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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."/> 93 94<link rel="canonical" href="https://dwayzer.netlify.app/posts/2021-06-15-tagging-the-abstracts-with-wikidata-items/"/> 95<link rel="license" href="https://creativecommons.org/licenses/by/4.0/"/> 96 97<!-- https://schema.org/Article --> 98<meta property="article:published" itemprop="datePublished" content="2021-06-16"/> 99<meta property="article:created" itemprop="dateCreated" content="2021-06-16"/> 100<meta name="article:author" content="Aleksei Lutai"/> 101 102<!-- https://developers.facebook.com/docs/sharing/webmasters#markup --> 103<meta property="og:title" content="ConviviaR Tools: Tagging the Scientific Abstracts with Wikidata Items"/> 104<meta property="og:type" content="article"/> 105<meta property="og:description" content="Here I am trying to build a script that process the short scientific texts (abstracts) and finds Wikidata items corresponding to the terms. 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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 !== " ") { 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. 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2596<script id="distill-front-matter" type="text/json"> 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":" ","affiliationURL":"#","orcidID":"0000-0003-1341-781X"}],"publishedDate":"2021-06-16T00:00:00.000+03:00","citationText":"Lutai, 2021"} 2598</script>
2598 2599 2600<!--/radix_placeholder_front_matter--> 2601<!--radix_placeholder_navigation_before_body--> 2602<header class="header header--fixed" role="banner"> 2603<nav class="distill-site-nav distill-site-header"> 2604<div class="nav-left"> 2605<span class="logo"> 2606<img src="../../images/dwayzer.png"/> 2607</span> 2608<a class='title' href='/'>ConviviaR Tools</a> 2609<input id="distill-search" class="nav-search hidden" type="text" placeholder="Search..."/> 2610</div> 2611<div class="nav-right"> 2612<a href='/'>Main</a> 2613<a href='/about'>About</a> 2614<a href="../../index.xml"> 2615<i class="fa fa-rss" aria-hidden="true"></i> 2616</a> 2617<a href="javascript:void(0);" class="nav-toggle">☰</a> 2618</div> 2619</nav> 2620</header> 2621<!--/radix_placeholder_navigation_before_body--> 2622<!--radix_placeholder_site_before_body--> 2623<!--/radix_placeholder_site_before_body--> 2624 2625<div class="d-title"> 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> 2634</div> 2635<!--/radix_placeholder_categories--> 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: âIf Wikidata is an open database, there should be a lot of solutions, you just need to find a proper tutorialâ. 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/#/">Mixânâmatch</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 âmagicalâ 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 âfind itemâ 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&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&search=galaxy&language=en">âgalaxyâ</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 âsyntheticâ 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. Thatâs one of the best privilieges the neophytes can enjoy, isnât 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 articleâs 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. Letâs 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&sample=5&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'><-</span> <span class='va'>dir</span> <span class='op'>%>%</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'>%>%</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'>%>%</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'>%>%</span> 2696 <span class='fu'>map</span><span class='op'>(</span><span class='st'>"items"</span><span class='op'>)</span> <span class='op'>%>%</span> <span class='va'>.</span><span class='op'>$</span><span class='va'>message</span> <span class='op'>%>%</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'>"<.+?>"</span>,<span class='st'>""</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</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'>%>%</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'>%>%</span> 2702 <span class='co'>#mutate(abstract - substr(abstract, 1,250)) %>% </span> 2703 <span class='co'>
2703#summarize(abstracts = paste(abstract, collapse = " ...")) %>% </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 worldâs 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 &gt;50% of the worldâs rivers covering &gt;40% of the worldâs continental surface and &gt;37% of the worldâs river length, whereas &lt;14% of the worldâs 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 clusterâknockout 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 zâ5 when the Universe was 1.2 billion years old. This galaxyâs 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 (âwhichâ or â37â 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'><-</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'><-</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'><-</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'>$</span><span class='va'>file_model</span><span class='op'>)</span> 2736 2737 <span class='co'># udpipe breaks by hyphens, so I use str_extract_all with a regex expr.