1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 442 443 444 445 446 447 448 449 450 451 452 453 454 455 456 457 458 459 460 461 462 463 464 465 466 467 468 469 470 471 472 473 474 475 476 477 478 479 480 481 482 483 484 485 486 487 488 489 490 491 492 493 494 495 496 497 498 499 500 501 502 503 504 505 506 507 508 509 510 511 512 513 514 515 516 517 518 519 520 521 522 523 524 525 526 527 528 529 530 531 532 533 534 535 536 537 538 539 540 541 542 543 544 545 546 547 548 549 550 551 552 553 554 555 556 557 558 559 560 561 562 563 564 565 566 567 568 569 570 571 572 573 574 575 576 577 578 579 580 581 582 583 584 585 586 587 588 589 590 591 592 593 594 595 596 597 598 599 600 601 602 603 604 605 606 607 608 609 610 611 612 613 614 615 616 617 618 619 620 621 622 623 624 625 626 627 628 629 630 631 632 633 634 635 636 637 638 639 640 641 642 643 644 645 646 647 648 649 650 651 652 653 654 655 656 657 658 659 660 661 662 663 664 665 666 667 668 669 670 671 672 673 674 675 676 677 678 679 680 681 682 683 684 685 686 687 688 689 690 691 692 693 694 695 696 697 698 699 700 701 702 703 704 705 706 707 708 709 710 711 712 713 714 715 716 717 718 719 720 721 722 723 724 725 726 727 728 729 730 731 732 733 734 735 736 737 738 739 740 741 742 743 744 745 746 747 748 749 750 751 752 753 754 755 756 757 758 759 760 761 762 763 764 765 766 767 768 769 770 771 772 773 774 775 776 777 778 779 780 781 782 783 784 785 786 787 788 789 790 791 792 793 794 795 796 797 798 799 800 801 802 803 804 805 806 807 808 809 810 811 812 813 814 815 816 817 818 819 820 821 822 823 824 825 826 827 828 829 830 831 832 833 834 835 836 837 838 839 840 841 842 843 844 845 846 847 848 849 850 851 852 853 854 855 856 857 858 859 860 861 862 863 864 865 866 867 868 869 870 871 872 873 874 875 876 877 878 879 880 881 882 883 884 885 886 887 888 889 890 891 892 893 894 895 896 897 898 899 900 901 902 903 904 905 906 907 908 909 910 911 912 913 914 915 916 917 918 919 920 921 922 923 924 925 926 927 928 929 930 931 932 933 934 935 936 937 938 939 940 941 942 943 944 945 946 947 948 949 950 951 952 953 954 955 956 957 958 959 960 961 962 963 964 965 966 967 968 969 970 971 972 973 974 975 976 977 978 979 980 981 982 983 984 985 986 987 988 989 990 991 992 993 994 995 996 997 998 999 1000 1001 1002 1003 1004 1005 1006 1007 1008 1009 1010 1011 1012 1013 1014 1015 1016 1017 1018 1019 1020 1021 1022 1023 1024 1025 1026 1027 1028 1029 1030 1031 1032 1033 1034 1035 1036 1037 1038 1039 1040 1041 1042 1043 1044 1045 1046 1047 1048 1049 1050 1051 1052 1053 1054 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 1065 1066 1067 1068 1069 1070 1071 1072 1073 1074 1075 1076 1077 1078 1079 1080 1081 1082 1083 1084 1085 1086 1087 1088 1089 1090 1091 1092 1093 1094 1095 1096 1097 1098 1099 1100 1101 1102 1103 1104 1105 1106 1107 1108 1109 1110 1111 1112 1113 1114 1115 1116 1117 1118 1119 1120 1121 1122 1123 1124 1125 1126 1127 1128 1129 1130 1131 1132 1133 1134 1135 1136 1137 1138 1139 1140 1141 1142 1143 1144 1145 1146 1147 1148 1149 1150 1151 1152 1153 1154 1155 1156 1157 1158 1159 1160 1161 1162 1163 1164 1165 1166 1167 1168 1169 1170 1171 1172 1173 1174 1175 1176 1177 1178 1179 1180 1181 1182 1183 1184 1185 1186 1187 1188 1189 1190 1191 1192 1193 1194 1195 1196 1197 1198 1199 1200 1201 1202 1203 1204 1205 1206 1207 1208 1209 1210 1211 1212 1213 1214 1215 1216 1217 1218 1219 1220 1221 1222 1223 1224 1225 1226 1227 1228 1229 1230 1231 1232 1233 1234 1235 1236 1237 1238 1239 1240 1241 1242 1243 1244 1245 1246 1247 1248 1249 1250 1251 1252 1253 1254 1255 1256 1257 1258 1259 1260 1261 1262 1263 1264 1265 1266 1267 1268 1269 1270 1271 1272 1273 1274 1275 1276 1277 1278 1279 1280 1281 1282 1283 1284 1285 1286 1287 1288 1289 1290 1291 1292 1293 1294 1295 1296 1297 1298 1299 1300 1301 1302 1303 1304 1305 1306 1307 1308 1309 1310 1311 1312 1313 1314 1315 1316 1317 1318 1319 1320 1321 1322 1323 1324 1325 1326 1327 1328 1329 1330 1331 1332 1333 1334 1335 1336 1337 1338 1339 1340 1341 1342 1343 1344 1345 1346 1347 1348 1349 1350 1351 1352 1353 1354 1355 1356 1357 1358 1359 1360 1361 1362 1363 1364 1365 1366 1367 1368 1369 1370 1371 1372 1373 1374 1375 1376 1377 1378 1379 1380 1381 1382 1383 1384 1385 1386 1387 1388 1389 1390 1391 1392 1393 1394 1395 1396 1397 1398 1399 1400 1401 1402 1403 1404 1405 1406 1407 1408 1409 1410 1411 1412 1413 1414 1415 1416 1417 1418 1419 1420 1421 1422 1423 1424 1425 1426 1427 1428 1429 1430 1431 1432 1433 1434 1435 1436 1437 1438 1439 1440 1441 1442 1443 1444 1445 1446 1447 1448 1449 1450 1451 1452 1453 1454 1455 1456 1457 1458 1459 1460 1461 1462 1463 1464 1465 1466 1467 1468 1469 1470 1471 1472 1473 1474 1475 1476 1477 1478 1479 1480 1481 1482 1483 1484 1485 1486 1487 1488 1489 1490 1491 1492 1493 1494 1495 1496 1497 1498 1499 1500 1501 1502 1503 1504 1505 1506 1507 1508 1509 1510 1511 1512 1513 1514 1515 1516 1517 1518 1519 1520 1521 1522 1523 1524 1525 1526 1527 1528 1529 1530 1531 1532 1533 1534 1535 1536 1537 1538 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585
|
<!-- ============================================
::DATATOOL:: Generated from "docsum.asn"
::DATATOOL:: by application DATATOOL version 2.3.1
::DATATOOL:: on 04/01/2011 23:04:41
============================================ -->
<!-- ============================================ -->
<!-- This section is mapped from module "Docsum-3-3"
================================================= -->
<!--
============================================
::DATATOOL:: Generated from "docsum_3.3.xsd"
