</span><span class='op'>~</span><span class='fu'><a href='https://rdrr.io/pkg/udpipe/man/keywords_phrases.html'>keywords_phrases</a></span><span class='op'>(</span>x <span class='op'>=</span> <span class='va'>.x</span><span class='op'>$</span><span class='va'>phrase_tag</span>, term <span class='op'>=</span> <span class='va'>.x</span><span class='op'>$</span><span class='va'>lemma</span>, 
2756                      pattern <span class='op'>=</span> <span class='st'>"N|AN|NN"</span>, is_regex <span class='op'>=</span> <span class='cn'>TRUE</span>, 
2757                      ngram_max <span class='op'>=</span> <span class='fl'>2</span>, detailed <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2758          <span class='fu'>select</span><span class='op'>(</span><span class='va'>keyword</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/nchar.html'>nchar</a></span><span class='op'>(</span><span class='va'>keyword</span><span class='op'>)</span><span class='op'>&gt;</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span>
2759  
2760  <span class='co'># saving the results on disk as RDS file for further using </span>
2761  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>
2762    datax <span class='op'>=</span> <span class='va'>datax</span>,
2763    data_terms <span class='op'>=</span> <span class='va'>data_terms</span>
2764    <span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='fu'>write_rds</span><span class='op'>(</span><span class='va'>file_d_terms</span><span class='op'>)</span>
2765<span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span>
2766  <span class='va'>datax</span> <span class='op'>&lt;-</span> <span class='fu'>read_rds</span><span class='op'>(</span><span class='va'>file_d_terms</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='va'>.</span><span class='op'>
2766[[</span><span class='st'>"datax"</span><span class='op'>]</span><span class='op'>]</span> 
2767  <span class='va'>data_terms</span> <span class='op'>&lt;-</span> <span class='fu'>read_rds</span><span class='op'>(</span><span class='va'>file_d_terms</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='va'>.</span><span class='op'>[[</span><span class='st'>"data_terms"</span><span class='op'>]</span><span class='op'>]</span> 
2768<span class='op'>}</span>
2769</code></pre>
2770</div>
2771</details>
2772</div>
2773<p>For each abstract we produced 2 datasets (in my code packed in the lists), containing:</p>
2774<ol type="1">
2775<li>the results of lemmatization and POS-tagging</li>
2776</ol>
2777<div class="layout-chunk" data-layout="l-body">
2778<details>
2779<summary>Show code</summary>
2780<div class="sourceCode">
2781<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>datax</span><span class='op'>$</span><span class='va'>A</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span>
2782</code></pre>
2783</div>
2784</details>
2785<div id="htmlwidget-c3e75eb8c8b52e644388" style="width:100%;height:auto;" class="datatables html-widget"></div>
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2786
2787</div>
2788<ol start="2" type="1">
2789<li>the keyword phrases (N, N+N, A+N) to be used for searching Wikidata</li>
2790</ol>
2791<div class="layout-chunk" data-layout="l-body">
2792<details>
2793<summary>Show code</summary>
2794<div class="sourceCode">
2795<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>data_terms</span><span class='op'>$</span><span class='va'>A</span> <span class='op'>%&gt;%</span> <span class='fu'>summarize</span><span class='op'>(</span>keywords <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='va'>keyword</span>, collapse  <span class='op'>=</span> <span class='st'>" | "</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2796  <span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>dom <span class='op'>=</span> <span class='st'>"t"</span><span class='op'>)</span><span class='op'>)</span>
2797</code></pre>
2798</div>
2799</details>
2800<div id="htmlwidget-bb7a93b203df76a63424" style="width:100%;height:auto;" class="datatables html-widget"></div>
2801<script type="application/json" data-for="htmlwidget-bb7a93b203df76a63424">{"x":{"filter":"none","data":[["drug | sars-cov-2 | disease | x-ray | screen | mpro | compound | coronavirus | coronavirus disease | human suffering | suffering | date | effective drug | search | covid-19 | high-throughput x-ray | crystallographic screen | drug library | library | main protease | protease | protease mpro | viral replication | replication | contrast | x-ray fragment | fragment | experiment | molecule | low complexity | complexity | complexity screen | already-approved drug | clinical trial | trial | three-dimensional protein | protein | protein structure | structure | viral reduction | reduction | peptidomimetic | nonpeptidic compound | antiviral activity | activity | nontoxic concentration | concentration | allosteric | site | attractive target | target | drug development | development"]],"container":"<table class=\"display\">\n  <thead>\n    <tr>\n      <th>keywords<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"dom":"t","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"order":[],"orderClasses":false,"lengthMenu":[5,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>
2801
2802</div>
2803<p>The terms and phrases seems OK to me, except that I would qualify “allosteric” as an adjective.</p>
2804<p>Now as we have the terms it’s time to build a search function that will be retrieving the relevant Wikidata items.</p>
2805<h3 id="searching-a-term-in-wikidata">Searching a term in Wikidata</h3>
2806<p>In order to increase a specificity of search (i.e. to retrieve more scientific terms and less “footbal teams” or “rockstar aliases”), I decided to do queries in SPARQL via Wikidata Query Service withe special filters.</p>
2807<p>The SPARQL query has the following conditions that:</p>
2808<ol type="1">
2809<li><p>retrieve the search results from wikibase API</p></li>
2810<li><p>retrieve a number of site links for Wikidata item</p></li>
2811<li><p>check against the dictionaries and thesauri (a long chain of wdt:P_ in a code. Some thesauri have direct relations to the scientific concepts (like MeSH - P486, ChEBI ID - P683, Semantic Scholar topic ID - P6611), the others are rather dictionaries and encyclopedias (like Oxford Classical Dictionary - P9106, or Enciclopaedia Britannica - P1417). You should be aware that those terms are also not completely matched to Wikidata items (see <a href="https://mix-n-match.toolforge.org/#/">Mix’n’Match</a> for particular catallogues).</p></li>
2812<li><p>excludes disambiguation wikimedia pages (Q4167410) - there’s over <a href="https://query.wikidata.org/#SELECT%20%28COUNT%28%3Fitem%29%20as%20%3Fcount%29%20WHERE%20%7B%20%3Fitem%20wdt%3AP31%20wd%3AQ4167410.%7D%0A">1M such pages</a> in Wikidata.</p></li>
2813<li><p>filters only English terms</p></li>
2814<li><p>filters the terms found at least in 3 thesauri</p></li>
2815<li><p>filters the items that have the same start as the query (e.g. it retrieves not only “neutron” but also a “neutron star”). The filter based on the regular expression leaves a lot of flexibility - e.g. you can also set the strict matching by enframing the terms with ^ and $.</p></li>
2816<li><p>scores the filtered results based on a number of sitelinks (and further by number of dictionaries the term was found in).</p></li>
2817</ol>
2818<div class="layout-chunk" data-layout="l-body">
2819<details>
2820<summary>Show code</summary>
2821<div class="sourceCode">
2822<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>sparql_composer</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>term</span><span class='op'>)</span><span class='op'>{</span>
2823  <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>'SELECT ?item (SAMPLE(?itemLabel) as ?item_label)
2824          (SAMPLE(?typeLabel) as ?entity_type) ?itemDescription 
2825          ?sites (COUNT(distinct(?id)) AS ?count)
2826    WHERE {hint:Query hint:optimizer "None".
2827      SERVICE wikibase:mwapi {
2828          bd:serviceParam wikibase:endpoint "www.wikidata.org";
2829           wikibase:api "EntitySearch";
2830            mwapi:search "'</span>, <span class='va'>term</span>, <span class='st'>'"; 
2831            mwapi:language "en".
2832          ?item wikibase:apiOutputItem mwapi:item.
2833      }
2834      FILTER BOUND (?item)     
2835      optional{?item wikibase:sitelinks ?sites.}
2836      ?item wdt:P1417|wdt:P486|wdt:P683|wdt:P6366|wdt:P3916|
2837            wdt:P227|wdt:P6366|wdt:P244|wdt:P4732|wdt:P231|
2838            wdt:P1014|wdt:P7859|wdt:P949|wdt:P2671|wdt:P6611|
2839            wdt:P268|wdt:P2163|wdt:P2581|wdt:P5019|wdt:P646|
2840            wdt:P2924|wdt:P9106|wdt:P4212|wdt:P3123|wdt:P2347|
2841            wdt:P1692|wdt:P8814|wdt:P699|wdt:P3219 ?id.
2842      ?item wdt:P31|wdt:P279 ?type. 
2843      ?item rdfs:label ?itemLabel.
2844      FILTER(LANGMATCHES(LANG(?itemLabel), "en")).
2845      FILTER REGEX(LCASE(?itemLabel), "^'</span>, <span class='va'>term</span>, <span class='st'>'"). 
2846      MINUS {?item wdt:P31 wd:Q4167410}
2847      SERVICE wikibase:label {
2848          bd:serviceParam wikibase:language "en".
2849          ?type rdfs:label ?typeLabel.
2850          ?item schema:description ?itemDescription.
2851          }  
2852    }
2853    group by ?item ?itemDescription ?sites
2854    HAVING ( ?count &gt; 2 )
2855    ORDER BY DESC(?sites) DESC(?count) 
2856    LIMIT 2'</span><span class='op'>)</span>
2857<span class='op'>}</span> 
2858</code></pre>
2859</div>
2860</details>
2861</div>
2862<p>I tried to use the development version of WikidataR (<a href="https://github.com/TS404/WikidataR">https://github.com/TS404/WikidataR</a>) for SPARQL queries, but found that it contained a little bug that incorrectly processed the output results with 1 row and prevent putting the function under map_df() control. I updated the code a bit.</p>
2863<div class="layout-chunk" data-layout="l-body">
2864<details>
2865<summary>Show code</summary>
2866<div class="sourceCode">
2867<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>wd_query</span> <span class='op'>&lt;-</span> <span class='kw'>function</span><span class='op'>(</span><span class='va'>query</span>, <span class='va'>format</span> <span class='op'>=</span> <span class='st'>
2867"simple"</span>, <span class='va'>...</span><span class='op'>)</span><span class='op'>{</span>
2868  <span class='va'>output</span> <span class='op'>&lt;-</span> <span class='fu'>WikidataQueryServiceR</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/WikidataQueryServiceR/man/query_wikidata.html'>query_wikidata</a></span><span class='op'>(</span>sparql_query <span class='op'>=</span> <span class='va'>query</span>, 
2869                    format <span class='op'>=</span> <span class='va'>format</span>, <span class='va'>...</span><span class='op'>)</span>
2870  <span class='va'>output</span> <span class='op'>&lt;-</span> <span class='fu'>tibble</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/data.frame.html'>data.frame</a></span><span class='op'>(</span><span class='va'>output</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2871    <span class='fu'>mutate_all</span><span class='op'>(</span><span class='op'>~</span><span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/grep.html'>grepl</a></span><span class='op'>(</span><span class='st'>"Q\\d+$"</span>,<span class='va'>.x</span><span class='op'>)</span>, <span class='fu'>str_extract</span><span class='op'>(</span><span class='va'>.x</span>, <span class='st'>"Q\\d+$"</span><span class='op'>)</span>, <span class='va'>.x</span><span class='op'>)</span><span class='op'>)</span>
2872  <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>nrow</a></span><span class='op'>(</span><span class='va'>output</span><span class='op'>)</span> <span class='op'>==</span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span><span class='va'>output</span> <span class='op'>&lt;-</span> <span class='fu'>tibble</span><span class='op'>(</span>value <span class='op'>=</span> <span class='cn'>NA</span><span class='op'>)</span><span class='op'>}</span>
2873  <span class='kw'><a href='https://rdrr.io/r/base/function.html'>return</a></span><span class='op'>(</span><span class='va'>output</span><span class='op'>)</span>
2874<span class='op'>}</span>
2875</code></pre>
2876</div>
2877</details>
2878</div>
2879<p>Next I took a vector of unique terms and made a chain of queries with map_df (I could pass a full vector into the request but in that case I would not see in the results which result corrsponds to which term).</p>
2880<div class="layout-chunk" data-layout="l-body">
2881<details>
2882<summary>Show code</summary>
2883<div class="sourceCode">
2884<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>file_w_terms</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>dir</span>, <span class='st'>"/terms.csv"</span><span class='op'>)</span>
2885<span class='kw'>if</span><span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/files.html'>file.exists</a></span><span class='op'>(</span><span class='va'>file_w_terms</span><span class='op'>)</span><span class='op'>)</span><span class='op'>{</span>
2886  <span class='va'>wiki_terms</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/unlist.html'>unlist</a></span><span class='op'>(</span><span class='va'>data_terms</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/r/base/unique.html'>unique</a></span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2887    <span class='fu'>map_df</span><span class='op'>(</span><span class='op'>~</span><span class='fu'>wd_query</span><span class='op'>(</span><span class='fu'>sparql_composer</span><span class='op'>(</span><span class='va'>.x</span><span class='op'>)</span>, format <span class='op'>=</span> <span class='st'>"simple"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2888                  <span class='fu'>mutate</span><span class='op'>(</span>query <span class='op'>=</span> <span class='va'>.x</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2889                  <span class='fu'>mutate_all</span><span class='op'>(</span><span class='op'>~</span><span class='fu'><a href='https://rdrr.io/r/base/character.html'>as.character</a></span><span class='op'>(</span><span class='va'>.x</span><span class='op'>)</span><span class='op'>)</span>
2890                 <span class='op'>)</span> <span class='op'>%&gt;%</span>  
2891    <span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NA.html'>is.na</a></span><span class='op'>(</span><span class='va'>item</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2892    <span class='fu'>select</span><span class='op'>(</span><span class='va'>query</span>, <span class='va'>item</span>, <span class='va'>item_label</span>, <span class='va'>entity_type</span>, 
2893           <span class='va'>itemDescription</span>, <span class='va'>sites</span>, <span class='va'>count</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2894    <span class='fu'>arrange</span><span class='op'>(</span><span class='va'>query</span><span class='op'>)</span>
2895  <span class='fu'>write_excel_csv</span><span class='op'>(</span><span class='va'>wiki_terms</span>, <span class='va'>file_w_terms</span><span class='op'>)</span>
2896<span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span>
2897  <span class='va'>wiki_terms</span> <span class='op'>&lt;-</span> <span class='fu'>read_csv</span><span class='op'>(</span><span class='va'>file_w_terms</span><span class='op'>)</span>
2898<span class='op'>}</span>
2899
2900<span class='va'>data_edit</span> <span class='op'>&lt;-</span> <span class='va'>data_terms</span> <span class='op'>%&gt;%</span> 
2901  <span class='fu'>map</span><span class='op'>(</span><span class='op'>~</span><span class='va'>.x</span> <span class='op'>%&gt;%</span> 
2902        <span class='fu'>left_join</span><span class='op'>(</span><span class='va'>wiki_terms</span>, by <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"keyword"</span> <span class='op'>=</span> <span class='st'>"query"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2903        <span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/NA.html'>is.na</a></span><span class='op'>(</span><span class='va'>item</span><span class='op'>)</span><span class='op'>)</span>