</span> 2738 <span class='va'>datax</span> <span class='op'><-</span> <span class='va'>data</span><span class='op'>$</span><span class='va'>abstract</span> <span class='op'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'><-</span> <span class='va'>datax</span> <span class='op'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</span> 2758 <span class='fu'>select</span><span class='op'>(</span><span class='va'>keyword</span><span class='op'>)</span> <span class='op'>%>%</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'>></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'>%>%</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'><-</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'>%>%</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'><-</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'>%>%</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'>$</span><span class='va'>A</span> <span class='op'>%>%</span> <span class='fu'><a href='https://rdrr.io/pkg/DT/man/datatable.html'>datatable</a></span><span class='op'>(</span>rownames <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> 2782</code></pre> 2783</div> 2784</details> 2785<div id="htmlwidget-c3e75eb8c8b52e644388" style="width:100%;height:auto;" class="datatables html-widget"></div>
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2786 2787</div> 2788<ol start="2" type="1"> 2789<li>the keyword phrases (N, N+N, A+N) to be used for searching Wikidata</li> 2790</ol> 2791<div class="layout-chunk" data-layout="l-body"> 2792<details> 2793<summary>Show code</summary> 2794<div class="sourceCode"> 2795<pre class="sourceCode r"><code class="sourceCode r"><span class='va'>data_terms</span><span class='op'>$</span><span class='va'>A</span> <span class='op'>%>%</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'>%>%</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 âallostericâ as an adjective.</p> 2804<p>Now as we have the terms itâs 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 âfootbal teamsâ or ârockstar aliasesâ), 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/#/">MixânâMatch</a> for particular catallogues).</p></li> 2812<li><p>excludes disambiguation wikimedia pages (Q4167410) - thereâs 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 âneutronâ but also a âneutron starâ). 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'><-</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 > 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'><-</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'><-</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'><-</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'>%>%</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'><-</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'><-</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'><-</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'><-</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'><-</span> <span class='va'>data_terms</span> <span class='op'>%>%</span> 2901 <span class='fu'>map</span><span class='op'>(</span><span class='op'>~</span><span class='va'>.x</span> <span class='op'>%>%</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'>%>%</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 âyesâ 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'><-</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'><-</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'><-</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'><-</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'><-</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'>%>%</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'>%>%</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'><-</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'>'<span style="background-color: #FEE1E8">'</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'>'</span>'</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'><-</span> <span class='va'>y</span> <span class='op'>%>%</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'>"<b>label:</b> "</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'>"<b>type:</b> "</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'>"<i>
2954"</span>, <span class='va'>itemDescription</span>, <span class='st'>"<i>"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</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'>"</br>"</span><span class='op'>)</span> <span class='op'>%>%</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'><-</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'>%>%</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'>%>%</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'>%>%</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 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 ...","...cause by <span style=\"background-color: #FEE1E8\">sars-cov-2<\/span> be create ......against the <span style=\"background-color: #FEE1E8\">sars-cov-2<\/span> main protease ......development against <span style=\"background-color: #FEE1E8\">sars-cov-2<\/span>...","...the coronavirus <span style=\"background-color: #FEE1E8\">disease<\/span> covid-19 cause ......treat the <span style=\"background-color: #FEE1E8\">disease<\/span> in a ...","...the