::DATATOOL:: by application DATATOOL version 2.1.0
::DATATOOL:: on 03/03/2011 12:34:38
============================================
edited with XMLSPY v5 rel. 4 U (http://www.xmlspy.com) by Michael Kholodov (National Library of Medicine)
edited with XMLSpy v2005 rel. 3 U (http://www.altova.com) by Michael Feolo (NCBI/NLM/NIH)
-->
<!ELEMENT Assay (
Assay_attlist,
Assay_method,
Assay_taxonomy,
Assay_strains?,
Assay_comment?,
Assay_citation?)>
<!ELEMENT Assay_attlist (
Assay_attlist_handle?,
Assay_attlist_batch?,
Assay_attlist_batchId?,
Assay_attlist_batchType?,
Assay_attlist_molType?,
Assay_attlist_sampleSize?,
Assay_attlist_population?,
Assay_attlist_linkoutUrl?)>
<!ELEMENT Assay_attlist_handle (#PCDATA)>
<!ELEMENT Assay_attlist_batch (#PCDATA)>
<!ELEMENT Assay_attlist_batchId (%INTEGER;)>
<!ELEMENT Assay_attlist_batchType %ENUM;>
<!ATTLIST Assay_attlist_batchType value (
snpassay |
validation |
doublehit
) #REQUIRED >
<!ELEMENT Assay_attlist_molType %ENUM;>
<!ATTLIST Assay_attlist_molType value (
genomic |
cDNA |
mito |
chloro
) #REQUIRED >
<!ELEMENT Assay_attlist_sampleSize (%INTEGER;)>
<!ELEMENT Assay_attlist_population (#PCDATA)>
<!ELEMENT Assay_attlist_linkoutUrl (#PCDATA)>
<!ELEMENT Assay_method (
Assay_method_eMethod?)>
<!ELEMENT Assay_method_eMethod (
Assay_method_eMethod_attlist,
Assay_method_eMethod_exception)>
<!ELEMENT Assay_method_eMethod_attlist (
Assay_method_eMethod_attlist_name?,
Assay_method_eMethod_attlist_id?)>
<!--Submitters method identifier -->
<!ELEMENT Assay_method_eMethod_attlist_name (#PCDATA)>
<!--dbSNP method identifier -->
<!ELEMENT Assay_method_eMethod_attlist_id (#PCDATA)>
<!--
description of deviation from/addition to
given method
-->
<!ELEMENT Assay_method_eMethod_exception (#PCDATA)>
<!ELEMENT Assay_taxonomy (
Assay_taxonomy_attlist,
Assay_taxonomy_taxonomy)>
<!ELEMENT Assay_taxonomy_attlist (
Assay_taxonomy_attlist_id,
Assay_taxonomy_attlist_organism?)>
<!--
NCBI taxonomy ID for
variation
-->
<!ELEMENT Assay_taxonomy_attlist_id (%INTEGER;)>
<!ELEMENT Assay_taxonomy_attlist_organism (#PCDATA)>
<!ELEMENT Assay_taxonomy_taxonomy EMPTY>
<!ELEMENT Assay_strains (Assay_strains_E*)>
<!ELEMENT Assay_strains_E (#PCDATA)>
<!ELEMENT Assay_comment (#PCDATA)>
<!ELEMENT Assay_citation (Assay_citation_E*)>
<!ELEMENT Assay_citation_E (#PCDATA)>
<!--
A collection of genome sequence records (curated gene regions (NG's),
contigs (NWNT's) and chromosomes (NC/AC's) produced by a genome sequence project.
Structure is populated from ContigInfo tables.
-->
<!ELEMENT Assembly (
Assembly_attlist,
Assembly_component?,
Assembly_snpStat)>
<!ELEMENT Assembly_attlist (
Assembly_attlist_dbSnpBuild,
Assembly_attlist_genomeBuild,
Assembly_attlist_groupLabel?,
Assembly_attlist_assemblySource?,
Assembly_attlist_current?,
Assembly_attlist_reference?)>
<!--
dbSNP build number defining the rsid set aligned to this
assembly
-->
<!ELEMENT Assembly_attlist_dbSnpBuild (%INTEGER;)>
<!--
assembly build number with possible 'subbuild' version
numbers to reflect updates in gene annotation (human e.g. 34_3, 35_1,
36_1)
-->
<!ELEMENT Assembly_attlist_genomeBuild (#PCDATA)>
<!--
High-level classification of the assembly to distinguish
reference projects from alternate solutions. GroupLabel field from
organism/build-specific ContigInfo tables. "reference" is occasionally used
as the preferred assembly; standards will converge as additional organism
genome projects are finished. Note that some organism assembly names include
extended characters like '~' and '/' that may be incompatible with OS
filename conventions.
-->
<!ELEMENT Assembly_attlist_groupLabel (#PCDATA)>
<!--
Name of the group(s) or organization(s) that generated the
assembly
-->
<!ELEMENT Assembly_attlist_assemblySource (#PCDATA)>
<!--Marks the current genomic assembly -->
<!ELEMENT Assembly_attlist_current EMPTY>
<!ATTLIST Assembly_attlist_current value ( true | false ) #REQUIRED >
<!ELEMENT Assembly_attlist_reference EMPTY>
<!ATTLIST Assembly_attlist_reference value ( true | false ) #REQUIRED >
<!ELEMENT Assembly_component (Component*)>
<!ELEMENT Assembly_snpStat (
Assembly_snpStat_attlist,
Assembly_snpStat_snpStat)>
<!ELEMENT Assembly_snpStat_attlist (
Assembly_snpStat_attlist_mapWeight,
Assembly_snpStat_attlist_chromCount?,
Assembly_snpStat_attlist_placedContigCount?,
Assembly_snpStat_attlist_unplacedContigCount?,
Assembly_snpStat_attlist_seqlocCount?,
Assembly_snpStat_attlist_hapCount?)>
<!--
summary measure of placement precision in the
assembly
-->
<!ELEMENT Assembly_snpStat_attlist_mapWeight %ENUM;>
<!ATTLIST Assembly_snpStat_attlist_mapWeight value (
unmapped |
unique-in-contig |
two-hits-in-contig |
less-10-hits |
multiple-hits
) #REQUIRED >
<!--
number of distinct chromosomes in the
mapset
-->
<!ELEMENT Assembly_snpStat_attlist_chromCount (%INTEGER;)>
<!--
number of distinct contigs [ gi |
accession[.version] ] in the mapset
-->
<!ELEMENT Assembly_snpStat_attlist_placedContigCount (%INTEGER;)>
<!--
number of sequence postions to a contig with
unknown chromosomal assignment
-->
<!ELEMENT Assembly_snpStat_attlist_unplacedContigCount (%INTEGER;)>
<!--
total number of sequence positions in the
mapset
-->
<!ELEMENT Assembly_snpStat_attlist_seqlocCount (%INTEGER;)>
<!--
Number of hits to alternative genomic haplotypes
(e.g. HLA DR region, KIR, or pseudo-autosomal regions like PAR)
within the assembly mapset. Note that positions on haplotypes
defined in other assemblies (a different assembly_group_label
value) will not be counted in this value.