2904  <span class='op'>)</span>
2905</code></pre>
2906</div>
2907</details>
2908</div>
2909<h3 id="the-results">The results</h3>
2910<p>The retrieved results are still far from being 100% specific and need to be validated. For this I created a prototype of checking template - an interactive DT table that:</p>
2911<ul>
2912<li><p>shows the text excerpts containg the term (+/- 2 words around)</p></li>
2913<li><p>highlights the terms</p></li>
2914<li><p>provides a description of the found Wikidata item</p></li>
2915<li><p>can be edited (right here! Click on ? and change it to “yes” in valid? column)</p></li>
2916<li><p>can be downloaded to CSV or XLSX file with the introduced changes.</p></li>
2917</ul>
2918<div class="layout-chunk" data-layout="l-body">
2919<details>
2920<summary>Show code</summary>
2921<div class="sourceCode">
2922<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>tables_rds</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>dir</span>, <span class='st'>"editable_tables.rds"</span><span class='op'>)</span>
2923
2924<span class='kw'>if</span><span class='op'>(</span><span class='op'>!</span><span class='fu'><a href='https://rdrr.io/r/base/files.html'>file.exists</a></span><span class='op'>(</span><span class='va'>tables_rds</span><span class='op'>)</span><span class='op'>)</span><span class='op'>{</span>
2925  <span class='va'>tables</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='op'>)</span>
2926
2927  <span class='kw'>for</span> <span class='op'>(</span><span class='va'>m</span> <span class='kw'>in</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>nrow</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span><span class='op'>)</span><span class='op'>{</span>
2928    <span class='va'>lemma_text</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/chartr.html'>tolower</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/unlist.html'>unlist</a></span><span class='op'>(</span><span class='va'>datax</span><span class='op'>
2928[[</span><span class='va'>m</span><span class='op'>]</span><span class='op'>]</span><span class='op'>[</span><span class='st'>"lemma"</span><span class='op'>]</span><span class='op'>)</span>, collapse <span class='op'>=</span> <span class='st'>" "</span><span class='op'>)</span><span class='op'>)</span>
2929
2930    <span class='va'>y</span> <span class='op'>&lt;-</span> <span class='va'>data_edit</span><span class='op'>[[</span><span class='va'>m</span><span class='op'>]</span><span class='op'>]</span> <span class='op'>%&gt;%</span>
2931      <span class='fu'>mutate</span><span class='op'>(</span>seltext <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/grep.html'>gsub</a></span><span class='op'>(</span><span class='st'>" "</span>,<span class='st'>".{0,5}"</span>,<span class='va'>keyword</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2932      <span class='fu'>mutate</span><span class='op'>(</span>painter <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"^"</span>,<span class='va'>seltext</span>,<span class='st'>"|"</span>, <span class='va'>seltext</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
2933      <span class='fu'>mutate</span><span class='op'>(</span>extractor <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>'((?:\\S+\\s+){0,2}\\b'</span>,
2934                            <span class='va'>seltext</span>,
2935                      <span class='st'>'.??\\b(\\s*|\\.)(?:\\S+\\b\\s*){0,2})'</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2936      <span class='fu'>mutate</span><span class='op'>(</span>extractor <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>sapply</a></span><span class='op'>(</span><span class='va'>extractor</span>, 
2937                  <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"^"</span>,<span class='va'>extractor</span>,
2938                                     <span class='st'>"|"</span>, <span class='va'>extractor</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>  
2939      <span class='fu'>mutate</span><span class='op'>(</span>text <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span> 
2940  
2941    <span class='kw'>for</span> <span class='op'>(</span><span class='va'>i</span> <span class='kw'>in</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>nrow</a></span><span class='op'>(</span><span class='va'>y</span><span class='op'>)</span><span class='op'>)</span><span class='op'>{</span>
2942      <span class='va'>y</span><span class='op'>[</span><span class='va'>i</span>, <span class='st'>"text"</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='fu'>str_extract_all</span><span class='op'>(</span><span class='va'>lemma_text</span>, <span class='va'>y</span><span class='op'>$</span><span class='va'>extractor</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, 
2943                                      simplify <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2944        <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"..."</span>,<span class='va'>.</span>,<span class='st'>"..."</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span>collapse <span class='op'>=</span> <span class='st'>""</span><span class='op'>)</span>
2945      
2946      <span class='va'>y</span><span class='op'>[</span><span class='va'>i</span>, <span class='st'>"text"</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='fu'>str_replace_all</span><span class='op'>(</span><span class='va'>y</span><span class='op'>$</span><span class='va'>text</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>, <span class='va'>y</span><span class='op'>$</span><span class='va'>painter</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>,
2947                        <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>'&lt;span style="background-color: #FEE1E8"&gt;'</span>,
2948                               <span class='va'>y</span><span class='op'>$</span><span class='va'>keyword</span><span class='op'>[</span><span class='va'>i</span><span class='op'>]</span>,<span class='st'>'&lt;/span&gt;'</span><span class='op'>)</span><span class='op'>)</span>
2949    <span class='op'>}</span>  
2950
2951  <span class='va'>tables</span><span class='op'>[[</span><span class='va'>m</span><span class='op'>]</span><span class='op'>]</span> <span class='op'>&lt;-</span> <span class='va'>y</span> <span class='op'>%&gt;%</span> 
2952    <span class='fu'>mutate</span><span class='op'>(</span>item_label <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"&lt;b&gt;label:&lt;/b&gt; "</span>, <span class='fu'><a href='https://rdrr.io/r/base/chartr.html'>toupper</a></span><span class='op'>(</span><span class='va'>item_label</span><span class='op'>)</span><span class='op'>)</span>, 
2953           entity_type <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"&lt;b&gt;type:&lt;/b&gt; "</span>, <span class='va'>entity_type</span><span class='op'>)</span>,
2954           itemDescription <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"&lt;i&gt;
2954"</span>, <span class='va'>itemDescription</span>, <span class='st'>"&lt;i&gt;"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
2955    <span class='fu'>unite</span><span class='op'>(</span>col <span class='op'>=</span> <span class='st'>"details"</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"item_label"</span>, <span class='st'>"entity_type"</span>, 
2956                             <span class='st'>"itemDescription"</span><span class='op'>)</span>, sep <span class='op'>=</span> <span class='st'>"&lt;/br&gt;"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2957    <span class='fu'>mutate</span><span class='op'>(</span><span class='st'>"valid?"</span> <span class='op'>=</span> <span class='st'>"?"</span><span class='op'>)</span>
2958  <span class='op'>}</span>
2959  <span class='fu'>write_rds</span><span class='op'>(</span><span class='va'>tables</span>, <span class='va'>tables_rds</span><span class='op'>)</span>
2960  <span class='op'>}</span> <span class='kw'>else</span> <span class='op'>{</span>
2961    <span class='va'>tables</span> <span class='op'>&lt;-</span> <span class='fu'>read_rds</span><span class='op'>(</span><span class='va'>tables_rds</span><span class='op'>)</span>
2962  <span class='op'>}</span>
2963</code></pre>
2964</div>
2965</details>
2966</div>
2967<p>So there is an editable table in an automatically generated HTML-report that anyone can revise and save.</p>
2968<h3 id="case-1">Case 1</h3>
2969<div class="layout-chunk" data-layout="l-body-outset">
2970<details>
2971<summary>Show code</summary>
2972<div class="sourceCode">
2973<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>tables</span><span class='op'>[[</span><span class='fl'>1</span><span class='op'>]</span><span class='op'>]</span> <span class='op'>%&gt;%</span> 
2974  <span class='fu'>select</span><span class='op'>(</span><span class='va'>text</span>, <span class='va'>item</span>, <span class='va'>`valid?`</span>, <span class='va'>
2974details</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
2975  <span class='fu'>DT</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, escape <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='co'>#filter = 'top', </span>
2976            editable <span class='op'>=</span> <span class='cn'>TRUE</span>, class <span class='op'>=</span> <span class='st'>'compact striped'</span>,
2977             caption <span class='op'>=</span> <span class='fu'>htmltools</span><span class='fu'>::</span><span class='va'><a href='https://rdrr.io/pkg/htmltools/man/builder.html'>tags</a></span><span class='op'>$</span><span class='fu'>caption</span><span class='op'>(</span>style <span class='op'>=</span> <span class='st'>'caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;'</span>,
2978               <span class='st'>'Data: wikidata.org (see in the text).'</span><span class='op'>)</span>,
2979            extensions <span class='op'>=</span> <span class='st'>'Buttons'</span>,
2980            options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>searchHighlight <span class='op'>=</span> <span class='cn'>TRUE</span>,
2981                            dom <span class='op'>=</span> <span class='st'>'Bfrtip'</span>, buttons <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>'csv'</span>, <span class='st'>"excel"</span><span class='op'>)</span>, 
2982                           columnDefs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>
2983                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'300px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span>,
2984                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'500px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span>,
2985                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'65px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span>,
2986                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>className <span class='op'>=</span> <span class='st'>'dt-center'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
2987                  <span class='op'>)</span>
2988            <span class='op'>)</span> <span class='op'>%&gt;%</span> 
2989     <span class='fu'><a href='https://rdrr.io/pkg/DT/man/formatCurrency.html'>formatStyle</a></span><span class='op'>(</span><span class='st'>'valid?'</span>,  backgroundColor <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/DT/man/styleInterval.html'>styleEqual</a></span><span class='op'>(</span><span class='st'>'yes'</span>, <span class='st'>'#90ee90'</span><span class='op'>)</span>, fontWeight <span class='op'>=</span> <span class='st'>'bold'</span><span class='op'>)</span> 
2990</code></pre>
2991</div>
2992</details>
2993<div id="htmlwidget-eceb12ea86d0238cfe47" style="width:100%;height:auto;" class="datatables html-widget"></div>
2994<script type="application/json" data-for="htmlwidget-eceb12ea86d0238cfe47">{"x":{"filter":"none","extensions":["Buttons"],"caption":"<caption style=\"caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;\">Data: wikidata.org (see in the text).<\/caption>","editable":{"target":"cell","disable":{"columns":null}},"data":[["...no effective <span style=\"background-color: #FEE1E8\">drug<\/span> be available ......for a <span style=\"background-color: #FEE1E8\">drug<\/span> against covid-19 ......two repurpose <span style=\"background-color: #FEE1E8\">drug<\/span> library against ......test already-approved <span style=\"background-color: #FEE1E8\">drug<\/span> and <span style=\"background-color: #FEE1E8\">drug<\/span> ......target for <span style=\"background-color: #FEE1E8\">drug<\/span> development against ...","...no effective <span style=\"background-color: #FEE1E8\">drug<\/span> be available ......for a <span 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already-approved ...","...identify 37 <span style=\"background-color: #FEE1E8\">compound<\/span> that bind ......six nonpeptidic <span style=\"background-color: #FEE1E8\">compound<\/span> show antiviral ...","...identify 37 <span style=\"background-color: #FEE1E8\">compound<\/span> that bind ......six nonpeptidic <span style=\"background-color: #FEE1E8\">compound<\/span> show antiviral ...","...the <span style=\"background-color: #FEE1E8\">coronavirus<\/span> disease covid-19 ...","...the <span style=\"background-color: #FEE1E8\">coronavirus<\/span> disease covid-19 ...","...the <span style=\"background-color: #FEE1E8\">coronavirus disease<\/span> covid-19 cause ...","...tremendous human <span style=\"background-color: #FEE1E8\">suffering<\/span> to date ...","...suffering to <span style=\"background-color: #FEE1E8\">date<\/span> no effective ...","...suffering to <span style=\"background-color: #FEE1E8\">date<\/span> no effective ...","...in a <span style=\"background-color: #FEE1E8\">search<\/span> for a ...","...in a <span style=\"background-color: #FEE1E8\">search<\/span> for a ...","...coronavirus disease <span style=\"background-color: #FEE1E8\">covid-19<\/span> cause by ......drug against <span style=\"background-color: #FEE1E8\">covid-19<\/span> we have ...","...coronavirus disease <span style=\"background-color: #FEE1E8\">covid-19<\/span> cause by ......drug against <span style=\"background-color: #FEE1E8\">covid-19<\/span> we have ...","...repurpose drug <span style=\"background-color: #FEE1E8\">library<\/span> against the ...","...repurpose drug <span style=\"background-color: #FEE1E8\">library<\/span> against the ...","...replication in <span style=\"background-color: #FEE1E8\">contrast<\/span> to commonly ...","...replication in <span style=\"background-color: #FEE1E8\">contrast<\/span> to commonly ...","...fragment screen <span style=\"background-color: #FEE1E8\">experiment<\/span> with molecule ...","...fragment screen <span style=\"background-color: #FEE1E8\">experiment<\/span> with molecule ...","...experiment with <span style=\"background-color: #FEE1E8\">molecule<\/span> of low ...","...of low <span style=\"background-color: #FEE1E8\">complexity<\/span> we screen ...","...of low <span style=\"background-color: #FEE1E8\">complexity<\/span> we screen ...","...drug in <span style=\"background-color: #FEE1E8\">clinical trial<\/span> from the ...","...in clinical <span style=\"background-color: #FEE1E8\">trial<\/span> from the ...","...in clinical <span style=\"background-color: #FEE1E8\">trial<\/span> from the ...","...the three-dimensional <span style=\"background-color: #FEE1E8\">protein<\/span> structure we ...","...the three-dimensional <span style=\"background-color: #FEE1E8\">protein<\/span> structure we ...","...three-dimensional protein <span style=\"background-color: #FEE1E8\">structure<\/span> we identify ...","...three-dimensional protein <span style=\"background-color: #FEE1E8\">structure<\/span> we identify ...","...cell-based viral <span style=\"background-color: #FEE1E8\">reduction<\/span> assay one ...","...cell-based viral <span style=\"background-color: #FEE1E8\">reduction<\/span> assay one ...","...show antiviral <span style=\"background-color: #FEE1E8\">activity<\/span> at nontoxic ...","...show antiviral <span style=\"background-color: #FEE1E8\">activity<\/span> at nontoxic ...","...at nontoxic <span style=\"background-color: #FEE1E8\">concentration<\/span> we identify ...","...at nontoxic <span style=\"background-color: #FEE1E8\">concentration<\/span> we identify ...","...identify two <span style=\"background-color: #FEE1E8\">allosteric<\/span> binding site ...","...allosteric binding <span style=\"background-color: #FEE1E8\">site<\/span> represent attractive ...","...represent attractive <span style=\"background-color: #FEE1E8\">target<\/span> for drug ...","...represent attractive <span style=\"background-color: #FEE1E8\">target<\/span> for drug ...","...for drug <span style=\"background-color: #FEE1E8\">development<\/span> against sars-cov-2...","...for drug <span style=\"background-color: #FEE1E8\">development<\/span> against sars-cov-2..."],["Q8386","Q622899","Q82069695","Q12136","Q810254","Q34777","Q826582","Q28389","Q103076","Q942537","Q959606","Q89469904","Q18975243","Q18975243","Q5780945","Q1652093","Q311183","Q19541","Q180711","Q81068910","Q84263196","Q7075","Q131454","Q690182","Q6849688","Q101965","Q790192","Q11369","Q723897","Q908207","Q30612","Q40745","Q8016240","Q8054","Q211935","Q47607","Q6671777","Q912546","Q1425997","Q423220","Q317949","Q152081","Q3686031","Q845326","Q2740415","Q104