coronavirus <span style=\"background-color: #FEE1E8\">disease<\/span> covid-19 cause ......treat the <span style=\"background-color: #FEE1E8\">disease<\/span> in a ...","...a high-throughput <span style=\"background-color: #FEE1E8\">x-ray<\/span> crystallographic screen ......commonly apply <span style=\"background-color: #FEE1E8\">x-ray<\/span> fragment screen ...","...a high-throughput <span style=\"background-color: #FEE1E8\">x-ray<\/span> crystallographic screen ......commonly apply <span style=\"background-color: #FEE1E8\">x-ray<\/span> fragment screen ...","...x-ray crystallographic <span style=\"background-color: #FEE1E8\">screen<\/span> of two ......x-ray fragment <span style=\"background-color: #FEE1E8\">screen<\/span> experiment with ......complexity we <span style=\"background-color: #FEE1E8\">screen<\/span> test already-approved ...","...x-ray crystallographic <span style=\"background-color: #FEE1E8\">screen<\/span> of two ......x-ray fragment <span style=\"background-color: #FEE1E8\">screen<\/span> experiment with ......complexity we <span style=\"background-color: #FEE1E8\">screen<\/span> test 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: 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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: 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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>
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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'>%>%</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'>%>%</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'>%>%</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>
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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 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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'>%>%</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'>%>%</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'>%>%</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 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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 âorthodoxâ 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
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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'>%>%</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'>%>%</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'>%>%</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>
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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
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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'>%>%</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'>%>%</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'>%>%</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'><-</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>%>%</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'>"(?<=label:).+?(?=type)"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</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'>%>%</span> <span class='fu'>distinct</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</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'>%>%</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'>%>%</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'>#'<span style="background-color: #90ee90">', </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'>#'</span>',</span> 3126 <span class='st'>' : (<a href='</span>,<span class='va'>url</span>, <span class='st'>' target="_blank">'</span>, 3127 <span class='va'>item</span>,<span class='st'>'</a>)'</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span> 3128 <span class='fu'>group_by</span><span class='op'>(</span><span class='va'>no</span><span class='op'>)</span> <span class='op'>%>%</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'>"</br>"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>%>%</span> 3130 <span class='fu'>ungroup</span><span class='op'>(</span><span class='op'>)</span> <span class='op'>%>%</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'>%>%</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 worldâs 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 >50% of the worldâs rivers covering >40% of the worldâs continental surface and >37% of the worldâs river length, whereas <14% of the worldâs 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 clusterâknockout 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 zâ5 when the Universe was 1.2 billion years old. This galaxyâs 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 havenât 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 videosâ¦</a></p> 3155<h3 id="acknowledgments" class="appendix">Acknowledgments</h3> 3156<p>Allaire J, Iannone R, Presmanes Hill A, Xie Y (2021). <em>distill: âR Markdownâ Format for Scientific and Technical Writing</em>. R package version 1.2, <URL: <a href="https://CRAN.R-project.org/package=distill" class="uri">https://CRAN.R-project.org/package=distill</a>>.</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, <URL: <a href="https://github.com/rstudio/rmarkdown" class="uri">https://github.com/rstudio/rmarkdown</a>>.