-->
<!ELEMENT Assembly_snpStat_attlist_hapCount (%INTEGER;)>
<!ELEMENT Assembly_snpStat_snpStat EMPTY>
<!--
URL value from dbSNP_main.BaseURL links table. attributes provide
context information and URL id that is referenced within individual refSNP
objects.
-->
<!ELEMENT BaseURL (
BaseURL_attlist,
BaseURL_baseURL)>
<!ELEMENT BaseURL_attlist (
BaseURL_attlist_urlId?,
BaseURL_attlist_resourceName?,
BaseURL_attlist_resourceId?)>
<!--
Resource identifier from
dbSNP_main.baseURL.
-->
<!ELEMENT BaseURL_attlist_urlId (%INTEGER;)>
<!--Name of linked resource -->
<!ELEMENT BaseURL_attlist_resourceName (#PCDATA)>
<!--
identifier expected by resource for
URL
-->
<!ELEMENT BaseURL_attlist_resourceId (#PCDATA)>
<!--
URL value from dbSNP_main.BaseURL links table. attributes provide
context information and URL id that is referenced within individual refSNP
objects.
-->
<!ELEMENT BaseURL_baseURL (#PCDATA)>
<!ELEMENT Component (
Component_attlist,
Component_mapLoc)>
<!ELEMENT Component_attlist (
Component_attlist_componentType?,
Component_attlist_ctgId?,
Component_attlist_accession?,
Component_attlist_name?,
Component_attlist_chromosome?,
Component_attlist_start?,
Component_attlist_end?,
Component_attlist_orientation?,
Component_attlist_gi?,
Component_attlist_groupTerm?,
Component_attlist_contigLabel?)>
<!--
type of component: chromosome, contig, gene_region,
etc.
-->
<!ELEMENT Component_attlist_componentType %ENUM;>
<!ATTLIST Component_attlist_componentType value (
contig |
mrna
) #REQUIRED >
<!--
dbSNP contig_id used to join on contig hit / mapset data to
these assembly properties
-->
<!ELEMENT Component_attlist_ctgId (%INTEGER;)>
<!--
Accession[.version] for the sequence
component
-->
<!ELEMENT Component_attlist_accession (#PCDATA)>
<!--
contig name defined as either a submitter local id, element
of a whole genome assembly set, or internal NCBI local
id
-->
<!ELEMENT Component_attlist_name (#PCDATA)>
<!--
Organism appropriate chromosome tag, 'Un' reserved for
default case of unplaced components
-->
<!ELEMENT Component_attlist_chromosome (#PCDATA)>
<!--
component starting position on the chromosome (base 0
inclusive)
-->
<!ELEMENT Component_attlist_start (%INTEGER;)>
<!--
component ending position on the chromosome (base 0
inclusive)
-->
<!ELEMENT Component_attlist_end (%INTEGER;)>
<!--
orientation of this component to chromosome, forward (fwd) =
0, reverse (rev) = 1, unknown = NULL in
ContigInfo.orient.
-->
<!ELEMENT Component_attlist_orientation %ENUM;>
<!ATTLIST Component_attlist_orientation value (
fwd |
rev |
unknown
) #REQUIRED >
<!--
NCBI gi for component sequence (equivalent to
accession.version) for nucleotide sequence.
-->
<!ELEMENT Component_attlist_gi (#PCDATA)>
<!--
Identifier label for the genome assembly that defines the
contigs in this mapset and their placement within the organism genome.
-->
<!ELEMENT Component_attlist_groupTerm (#PCDATA)>
<!--Display label for component -->
<!ELEMENT Component_attlist_contigLabel (#PCDATA)>
<!ELEMENT Component_mapLoc (MapLoc*)>
<!--Set of dbSNP refSNP docsums, version 3.2 -->
<!ELEMENT ExchangeSet (
ExchangeSet_attlist,
ExchangeSet_sourceDatabase,
ExchangeSet_rs?,
ExchangeSet_assay?,
ExchangeSet_query?,
ExchangeSet_summary,
ExchangeSet_baseURL)>
<!ELEMENT ExchangeSet_attlist (
ExchangeSet_attlist_setType?,
ExchangeSet_attlist_setDepth?,
ExchangeSet_attlist_specVersion?,
ExchangeSet_attlist_dbSnpBuild?,
ExchangeSet_attlist_generated?)>
<!--
set-type: full dump; from query; single
refSNP
-->
<!ELEMENT ExchangeSet_attlist_setType (#PCDATA)>
<!--
content depth: brief XML (only refSNP properties and summary
subSNP element content); full XML (full refSNP, full subSNP content; all
flanking sequences)
-->
<!ELEMENT ExchangeSet_attlist_setDepth (#PCDATA)>
<!--
version number of docsum.asn/docsum.dtd
specification
-->
<!ELEMENT ExchangeSet_attlist_specVersion (#PCDATA)>
<!--build number of database for this export -->
<!ELEMENT ExchangeSet_attlist_dbSnpBuild (%INTEGER;)>
<!--Generated date -->
<!ELEMENT ExchangeSet_attlist_generated (#PCDATA)>
<!ELEMENT ExchangeSet_sourceDatabase (
ExchangeSet_sourceDatabase_attlist,
ExchangeSet_sourceDatabase_sourceDatabase)>
<!ELEMENT ExchangeSet_sourceDatabase_attlist (
ExchangeSet_sourceDatabase_attlist_taxId,
ExchangeSet_sourceDatabase_attlist_organism,
ExchangeSet_sourceDatabase_attlist_dbSnpOrgAbbr?,
ExchangeSet_sourceDatabase_attlist_gpipeOrgAbbr?)>
<!--
NCBI taxonomy ID for
variation
-->
<!ELEMENT ExchangeSet_sourceDatabase_attlist_taxId (%INTEGER;)>
<!--
common name for species used as part of database
name.
-->
<!ELEMENT ExchangeSet_sourceDatabase_attlist_organism (#PCDATA)>
<!--organism abbreviation used in dbSNP. -->
<!ELEMENT ExchangeSet_sourceDatabase_attlist_dbSnpOrgAbbr (#PCDATA)>
<!--
organism abbreviation used within NCBI genome
pipeline data dumps.