29946951","Q17563434","Q175002","Q213713"],["?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?"],["<b>label:<\/b> DRUG<\/br><b>type:<\/b> xenobiotic<\/br><i>chemical substance having an effect on the body<i>","<b>label:<\/b> DRUG ENFORCEMENT ADMINISTRATION<\/br><b>type:<\/b> federal law enforcement agency of the United States<\/br><i>United States federal agency<i>","<b>label:<\/b> SARS-COV-2<\/br><b>type:<\/b> group or class of strains<\/br><i>strain of virus causing the ongoing pandemic of coronavirus disease 2019 (COVID-19)<i>","<b>label:<\/b> DISEASE<\/br><b>type:<\/b> health problem<\/br><i>abnormal condition negatively affecting organisms<i>","<b>label:<\/b> DISEASE-MODIFYING ANTIRHEUMATIC DRUG<\/br><b>type:<\/b> therapeutic use<\/br><i>drugs used to treat rheumatoid arthritis<i>","<b>label:<\/b> X-RAY<\/br><b>type:<\/b> electromagnetic radiation<\/br><i>electromagnetic radiation of wavelength ranging from 10 pm to 10 nm<i>","<b>label:<\/b> X-RAY CRYSTALLOGRAPHY<\/br><b>type:<\/b> crystallography<\/br><i>technique used for determining the atomic and molecular structure of a crystal, in which the crystalline atoms cause a beam of incident X-rays to diffract into many specific directions<i>","<b>label:<\/b> SCREENWRITER<\/br><b>type:<\/b> writer<\/br><i>writer who writes for TV, films, radio, comics or games<i>","<b>label:<\/b> SCREENPLAY<\/br><b>type:<\/b> literary genre<\/br><i>written work by screenwriters for a film or television program<i>","<b>label:<\/b> COMPOUND EYE<\/br><b>type:<\/b> eye<\/br><i>arthropod eye<i>","<b>label:<\/b> COMPOUND INTEREST<\/br><b>type:<\/b> interest<\/br><i>when interest is added to the principal of a deposit or loan, so that, from that moment on, the interest that has been added also earns interest<i>","<b>label:<\/b> CORONAVIRUS<\/br><b>type:<\/b> organisms known by a particular common name<\/br><i>group of related viruses that cause diseases in mammals and birds<i>","<b>label:<\/b> CORONAVIRUS DISEASE<\/br><b>type:<\/b> Coronaviridae infectious disease<\/br><i>diseases caused by coronaviruses<i>","<b>label:<\/b> CORONAVIRUS DISEASE<\/br><b>type:<\/b> infectious disease<\/br><i>diseases caused by coronaviruses<i>","<b>label:<\/b> SUFFERING<\/br><b>type:<\/b> qualia<\/br><i>pain, mental, or emotional unhappiness caused by bad things happening<i>","<b>label:<\/b> DATE<\/br><b>type:<\/b> Q29043273<\/br><i>edible fruit of a date palm<i>","<b>label:<\/b> DATE MASAMUNE<\/br><b>type:<\/b> human<\/br><i>daimyo of the Sengoku period to early-Edo period; 1st lord of Sendai<i>","<b>label:<\/b> SEARCH ENGINE<\/br><b>type:<\/b> software<\/br><i>application that collects and allows the searching of information on a computer system<i>","<b>label:<\/b> SEARCH ENGINE OPTIMISATION<\/br><b>type:<\/b> Internet marketing<\/br><i>practice of increasing online visibility in search engine results pages<i>","<b>label:<\/b> COVID-19 PANDEMIC<\/br><b>type:<\/b> public health emergency of international concern<\/br><i>ongoing pandemic of COVID-19, caused by the virus SARS-CoV-2<i>","<b>label:<\/b> COVID-19<\/br><b>type:<\/b> coronavirus disease<\/br><i>respiratory syndrome and infectious disease in humans, caused by SARS coronavirus 2<i>","<b>label:<\/b> LIBRARY<\/br><b>type:<\/b> facility<\/br><i>institution charged with the care of a collection of literary, musical, artistic, or reference materials, such as books, manuscripts, recordings, or films<i>","<b>label:<\/b> LIBRARY OF CONGRESS<\/br><b>type:<\/b> parliamentary archive<\/br><i>(de facto) national library of the United States of America<i>","<b>label:<\/b> CONTRAST<\/br><b>type:<\/b> difference<\/br><i>difference in luminance and/or color that makes objects visually distinguishable<i>","<b>label:<\/b> CONTRAST AGENT<\/br><b>type:<\/b> class of chemical substances by use<\/br><i>substance used in medical imaging to enhance the contrast of structures or fluids within the body<i>","<b>label:<\/b> EXPERIMENT<\/br><b>type:<\/b> test<\/br><i>
2994scientific procedure carried out to support, refute, or validate a hypothesis<i>","<b>label:<\/b> EXPERIMENTAL FILM<\/br><b>type:<\/b> film genre<\/br><i>cinematic works that are experimental form or content<i>","<b>label:<\/b> MOLECULE<\/br><b>type:<\/b> molecular entity<\/br><i>electrically neutral entity consisting of more than one atom (n > 1); rigorously, a molecule, in which n > 1 must correspond to a depression on the potential energy surface that is deep enough to confine at least one vibrational state<i>","<b>label:<\/b> COMPLEXITY<\/br><b>type:<\/b> type of property<\/br><i>properties of systems that cannot be simply described or modeled<i>","<b>label:<\/b> COMPLEXITY CLASS<\/br><b>type:<\/b> class<\/br><i>set of problems in computational complexity theory of related resource-based complexity<i>","<b>label:<\/b> CLINICAL TRIAL<\/br><b>type:<\/b> product testing<\/br><i>interventional study in clinical research<i>","<b>label:<\/b> TRIAL BY ORDEAL<\/br><b>type:<\/b> trial<\/br><i>ancient judicial practice to determine guilt through an unpleasant experience<i>","<b>label:<\/b> TRIAL<\/br><b>type:<\/b> legal proceeding<\/br><i>coming together of parties to a dispute, to present information in a tribunal<i>","<b>label:<\/b> PROTEIN<\/br><b>type:<\/b> second-order class<\/br><i>biological molecule consisting of chains of amino acid residues<i>","<b>label:<\/b> PROTEIN BIOSYNTHESIS<\/br><b>type:<\/b> biological process<\/br><i>cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain<i>","<b>label:<\/b> STRUCTURED QUERY LANGUAGE<\/br><b>type:<\/b> programming language<\/br><i>programming language for management and use of relational databases<i>","<b>label:<\/b> STRUCTURE<\/br><b>type:<\/b> entity<\/br><i>arrangement and organization of interrelated elements in an object or system, or the object or system so organized<i>","<b>label:<\/b> REDUCTION<\/br><b>type:<\/b> chemical reaction<\/br><i>gain of electrons in a chemical reaction<i>","<b>label:<\/b> REDUCTION<\/br><b>type:<\/b> arrangement<\/br><i>music term; arrangement or transcription of an existing score or composition in which complexity is lessened to make analysis, performance, or practice easier or clearer<i>","<b>label:<\/b> ACTIVITY<\/br><b>type:<\/b> intensive quantity<\/br><i>measure of the effective concentration of a species in a mixture<i>","<b>label:<\/b> ACTIVITY<\/br><b>type:<\/b> rate<\/br><i>physical quantity in nuclear physics, measured in becquerel<i>","<b>label:<\/b> CONCENTRATION CAMP<\/br><b>type:<\/b> camp<\/br><i>camp in which people are imprisoned or confined, commonly in large groups, without trial<i>","<b>label:<\/b> CONCENTRATION<\/br><b>type:<\/b> volumetric quantity<\/br><i>type of physical property; the abundance of a constituent divided by the total volume of a mixture<i>","<b>label:<\/b> ALLOSTERIC REGULATION<\/br><b>type:<\/b> regulation of catalytic activity<\/br><i>type of regulation of enzyme activity<i>","<b>label:<\/b> SITE-SPECIFIC ART<\/br><b>type:<\/b> art<\/br><i>artwork created for a certain place<i>","<b>label:<\/b> TARGET<\/br><b>type:<\/b> supermarket chain<\/br><i>a shopping center in the United States<i>","<b>label:<\/b> TARGET<\/br><b>type:<\/b> target<\/br><i>goal in archery and other sports<i>","<b>label:<\/b> DEVELOPMENTAL PSYCHOLOGY<\/br><b>type:<\/b> branch of psychology<\/br><i>scientific study of changes that occur in human beings over the course of their lives<i>","<b>label:<\/b> DEVELOPMENTAL BIOLOGY<\/br><b>type:<\/b> biology<\/br><i>explores the processes by which individual organisms grow and develop (ontogeny)<i>"]],"container":"<table class=\"compact striped\">\n  <thead>\n    <tr>\n      <th>text<\/th>\n      <th>item<\/th>\n      <th>valid?<\/th>\n      <th>details<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"dom":"Bfrtip","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"searchHighlight":true,"buttons":["csv","excel"],"columnDefs":[{"width":"300
2994px","targets":0},{"width":"500px","targets":3},{"width":"65px","targets":[1,2]},{"className":"dt-center","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[5,10,25,50,100],"rowCallback":"function(row, data) {\nvar value=data[2]; $(this.api().cell(row, 2).node()).css({'font-weight':'bold','background-color':value == \"yes\" ? \"#90ee90\" : null});\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
2994
2995</div>
2996<h3 id="case-2">Case 2</h3>
2997<div class="layout-chunk" data-layout="l-body-outset">
2998<details>
2999<summary>Show code</summary>
3000<div class="sourceCode">
3001<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>tables</span><span class='op'>[[</span><span class='fl'>2</span><span class='op'>]</span><span class='op'>]</span> <span class='op'>%&gt;%</span> 
3002  <span class='fu'>select</span><span class='op'>(</span><span class='va'>text</span>, <span class='va'>item</span>, <span class='va'>`valid?`</span>, <span class='va'>details</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3003  <span class='fu'>DT</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, escape <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='co'>#filter = 'top', </span>
3004            editable <span class='op'>=</span> <span class='cn'>TRUE</span>, class <span class='op'>=</span> <span class='st'>'compact striped'</span>,
3005             caption <span class='op'>=</span> <span class='fu'>htmltools</span><span class='fu'>::</span><span class='va'><a href='https://rdrr.io/pkg/htmltools/man/builder.html'>tags</a></span><span class='op'>$</span><span class='fu'>caption</span><span class='op'>(</span>style <span class='op'>=</span> <span class='st'>'caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;'</span>,
3006               <span class='st'>'Data: wikidata.org (see in the text).'</span><span class='op'>)</span>,
3007            extensions <span class='op'>=</span> <span class='st'>'Buttons'</span>,
3008            options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>searchHighlight <span class='op'>=</span> <span class='cn'>TRUE</span>,
3009                            dom <span class='op'>=</span> <span class='st'>'Bfrtip'</span>, buttons <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>'csv'</span>, <span class='st'>"excel"</span><span class='op'>)</span>, 
3010                           columnDefs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>
3011                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'300px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span>,
3012                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'500px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span>,
3013                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'65px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span>,
3014                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>className <span class='op'>=</span> <span class='st'>'dt-center'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
3015                  <span class='op'>)</span>
3016            <span class='op'>)</span> <span class='op'>%&gt;%</span> 
3017     <span class='fu'><a href='https://rdrr.io/pkg/DT/man/formatCurrency.html'>formatStyle</a></span><span class='op'>(</span><span class='st'>'valid?'</span>,  backgroundColor <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/DT/man/styleInterval.html'>styleEqual</a></span><span class='op'>(</span><span class='st'>'yes'</span>, <span class='st'>'#90ee90'</span><span class='op'>)</span>, fontWeight <span class='op'>=</span> <span class='st'>'bold'</span><span class='op'>)</span> 
3018</code></pre>
3019</div>
3020</details>
3021<div id="htmlwidget-dc6e35a8d8cf6d3c3d0f" style="width:100%;height:auto;" class="datatables html-widget"></div>
3022<script type="application/json" data-for="htmlwidget-dc6e35a8d8cf6d3c3d0f">{"x":{"filter":"none","extensions":["Buttons"],"caption":"<caption style=\"caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;\">Data: wikidata.org (see in the text).<\/caption>","editable":{"target":"cell","disable":{"columns":null}},"data":[["...of the <span style=\"background-color: #FEE1E8\">world<\/span> 's vertebrate ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's rivers ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's continental ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's river ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's surface ...","...of the <span style=\"background-color: #FEE1E8\">world<\/span> 's vertebrate ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's rivers ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's continental ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's river ......of the <span style=\"background-color: #FEE1E8\">world<\/span> 's surface ...","...index cumulative <span style=\"background-color: #FEE1E8\">change<\/span> in biodiversity ......reveal mark <span style=\"background-color: #FEE1E8\">change<\/span> in biodiversity ......greatest biodiversity <span style=\"background-color: #FEE1E8\">change<\/span> be primarily ...","...index cumulative <span style=\"background-color: #FEE1E8\">change<\/span> in biodiversity ......reveal mark <span style=\"background-color: #FEE1E8\">change<\/span> in biodiversity ......greatest biodiversity <span style=\"background-color: #FEE1E8\">change<\/span> be primarily ...","...change in <span style=\"background-color: #FEE1E8\">biodiversity<\/span> facets reveal ......change in <span style=\"background-color: #FEE1E8\">biodiversity<\/span> in gt ......be greatest <span style=\"background-color: #FEE1E8\">biodiversity<\/span> change be ...","...change in <span style=\"background-color: #FEE1E8\">biodiversity<\/span> facets reveal ......change in <span style=\"background-color: #FEE1E8\">biodiversity<\/span> in gt ......be greatest <span style=\"background-color: #FEE1E8\">biodiversity<\/span> change be ...","...world 's <span style=\"background-color: #FEE1E8\">rivers<\/span> cover gt ......impacte present-day <span style=\"background-color: #FEE1E8\">rivers<\/span> be more ......in temperate <span style=\"background-color: #FEE1E8\">rivers<\/span> where the ...","...world 's <span style=\"background-color: #FEE1E8\">rivers<\/span> cover gt ......impacte present-day <span style=\"background-color: #FEE1E8\">rivers<\/span> be more ......in temperate <span style=\"background-color: #FEE1E8\">rivers<\/span> where the ...","...world 's <span style=\"background-color: #FEE1E8\">river<\/span>s cover gt ......world 's <span style=\"background-color: #FEE1E8\">river<\/span> length whereas ......surface and <span style=\"background-color: #FEE1E8\">river<\/span> length aremain ......impacte present-day <span style=\"background-color: #FEE1E8\">river<\/span>s be more ......in temperate <span style=\"background-color: #FEE1E8\">river<\/span>s where the ......due to <span style=\"background-color: #FEE1E8\">river<\/span> fragmentation and ...","...world 's <span style=\"background-color: #FEE1E8\">river<\/span>s cover gt ......world 's <span style=\"background-color: #FEE1E8\">river<\/span> length whereas ......surface and <span style=\"background-color: #FEE1E8\">river<\/span> length aremain ......impacte present-day <span style=\"background-color: #FEE1E8\">river<\/span>s be more ......in temperate <span style=\"background-color: #FEE1E8\">river<\/span>s where the ......due to <span style=\"background-color: #FEE1E8\">river<\/span> fragmentation and ...","...freshwater <span style=\"background-color: #FEE1E8\">fish<\/span> represent one-fourth ......have more <span style=\"background-color: #FEE1E8\">fish<\/span> species with ...","...freshwater <span style=\"background-color: #FEE1E8\">fish<\/span> represent one-fourth ......have more <span style=\"background-color: #FEE1E8\">fish<\/span> species with ...","...'s continental <span style=\"background-color: #FEE1E8\">surface<\/span> and gt ......world 's <span style=\"background-color: #FEE1E8\">surface<\/span> and river ...","...'s continental <span style=\"background-color: #FEE1E8\">surface<\/span> and gt ......world 's <span style=\"background-color: #FEE1E8\">surface<\/span> and river ...","...'s river <span style=\"background-color: #FEE1E8\">length<\/span> whereas lt ......and river <span style=\"background-color: #FEE1E8\">length<\/span> aremain least ...","...'s river <span style=\"background-color: #FEE1E8\">length<\/span> whereas lt ......and river <span style=\"background-color: #FEE1E8\">length<\/span> aremain least ...","...more fish <span style=\"background-color: #FEE1E8\">species<\/span> with more ......of non-native <span style=\"background-color: #FEE1E8\">species<\/span>...","...more fish <span style=\"background-color: #FEE1E8\">species<\/span> with more ......of non-native <span style=\"background-color: #FEE1E8\">species<\/span>...","...<span style=\"background-color: #FEE1E8\">freshwater fish<\/span> represent one-fourth ...","...<span style=\"background-color: #FEE1E8\">freshwater fish<\/span> represent one-fourth ...","...world 's <span style=\"background-color: #FEE1E8\">vertebrate<\/span> and provide ...","...world 's <span style=\"background-color: #FEE1E8\">vertebrate<\/span>