</p> 3158<p>Henry L, Wickham H (2020). <em>purrr: Functional Programming Tools</em>. R package version 0.3.4, <URL: <a href="https://CRAN.R-project.org/package=purrr" class="uri">https://CRAN.R-project.org/package=purrr</a>>.</p> 3159<p>Popov M (2020). <em>WikidataQueryServiceR: API Client Library for âWikidata Query Serviceâ</em>. R package version 1.0.0, <URL: <a href="https://CRAN.R-project.org/package=WikidataQueryServiceR" class="uri">https://CRAN.R-project.org/package=WikidataQueryServiceR</a>>.</p> 3160<p>Shafee T, Keyes O, Signorelli S, Lum A, Graul C, Popov M (2021). <em>WikidataR: Read-Write API Client Library for âWikidataâ</em>. R package version 2.2.0, <URL: <a href="https://github.com/TS404/WikidataR/issues" class="uri">https://github.com/TS404/WikidataR/issues</a>>.</p> 3161<p>Wickham H (2020). <em>tidyr: Tidy Messy Data</em>. R package version 1.1.2, <URL: <a href="https://CRAN.R-project.org/package=tidyr" class="uri">https://CRAN.R-project.org/package=tidyr</a>>.</p> 3162<p>Wickham H (2019). <em>stringr: Simple, Consistent Wrappers for Common String Operations</em>. R package version 1.4.0, <URL: <a href="https://CRAN.R-project.org/package=stringr" class="uri">https://CRAN.R-project.org/package=stringr</a>>.</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, <URL: <a href="https://CRAN.R-project.org/package=dplyr" class="uri">https://CRAN.R-project.org/package=dplyr</a>>.</p> 3164<p>Wickham H, Hester J (2020). <em>readr: Read Rectangular Text Data</em>. R package version 1.4.0, <URL: <a href="https://CRAN.R-project.org/package=readr" class="uri">https://CRAN.R-project.org/package=readr</a>>.</p> 3165<p>Wijffels J (2021). <em>udpipe: Tokenization, Parts of Speech Tagging, Lemmatization and Dependency Parsing with the âUDPipeâ âNLPâ Toolkit</em>. R package version 0.8.6, <URL: <a href="https://CRAN.R-project.org/package=udpipe" class="uri">
3165https://CRAN.R-project.org/package=udpipe</a>>.</p> 3166<p>Xie Y (2020). <em>knitr: A General-Purpose Package for Dynamic Report Generation in R</em>. R package version 1.30, <URL: <a href="https://yihui.org/knitr/" class="uri">https://yihui.org/knitr/</a>>.</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, <URL: <a href="https://yihui.org/knitr/" class="uri">https://yihui.org/knitr/</a>>.</p> 3168<p>Xie Y (2014). âknitr: A Comprehensive Tool for Reproducible Research in R.â In Stodden V, Leisch F, Peng RD (eds.), <em>Implementing Reproducible Computational Research</em>. Chapman and Hall/CRC. ISBN 978-1466561595, <URL: <a href="http://www.crcpress.com/product/isbn/9781466561595" class="uri">http://www.crcpress.com/product/isbn/9781466561595</a>>.</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, <URL: <a href="https://bookdown.org/yihui/rmarkdown" class="uri">https://bookdown.org/yihui/rmarkdown</a>>.</p> 3170<p>Xie Y, Cheng J, Tan X (2021). <em>DT: A Wrapper of the JavaScript Library âDataTablesâ</em>. R package version 0.17, <URL: <a href="https://CRAN.R-project.org/package=DT" class="uri">https://CRAN.R-project.org/package=DT</a>>.</p> 3171<p>Xie Y, Dervieux C, Riederer E (2020). <em>R Markdown Cookbook</em>. Chapman and Hall/CRC, Boca Raton, Florida. ISBN 9780367563837, <URL: <a href="https://bookdown.org/yihui/rmarkdown-cookbook" class="uri">https://bookdown.org/yihui/rmarkdown-cookbook</a>>.</p> 3172<div class="sourceCode" id="cb1"><pre class="sourceCode r distill-force-highlighting-css"><code class="sourceCode r"></code></pre></div> 3173<!--radix_placeholder_article_footer--> 3174<div class="article-footer"> 3175 <p class="social_footer"> 3176 <span class="article-sharing"> 3177 Share: 3178 <a href="https://twitter.com/share?text=Tagging%20the%20Scientific%20Abstracts%20with%20Wikidata%20Items&url=https%3A%2F%2Fdwayzer.netlify.app%2Fposts%2F2021-06-15-tagging-the-abstracts-with-wikidata-items%2F" aria-label="share on twitter"> 3179 <i class="fab fa-twitter" aria-hidden="true"></i> 3180 </a> 3181 <a href="https://www.linkedin.com/shareArticle?mini=true&url=https%3A%2F%2Fdwayzer.netlify.app%2Fposts%2F2021-06-15-tagging-the-abstracts-with-wikidata-items%2F&title=Tagging%20the%20Scientific%20Abstracts%20with%20Wikidata%20Items" aria-label="share on linkedin"> 3182 <i class="fab fa-linkedin" aria-hidden="true"></i> 3183 </a> 3184 <a href="https://www.facebook.com/sharer/sharer.php?s=100&p[url]=https%3A%2F%2Fdwayzer.netlify.app%2Fposts%2F2021-06-15-tagging-the-abstracts-with-wikidata-items%2F" aria-label="share on facebook"> 3185 <i class="fab fa-facebook" aria-hidden="true"></i> 3186 </a> 3187 </span> 3188 </p> 3189</div> 3190<!--/radix_placeholder_article_footer--> 3191</div> 3192 3193<div class="d-appendix"> 3194</div> 3195 3196 3197<!--radix_placeholder_site_after_body--> 3198<!--/radix_placeholder_site_after_body--> 3199<!--radix_placeholder_appendices--> 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> 3213</div> 3214<!--/radix_placeholder_appendices--> 3215<!--radix_placeholder_navigation_after_body--> 3216<!--/radix_placeholder_navigation_after_body--> 3217 3218</body> 3219 3220</html>
Line numbers count LF bytes from the start of the resource, as the search results do. Vendor segments are library code the classifier recognised; they are stored but not indexed. Bytes are shown as Latin1 characters, one per byte.