-->
<!ELEMENT ExchangeSet_sourceDatabase_attlist_gpipeOrgAbbr (#PCDATA)>
<!ELEMENT ExchangeSet_sourceDatabase_sourceDatabase EMPTY>
<!ELEMENT ExchangeSet_rs (Rs*)>
<!ELEMENT ExchangeSet_assay (Assay)>
<!ELEMENT ExchangeSet_query (
ExchangeSet_query_attlist,
ExchangeSet_query_query)>
<!ELEMENT ExchangeSet_query_attlist (
ExchangeSet_query_attlist_date?,
ExchangeSet_query_attlist_string?)>
<!--yyyy-mm-dd -->
<!ELEMENT ExchangeSet_query_attlist_date (#PCDATA)>
<!--
Query terms or search
constraints
-->
<!ELEMENT ExchangeSet_query_attlist_string (#PCDATA)>
<!ELEMENT ExchangeSet_query_query EMPTY>
<!ELEMENT ExchangeSet_summary (
ExchangeSet_summary_attlist,
ExchangeSet_summary_summary)>
<!ELEMENT ExchangeSet_summary_attlist (
ExchangeSet_summary_attlist_numRsIds?,
ExchangeSet_summary_attlist_totalSeqLength?,
ExchangeSet_summary_attlist_numContigHits?,
ExchangeSet_summary_attlist_numGeneHits?,
ExchangeSet_summary_attlist_numGiHits?,
ExchangeSet_summary_attlist_num3dStructs?,
ExchangeSet_summary_attlist_numAlleleFreqs?,
ExchangeSet_summary_attlist_numStsHits?,
ExchangeSet_summary_attlist_numUnigeneCids?)>
<!--Total number of refsnp-ids in this exchange set -->
<!ELEMENT ExchangeSet_summary_attlist_numRsIds (%INTEGER;)>
<!--
Total length of exemplar flanking
sequences
-->
<!ELEMENT ExchangeSet_summary_attlist_totalSeqLength (%INTEGER;)>
<!--
Total number of contig locations from
SNPContigLoc
-->
<!ELEMENT ExchangeSet_summary_attlist_numContigHits (%INTEGER;)>
<!--
Total number of locus ids from
SNPContigLocusId
-->
<!ELEMENT ExchangeSet_summary_attlist_numGeneHits (%INTEGER;)>
<!--
Total number of gi hits from
MapLink
-->
<!ELEMENT ExchangeSet_summary_attlist_numGiHits (%INTEGER;)>
<!--
Total number of 3D structures from
SNP3D
-->
<!ELEMENT ExchangeSet_summary_attlist_num3dStructs (%INTEGER;)>
<!--
Total number of allele frequences from
SubPopAllele
-->
<!ELEMENT ExchangeSet_summary_attlist_numAlleleFreqs (%INTEGER;)>
<!--
Total number of STS hits from
SnpInSts
-->
<!ELEMENT ExchangeSet_summary_attlist_numStsHits (%INTEGER;)>
<!--
Total number of unigene cluster ids from
UnigeneSnp
-->
<!ELEMENT ExchangeSet_summary_attlist_numUnigeneCids (%INTEGER;)>
<!ELEMENT ExchangeSet_summary_summary EMPTY>
<!ELEMENT ExchangeSet_baseURL (BaseURL*)>
<!--
functional relationship of SNP (and possibly alleles) to genes at
contig location as defined in organism-specific bxxx_SNPContigLocusId_xxx
tables.
-->
<!ELEMENT FxnSet (
FxnSet_attlist,
FxnSet_fxnSet)>
<!ELEMENT FxnSet_attlist (
FxnSet_attlist_geneId?,
FxnSet_attlist_symbol?,
FxnSet_attlist_mrnaAcc?,
FxnSet_attlist_mrnaVer?,
FxnSet_attlist_protAcc?,
FxnSet_attlist_protVer?,
FxnSet_attlist_fxnClass?,
FxnSet_attlist_readingFrame?,
FxnSet_attlist_allele?,
FxnSet_attlist_residue?,
FxnSet_attlist_aaPosition?,
FxnSet_attlist_mrnaPosition?)>
<!--gene-id of gene as aligned to contig -->
<!ELEMENT FxnSet_attlist_geneId (%INTEGER;)>
<!--
symbol (official if present in Entrez Gene) of
gene
-->
<!ELEMENT FxnSet_attlist_symbol (#PCDATA)>
<!--mRNA accession if variation in transcript -->
<!ELEMENT FxnSet_attlist_mrnaAcc (#PCDATA)>
<!--
mRNA sequence version if variation is in
transcripot
-->
<!ELEMENT FxnSet_attlist_mrnaVer (%INTEGER;)>
<!--protein accession if variation in protein -->
<!ELEMENT FxnSet_attlist_protAcc (#PCDATA)>
<!--
protein version if variation is in
protein
-->
<!ELEMENT FxnSet_attlist_protVer (%INTEGER;)>
<!--
variation in region of gene, but not in
transcript - deprecated
-->
<!ELEMENT FxnSet_attlist_fxnClass %ENUM;>
<!ATTLIST FxnSet_attlist_fxnClass value (
locus-region |
coding-unknown |
synonymous-codon |
non-synonymous-codon |
mrna-utr |
intron-variant |
splice-region-variant |
reference |
coding-exception |
coding-sequence-variant |
nc-transcript-variant |
downstream-variant-500B |
upstream-variant-2KB |
stop-gained |
missense |
frameshift-variant |
utr-variant-3-prime |
upstream-variant-5KB |
splice-acceptor-variant |
splice-donor-variant |
cds-indel |
downstream-variant-5KB |
complex-change-in-transcript |
stop-lost |
incomplete-terminal-codon-variant |
nmd-transcript-variant |
mature-miRNA-variant
) #REQUIRED >
<!ELEMENT FxnSet_attlist_readingFrame (%INTEGER;)>
<!--
variation allele: * suffix indicates allele of contig at this
location
-->
<!ELEMENT FxnSet_attlist_allele (#PCDATA)>
<!--translated amino acid residue for allele -->
<!ELEMENT FxnSet_attlist_residue (#PCDATA)>
<!--
position of the variant residue in peptide
sequence
-->
<!ELEMENT FxnSet_attlist_aaPosition (%INTEGER;)>
<!ELEMENT FxnSet_attlist_mrnaPosition (%INTEGER;)>
<!--
functional relationship of SNP (and possibly alleles) to genes at
contig location as defined in organism-specific bxxx_SNPContigLocusId_xxx
tables.