3022 and provide ...","...provide irreplaceable <span style=\"background-color: #FEE1E8\">goods<\/span> and service ...","...provide irreplaceable <span style=\"background-color: #FEE1E8\">goods<\/span> and service ...","...goods and <span style=\"background-color: #FEE1E8\">service<\/span> but be ...","...goods and <span style=\"background-color: #FEE1E8\">service<\/span> but be ...","...by human <span style=\"background-color: #FEE1E8\">activity<\/span> a new ...","...by human <span style=\"background-color: #FEE1E8\">activity<\/span> a new ...","...a new <span style=\"background-color: #FEE1E8\">index<\/span> cumulative change ...","...a new <span style=\"background-color: #FEE1E8\">index<\/span> cumulative change ...","...in biodiversity <span style=\"background-color: #FEE1E8\">facets<\/span> reveal mark ...","...more diverse <span style=\"background-color: #FEE1E8\">morphology<\/span> and longer ...","...more diverse <span style=\"background-color: #FEE1E8\">morphology<\/span> and longer ...","...longer evolutionary <span style=\"background-color: #FEE1E8\">legacy<\/span> in temperate ...","...aremain least <span style=\"background-color: #FEE1E8\">impact<\/span>e present-day rivers ......where the <span style=\"background-color: #FEE1E8\">impact<\/span> have be ...","...aremain least <span style=\"background-color: #FEE1E8\">impact<\/span>e present-day rivers ......where the <span style=\"background-color: #FEE1E8\">impact<\/span> have be ...","...to river <span style=\"background-color: #FEE1E8\">fragmentation<\/span> and introduction ..."],["Q362","Q361","Q1150070","Q2314651","Q47041","Q864294","Q49243","Q108111","Q4022","Q19686","Q152","Q14373","Q484298","Q170749","Q36253","Q836595","Q7432","Q203986","Q1072742","Q863904","Q25241","Q3634677","Q28877","Q9166501","Q7406919","Q1220872","Q423220","Q317949","Q184848","Q873506","Q5428531","Q38311","Q183252","Q2358400","Q55818","Q4115667","Q2274559"],["?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?"],["<b>label:<\/b> WORLD WAR II<\/br><b>type:<\/b> historical period<\/br><i>1939–1945 global war between the Allied and Axis Powers<i>","<b>label:<\/b> WORLD WAR I<\/br><b>type:<\/b> historical period<\/br><i>1914–1918 global war, centered in Europe, between the Allied and Central Powers<i>","<b>label:<\/b> CHANGE<\/br><b>type:<\/b> philosophical concept<\/br><i>process, event or action that deviates from the present state<i>","<b>label:<\/b> CHANGE<\/br><b>type:<\/b> musical group<\/br><i>Italian-American post-disco group<i>","<b>label:<\/b> BIODIVERSITY<\/br><b>type:<\/b> diversity<\/br><i>degree of variation of life forms<i>","<b>label:<\/b> BIODIVERSITY HOTSPOT<\/br><b>type:<\/b> bioregion<\/br><i>biogeographic region with significant levels of biodiversity<i>","<b>label:<\/b> RIVERSIDE, CALIFORNIA<\/br><b>type:<\/b> charter city<\/br><i>county seat of Riverside County, California, United States<i>","<b>label:<\/b> RIVERSIDE COUNTY<\/br><b>type:<\/b> county of California<\/br><i>county in California, United States<i>","<b>label:<\/b> RIVER<\/br><b>type:<\/b> natural watercourse<\/br><i>larger natural watercourse<i>","<b>label:<\/b> RIVER THAMES<\/br><b>type:<\/b> river<\/br><i>river in southern England<i>","<b>label:<\/b> FISH<\/br><b>type:<\/b> aquatic animal<\/br><i>vertebrate animal that lives in water and (typically) has gills<i>","<b>label:<\/b> FISHING<\/br><b>type:<\/b> hunting<\/br><i>activity of trying to catch fish<i>","<b>label:<\/b> SURFACE<\/br><b>type:<\/b> topological manifold<\/br><i>two-dimensional manifold, and, as such, may be an \"abstract surface\" not embedded in any Euclidean space<i>","<b>label:<\/b> SURFACE TENSION<\/br><b>type:<\/b> physical phenomenon<\/br><i>elastic tendency of a fluid surface which makes it acquire the least surface area possible<i>","<b>label:<\/b> LENGTH<\/br><b>type:<\/b> ISQ base quantity<\/br><i>measured dimension of an object in a physical space<i>","<b>label:<\/b> LENGTH CONTRACTION<\/br><b>type:<\/b> physical phenomenon<\/br><i>The contraction of length in the direction of propagation in Minkowski space<i>","<b>label:<\/b> SPECIES<\/br><b>type:<\/b> rank<\/br><i>one of the basic units of biological classification and a taxonomic rank<i>","<b>label:<\/b> SPECIESISM<\/br><b>type:<\/b> discrimination<\/br><i>special consideration to individuals solely on the basis of their species membership<i>","<b>label:<\/b> FRESHWATER FISH<\/br><b>type:<\/b> fish<\/br><i>fish that live all or much of their lives in freshwater<i>","<b>label:<\/b> FRESHWATER FISHING<\/br><b>type:<\/b> fishing<\/br><i>NA<i>","<b>label:<\/b> VERTEBRATE<\/br><b>type:<\/b> Chordata<\/br><i>subphylum of chordates<i>","<b>label:<\/b> VERTEBRATE PALEONTOLOGY<\/br><b>type:<\/b> vertebrate zoology<\/br><i>scientific study of prehistoric and fossil vertebrates<i>","<b>label:<\/b> GOODS<\/br><b>type:<\/b> goods and services<\/br><i>tangible and intangible thing, except labor tied services, that satisfies human wants and provides utility<i>","<b>label:<\/b> GOODS WAGON<\/br><b>type:<\/b> railroad car<\/br><i>unpowered railway vehicle used for freight transport<i>","<b>label:<\/b> SERVICE<\/br><b>type:<\/b> spatio-temporal entity<\/br><i>activity that directly satisfies wants without producing a lasting asset<i>","<b>label:<\/b> SERVICE<\/br><b>type:<\/b> software component<\/br><i>set of related software functionalities made available to be reused for different purposes<i>","<b>label:<\/b> ACTIVITY<\/br><b>type:<\/b> intensive quantity<\/br><i>measure of the effective concentration of a species in a mixture<i>","<b>label:<\/b> ACTIVITY<\/br><b>type:<\/b> rate<\/br><i>physical quantity in nuclear physics, measured in becquerel<i>","<b>label:<\/b> INDEX FINGER<\/br><b>type:<\/b> finger<\/br><i>finger<i>","<b>label:<\/b> INDEX<\/br><b>type:<\/b> list<\/br><i>list of words or phrases<i>","<b>label:<\/b> FACETS MULTI-MEDIA<\/br><b>type:<\/b> cinematheque<\/br><i>cinemathèque in Chicago, Illinois, United States<i>","<b>label:<\/b> MORPHOLOGY<\/br><b>type:<\/b> linguistics<\/br><i>linguistics: the identification, analysis and description of the structure of a given language's morphemes and other linguistic units<i>","<b>label:<\/b> MORPHOLOGY<\/br><b>type:<\/b> biology<\/br><i>biology: the structure and form of organisms<i>","<b>label:<\/b> LEGACY<\/br><b>type:<\/b> record label<\/br><i>US record label; imprint of Sony Music Entertainment<i>","<b>label:<\/b> IMPACT CRATER<\/br><b>type:<\/b> astronomical object type<\/br><i>circular depression on a celestial object formed by a hypervelocity impact of a smaller body<i>","<b>label:<\/b> IMPACT<\/br><b>type:<\/b> occurrence<\/br><i>high force or shock applied over a short time period when two or more bodies collide<i>","<b>label:<\/b> FRAGMENTATION<\/br><b>type:<\/b> fission<\/br><i>Form of asexual reproduction<i>"]],"container":"<table class=\"compact striped\">\n  <thead>\n    <tr>\n      <th>text<\/th>\n      <th>item<\/th>\n      <th>valid?<\/th>\n      <th>details<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"dom":"Bfrtip","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"searchHighlight":true,"buttons":["csv","excel"],"columnDefs":[{"width":"300
3022px","targets":0},{"width":"500px","targets":3},{"width":"65px","targets":[1,2]},{"className":"dt-center","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[5,10,25,50,100],"rowCallback":"function(row, data) {\nvar value=data[2]; $(this.api().cell(row, 2).node()).css({'font-weight':'bold','background-color':value == \"yes\" ? \"#90ee90\" : null});\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
3022
3023</div>
3024<h3 id="case-3">Case 3</h3>
3025<div class="layout-chunk" data-layout="l-body-outset">
3026<details>
3027<summary>Show code</summary>
3028<div class="sourceCode">
3029<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>tables</span><span class='op'>[[</span><span class='fl'>3</span><span class='op'>]</span><span class='op'>]</span> <span class='op'>%&gt;%</span> 
3030  <span class='fu'>select</span><span class='op'>(</span><span class='va'>text</span>, <span class='va'>item</span>, <span class='va'>`valid?`</span>, <span class='va'>details</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3031  <span class='fu'>DT</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, escape <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='co'>#filter = 'top', </span>
3032            editable <span class='op'>=</span> <span class='cn'>TRUE</span>, class <span class='op'>=</span> <span class='st'>'compact striped'</span>,
3033             caption <span class='op'>=</span> <span class='fu'>htmltools</span><span class='fu'>::</span><span class='va'><a href='https://rdrr.io/pkg/htmltools/man/builder.html'>tags</a></span><span class='op'>$</span><span class='fu'>caption</span><span class='op'>(</span>style <span class='op'>=</span> <span class='st'>'caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;'</span>,
3034               <span class='st'>'Data: wikidata.org (see in the text).'</span><span class='op'>)</span>,
3035            extensions <span class='op'>=</span> <span class='st'>'Buttons'</span>,
3036            options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>searchHighlight <span class='op'>=</span> <span class='cn'>TRUE</span>,
3037                            dom <span class='op'>=</span> <span class='st'>'Bfrtip'</span>, buttons <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>'csv'</span>, <span class='st'>"excel"</span><span class='op'>)</span>, 
3038                           columnDefs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>
3039                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'300px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span>,
3040                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'500px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span>,
3041                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'65px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span>,
3042                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>className <span class='op'>=</span> <span class='st'>'dt-center'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
3043                  <span class='op'>)</span>
3044            <span class='op'>)</span> <span class='op'>%&gt;%</span> 
3045     <span class='fu'><a href='https://rdrr.io/pkg/DT/man/formatCurrency.html'>formatStyle</a></span><span class='op'>(</span><span class='st'>'valid?'</span>,  backgroundColor <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/DT/man/styleInterval.html'>styleEqual</a></span><span class='op'>(</span><span class='st'>'yes'</span>, <span class='st'>'#90ee90'</span><span class='op'>)</span>, fontWeight <span class='op'>=</span> <span class='st'>'bold'</span><span class='op'>)</span> 
3046</code></pre>
3047</div>
3048</details>
3049<div id="htmlwidget-cebcacfa094714c7b16c" style="width:100%;height:auto;" class="datatables html-widget"></div>
3050<script type="application/json" data-for="htmlwidget-cebcacfa094714c7b16c">{"x":{"filter":"none","extensions":["Buttons"],"caption":"<caption style=\"caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;\">Data: wikidata.org (see in the text).<\/caption>","editable":{"target":"cell","disable":{"columns":null}},"data":[["...surface of <span style=\"background-color: #FEE1E8\">neutron<\/span>-rich heavy ......with a <span style=\"background-color: #FEE1E8\">neutron<\/span> skin create ......by excess <span style=\"background-color: #FEE1E8\">neutron<\/span> provide a ......study dilute <span style=\"background-color: #FEE1E8\">neutron<\/span>-rich matter ......surface of <span style=\"background-color: #FEE1E8\">neutron<\/span>-rich tin ......and the <span style=\"background-color: #FEE1E8\">neutron<\/span> skin this ......between the <span style=\"background-color: #FEE1E8\">neutron<\/span>-skin thickness ......for understanding <span style=\"background-color: #FEE1E8\">neutron<\/span> star our ...","...surface of <span style=\"background-color: #FEE1E8\">neutron<\/span>-rich heavy ......with a <span style=\"background-color: #FEE1E8\">neutron<\/span> skin create ......by excess <span style=\"background-color: #FEE1E8\">neutron<\/span> provide a ......study dilute <span style=\"background-color: #FEE1E8\">neutron<\/span>-rich matter ......surface of <span style=\"background-color: #FEE1E8\">neutron<\/span>-rich tin ......and the <span style=\"background-color: #FEE1E8\">neutron<\/span> skin this ......between the <span style=\"background-color: #FEE1E8\">neutron<\/span>-skin thickness ......for understanding <span style=\"background-color: #FEE1E8\">neutron<\/span> star our ...","...the <span style=\"background-color: #FEE1E8\">surface<\/span> of neutron-rich ......at the <span style=\"background-color: #FEE1E8\">surface<\/span> of neutron-rich ...","...the <span style=\"background-color: #FEE1E8\">surface<\/span> of neutron-rich ......at the <span style=\"background-color: #FEE1E8\">surface<\/span> of neutron-rich ...","...a neutron <span style=\"background-color: #FEE1E8\">skin<\/span> create by ......the neutron <span style=\"background-color: #FEE1E8\">skin<\/span> this result ......<span style=\"background-color: #FEE1E8\">skin<\/span> thickness and ...","...a neutron <span style=\"background-color: #FEE1E8\">skin<\/span> create by ......the neutron <span style=\"background-color: #FEE1E8\">skin<\/span> this result ......<span style=\"background-color: #FEE1E8\">skin<\/span> thickness and ...","...quasi-free a <span style=\"background-color: #FEE1E8\">cluster<\/span> knockout reaction ......of a <span style=\"background-color: #FEE1E8\">cluster<\/span> at the ......<span style=\"background-color: #FEE1E8\">cluster<\/span> formation and ...","...quasi-free a <span style=\"background-color: #FEE1E8\">cluster<\/span> knockout reaction ......of a <span style=\"background-color: #FEE1E8\">cluster<\/span> at the ......