-->
<!ELEMENT FxnSet_fxnSet EMPTY>
<!--
Position of a single hit of a variation on a
contig
-->
<!ELEMENT MapLoc (
MapLoc_attlist,
MapLoc_fxnSet?)>
<!ELEMENT MapLoc_attlist (
MapLoc_attlist_asnFrom,
MapLoc_attlist_asnTo,
MapLoc_attlist_locType,
MapLoc_attlist_alnQuality?,
MapLoc_attlist_orient?,
MapLoc_attlist_physMapInt?,
MapLoc_attlist_leftFlankNeighborPos?,
MapLoc_attlist_rightFlankNeighborPos?,
MapLoc_attlist_leftContigNeighborPos?,
MapLoc_attlist_rightContigNeighborPos?,
MapLoc_attlist_numberOfMismatches?,
MapLoc_attlist_numberOfDeletions?,
MapLoc_attlist_numberOfInsertions?)>
<!--
beginning of variation as feature on
contig
-->
<!ELEMENT MapLoc_attlist_asnFrom (%INTEGER;)>
<!--
end position of variation as feature on
contig
-->
<!ELEMENT MapLoc_attlist_asnTo (%INTEGER;)>
<!--
defines the seq-loc symbol if asn_from !=
asn_to
-->
<!ELEMENT MapLoc_attlist_locType %ENUM;>
<!ATTLIST MapLoc_attlist_locType value (
insertion |
exact |
deletion |
range-ins |
range-exact |
range-del
) #REQUIRED >
<!--alignment qualiity -->
<!ELEMENT MapLoc_attlist_alnQuality (%REAL;)>
<!--
orientation of refSNP sequence to contig
sequence
-->
<!ELEMENT MapLoc_attlist_orient %ENUM;>
<!ATTLIST MapLoc_attlist_orient value (
forward |
reverse
) #REQUIRED >
<!--
chromosome position as integer for
sorting
-->
<!ELEMENT MapLoc_attlist_physMapInt (%INTEGER;)>
<!--
nearest aligned position in 5' flanking sequence of
snp
-->
<!ELEMENT MapLoc_attlist_leftFlankNeighborPos (%INTEGER;)>
<!--nearest aligned position in 3' flanking sequence of snp -->
<!ELEMENT MapLoc_attlist_rightFlankNeighborPos (%INTEGER;)>
<!--
nearest aligned position in 5' contig alignment of
snp
-->
<!ELEMENT MapLoc_attlist_leftContigNeighborPos (%INTEGER;)>
<!--
nearest aligned position in 3' contig alignment of
snp
-->
<!ELEMENT MapLoc_attlist_rightContigNeighborPos (%INTEGER;)>
<!--
number of Mismatched positions in this
alignment
-->
<!ELEMENT MapLoc_attlist_numberOfMismatches (%INTEGER;)>
<!--number of deletions in this alignment -->
<!ELEMENT MapLoc_attlist_numberOfDeletions (%INTEGER;)>
<!--number of insetions in this alignment -->
<!ELEMENT MapLoc_attlist_numberOfInsertions (%INTEGER;)>
<!ELEMENT MapLoc_fxnSet (FxnSet*)>
<!ELEMENT PrimarySequence (
PrimarySequence_attlist,
PrimarySequence_mapLoc)>
<!ELEMENT PrimarySequence_attlist (
PrimarySequence_attlist_dbSnpBuild,
PrimarySequence_attlist_gi,
PrimarySequence_attlist_source?,
PrimarySequence_attlist_accession?)>
<!ELEMENT PrimarySequence_attlist_dbSnpBuild (%INTEGER;)>
<!ELEMENT PrimarySequence_attlist_gi (%INTEGER;)>
<!ELEMENT PrimarySequence_attlist_source %ENUM;>
<!ATTLIST PrimarySequence_attlist_source value (
submitter |
blastmb |
xm |
remap |
hgvs
) #REQUIRED >
<!ELEMENT PrimarySequence_attlist_accession (#PCDATA)>
<!ELEMENT PrimarySequence_mapLoc (MapLoc*)>
<!--
defines the docsum structure for refSNP clusters, where a refSNP
cluster (rs) is a grouping of individual dbSNP submissions that all refer to the
same variation. The refsnp provides a single unified record for annotation of NCBI
resources such as reference genome sequence.
-->
<!ELEMENT Rs (
Rs_attlist,
Rs_het?,
Rs_validation,
Rs_create,
Rs_update?,
Rs_sequence,
Rs_ss,
Rs_assembly?,
Rs_primarySequence?,
Rs_rsStruct?,
Rs_rsLinkout?,
Rs_mergeHistory?,
Rs_hgvs?,
Rs_alleleOrigin?,
Rs_phenotype?,
Rs_bioSource?,
Rs_frequency?)>
<!ELEMENT Rs_attlist (
Rs_attlist_rsId,
Rs_attlist_snpClass,
Rs_attlist_snpType,
Rs_attlist_molType,
Rs_attlist_validProbMin?,
Rs_attlist_validProbMax?,
Rs_attlist_genotype?,
Rs_attlist_bitField?,
Rs_attlist_taxId?)>
<!--refSNP (rs) number -->
<!ELEMENT Rs_attlist_rsId (%INTEGER;)>
<!ELEMENT Rs_attlist_snpClass %ENUM;>
<!ATTLIST Rs_attlist_snpClass value (
snp |
in-del |
heterozygous |
microsatellite |
named-locus |
no-variation |
mixed |
multinucleotide-polymorphism
) #REQUIRED >
<!ELEMENT Rs_attlist_snpType %ENUM;>
<!ATTLIST Rs_attlist_snpType value (
notwithdrawn |
artifact |
gene-duplication |
duplicate-submission |
notspecified |
ambiguous-location |
low-map-quality
) #REQUIRED >
<!ELEMENT Rs_attlist_molType %ENUM;>
<!ATTLIST Rs_attlist_molType value (
genomic |
cDNA |
mito |
chloro |
unknown
) #REQUIRED >
<!--
minimum reported success rate of all submissions in
cluster
-->
<!ELEMENT Rs_attlist_validProbMin (%INTEGER;)>
<!--
maximum reported success rate of all submissions in
cluster
-->
<!ELEMENT Rs_attlist_validProbMax (%INTEGER;)>
<!--
at least one genotype reported for this
refSNP
-->
<!ELEMENT Rs_attlist_genotype EMPTY>
<!ATTLIST Rs_attlist_genotype value ( true | false ) #REQUIRED >
<!ELEMENT Rs_attlist_bitField (#PCDATA)>
<!ELEMENT Rs_attlist_taxId (%INTEGER;)>
<!ELEMENT Rs_het (
Rs_het_attlist,
Rs_het_het)>
<!ELEMENT Rs_het_attlist (
Rs_het_attlist_type,
Rs_het_attlist_value,
Rs_het_attlist_stdError?)>
<!--
Est=Estimated average het from allele
frequencies, Obs=Observed from genotype data
-->
<!ELEMENT Rs_het_attlist_type %ENUM;>
<!ATTLIST Rs_het_attlist_type value (
est |
obs
) #REQUIRED >
<!--Heterozygosity -->
<!ELEMENT Rs_het_attlist_value (%REAL;)>
<!--
Standard error of Het
estimate
-->
<!ELEMENT Rs_het_attlist_stdError (%REAL;)>
<!ELEMENT Rs_het_het EMPTY>
<!ELEMENT Rs_validation (
Rs_validation_attlist,
Rs_validation_otherPopBatchId?,
Rs_validation_twoHit2AlleleBatchId?,
Rs_validation_frequencyClass?,
Rs_validation_hapMapPhase?,
Rs_validation_tGPPhase?,
Rs_validation_suspectEvidence?)>
<!ELEMENT Rs_validation_attlist (
Rs_validation_attlist_byCluster?,
Rs_validation_attlist_byFrequency?,
Rs_validation_attlist_byOtherPop?,
Rs_validation_attlist_by2Hit2Allele?,
Rs_validation_attlist_byHapMap?,
Rs_validation_attlist_by1000G?,
Rs_validation_attlist_suspect?)>
<!--
at least one subsnp in cluster has frequency data
submitted
-->
<!ELEMENT Rs_validation_attlist_byCluster EMPTY>
<!ATTLIST Rs_validation_attlist_byCluster value ( true | false ) #REQUIRED >
<!--Validated by allele frequency -->
<!ELEMENT Rs_validation_attlist_byFrequency EMPTY>
<!ATTLIST Rs_validation_attlist_byFrequency value ( true | false ) #REQUIRED >
<!ELEMENT Rs_validation_attlist_byOtherPop EMPTY>
<!ATTLIST Rs_validation_attlist_byOtherPop value ( true | false ) #REQUIRED >
<!--
cluster has 2+ submissions, with 1+ submissions
assayed with a non-computational method
-->
<!ELEMENT Rs_validation_attlist_by2Hit2Allele EMPTY>
<!ATTLIST Rs_validation_attlist_by2Hit2Allele value ( true | false ) #REQUIRED >
<!--Validated by HapMap Project -->
<!ELEMENT Rs_validation_attlist_byHapMap EMPTY>
<!ATTLIST Rs_validation_attlist_byHapMap value ( true | false ) #REQUIRED >
<!--Validated by 1000 Genomes Project -->
<!ELEMENT Rs_validation_attlist_by1000G EMPTY>
<!ATTLIST Rs_validation_attlist_by1000G value ( true | false ) #REQUIRED >
<!--Suspected to be false SNP -->
<!ELEMENT Rs_validation_attlist_suspect EMPTY>
<!ATTLIST Rs_validation_attlist_suspect value ( true | false ) #REQUIRED >
<!--
dbSNP batch-id's for other pop snp validation
data.
-->
<!ELEMENT Rs_validation_otherPopBatchId (Rs_validation_otherPopBatchId_E*)>
<!ELEMENT Rs_validation_otherPopBatchId_E (%INTEGER;)>
<!--
dbSNP batch-id's for double-hit snp
validation data. Use batch-id to get methods, etc.
-->
<!ELEMENT Rs_validation_twoHit2AlleleBatchId (Rs_validation_twoHit2AlleleBatchId_E*)>
<!ELEMENT Rs_validation_twoHit2AlleleBatchId_E (%INTEGER;)>
<!--
Frequency validation class (1) low frequency
variation that is cited in journal and other reputable
sources (2) greater than 5 percent minor allele freq in each
and all populations (4) greater than 5 percent minor allele
freq in 1+ populations (8) if the variant has 2+ minor
allele count based on freq or genotype data (16) less than 1
percent minor allele freq in each and all populations (32)
less than 1 percent minor freq in 1+ populations
-->
<!ELEMENT Rs_validation_frequencyClass (Rs_validation_frequencyClass_E*)>
<!ELEMENT Rs_validation_frequencyClass_E (%INTEGER;)>
<!--
alidated by HapMap Project phase1-genotyped
(1), Phase 1 genotyped; filtered, non-redundant
phase2-genotyped (2), Phase 2 genotyped; filtered,
non-redundant phase3-genotyped (4) Phase 3 genotyped;
filtered, non-redundant
-->
<!ELEMENT Rs_validation_hapMapPhase (Rs_validation_hapMapPhase_E*)>
<!ELEMENT Rs_validation_hapMapPhase_E (%INTEGER;)>
<!--
Validated by 1000 Genomes Project (TGP) pilot
1 (1), pilot 2 (2), pilot 3 (4)
-->
<!ELEMENT Rs_validation_tGPPhase (Rs_validation_tGPPhase_E*)>
<!ELEMENT Rs_validation_tGPPhase_E (%INTEGER;)>
<!--
Suspected to be false SNP evidence Single
Nucleotide Difference - paralogous genes (1), Genotype or
base calling errors (2), Submission evidence or errors (4),
Others (8)
-->
<!ELEMENT Rs_validation_suspectEvidence (Rs_validation_suspectEvidence_E*)>
<!ELEMENT Rs_validation_suspectEvidence_E (#PCDATA)>
<!--
date the refsnp cluster was
instantiated
date the refsnp cluster was
instantiated
-->
<!ELEMENT Rs_create (
Rs_create_attlist,
Rs_create_create)>
<!ELEMENT Rs_create_attlist (
Rs_create_attlist_build?,
Rs_create_attlist_date?)>
<!--
build number when the cluster was
created
-->
<!ELEMENT Rs_create_attlist_build (%INTEGER;)>
<!--yyyy-mm-dd -->
<!ELEMENT Rs_create_attlist_date (#PCDATA)>
<!--
date the refsnp cluster was
instantiated
-->
<!ELEMENT Rs_create_create EMPTY>
<!--
most recent date the cluster was updated (member added or
deleted)
most recent date the cluster was updated (member added or
deleted)
-->
<!ELEMENT Rs_update (
Rs_update_attlist,
Rs_update_update)>
<!ELEMENT Rs_update_attlist (
Rs_update_attlist_build?,
Rs_update_attlist_date?)>
<!--
build number when the cluster was
updated
-->
<!ELEMENT Rs_update_attlist_build (%INTEGER;)>
<!--yyyy-mm-dd -->
<!ELEMENT Rs_update_attlist_date (#PCDATA)>
<!--
most recent date the cluster was updated (member added or
deleted)
-->
<!ELEMENT Rs_update_update EMPTY>
<!ELEMENT Rs_sequence (
Rs_sequence_attlist,
Rs_sequence_seq5?,
Rs_sequence_observed,
Rs_sequence_seq3?)>
<!ELEMENT Rs_sequence_attlist (
Rs_sequence_attlist_exemplarSs,
Rs_sequence_attlist_ancestralAllele?)>
<!--
dbSNP ss# selected as source of refSNP flanking
sequence, ss# part of ss-list below
-->