<span style=\"background-color: #FEE1E8\">cluster<\/span> formation and ...","...cluster knockout <span style=\"background-color: #FEE1E8\">reaction<\/span> we obtain ......of the <span style=\"background-color: #FEE1E8\">reaction<\/span> cross section ...","...cluster knockout <span style=\"background-color: #FEE1E8\">reaction<\/span> we obtain ......of the <span style=\"background-color: #FEE1E8\">reaction<\/span> cross section ...","...for the <span style=\"background-color: #FEE1E8\">formation<\/span> of a ......between a-cluster <span style=\"background-color: #FEE1E8\">formation<\/span> and the ...","...neutron-rich heavy <span style=\"background-color: #FEE1E8\">nuclei<\/span> with a ...","...neutron-rich heavy <span style=\"background-color: #FEE1E8\">nuclei<\/span> with a ...","...create by <span style=\"background-color: #FEE1E8\">excess<\/span> neutron provide ...","...a important <span style=\"background-color: #FEE1E8\">terrestrial<\/span> model system ...","...a important <span style=\"background-color: #FEE1E8\">terrestrial<\/span> model system ...","...important terrestrial <span style=\"background-color: #FEE1E8\">model<\/span> system to ...","...important terrestrial <span style=\"background-color: #FEE1E8\">model<\/span> system to ...","...terrestrial model <span style=\"background-color: #FEE1E8\">system<\/span> to study ...","...terrestrial model <span style=\"background-color: #FEE1E8\">system<\/span> to study ...","...dilute neutron-rich <span style=\"background-color: #FEE1E8\">matter<\/span> by use ...","...dilute neutron-rich <span style=\"background-color: #FEE1E8\">matter<\/span> by use ...","...a cluster <span style=\"background-color: #FEE1E8\">knockout<\/span> reaction we ...","...direct experimental <span style=\"background-color: #FEE1E8\">evidence<\/span> for the ...","...direct experimental <span style=\"background-color: #FEE1E8\">evidence<\/span> for the ...","...of neutron-rich <span style=\"background-color: #FEE1E8\">tin<\/span> isotope the ...","...of neutron-rich <span style=\"background-color: #FEE1E8\">tin<\/span> isotope the ...","...the reaction <span style=\"background-color: #FEE1E8\">cross<\/span> section with ...","...the reaction <span style=\"background-color: #FEE1E8\">cross<\/span> section with ...","...the reaction <span style=\"background-color: #FEE1E8\">cross section<\/span> with increase ...","...reaction cross <span style=\"background-color: #FEE1E8\">section<\/span> with increase ...","...reaction cross <span style=\"background-color: #FEE1E8\">section<\/span> with increase ...","...with increase <span style=\"background-color: #FEE1E8\">mass number<\/span> in excellent ...","...increase mass <span style=\"background-color: #FEE1E8\">number<\/span> in excellent ...","...increase mass <span style=\"background-color: #FEE1E8\">number<\/span> in excellent ...","...in excellent <span style=\"background-color: #FEE1E8\">agreement<\/span> with the ...","...in excellent <span style=\"background-color: #FEE1E8\">agreement<\/span> with the ...","...the theoretical <span style=\"background-color: #FEE1E8\">prediction<\/span> imply a ...","...in turn <span style=\"background-color: #FEE1E8\">call<\/span> for a ...","...in turn <span style=\"background-color: #FEE1E8\">call<\/span> for a ...","...for a <span style=\"background-color: #FEE1E8\">revision<\/span> of the ...","...of the <span style=\"background-color: #FEE1E8\">correlation<\/span> between the ...","...the neutron-skin <span style=\"background-color: #FEE1E8\">thickness<\/span> and the ...","...and the <span style=\"background-color: #FEE1E8\">density<\/span>
3050 dependence of ...","...and the <span style=\"background-color: #FEE1E8\">density<\/span> dependence of ...","...the symmetry <span style=\"background-color: #FEE1E8\">energy<\/span> which be ...","...the symmetry <span style=\"background-color: #FEE1E8\">energy<\/span> which be ...","...a natural <span style=\"background-color: #FEE1E8\">explanation<\/span> for the ...","...of a <span style=\"background-color: #FEE1E8\">particle<\/span> in a ...","...of a <span style=\"background-color: #FEE1E8\">particle<\/span> in a ..."],["Q2348","Q4202","Q484298","Q170749","Q1074","Q238020","Q184158","Q622825","Q192957","Q3394849","Q736917","Q123619","Q863908","Q92628454","Q128207","Q1060363","Q4610556","Q213907","Q58778","Q3516404","Q35758","Q1374","Q1364740","Q176763","Q1347572","Q1096","Q131814","Q40843","Q179687","Q17128025","Q1086353","Q1930808","Q101395","Q11563","Q12479","Q331647","Q829903","Q748250","Q12681","Q105037","Q2083688","Q186290","Q3589038","Q29539","Q1048589","Q11379","Q192704","Q7958","Q18334","Q130825"],["?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?"],["<b>label:<\/b> NEUTRON<\/br><b>type:<\/b> nucleon<\/br><i>nucleon (constituent of the nucleus of the atom) that has neutral electric charge (no charge); symbol n<i>","<b>label:<\/b> NEUTRON STAR<\/br><b>type:<\/b> compact star<\/br><i>Collapsed core of a massive star<i>","<b>label:<\/b> SURFACE<\/br><b>type:<\/b> topological manifold<\/br><i>two-dimensional manifold, and, as such, may be an \"abstract surface\" not embedded in any Euclidean space<i>","<b>label:<\/b> SURFACE TENSION<\/br><b>type:<\/b> physical phenomenon<\/br><i>elastic tendency of a fluid surface which makes it acquire the least surface area possible<i>","<b>label:<\/b> SKIN<\/br><b>type:<\/b> anatomical structure<\/br><i>soft outer covering organ of vertebrates<i>","<b>label:<\/b> SKIN<\/br><b>type:<\/b> human<\/br><i>English singer<i>","<b>label:<\/b> CLUSTER MUNITION<\/br><b>type:<\/b> bomb<\/br><i>munition containing multiple submunitions meant to disperse effects of the munitions<i>","<b>label:<\/b> CLUSTER ANALYSIS<\/br><b>type:<\/b> data analysis<\/br><i>task of grouping a set of objects in such a way that objects in the same group (called a cluster) are more similar (in some sense or another) to each other than to those in other groups (clusters)<i>","<b>label:<\/b> REACTIONARY<\/br><b>type:<\/b> political ideology<\/br><i>describes a political view that favors previous political aspects or states over present ones<i>","<b>label:<\/b> REACTION RATE<\/br><b>type:<\/b> scalar quantity<\/br><i>for a reactant or product in a particular reaction is intuitively defined as how quickly or slowly a reaction takes place<i>","<b>label:<\/b> FORMATION<\/br><b>type:<\/b> lithostratigraphic unit<\/br><i>body of rock identified by lithic characteristics and stratigraphic position; it is usually but not necessarily tabular and is mappable at the Earth's surface or traceable in the subsurface. Smaller than a subgroup<i>","<b>label:<\/b> NUCLEIC ACID<\/br><b>type:<\/b> structural class of chemical compounds<\/br><i>large biomolecules essential to known life<i>","<b>label:<\/b> NUCLEIC ACID SEQUENCE<\/br><b>type:<\/b> nucleic acid structure<\/br><i>succession of letters that indicate the order of nucleotides within a DNA (using GACT) or RNA (GACU) molecule<i>","<b>label:<\/b> EXCESS<\/br><b>type:<\/b> lifestyle<\/br><i>lack of moderation<i>","<b>label:<\/b> TERRESTRIAL PLANET<\/br><b>type:<\/b> astronomical object type<\/br><i>planet that is composed primarily of silicate rocks or metals. Within the Solar System, the terrestrial planets are the inner planets closest to the Sun, i.e. Mercury, Venus, Earth, and Mars<i>","<b>label:<\/b> TERRESTRIAL TRUNKED RADIO<\/br><b>type:<\/b> European norm<\/br><i>standard for a trunked radio systems<i>","<b>label:<\/b> MODEL<\/br><b>type:<\/b> profession<\/br><i>person employed to display, advertise and promote products, or to serve as a visual aid<i>","<b>label:<\/b> MODEL ORGANISM<\/br><b>type:<\/b> research object<\/br><i>organisms used to study biology across species<i>","<b>label:<\/b> SYSTEM<\/br><b>type:<\/b> structure<\/br><i>set of interacting or interdependent components<i>","<b>label:<\/b> SYSTEMATICS<\/br><b>type:<\/b> systematics<\/br><i>study of relationships between organisms<i>","<b>label:<\/b> MATTER<\/br><b>type:<\/b> material substance<\/br><i>
3050substance that has rest mass and volume, or several other definitions<i>","<b>label:<\/b> MATTERHORN<\/br><b>type:<\/b> tourist attraction<\/br><i>mountain in the Pennine Alps on the border between Switzerland and Italy<i>","<b>label:<\/b> KNOCKOUT MOUSE<\/br><b>type:<\/b> genetically modified mouse<\/br><i>genetically modified mouse used in gene research<i>","<b>label:<\/b> EVIDENCE<\/br><b>type:<\/b> product<\/br><i>body of facts in a legal proceding<i>","<b>label:<\/b> EVIDENCE<\/br><b>type:<\/b> source of information<\/br><i>anything presented in support of an assertion<i>","<b>label:<\/b> TIN<\/br><b>type:<\/b> metal<\/br><i>element with the atomic number of 50<i>","<b>label:<\/b> TINA TURNER<\/br><b>type:<\/b> human<\/br><i>American-born singer, dancer, actress, and author; naturalized Swiss citizen<i>","<b>label:<\/b> CROSS<\/br><b>type:<\/b> religious symbol<\/br><i>geometrical figure<i>","<b>label:<\/b> CROSS-COUNTRY SKIING<\/br><b>type:<\/b> type of sport<\/br><i>competitive winter sport<i>","<b>label:<\/b> CROSS SECTION<\/br><b>type:<\/b> physical quantity<\/br><i>measure of probability that a specific process will take place in a collision of two particles<i>","<b>label:<\/b> SECTION D'OR<\/br><b>type:<\/b> art group<\/br><i>art group<i>","<b>label:<\/b> SECTION MODULUS<\/br><b>type:<\/b> physical quantity<\/br><i>NA<i>","<b>label:<\/b> MASS NUMBER<\/br><b>type:<\/b> count variable<\/br><i>number of heavy particles in the atomic nucleus<i>","<b>label:<\/b> NUMBER<\/br><b>type:<\/b> quantity<\/br><i>mathematical object used to count, label, and measure<i>","<b>label:<\/b> NUMBER THEORY<\/br><b>type:<\/b> area of mathematics<\/br><i>branch of pure mathematics devoted primarily to the study of the integers<i>","<b>label:<\/b> AGREEMENT ON TRADE-RELATED ASPECTS OF INTELLECTUAL PROPERTY RIGHTS<\/br><b>type:<\/b> treaty<\/br><i>treaty of the WTO<i>","<b>label:<\/b> AGREEMENT<\/br><b>type:<\/b> inflection<\/br><i>-or versus -er<i>","<b>label:<\/b> PREDICTION<\/br><b>type:<\/b> occurrence<\/br><i>statement about an uncertain event, which is often based upon experience or knowledge<i>","<b>label:<\/b> CALLIGRAPHY<\/br><b>type:<\/b> art genre<\/br><i>visual art related to writing<i>","<b>label:<\/b> CALLAO<\/br><b>type:<\/b> seaport<\/br><i>city and main seaport in Peru<i>","<b>label:<\/b> REVISIONISM<\/br><b>type:<\/b> political ideology<\/br><i>various ideas, principles and theories that are based on a significant revision of fundamental Marxist premises; often used as a derogatory term by more “orthodox” Marxists<i>","<b>label:<\/b> CORRELATION<\/br><b>type:<\/b> relation<\/br><i>any statistical relationship, whether causal or not, between two random variables or bivariate data<i>","<b>label:<\/b> THICKNESS<\/br><b>type:<\/b> size<\/br><i>extent from one surface to the opposite, usually in the smallest solid dimension<i>","<b>label:<\/b> DENSITY<\/br><b>type:<\/b> measured quantity<\/br><i>mass per volume<i>","<b>label:<\/b> DENSITY FUNCTIONAL THEORY<\/br><b>type:<\/b> theory<\/br><i>computational quantum mechanical modelling method to investigate the electronic structure<i>","<b>label:<\/b> ENERGY<\/br><b>type:<\/b> physical quantity<\/br><i>measure for the ability of a system to do work<i>","<b>label:<\/b> ENERGY EFFICIENCY<\/br><b>type:<\/b> effectiveness<\/br><i>ratio between the useful output and the input of a machine<i>","<b>label:<\/b> EXPLANATION<\/br><b>type:<\/b> description<\/br><i>set of statements constructed to describe a set of facts<i>","<b>label:<\/b> PARTICLE PHYSICS<\/br><b>type:<\/b> physics<\/br><i>branch of physics<i>","<b>label:<\/b> PARTICLE ACCELERATOR<\/br><b>type:<\/b> facility<\/br><i>device to propel charged particles to high speeds<i>"]],"container":"<table class=\"compact striped\">\n  <thead>\n    <tr>\n      <th>text<\/th>\n      <th>item<\/th>\n      <th>valid?<\/th>\n      <th>details<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"dom":"Bfrtip","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"searchHighlight":true,"buttons":["csv","excel"],"columnDefs":[{"width":"300
3050px","targets":0},{"width":"500px","targets":3},{"width":"65px","targets":[1,2]},{"className":"dt-center","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[5,10,25,50,100],"rowCallback":"function(row, data) {\nvar value=data[2]; $(this.api().cell(row, 2).node()).css({'font-weight':'bold','background-color':value == \"yes\" ? \"#90ee90\" : null});\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
3050
3051</div>
3052<h3 id="case-4">Case 4</h3>
3053<div class="layout-chunk" data-layout="l-body-outset">
3054<details>
3055<summary>Show code</summary>
3056<div class="sourceCode">
3057<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>tables</span><span class='op'>[[</span><span class='fl'>4</span><span class='op'>]</span><span class='op'>]</span> <span class='op'>%&gt;%</span> 
3058  <span class='fu'>select</span><span class='op'>(</span><span class='va'>text</span>, <span class='va'>item</span>, <span class='va'>`valid?`</span>, <span class='va'>details</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3059  <span class='fu'>DT</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, escape <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='co'>#filter = 'top', </span>
3060            editable <span class='op'>=</span> <span class='cn'>TRUE</span>, class <span class='op'>=</span> <span class='st'>'compact striped'</span>,
3061             caption <span class='op'>=</span> <span class='fu'>htmltools</span><span class='fu'>::</span><span class='va'><a href='https://rdrr.io/pkg/htmltools/man/builder.html'>tags</a></span><span class='op'>$</span><span class='fu'>caption</span><span class='op'>(</span>style <span class='op'>=</span> <span class='st'>'caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;'</span>,
3062               <span class='st'>'Data: wikidata.org (see in the text).'</span><span class='op'>)</span>,
3063            extensions <span class='op'>=</span> <span class='st'>'Buttons'</span>,
3064            options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>searchHighlight <span class='op'>=</span> <span class='cn'>TRUE</span>,
3065                            dom <span class='op'>=</span> <span class='st'>'Bfrtip'</span>, buttons <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>'csv'</span>, <span class='st'>"excel"</span><span class='op'>)</span>, 
3066                           columnDefs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>
3067                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'300px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span>,
3068                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'500px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span>,
3069                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'65px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span>,
3070                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>className <span class='op'>=</span> <span class='st'>'dt-center'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
3071                  <span class='op'>)</span>
3072            <span class='op'>)</span> <span class='op'>%&gt;%</span> 
3073     <span class='fu'><a href='https://rdrr.io/pkg/DT/man/formatCurrency.html'>formatStyle</a></span><span class='op'>(</span><span class='st'>'valid?'</span>,  backgroundColor <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/DT/man/styleInterval.html'>styleEqual</a></span><span class='op'>(</span><span class='st'>'yes'</span>, <span class='st'>'#90ee90'</span><span class='op'>)</span>, fontWeight <span class='op'>=</span> <span class='st'>'bold'</span><span class='op'>)</span> 
3074</code></pre>
3075</div>
3076</details>
3077<div id="htmlwidget-5effa923a5624bdd1235" style="width:100%;height:auto;" class="datatables html-widget"></div>