<!ELEMENT Rs_sequence_attlist_exemplarSs (%INTEGER;)>
<!ELEMENT Rs_sequence_attlist_ancestralAllele (#PCDATA)>
<!--
5' sequence that flanks the
variation
-->
<!ELEMENT Rs_sequence_seq5 (#PCDATA)>
<!--
list of all nucleotide alleles observed in
ss-list members, correcting for reverse complementation of
members reported in reverse orientation
-->
<!ELEMENT Rs_sequence_observed (#PCDATA)>
<!--
3' sequence that flanks the
variation
-->
<!ELEMENT Rs_sequence_seq3 (#PCDATA)>
<!ELEMENT Rs_ss (Ss*)>
<!ELEMENT Rs_assembly (Assembly*)>
<!ELEMENT Rs_primarySequence (PrimarySequence*)>
<!ELEMENT Rs_rsStruct (RsStruct*)>
<!ELEMENT Rs_rsLinkout (RsLinkout*)>
<!ELEMENT Rs_mergeHistory (Rs_mergeHistory_E*)>
<!ELEMENT Rs_mergeHistory_E (
Rs_mergeHistory_E_attlist,
Rs_mergeHistory_E_mergeHistory)>
<!ELEMENT Rs_mergeHistory_E_attlist (
Rs_mergeHistory_E_attlist_rsId,
Rs_mergeHistory_E_attlist_buildId?,
Rs_mergeHistory_E_attlist_orientFlip?)>
<!--
previously issued rs id whose member assays have
now been merged
-->
<!ELEMENT Rs_mergeHistory_E_attlist_rsId (%INTEGER;)>
<!--
build id when rs id was merged into parent
rs
-->
<!ELEMENT Rs_mergeHistory_E_attlist_buildId (%INTEGER;)>
<!--
TRUE if strand of rs id is reverse to parent
object's current strand
-->
<!ELEMENT Rs_mergeHistory_E_attlist_orientFlip EMPTY>
<!ATTLIST Rs_mergeHistory_E_attlist_orientFlip value ( true | false ) #REQUIRED >
<!ELEMENT Rs_mergeHistory_E_mergeHistory EMPTY>
<!-- HGVS name list -->
<!ELEMENT Rs_hgvs (Rs_hgvs_E*)>
<!ELEMENT Rs_hgvs_E (#PCDATA)>
<!--
origin of this allele, if known
note that these are powers-of-two, and represent bits; thus, we can
represent more than one state simultaneously through a bitwise OR
unknown (0),
germline (1),
somatic (2),
inherited (4),
paternal (8),
maternal (16),
de-novo (32),
biparental (64),
uniparental (128),
not-tested (256),
tested-inconclusive (512),
origin of this allele, if known
note that these are powers-of-two, and represent bits; thus, we can
represent more than one state simultaneously through a bitwise OR
unknown (0),
germline (1),
somatic (2),
inherited (4),
paternal (8),
maternal (16),
de-novo (32),
biparental (64),
uniparental (128),
not-tested (256),
tested-inconclusive (512),
-->
<!ELEMENT Rs_alleleOrigin (Rs_alleleOrigin_E*)>
<!ELEMENT Rs_alleleOrigin_E (
Rs_alleleOrigin_E_attlist,
Rs_alleleOrigin_E_alleleOrigin)>
<!ELEMENT Rs_alleleOrigin_E_attlist (
Rs_alleleOrigin_E_attlist_allele?)>
<!ELEMENT Rs_alleleOrigin_E_attlist_allele (#PCDATA)>
<!--
origin of this allele, if known
note that these are powers-of-two, and represent bits; thus, we can
represent more than one state simultaneously through a bitwise OR
unknown (0),
germline (1),
somatic (2),
inherited (4),
paternal (8),
maternal (16),
de-novo (32),
biparental (64),
uniparental (128),
not-tested (256),
tested-inconclusive (512),
-->
<!ELEMENT Rs_alleleOrigin_E_alleleOrigin (%INTEGER;)>
<!ELEMENT Rs_phenotype (Rs_phenotype_E*)>
<!ELEMENT Rs_phenotype_E (
Rs_phenotype_E_clinicalSignificance?)>
<!--
unknown (0),
untested (1),
non-pathogenic (2),
probable-non-pathogenic (3),
probable-pathogenic (4),
pathogenic (5),
drug response (6),
other (255)
-->
<!ELEMENT Rs_phenotype_E_clinicalSignificance (Rs_phenotype_E_clinicalSignificance_E*)>
<!ELEMENT Rs_phenotype_E_clinicalSignificance_E (#PCDATA)>
<!ELEMENT Rs_bioSource (Rs_bioSource_E*)>
<!ELEMENT Rs_bioSource_E (
Rs_bioSource_E_genome?,
Rs_bioSource_E_origin?)>
<!--
unknown (0) ,
genomic (1) ,
chloroplast (2) ,
chromoplast (3) ,
kinetoplast (4) ,
mitochondrion (5) ,
plastid (6) ,
macronuclear (7) ,
extrachrom (8) ,
plasmid (9) ,
transposon (10) ,
insertion-seq (11) ,
cyanelle (12) ,
proviral (13) ,
virion (14) ,
nucleomorph (15) ,
apicoplast (16) ,
leucoplast (17) ,
proplastid (18) ,
endogenous-virus (19) ,
hydrogenosome (20) ,
chromosome (21) ,
chromatophore (22)
-->
<!ELEMENT Rs_bioSource_E_genome (Rs_bioSource_E_genome_E*)>
<!ELEMENT Rs_bioSource_E_genome_E (#PCDATA)>
<!--
unknown (0) ,
natural (1) , normal biological entity
natmut (2) , naturally occurring mutant
mut (3) , artificially mutagenized
artificial (4) , artificially engineered
synthetic (5) , purely synthetic
other (255)
-->
<!ELEMENT Rs_bioSource_E_origin (Rs_bioSource_E_origin_E*)>
<!ELEMENT Rs_bioSource_E_origin_E (#PCDATA)>
<!ELEMENT Rs_frequency (Rs_frequency_E*)>
<!ELEMENT Rs_frequency_E (
Rs_frequency_E_attlist,
Rs_frequency_E_frequency)>
<!ELEMENT Rs_frequency_E_attlist (
Rs_frequency_E_attlist_freq?,
Rs_frequency_E_attlist_allele?,
Rs_frequency_E_attlist_popId?,
Rs_frequency_E_attlist_sampleSize?)>
<!ELEMENT Rs_frequency_E_attlist_freq (%REAL;)>
<!ELEMENT Rs_frequency_E_attlist_allele (#PCDATA)>
<!--dbSNP Populaton ID -->
<!ELEMENT Rs_frequency_E_attlist_popId (%INTEGER;)>
<!ELEMENT Rs_frequency_E_attlist_sampleSize (%INTEGER;)>
<!ELEMENT Rs_frequency_E_frequency EMPTY>
<!--link data for another resource -->
<!ELEMENT RsLinkout (
RsLinkout_attlist,
RsLinkout_rsLinkout)>
<!ELEMENT RsLinkout_attlist (
RsLinkout_attlist_resourceId,
RsLinkout_attlist_linkValue)>
<!--BaseURLList.url_id -->
<!ELEMENT RsLinkout_attlist_resourceId (#PCDATA)>
<!--
value to append to ResourceURL.base-url for complete
link
-->
<!ELEMENT RsLinkout_attlist_linkValue (#PCDATA)>
<!--link data for another resource -->
<!ELEMENT RsLinkout_rsLinkout EMPTY>
<!--structure information for SNP -->
<!ELEMENT RsStruct (
RsStruct_attlist,
RsStruct_rsStruct)>
<!ELEMENT RsStruct_attlist (
RsStruct_attlist_protAcc?,
RsStruct_attlist_protGi?,
RsStruct_attlist_protLoc?,
RsStruct_attlist_protResidue?,
RsStruct_attlist_rsResidue?,
RsStruct_attlist_structGi?,
RsStruct_attlist_structLoc?,
RsStruct_attlist_structResidue?)>
<!--accession of the protein with variation -->
<!ELEMENT RsStruct_attlist_protAcc (#PCDATA)>
<!--GI of the protein with variation -->
<!ELEMENT RsStruct_attlist_protGi (%INTEGER;)>
<!--
position of the residue for the protein
GI
-->
<!ELEMENT RsStruct_attlist_protLoc (%INTEGER;)>
<!--
residue specified for protein at prot-loc
location
-->
<!ELEMENT RsStruct_attlist_protResidue (#PCDATA)>
<!--
alternative residue specified by variation
sequence
-->
<!ELEMENT RsStruct_attlist_rsResidue (#PCDATA)>
<!--GI of the structure neighbor -->
<!ELEMENT RsStruct_attlist_structGi (%INTEGER;)>
<!--
position of the residue for the structure
GI
-->
<!ELEMENT RsStruct_attlist_structLoc (%INTEGER;)>
<!--
residue specified for protein at struct-loc
location
-->
<!ELEMENT RsStruct_attlist_structResidue (#PCDATA)>
<!--structure information for SNP -->
<!ELEMENT RsStruct_rsStruct EMPTY>
<!--data for an individual submission to dbSNP -->
<!ELEMENT Ss (
Ss_attlist,
Ss_sequence)>
<!ELEMENT Ss_attlist (
Ss_attlist_ssId,
Ss_attlist_handle,
Ss_attlist_batchId,
Ss_attlist_locSnpId?,
Ss_attlist_subSnpClass?,
Ss_attlist_orient?,
Ss_attlist_strand?,
Ss_attlist_molType?,
Ss_attlist_buildId?,
Ss_attlist_methodClass?,
Ss_attlist_validated?,
Ss_attlist_linkoutUrl?,
Ss_attlist_ssAlias?,
Ss_attlist_alleleOrigin?,
Ss_attlist_clinicalSignificance?)>
<!--dbSNP accession number for submission -->
<!ELEMENT Ss_attlist_ssId (%INTEGER;)>
<!--Tag for the submitting laboratory -->
<!ELEMENT Ss_attlist_handle (#PCDATA)>
<!--dbSNP number for batch submission -->
<!ELEMENT Ss_attlist_batchId (%INTEGER;)>
<!--submission (ss#) submitter ID -->
<!ELEMENT Ss_attlist_locSnpId (#PCDATA)>
<!--
SubSNP classification by type of
variation
-->
<!ELEMENT Ss_attlist_subSnpClass %ENUM;>
<!ATTLIST Ss_attlist_subSnpClass value (
snp |
in-del |
heterozygous |
microsatellite |
named-locus |
no-variation |
mixed |
multinucleotide-polymorphism
) #REQUIRED >
<!--
orientation of refsnp cluster members to refsnp cluster
sequence
-->
<!ELEMENT Ss_attlist_orient %ENUM;>
<!ATTLIST Ss_attlist_orient value (
forward |
reverse
) #REQUIRED >
<!--
strand is defined as TOP/BOTTOM by nature of flanking
nucleotide sequence
-->
<!ELEMENT Ss_attlist_strand %ENUM;>
<!ATTLIST Ss_attlist_strand value (
top |
bottom
) #REQUIRED >
<!--moltype from Batch table -->
<!ELEMENT Ss_attlist_molType %ENUM;>
<!ATTLIST Ss_attlist_molType value (
genomic |
cDNA |
mito |
chloro |
unknown
) #REQUIRED >
<!--
dbSNP build number when ss# was added to a refSNP (rs#)
cluster
-->
<!ELEMENT Ss_attlist_buildId (%INTEGER;)>
<!--
class of method used to assay for the
variation
-->
<!ELEMENT Ss_attlist_methodClass %ENUM;>
<!ATTLIST Ss_attlist_methodClass value (
dHPLC |
hybridize |
computed |
sSCP |
other |
unknown |
rFLP |
sequence
) #REQUIRED >
<!--
subsnp has been experimentally validated by
submitter
-->
<!ELEMENT Ss_attlist_validated %ENUM;>
<!ATTLIST Ss_attlist_validated value (
by-submitter |
by-frequency |
by-cluster
) #REQUIRED >
<!--
append loc-snp-id to this base URL to construct a pointer to
submitter data.
-->
<!ELEMENT Ss_attlist_linkoutUrl (#PCDATA)>
<!ELEMENT Ss_attlist_ssAlias (#PCDATA)>
<!--
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="unknown"/>
<xsd:enumeration value="germline"/>
<xsd:enumeration value="somatic"/>
<xsd:enumeration value="inherited"/>
<xsd:enumeration value="paternal"/>
<xsd:enumeration value="maternal"/>
<xsd:enumeration value="de-novo"/>
<xsd:enumeration value="other"/>
</xsd:restriction>
</xsd:simpleType>
-->
<!ELEMENT Ss_attlist_alleleOrigin (%INTEGER;)>
<!--
<xsd:simpleType>
<xsd:restriction base="xsd:string">
<xsd:enumeration value="unknown"/>
<xsd:enumeration value="untested"/>
<xsd:enumeration value="non-pathogenic"/>
<xsd:enumeration value="probable-non-pathogenic"/>
<xsd:enumeration value="probable-pathogenic"/>
<xsd:enumeration value="pathogenic"/>
<xsd:enumeration value="other"/>
</xsd:restriction>
</xsd:simpleType>
-->
<!ELEMENT Ss_attlist_clinicalSignificance (#PCDATA)>
<!ELEMENT Ss_sequence (
Ss_sequence_seq5?,
Ss_sequence_observed,
Ss_sequence_seq3?)>
<!--
5' sequence that flanks the
variation
-->
<!ELEMENT Ss_sequence_seq5 (#PCDATA)>
<!--
list of all nucleotide alleles observed in
ss-list members, correcting for reverse complementation of
memebers reported in reverse orientation
-->
<!ELEMENT Ss_sequence_observed (#PCDATA)>
<!--
3' sequence that flanks the
variation
-->
<!ELEMENT Ss_sequence_seq3 (#PCDATA)>
|