3078<script type="application/json" data-for="htmlwidget-5effa923a5624bdd1235">{"x":{"filter":"none","extensions":["Buttons"],"caption":"<caption style=\"caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;\">Data: wikidata.org (see in the text).<\/caption>","editable":{"target":"cell","disable":{"columns":null}},"data":[["...we use <span style=\"background-color: #FEE1E8\">time<\/span> series to ......mean exit <span style=\"background-color: #FEE1E8\">time<\/span> from the ......at a <span style=\"background-color: #FEE1E8\">time<\/span> when high-resolution ......<span style=\"background-color: #FEE1E8\">time<\/span> series be ...","...we use <span style=\"background-color: #FEE1E8\">time<\/span> series to ......mean exit <span style=\"background-color: #FEE1E8\">time<\/span> from the ......at a <span style=\"background-color: #FEE1E8\">time<\/span> when high-resolution ......<span style=\"background-color: #FEE1E8\">time<\/span> series be ...","...by a <span style=\"background-color: #FEE1E8\">series<\/span> of minor ......use time <span style=\"background-color: #FEE1E8\">series<\/span> to fit ......high-resolution time <span style=\"background-color: #FEE1E8\">series<\/span> be become ...","...the largest <span style=\"background-color: #FEE1E8\">perturbation<\/span> from which ......minor synergistic <span style=\"background-color: #FEE1E8\">perturbation<\/span> rather than ...","...its original <span style=\"background-color: #FEE1E8\">state<\/span> however a ......into another <span style=\"background-color: #FEE1E8\">state<\/span> may often ...","...however a <span style=\"background-color: #FEE1E8\">transition<\/span> into another ......a critical <span style=\"background-color: #FEE1E8\">transition<\/span> at a ...","...we use <span style=\"background-color: #FEE1E8\">time series<\/span> to fit ......when high-resolution <span style=\"background-color: #FEE1E8\">time series<\/span> be become ...","...fit a <span style=\"background-color: #FEE1E8\">model<\/span> that capture ......component the <span style=\"background-color: #FEE1E8\">model<\/span> be then ...","...fit a <span style=\"background-color: #FEE1E8\">model<\/span> that capture ......component the <span style=\"background-color: #FEE1E8\">model<\/span> be then ...","...<span style=\"background-color: #FEE1E8\">ecological resilience<\/span> be the ...","...be the <span style=\"background-color: #FEE1E8\">magnitude<\/span> of the ...","...be the <span style=\"background-color: #FEE1E8\">magnitude<\/span> of the ...","...which a <span style=\"background-color: #FEE1E8\">system<\/span> can still ...","...which a <span style=\"background-color: #FEE1E8\">system<\/span> can still ...","...a single <span style=\"background-color: #FEE1E8\">big one<\/span> we show ...","...single big <span style=\"background-color: #FEE1E8\">one<\/span> we show ...","...single big <span style=\"background-color: #FEE1E8\">one<\/span> we show ...","...estimate in <span style=\"background-color: #FEE1E8\">term<\/span> of average ...","...estimate in <span style=\"background-color: #FEE1E8\">term<\/span> of average ...","...of average <span style=\"background-color: #FEE1E8\">life<\/span> expectancy accounting ...","...of average <span style=\"background-color: #FEE1E8\">life<\/span> expectancy accounting ...","...of average <span style=\"background-color: #FEE1E8\">life expectancy<\/span> accounting for ...","...life expectancy <span style=\"background-color: #FEE1E8\">accounting<\/span> for this ...","...life expectancy <span style=\"background-color: #FEE1E8\">accounting<\/span> for this ...","...this natural <span style=\"background-color: #FEE1E8\">regime<\/span> of variability ...","...this natural <span style=\"background-color: #FEE1E8\">regime<\/span> of variability ...","...the deterministic <span style=\"background-color: #FEE1E8\">component<\/span> the model ...","...from the <span style=\"background-color: #FEE1E8\">basin<\/span> of attraction ...","...from the <span style=\"background-color: #FEE1E8\">basin<\/span> of attraction ...","...a fresh <span style=\"background-color: #FEE1E8\">angle<\/span> to anticipat ...","...a fresh <span style=\"background-color: #FEE1E8\">angle<\/span> to anticipat ...","...anticipat the <span style=\"background-color: #FEE1E8\">chance<\/span> of a ...","...anticipat the <span style=\"background-color: #FEE1E8\">chance<\/span> of a ..."],["Q11471","Q43297","Q170198","Q911364","Q7275","Q19588","Q186588","Q4610556","Q213907","Q4105196","Q2028919","Q2091629","Q58778","Q3516404","Q689040","Q11237288","Q1133343","Q546583","Q170564","Q3","Q188419","Q188419","Q4116214","Q1779838","Q52371","Q5589178","Q1310239","Q810196","Q988558","Q11352","Q168159","Q12470060","Q16301153"],["?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?"],["<b>label:<\/b> TIME<\/br><b>type:<\/b> series<\/br><i>dimension in which events can be ordered from the past through the present into the future<i>","<b>label:<\/b> TIME<\/br><b>type:<\/b> print news magazine<\/br><i>American weekly news magazine<i>","<b>label:<\/b> SERIES<\/br><b>type:<\/b> mathematical concept<\/br><i>Infinite sum<i>","<b>label:<\/b>
3078 PERTURBATION THEORY<\/br><b>type:<\/b> scientific theory<\/br><i>quantum mechanics<i>","<b>label:<\/b> STATE<\/br><b>type:<\/b> state (former or current)<\/br><i>organised community living under a system of government; either a sovereign state, constituent state, or federated state<i>","<b>label:<\/b> TRANSITION METAL<\/br><b>type:<\/b> metal<\/br><i>series of chemical elements<i>","<b>label:<\/b> TIME SERIES<\/br><b>type:<\/b> data set<\/br><i>set of data indexed in time order<i>","<b>label:<\/b> MODEL<\/br><b>type:<\/b> profession<\/br><i>person employed to display, advertise and promote products, or to serve as a visual aid<i>","<b>label:<\/b> MODEL ORGANISM<\/br><b>type:<\/b> research object<\/br><i>organisms used to study biology across species<i>","<b>label:<\/b> ECOLOGICAL RESILIENCE<\/br><b>type:<\/b> resilience (general concept)<\/br><i>capacity of an ecosystem to respond to a perturbation or disturbance by resisting damage and recovering quickly<i>","<b>label:<\/b> MAGNITUDE (ASTRONOMY)<\/br><b>type:<\/b> logarithmic scale<\/br><i>Logarithmic measure of the brightness of an astronomical object<i>","<b>label:<\/b> MAGNITUDE<\/br><b>type:<\/b> property<\/br><i>mathematical concept related to comparison and ordering<i>","<b>label:<\/b> SYSTEM<\/br><b>type:<\/b> structure<\/br><i>set of interacting or interdependent components<i>","<b>label:<\/b> SYSTEMATICS<\/br><b>type:<\/b> systematics<\/br><i>study of relationships between organisms<i>","<b>label:<\/b> BIG ONE<\/br><b>type:<\/b> steel roller coaster<\/br><i>Steel roller coaster at Blackpool Pleasure Beach<i>","<b>label:<\/b> ONE<\/br><b>type:<\/b> human<\/br><i>Japanese manga artist<i>","<b>label:<\/b> ONE CAMPAIGN<\/br><b>type:<\/b> organization<\/br><i>organization<i>","<b>label:<\/b> TERMITE<\/br><b>type:<\/b> taxon<\/br><i>insect<i>","<b>label:<\/b> TERMINATOR 2: JUDGMENT DAY<\/br><b>type:<\/b> film<\/br><i>1991 American science fiction action film directed by James Cameron<i>","<b>label:<\/b> LIFE<\/br><b>type:<\/b> property<\/br><i>matter capable of extracting energy from the environment for replication<i>","<b>label:<\/b> LIFE EXPECTANCY<\/br><b>type:<\/b> assessment method<\/br><i>statistical measure of how long a person or organism may live, based on factors of their life<i>","<b>label:<\/b> LIFE EXPECTANCY<\/br><b>type:<\/b> lifetime<\/br><i>statistical measure of how long a person or organism may live, based on factors of their life<i>","<b>label:<\/b> ACCOUNTING<\/br><b>type:<\/b> academic discipline<\/br><i>measurement, processing and communication of financial information about economic entities<i>","<b>label:<\/b> ACCOUNTING STANDARD<\/br><b>type:<\/b> technical standard<\/br><i>the specific accouning discipline followed (IFRS, US GAAP, Chinese AS, France GAAP, Germany GAAP, Russian GAAP, UK GAAP, etc.)<i>","<b>label:<\/b> REGIMENT<\/br><b>type:<\/b> size-specific military unit<\/br><i>military unit size designation<i>","<b>label:<\/b> REGIME<\/br><b>type:<\/b> form of state<\/br><i>form of government or the set of rules, cultural or social norms, etc. that regulate the operation of a government or institution and its interactions with society<i>","<b>label:<\/b> COMPONENT<\/br><b>type:<\/b> part<\/br><i>smaller, self-contained part of technical entity consisting of components<i>","<b>label:<\/b> BASINGSTOKE<\/br><b>type:<\/b> unparished area<\/br><i>town in Hampshire, England<i>","<b>label:<\/b> BASIN<\/br><b>type:<\/b> town of the United States<\/br><i>town and county seat of Big Horn County, Wyoming, United States<i>","<b>label:<\/b> ANGLE<\/br><b>type:<\/b> geometric shape<\/br><i>something that is formed when two rays meet at a single or same point<i>","<b>label:<\/b> ANGLESEY<\/br><b>type:<\/b> administrative territorial entity<\/br><i>island in north-west Wales<i>","<b>label:<\/b> CHANCE THE RAPPER<\/br><b>type:<\/b> human<\/br><i>American rapper and philanthropist from Illinois<i>","<b>label:<\/b> CHANCE<\/br><b>type:<\/b> emotion<\/br><i>emotion caused by random occurence<i>"]],"container":"<table class=\"compact striped\">\n  <thead>\n    <tr>\n      <th>text<\/th>\n      <th>item<\/th>\n      <th>valid?<\/th>\n      <th>details<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"dom":"Bfrtip","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"searchHighlight":true,"buttons":["csv","excel"],"columnDefs":[{"width":"300
3078px","targets":0},{"width":"500px","targets":3},{"width":"65px","targets":[1,2]},{"className":"dt-center","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[5,10,25,50,100],"rowCallback":"function(row, data) {\nvar value=data[2]; $(this.api().cell(row, 2).node()).css({'font-weight':'bold','background-color':value == \"yes\" ? \"#90ee90\" : null});\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
3078
3079</div>
3080<h3 id="case-5">Case 5</h3>
3081<div class="layout-chunk" data-layout="l-body-outset">
3082<details>
3083<summary>Show code</summary>
3084<div class="sourceCode">
3085<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>tables</span><span class='op'>[[</span><span class='fl'>5</span><span class='op'>]</span><span class='op'>]</span> <span class='op'>%&gt;%</span> 
3086  <span class='fu'>select</span><span class='op'>(</span><span class='va'>text</span>, <span class='va'>item</span>, <span class='va'>`valid?`</span>, <span class='va'>details</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3087  <span class='fu'>DT</span><span class='fu'>::</span><span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, escape <span class='op'>=</span> <span class='cn'>FALSE</span>, <span class='co'>#filter = 'top', </span>
3088            editable <span class='op'>=</span> <span class='cn'>TRUE</span>, class <span class='op'>=</span> <span class='st'>'compact striped'</span>,
3089             caption <span class='op'>=</span> <span class='fu'>htmltools</span><span class='fu'>::</span><span class='va'><a href='https://rdrr.io/pkg/htmltools/man/builder.html'>tags</a></span><span class='op'>$</span><span class='fu'>caption</span><span class='op'>(</span>style <span class='op'>=</span> <span class='st'>'caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;'</span>,
3090               <span class='st'>'Data: wikidata.org (see in the text).'</span><span class='op'>)</span>,
3091            extensions <span class='op'>=</span> <span class='st'>'Buttons'</span>,
3092            options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>searchHighlight <span class='op'>=</span> <span class='cn'>TRUE</span>,
3093                            dom <span class='op'>=</span> <span class='st'>'Bfrtip'</span>, buttons <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>'csv'</span>, <span class='st'>"excel"</span><span class='op'>)</span>, 
3094                           columnDefs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>
3095                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'300px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span>,
3096                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'500px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>3</span><span class='op'>)</span><span class='op'>)</span>,
3097                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'65px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span>,<span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span>,
3098                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>className <span class='op'>=</span> <span class='st'>'dt-center'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>2</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
3099                  <span class='op'>)</span>
3100            <span class='op'>)</span> <span class='op'>%&gt;%</span> 
3101     <span class='fu'><a href='https://rdrr.io/pkg/DT/man/formatCurrency.html'>formatStyle</a></span><span class='op'>(</span><span class='st'>'valid?'</span>,  backgroundColor <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/DT/man/styleInterval.html'>styleEqual</a></span><span class='op'>(</span><span class='st'>'yes'</span>, <span class='st'>'#90ee90'</span><span class='op'>)</span>, fontWeight <span class='op'>=</span> <span class='st'>'bold'</span><span class='op'>)</span> 
3102</code></pre>
3103</div>
3104</details>
3105<div id="htmlwidget-00b47515bea8e029e3e4" style="width:100%;height:auto;" class="datatables html-widget"></div>
3106<script type="application/json" data-for="htmlwidget-00b47515bea8e029e3e4">{"x":{"filter":"none","extensions":["Buttons"],"caption":"<caption style=\"caption-side: bottom; text-align: left; font-size: 80%; color: #969696; font-family: Roboto Condensed;\">Data: wikidata.org (see in the text).<\/caption>","editable":{"target":"cell","disable":{"columns":null}},"data":[["...predict that <span style=\"background-color: #FEE1E8\">galaxy<\/span> form in ......feedback process <span style=\"background-color: #FEE1E8\">galaxy<\/span> bulge may ......a starburst <span style=\"background-color: #FEE1E8\">galaxy<\/span> at redshift ......old this <span style=\"background-color: #FEE1E8\">galaxy<\/span> 's cold ......motion the <span style=\"background-color: #FEE1E8\">galaxy<\/span> rotation curve ......model of <span style=\"background-color: #FEE1E8\">galaxy<\/span> formation...","...predict that <span style=\"background-color: #FEE1E8\">galaxy<\/span> form in ......feedback process <span style=\"background-color: #FEE1E8\">galaxy<\/span> bulge may ......a starburst <span style=\"background-color: #FEE1E8\">galaxy<\/span> at redshift ......old this <span style=\"background-color: #FEE1E8\">galaxy<\/span> 's cold ......motion the <span style=\"background-color: #FEE1E8\">galaxy<\/span> rotation curve ......model of <span style=\"background-color: #FEE1E8\">galaxy<\/span> formation...","...the early <span style=\"background-color: #FEE1E8\">universe<\/span> experience a ......when the <span style=\"background-color: #FEE1E8\">universe<\/span> be 1 ......the early <span style=\"background-color: #FEE1E8\">universe<\/span> than predict ...","...phase of <span style=\"background-color: #FEE1E8\">gas<\/span> accretion and ......follow by <span style=\"background-color: #FEE1E8\">gas<\/span> ejection due ......'s cold <span style=\"background-color: #FEE1E8\">gas<\/span> form a ...","...phase of <span style=\"background-color: #FEE1E8\">gas<\/span> accretion and ......follow by <span style=\"background-color: #FEE1E8\">gas<\/span> ejection due ......'s cold <span style=\"background-color: #FEE1E8\">gas<\/span> form a ...","...regularly rotating <span style=\"background-color: #FEE1E8\">disk<\/span> with negligible ......a star-forming <span style=\"background-color: #FEE1E8\">disk<\/span> we conclude ......regularly rotat <span style=\"background-color: #FEE1E8\">disk<\/span> can form ...","...regularly rotating <span style=\"background-color: #FEE1E8\">disk<\/span> with negligible ......a star-forming <span style=\"background-color: #FEE1E8\">disk<\/span> we conclude ......regularly rotat <span style=\"background-color: #FEE1E8\">disk<\/span> can form ...","...and star <span style=\"background-color: #FEE1E8\">formation<\/span> follow by ......of galaxy <span style=\"background-color: #FEE1E8\">formation<\/span>...","...cosmological <span style=\"background-color: #FEE1E8\">models<\/span> predict that ...","...early universe <span style=\"background-color: #FEE1E8\">experience<\/span> a chaotic ...","...a chaotic <span style=\"background-color: #FEE1E8\">phase<\/span> of gas ...","...a chaotic <span style=\"background-color: #FEE1E8\">phase<\/span> of gas ...","...of gas <span style=\"background-color: #FEE1E8\">accretion<\/span> and star ...","...of gas <span style=\"background-color: #FEE1E8\">accretion<\/span> and star ...","...accretion and <span style=\"background-color: #FEE1E8\">star<\/span> formation follow ......to a <span style=\"background-color: #FEE1E8\">star<\/span>-forming disk ...","...accretion and <span style=\"background-color: #FEE1E8\">star<\/span> formation follow ......to a <span style=\"background-color: #FEE1E8\">star<\/span>-forming disk ...","...accretion and <span style=\"background-color: #FEE1E8\">star formation<\/span> follow by ...","...by gas <span style=\"background-color: #FEE1E8\">ejection<\/span> due to ...","...due to <span style=\"background-color: #FEE1E8\">feedback<\/span> process galaxy ...","...to feedback <span style=\"background-color: #FEE1E8\">process<\/span> galaxy bulge ...","...to feedback <span style=\"background-color: #FEE1E8\">process<\/span> galaxy bulge ...","...later via <span style=\"background-color: #FEE1E8\">merger<\/span> or internal ...","...or internal <span style=\"background-color: #FEE1E8\">evolution<\/span> here we ...","...we present <span style=\"background-color: #FEE1E8\">submillimeter<\/span> observation with ...","...present submillimeter <span style=\"background-color: #FEE1E8\">observation<\/span> with spatial ...","...present submillimeter <span style=\"background-color: #FEE1E8\">observation<\/span> with spatial ...","...with spatial <span style=\"background-color: #FEE1E8\">resolution<\/span> of 700 ...","...with spatial <span style=\"background-color: #FEE1E8\">resolution<\/span> of 700 ...","...of 700 <span style=\"background-color: #FEE1E8\">
3106parsec<\/span> of aless ...","...parsec of <span style=\"background-color: #FEE1E8\">aless<\/span> 073 1 ...","...parsec of <span style=\"background-color: #FEE1E8\">aless<\/span> 073 1 ...","...1 a <span style=\"background-color: #FEE1E8\">starburst galaxy<\/span> at redshift ...","...galaxy at <span style=\"background-color: #FEE1E8\">redshift<\/span> z 5 ...","...2 billion <span style=\"background-color: #FEE1E8\">year<\/span> old this ...","...2 billion <span style=\"background-color: #FEE1E8\">year<\/span> old this ...","...that galaxy <span style=\"background-color: #FEE1E8\">form<\/span> in the ......cold gas <span style=\"background-color: #FEE1E8\">form<\/span> a regularly ......disk can <span style=\"background-color: #FEE1E8\">form<\/span> more rapidly ...","...that galaxy <span style=\"background-color: #FEE1E8\">form<\/span> in the ......cold gas <span style=\"background-color: #FEE1E8\">form<\/span> a regularly ......disk can <span style=\"background-color: #FEE1E8\">form<\/span> more rapidly ...","...negligible noncircular <span style=\"background-color: #FEE1E8\">motion<\/span> the galaxy ...","...negligible noncircular <span style=\"background-color: #FEE1E8\">motion<\/span> the galaxy ...","...the galaxy <span style=\"background-color: #FEE1E8\">rotation<\/span> curve require ...","...the galaxy <span style=\"background-color: #FEE1E8\">rotation<\/span> curve require ...","...galaxy rotation <span style=\"background-color: #FEE1E8\">curve<\/span> require the ...","...galaxy rotation <span style=\"background-color: #FEE1E8\">curve<\/span> require the ...","...bulge in <span style=\"background-color: #FEE1E8\">addition<\/span> to a ...","...bulge in <span style=\"background-color: #FEE1E8\">addition<\/span> to a ...","...cosmological <span style=\"background-color: #FEE1E8\">model<\/span>s predict that ......predict by <span style=\"background-color: #FEE1E8\">model<\/span> of galaxy ...","...cosmological <span style=\"background-color: #FEE1E8\">model<\/span>s predict that ......predict by <span style=\"background-color: #FEE1E8\">model<\/span> of galaxy ...","...model of <span style=\"background-color: #FEE1E8\">galaxy formation<\/span>..."],["Q318","Q204107","Q1","Q11432","Q39558","Q238231","Q1228827","Q736917","Q4044426","Q164359","Q42339","Q26388","Q237604","Q419990","Q523","Q462","Q16744","Q641303","Q183635","Q205663","Q898830","Q731112","Q1063","Q1205241","Q193181","Q818557","Q2751586","Q1051925","Q12129","Q680","Q1064","Q726611","Q76250","Q577","Q228891","Q161210","Q736917","Q79782","Q4300759","Q107617","Q848368","Q161973","Q1506584","Q32043","Q212745","Q4610556","Q213907","Q1995140"],["?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?","?"],["<b>label:<\/b> GALAXY<\/br><b>type:<\/b> deep-sky object<\/br><i>astronomical structure<i>","<b>label:<\/b> GALAXY CLUSTER<\/br><b>type:<\/b> astronomical object type<\/br><i>structure made up of a gravitationally-bound aggregation of hundreds of galaxies; is larger than a galaxy group<i>","<b>label:<\/b> UNIVERSE<\/br><b>type:<\/b> universe<\/br><i>totality consisting of space, time, matter and energy<i>","<b>label:<\/b> GAS<\/br><b>type:<\/b> fluid<\/br><i>one of the four fundamental states of matter<i>","<b>label:<\/b> GASOLINE<\/br><b>type:<\/b> petroleum product<\/br><i>petroleum-derived liquid used primarily as a fuel<i>","<b>label:<\/b> DISK<\/br><b>type:<\/b> geometric shape<\/br><i>plane figure, bounded by circle<i>","<b>label:<\/b> DISKO ISLAND<\/br><b>type:<\/b> island<\/br><i>island<i>","<b>label:<\/b> FORMATION<\/br><b>type:<\/b> lithostratigraphic unit<\/br><i>body of rock identified by lithic characteristics and stratigraphic position; it is usually but not necessarily tabular and is mappable at the Earth's surface or traceable in the subsurface. Smaller than a subgroup<i>","<b>label:<\/b> MODELS<\/br><b>type:<\/b> musical group<\/br><i>australian rock band<i>","<b>label:<\/b> EXPERIENCE<\/br><b>type:<\/b> knowledge<\/br><i>knowledge or mastery of an event or subject gained through involvement in or exposure to it<i>","<b>label:<\/b> PHASEOLUS VULGARIS<\/br><b>type:<\/b> taxon<\/br><i>species of plant<i>","<b>label:<\/b> PHASE OF THE MOON<\/br><b>type:<\/b> shape<\/br><i>shape of the sunlit portion of the Moon as viewed from Earth<i>","<b>label:<\/b> ACCRETION DISC<\/br><b>type:<\/b> astronomical object<\/br><i>structure formed by diffuse material in orbital motion around a massive central body<i>","<b>label:<\/b> ACCRETIONARY WEDGE<\/br><b>type:<\/b> physico-geographical object<\/br><i>sediments accreted onto the non-subducting tectonic plate at a convergent plate boundary<i>","<b>label:<\/b> STAR<\/br><b>type:<\/b> fusor<\/br><i>
3106astronomical object consisting of a luminous spheroid of plasma held together by its own gravity<i>","<b>label:<\/b> STAR WARS<\/br><b>type:<\/b> brand<\/br><i>epic science fantasy space opera saga and media franchise<i>","<b>label:<\/b> STAR FORMATION<\/br><b>type:<\/b> creation<\/br><i>process of forming stars<i>","<b>label:<\/b> EJECTION FRACTION<\/br><b>type:<\/b> biomedical measurand type<\/br><i>fraction of blood ejected from a ventricle of the heart with each heartbeat<i>","<b>label:<\/b> FEEDBACK<\/br><b>type:<\/b> interaction<\/br><i>process in which information about the past or the present influences the same phenomenon in the present or future;occurs when outputs of a system are routed back as inputs as part of a chain of cause-and-effect that forms a circuit or loop<i>","<b>label:<\/b> PROCESS<\/br><b>type:<\/b> computer science term<\/br><i>particular execution of a computer program<i>","<b>label:<\/b> PROCESSION<\/br><b>type:<\/b> event<\/br><i>organized body of people walking in a formal or ceremonial manner<i>","<b>label:<\/b> MERGERS AND ACQUISITIONS<\/br><b>type:<\/b> redistribution of property<\/br><i>transactions in which the ownership of companies, other business organizations or their operating units are transferred or combined<i>","<b>label:<\/b> EVOLUTION<\/br><b>type:<\/b> evolution<\/br><i>change in the inherited characteristics of biological populations over successive generations<i>","<b>label:<\/b> SUBMILLIMETER ARRAY<\/br><b>type:<\/b> radio interferometer<\/br><i>Array of radio telescopes in Hawaii<i>","<b>label:<\/b> OBSERVATION<\/br><b>type:<\/b> perception<\/br><i>active acquisition of information from a primary source<i>","<b>label:<\/b> OBSERVATIONAL ASTRONOMY<\/br><b>type:<\/b> astronomy<\/br><i>field of astronomy concerned with recording data about the observable universe<i>","<b>label:<\/b> RESOLUTION<\/br><b>type:<\/b> motion<\/br><i>written declaration adopted by a deliberative body<i>","<b>label:<\/b> RESOLUTION<\/br><b>type:<\/b> rule of inference<\/br><i>in logic, rule of inference<i>","<b>label:<\/b> PARSEC<\/br><b>type:<\/b> UCUM derived unit<\/br><i>unit of length used in astronomy<i>","<b>label:<\/b> ALESSANDRO VOLTA<\/br><b>type:<\/b> human<\/br><i>Italian physicist, chemist, and pioneer of electricity and power<i>","<b>label:<\/b> ALESSANDRO MANZONI<\/br><b>type:<\/b> human<\/br><i>Italian poet and novelist (1785-1873)<i>","<b>label:<\/b> STARBURST GALAXY<\/br><b>type:<\/b> galaxy<\/br><i>galaxy undergoing an exceptionally high rate of star formation<i>","<b>label:<\/b> REDSHIFT<\/br><b>type:<\/b> physical law<\/br><i>relative increase in wavelength of electromagnetic radiation in the emission spectrum of astronomical objects<i>","<b>label:<\/b> YEAR<\/br><b>type:<\/b> time interval<\/br><i>estimated period of time for the Earth's orbit around the Sun and observed at a fixed geographic point (averaging 365.24 days); base later modified to define or adjust various calendars<i>","<b>label:<\/b> YEARDLEY SMITH<\/br><b>type:<\/b> human<\/br><i>voice actor<i>","<b>label:<\/b> FORMALDEHYDE<\/br><b>type:<\/b> occupational carcinogen<\/br><i>chemical compound<i>","<b>label:<\/b> FORMATION<\/br><b>type:<\/b> lithostratigraphic unit<\/br><i>body of rock identified by lithic characteristics and stratigraphic position; it is usually but not necessarily tabular and is mappable at the Earth's surface or traceable in the subsurface. Smaller than a subgroup<i>","<b>label:<\/b> MOTION<\/br><b>type:<\/b> move<\/br><i>change in position of an object over time; a body is said to be in motion if it changes its position with respect to its immediate surroundings<i>","<b>label:<\/b> MOTION<\/br><b>type:<\/b> coordinates transformation<\/br><i>isometry of a metric space<i>","<b>label:<\/b> ROTATION<\/br><b>type:<\/b> motion<\/br><i>circular movement of an object around an axis of rotation<i>","<b>label:<\/b> ROTATION<\/br><b>type:<\/b> motion<\/br><i>concept originating in geometry; motion of a certain space that preserves at least one point<i>","<b>label:<\/b> CURVE<\/br><b>type:<\/b> geometric concept<\/br><i>mathematical idealization of the trace left by a moving point<i>","<b>label:<\/b> CURVED MIRROR<\/br><b>type:<\/b> mirror<\/br><i>mirror with a curved reflecting surface<i>","<b>label:<\/b> ADDITION<\/br><b>type:<\/b> binary operation<\/br><i>arithmetic operation<i>","<b>label:<\/b> ADDITION REACTION<\/br><b>type:<\/b> addition<\/br><i>
3106chemical reaction where two or more molecules combine to form a larger one (the adduct)<i>","<b>label:<\/b> MODEL<\/br><b>type:<\/b> profession<\/br><i>person employed to display, advertise and promote products, or to serve as a visual aid<i>","<b>label:<\/b> MODEL ORGANISM<\/br><b>type:<\/b> research object<\/br><i>organisms used to study biology across species<i>","<b>label:<\/b> GALAXY FORMATION AND EVOLUTION<\/br><b>type:<\/b> academic discipline<\/br><i>area of study in astrophysics<i>"]],"container":"<table class=\"compact striped\">\n  <thead>\n    <tr>\n      <th>text<\/th>\n      <th>item<\/th>\n      <th>valid?<\/th>\n      <th>details<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":5,"dom":"Bfrtip","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"searchHighlight":true,"buttons":["csv","excel"],"columnDefs":[{"width":"300px","targets":0},{"width":"500px","targets":3},{"width":"65px","targets":[1,2]},{"className":"dt-center","targets":2}],"order":[],"orderClasses":false,"lengthMenu":[5,10,25,50,100],"rowCallback":"function(row, data) {\nvar value=data[2]; $(this.api().cell(row, 2).node()).css({'font-weight':'bold','background-color':value == \"yes\" ? \"#90ee90\" : null});\n}"}},"evals":["options.rowCallback"],"jsHooks":[]}</script>
3106
3107</div>
3108<h3 id="final-results">Final Results</h3>
3109<p>After the editor have checked the results (ok, that was me) and saved CSV files with the selected matches, the files are merged into a joint table for a final demonstration. Here you are - list the pages to see which Wikidata items are found for the abstracts.</p>
3110<div class="layout-chunk" data-layout="l-body-outset">
3111<details>
3112<summary>Show code</summary>
3113<div class="sourceCode">
3114<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>final_table</span> <span class='op'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='va'>dir</span>, <span class='st'>"/csvs/"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3115  <span class='fu'><a href='https://rdrr.io/r/base/list.files.html'>list.files</a></span><span class='op'>(</span>full.names <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3116  <span class='fu'>map_df</span><span class='op'>(</span><span class='op'>~</span><span class='fu'>read_csv</span><span class='op'>(</span><span class='va'>.x</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='fu'>mutate</span><span class='op'>(</span>no <span class='op'>=</span> <span class='va'>.x</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3117  <span class='fu'><a href='https://rdrr.io/r/stats/filter.html'>filter</a></span><span class='op'>(</span><span class='va'>`valid?`</span><span class='op'>==</span><span class='st'>"yes"</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3118  <span class='fu'>mutate</span><span class='op'>(</span>details <span class='op'>=</span> <span class='fu'>str_extract</span><span class='op'>(</span><span class='va'>
3118details</span>, 
3119                               <span class='st'>"(?&lt;=label:).+?(?=type)"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3120  <span class='fu'>select</span><span class='op'>(</span><span class='op'>-</span><span class='va'>text</span><span class='op'>)</span> <span class='op'>%&gt;%</span> <span class='fu'>distinct</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3121  <span class='fu'>mutate</span><span class='op'>(</span>no <span class='op'>=</span> <span class='fu'>str_extract</span><span class='op'>(</span><span class='va'>no</span>, <span class='st'>"\\d(?=.csv)"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
3122  <span class='fu'>mutate</span><span class='op'>(</span>url <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>'https://www.wikidata.org/wiki/'</span>, <span class='va'>item</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3123  <span class='fu'>mutate</span><span class='op'>(</span>txt <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='co'>#'&lt;span style="background-color: #90ee90"&gt;', </span>
3124                       <span class='fu'><a href='https://rdrr.io/r/base/chartr.html'>tolower</a></span><span class='op'>(</span><span class='va'>
3124details</span><span class='op'>)</span>,
3125                       <span class='co'>#'&lt;/span&gt;',</span>
3126                        <span class='st'>' :  (&lt;a href='</span>,<span class='va'>url</span>, <span class='st'>' target="_blank"&gt;'</span>,
3127                      <span class='va'>item</span>,<span class='st'>'&lt;/a&gt;)'</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3128  <span class='fu'>group_by</span><span class='op'>(</span><span class='va'>no</span><span class='op'>)</span> <span class='op'>%&gt;%</span>
3129  <span class='fu'>summarize</span><span class='op'>(</span>wikidata_items <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste</a></span><span class='op'>(</span><span class='va'>txt</span>, collapse <span class='op'>=</span> <span class='st'>"&lt;/br&gt;"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3130  <span class='fu'>ungroup</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3131  <span class='fu'><a href='https://rdrr.io/r/base/cbind.html'>cbind</a></span><span class='op'>(</span><span class='va'>data</span><span class='op'>)</span> <span class='op'>%&gt;%</span> 
3132  <span class='fu'>select</span><span class='op'>(</span><span class='va'>abstract</span>, <span class='va'>wikidata_items</span><span class='op'>)</span>
3133
3134<span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span><span class='va'>final_table</span>, rownames <span class='op'>=</span> <span class='cn'>FALSE</span>, escape <span class='op'>=</span> <span class='cn'>FALSE</span>, 
3135            editable <span class='op'>=</span> <span class='cn'>TRUE</span>, class <span class='op'>=</span> <span class='st'>'compact striped'</span>, 
3136          options <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pageLength <span class='op'>=</span> <span class='fl'>1</span>, dom <span class='op'>=</span> <span class='st'>"tip"</span>,
3137                        columnDefs <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>
3138                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'550px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>0</span><span class='op'>)</span><span class='op'>)</span>,
3139                  <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>width <span class='op'>=</span> <span class='st'>'300px'</span>, targets <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span><span class='op'>)</span>
3140                  <span class='op'>)</span><span class='op'>)</span>
3141</code></pre>
3142</div>
3143</details>
3144<div id="htmlwidget-a261add0491c285bdc49" style="width:100%;height:auto;" class="datatables html-widget"></div>
3145<script type="application/json" data-for="htmlwidget-a261add0491c285bdc49">{"x":{"filter":"none","editable":{"target":"cell","disable":{"columns":null}},"data":[["The coronavirus disease (COVID-19) caused by SARS-CoV-2 is creating tremendous human suffering. To date, no effective drug is available to directly treat the disease. In a search for a drug against COVID-19, we have performed a high-throughput x-ray crystallographic screen of two repurposing drug libraries against the SARS-CoV-2 main protease (Mpro), which is essential for viral replication. In contrast to commonly applied x-ray fragment screening experiments with molecules of low complexity, our screen tested already-approved drugs and drugs in clinical trials. From the three-dimensional protein structures, we identified 37 compounds that bind to Mpro. In subsequent cell-based viral reduction assays, one peptidomimetic and six nonpeptidic compounds showed antiviral activity at nontoxic concentrations. We identified two allosteric binding sites representing attractive targets for drug development against SARS-CoV-2.","Freshwater fish represent one-fourth of the world’s vertebrates and provide irreplaceable goods and services but are increasingly affected by human activities. A new index, Cumulative 
3145Change in Biodiversity Facets, revealed marked changes in biodiversity in &gt;50% of the world’s rivers covering &gt;40% of the world’s continental surface and &gt;37% of the world’s river length, whereas &lt;14% of the world’s surface and river length remain least impacted. Present-day rivers are more similar to each other and have more fish species with more diverse morphologies and longer evolutionary legacies. In temperate rivers, where the impact has been greatest, biodiversity changes were primarily due to river fragmentation and introduction of non-native species.","The surface of neutron-rich heavy nuclei, with a neutron skin created by excess neutrons, provides an important terrestrial model system to study dilute neutron-rich matter. By using quasi-free a cluster–knockout reactions, we obtained direct experimental evidence for the formation of a clusters at the surface of neutron-rich tin isotopes. The observed monotonous decrease of the reaction cross sections with increasing mass number, in excellent agreement with the theoretical prediction, implies a tight interplay between a-cluster formation and the neutron skin. This result, in turn, calls for a revision of the correlation between the neutron-skin thickness and the density dependence of the symmetry energy, which is essential for understanding neutron stars. Our result also provides a natural explanation for the origin of a particles in a decay.","Ecological resilience is the magnitude of the largest perturbation from which a system can still recover to its original state. However, a transition into another state may often be invoked by a series of minor synergistic perturbations rather than a single big one. We show how resilience can be estimated in terms of average life expectancy, accounting for this natural regime of variability. We use time series to fit a model that captures the stochastic as well as the deterministic components. The model is then used to estimate the mean exit time from the basin of attraction. This approach offers a fresh angle to anticipating the chance of a critical transition at a time when high-resolution time series are becoming increasingly available.","Cosmological models predict that galaxies forming in the early Universe experience a chaotic phase of gas accretion and star formation, followed by gas ejection due to feedback processes. Galaxy bulges may assemble later via mergers or internal evolution. Here we present submillimeter observations (with spatial resolution of 700 parsecs) of ALESS 073.1, a starburst galaxy at redshift z≃5 when the Universe was 1.2 billion years old. This galaxy’s cold gas forms a regularly rotating disk with negligible noncircular motions. The galaxy rotation curve requires the presence of a central bulge in addition to a star-forming disk. We conclude that massive bulges and regularly rotating disks can form more rapidly in the early Universe than predicted by models of galaxy formation."],[" drug :  (<a href=https://www.wikidata.org/wiki/Q8386 target=\"_blank\">Q8386<\/a>)<\/br> sars-cov-2 :  (<a href=https://www.wikidata.org/wiki/Q82069695 target=\"_blank\">Q82069695<\/a>)<\/br> x-ray crystallography :  (<a href=https://www.wikidata.org/wiki/Q826582 target=\"_blank\">Q826582<\/a>)<\/br> coronavirus :  (<a href=https://www.wikidata.org/wiki/Q89469904 target=\"_blank\">Q89469904<\/a>)<\/br> coronavirus disease :  (<a href=https://www.wikidata.org/wiki/Q18975243 target=\"_blank\">Q18975243<\/a>)<\/br> covid-19 pandemic :  (<a href=https://www.wikidata.org/wiki/Q81068910 target=\"_blank\">Q81068910<\/a>)<\/br> covid-19 :  (<a href=https://www.wikidata.org/wiki/Q84263196 target=\"_blank\">Q84263196<\/a>)<\/br> allosteric regulation :  (<a href=https://www.wikidata.org/wiki/Q845326 target=\"_blank\">Q845326<\/a>)"," biodiversity :  (<a href=https://www.wikidata.org/wiki/Q47041 target=\"_blank\">Q47041<\/a>)<\/br> river :  (<a href=https://www.wikidata.org/wiki/Q4022 target=\"_blank\">Q4022<\/a>)<\/br> fish :  (<a href=https://www.wikidata.org/wiki/Q152 target=\"_blank\">Q152<\/a>)<\/br> freshwater fish :  (<a href=https://www.wikidata.org/wiki/Q1072742 target=\"_blank\">Q1072742<\/a>)"," neutron :  (<a href=https://www.wikidata.org/wiki/Q2348 target=\"_blank\">Q2348<\/a>)<\/br> tin :  (<a href=https://www.wikidata.org/wiki/Q1096 target=\"_blank\">Q1096<\/a>)<\/br>
3145 cross section :  (<a href=https://www.wikidata.org/wiki/Q17128025 target=\"_blank\">Q17128025<\/a>)<\/br> mass number :  (<a href=https://www.wikidata.org/wiki/Q101395 target=\"_blank\">Q101395<\/a>)<\/br> particle physics :  (<a href=https://www.wikidata.org/wiki/Q18334 target=\"_blank\">Q18334<\/a>)"," ecological resilience :  (<a href=https://www.wikidata.org/wiki/Q4105196 target=\"_blank\">Q4105196<\/a>)<\/br> life expectancy :  (<a href=https://www.wikidata.org/wiki/Q188419 target=\"_blank\">Q188419<\/a>)"," galaxy :  (<a href=https://www.wikidata.org/wiki/Q318 target=\"_blank\">Q318<\/a>)<\/br> accretion disc :  (<a href=https://www.wikidata.org/wiki/Q237604 target=\"_blank\">Q237604<\/a>)<\/br> star :  (<a href=https://www.wikidata.org/wiki/Q523 target=\"_blank\">Q523<\/a>)<\/br> star formation :  (<a href=https://www.wikidata.org/wiki/Q16744 target=\"_blank\">Q16744<\/a>)<\/br> submillimeter array :  (<a href=https://www.wikidata.org/wiki/Q1205241 target=\"_blank\">Q1205241<\/a>)<\/br> starburst galaxy :  (<a href=https://www.wikidata.org/wiki/Q726611 target=\"_blank\">Q726611<\/a>)<\/br> redshift :  (<a href=https://www.wikidata.org/wiki/Q76250 target=\"_blank\">Q76250<\/a>)<\/br> galaxy formation and evolution :  (<a href=https://www.wikidata.org/wiki/Q1995140 target=\"_blank\">Q1995140<\/a>)"]],"container":"<table class=\"compact striped\">\n  <thead>\n    <tr>\n      <th>abstract<\/th>\n      <th>wikidata_items<\/th>\n    <\/tr>\n  <\/thead>\n<\/table>","options":{"pageLength":1,"dom":"tip","deferRender":true,"ordering":true,"autoWidth":true,"scrollX":true,"columnDefs":[{"width":"550px","targets":0},{"width":"300px","targets":1}],"order":[],"orderClasses":false,"lengthMenu":[1,10,25,50,100]}},"evals":[],"jsHooks":[]}</script>
3145
3146</div>
3147<h3 id="limitations">Limitations</h3>
3148<ol type="1">
3149<li><p>there could be more relevant items for the terms, but I have not found it. Sure. So far this can be viewed as an initial suggestion and a pointer. Each item in the table above directs via URL to a Wikidata page where the related items can further be found.</p></li>
3150<li><p>Not all dictionaries were included in SPARQL. True. I listed those that I met first while investigating some random Wikidata items. This is a customized option - a list of catalogues for searching only the biomedical terms would require less catalogues, etc.</p></li>
3151<li><p>There are special properties which points at the scientific terms with high probability. This is TRUE, of course. I tried to play with <a href="https://www.wikidata.org/wiki/Property:P2579">studied by, P2579</a>, but the problem of using it that many terms have no such property. For example, <a href="https://www.wikidata.org/wiki/Q2348">neutron, Q2348</a> has no P2579 property. But neutron is a subclass of <a href="https://www.wikidata.org/wiki/Q37147">atomic nucleus, Q37147</a> which Wikidata record has P2579 statements referring to the subject area. I skipped it.</p></li>
3152</ol>
3153<p>Another option that I haven’t tried is to check if the items retrieved by initial API request are <a href="https://www.wikidata.org/wiki/Property:P921">main subjects, P921</a> present in any <a href="https://www.wikidata.org/wiki/Q13442814">scientific articles, Q13442814</a> or (more generally) with the items <a href="https://www.wikidata.org/wiki/Property:P1433">published, P1433</a> in the <a href="https://www.wikidata.org/wiki/Q5633421">academic journals, Q5633421</a>.</p>
3154<p>I really need to watch <a href="https://www.youtube.com/channel/UCa5oYsCabGo7XwwKGqo7Qcw">those videos…</a></p>
3155<h3 id="acknowledgments" class="appendix">Acknowledgments</h3>
3156<p>Allaire J, Iannone R, Presmanes Hill A, Xie Y (2021). <em>distill: ‘R Markdown’ Format for Scientific and Technical Writing</em>. R package version 1.2, &lt;URL: <a href="https://CRAN.R-project.org/package=distill" class="uri">https://CRAN.R-project.org/package=distill</a>&gt;.</p>
3157<p>Allaire J, Xie Y, McPherson J, Luraschi J, Ushey K, Atkins A, Wickham H, Cheng J, Chang W, Iannone R (2021). <em>rmarkdown: Dynamic Documents for R</em>. R package version 2.7, &lt;URL: <a href="https://github.com/rstudio/rmarkdown" class="uri">https://github.com/rstudio/rmarkdown</a>&gt;.</p>
3158<p>Henry L, Wickham H (2020). <em>purrr: Functional Programming Tools</em>. R package version 0.3.4, &lt;URL: <a href="https://CRAN.R-project.org/package=purrr" class="uri">https://CRAN.R-project.org/package=purrr</a>&gt;.</p>
3159<p>Popov M (2020). <em>WikidataQueryServiceR: API Client Library for ‘Wikidata Query Service’</em>. R package version 1.0.0, &lt;URL: <a href="https://CRAN.R-project.org/package=WikidataQueryServiceR" class="uri">https://CRAN.R-project.org/package=WikidataQueryServiceR</a>&gt;.</p>
3160<p>Shafee T, Keyes O, Signorelli S, Lum A, Graul C, Popov M (2021). <em>WikidataR: Read-Write API Client Library for ‘Wikidata’</em>. R package version 2.2.0, &lt;URL: <a href="https://github.com/TS404/WikidataR/issues" class="uri">https://github.com/TS404/WikidataR/issues</a>&gt;.</p>
3161<p>Wickham H (2020). <em>tidyr: Tidy Messy Data</em>. R package version 1.1.2, &lt;URL: <a href="https://CRAN.R-project.org/package=tidyr" class="uri">https://CRAN.R-project.org/package=tidyr</a>&gt;.</p>
3162<p>Wickham H (2019). <em>stringr: Simple, Consistent Wrappers for Common String Operations</em>. R package version 1.4.0, &lt;URL: <a href="https://CRAN.R-project.org/package=stringr" class="uri">https://CRAN.R-project.org/package=stringr</a>&gt;.</p>
3163<p>Wickham H, Francois R, Henry L, Muller K (2021). <em>dplyr: A Grammar of Data Manipulation</em>. R package version 1.0.3, &lt;URL: <a href="https://CRAN.R-project.org/package=dplyr" class="uri">https://CRAN.R-project.org/package=dplyr</a>&gt;.</p>
3164<p>Wickham H, Hester J (2020). <em>readr: Read Rectangular Text Data</em>. R package version 1.4.0, &lt;URL: <a href="https://CRAN.R-project.org/package=readr" class="uri">https://CRAN.R-project.org/package=readr</a>&gt;.</p>
3165<p>Wijffels J (2021). <em>udpipe: Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the ‘UDPipe’ ‘NLP’ Toolkit</em>. R package version 0.8.6, &lt;URL: <a href="https://CRAN.R-project.org/package=udpipe" class="uri">
3165https://CRAN.R-project.org/package=udpipe</a>&gt;.</p>
3166<p>Xie Y (2020). <em>knitr: A General-Purpose Package for Dynamic Report Generation in R</em>. R package version 1.30, &lt;URL: <a href="https://yihui.org/knitr/" class="uri">https://yihui.org/knitr/</a>&gt;.</p>
3167<p>Xie Y (2015). <em>Dynamic Documents with R and knitr</em>, 2nd edition. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 978-1498716963, &lt;URL: <a href="https://yihui.org/knitr/" class="uri">https://yihui.org/knitr/</a>&gt;.</p>
3168<p>Xie Y (2014). “knitr: A Comprehensive Tool for Reproducible Research in R.” In Stodden V, Leisch F, Peng RD (eds.), <em>Implementing Reproducible Computational Research</em>. Chapman and Hall/CRC. ISBN 978-1466561595, &lt;URL: <a href="http://www.crcpress.com/product/isbn/9781466561595" class="uri">http://www.crcpress.com/product/isbn/9781466561595</a>&gt;.</p>
3169<p>Xie Y, Allaire J, Grolemund G (2018). <em>R Markdown: The Definitive Guide</em>. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 9781138359338, &lt;URL: <a href="https://bookdown.org/yihui/rmarkdown" class="uri">https://bookdown.org/yihui/rmarkdown</a>&gt;.</p>
3170<p>Xie Y, Cheng J, Tan X (2021). <em>DT: A Wrapper of the JavaScript Library ‘DataTables’</em>. R package version 0.17, &lt;URL: <a href="https://CRAN.R-project.org/package=DT" class="uri">https://CRAN.R-project.org/package=DT</a>&gt;.</p>
3171<p>Xie Y, Dervieux C, Riederer E (2020). <em>R Markdown Cookbook</em>. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 9780367563837, &lt;URL: <a href="https://bookdown.org/yihui/rmarkdown-cookbook" class="uri">https://bookdown.org/yihui/rmarkdown-cookbook</a>&gt;.</p>
3172<div class="sourceCode" id="cb1"><pre class="sourceCode r distill-force-highlighting-css"><code class="sourceCode r"></code></pre></div>
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3192
3193<div class="d-appendix">
3194</div>
3195
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3200<div class="appendix-bottom">
3201  <h3 id="reuse">Reuse</h3>
3202  <p>Text and figures are licensed under Creative Commons Attribution <a rel="license" href="https://creativecommons.org/licenses/by/4.0/">CC BY 4.0</a>. The figures that have been reused from other sources don't fall under this license and can be recognized by a note in their caption: "Figure from ...".</p>
3203  <h3 id="citation">Citation</h3>
3204  <p>For attribution, please cite this work as</p>
3205  <pre class="citation-appendix short">Lutai (2021, June 16). ConviviaR Tools: Tagging the Scientific Abstracts with Wikidata Items. Retrieved from https://dwayzer.netlify.app/posts/2021-06-15-tagging-the-abstracts-with-wikidata-items/</pre>
3206  <p>BibTeX citation</p>
3207  <pre class="citation-appendix long">@misc{lutai2021tagging,
3208  author = {Lutai, Aleksei},
3209  title = {ConviviaR Tools: Tagging the Scientific Abstracts with Wikidata Items},
3210  url = {https://dwayzer.netlify.app/posts/2021-06-15-tagging-the-abstracts-with-wikidata-items/},
3211  year = {2021}
3212}</pre>
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