设计模式¶
数据库模式¶
IRD主要存储了项目、样本、测序结果、样本表型、以及样本与比对参考基因的关系。实体关系图如下:
数据模式¶
sample(包含样本信息、项目信息、测序信息、表型信息)
形式如下:
- tables.sample
- sample
- project
- sequence
- phenotype
格式如下:
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 | {
sample_id: {
type: "string",
desc: "样本编号",
allow: "",
index: true,
level: "D5"
},
sample_name: {
type: "string",
desc: "样本名称",
allow: "",
index: false,
level: "D5"
},
project: {
name: {
type: "string",
desc: "项目名称",
allow: "",
index: false,
level: "D5"
},
sample_num: {
type: "string",
desc: "组成样本数",
allow: "",
index: false,
level: "D5"
},
type: {
type: "string",
desc: "项目类型",
allow: [
"TCR",
"BCR"
],
index: false,
level: "D5"
},
desc: {
type: "string",
desc: "项目描述",
allow: "",
index: false,
level: "D5"
}
},
sample_type: {
type: "string",
desc: "样本类型",
allow: [
"PBMC",
"whole_blood",
"lymphoid_tissue",
"non-lymphoid_tissue"
],
index: false,
level: "D5"
},
species: {
type: "string",
desc: "样本所属物种",
allow: "",
index: false,
level: "D5"
},
seq_type: {
type: "string",
desc: "测序样本类型",
allow: [
"DNA",
"RNA"
],
index: false,
level: "D5"
},
locus: {
type: "string",
desc: "目标序列类型",
allow: [
"TRCAD",
"TRCG",
"TCRB",
"IGH",
"IGL",
"IGK"
],
index: false,
level: "D5"
},
method: {
type: "string",
desc: "分析方法",
allow: [
"IMonitor"
],
index: false,
level: "D5"
},
method_para: {
type: "string",
desc: "流程方法的具体参数",
allow: "",
index: false,
level: "D3"
},
primer_set: {
type: "string",
desc: "引物名称",
allow: "",
index: false,
level: "D5"
},
time: {
type: "date",
desc: "取样时间",
allow: "",
index: false,
level: "D5"
},
amount_ng: {
type: "float",
desc: "样本量(ng)",
allow: "",
index: false,
level: "D5"
},
platforms: {
type: "string",
desc: "测序平台",
allow: [
"Hiseq",
"Proten",
"Zebra",
"Miseq"
],
index: false,
level: "D5"
},
in_frame_percentage: {
type: "float",
desc: "in frame数据百分比",
allow: "0-100",
index: false,
level: "D5"
},
total_in_frame_reads: {
type: "float",
desc: "in frame reads数",
allow: ">0",
index: false,
level: "D5"
},
out_frame_percentage: {
type: "float",
desc: "out frame数据百分比",
allow: "0-100",
index: false,
level: "D5"
},
total_out_frame_percentage: {
type: "float",
desc: "out frame reads数",
allow: ">0",
index: false,
level: "D5"
},
stop_codon_percentage: {
type: "float",
desc: "含有终止密码子数据百分比",
allow: "0-100",
index: false,
level: "D5"
},
total_stop_reads: {
type: "float",
desc: "含有终止密码子reads数",
allow: ">0",
index: false,
level: "D5"
},
v_alignment: {
type: "float",
desc: "V基因比对率",
allow: "0-100",
index: false,
level: "D5"
},
d_alignment: {
type: "float",
desc: "D基因比对率",
allow: "0-100",
index: false,
level: "D5"
},
j_alignment: {
type: "float",
desc: "J基因比对率",
allow: "0-100",
index: false,
level: "D5"
},
vj_alignment: {
type: "float",
desc: "VJ基因比对率",
allow: "0-100",
index: false,
level: "D5"
},
cdr3_nt_productive_entropy: {
type: "float",
desc: "有效数据CDR3 NT的香农熵",
allow: "0-30",
index: false,
level: "D5"
},
cdr3_aa_productive_entropy: {
type: "float",
desc: "有效数据CDR3 AA的香农熵",
allow: "0-30",
index: false,
level: "D5"
},
seq_nt_uniq_number: {
type: "float",
desc: "碱基序列unique number",
allow: ">0",
index: false,
level: "D5"
},
seq_aa_uniq_number: {
type: "float",
desc: "氨基酸序列unique number",
allow: ">0",
index: false,
level: "D5"
},
cdr3_nt_uniq_number: {
type: "string",
desc: "CDR3 NT unique number",
allow: ">0",
index: false,
level: "D5"
},
cdr3_aa_uniq_number: {
type: "float",
desc: "CDR3 AA unique number",
allow: ">0",
index: false,
level: "D5"
},
sequence_result_status: {
type: "string",
desc: "数据录入时的状态",
allow: [
"published",
"unpublished"
],
index: false,
level: "D5"
},
upload_date: {
type: "date",
desc: "样本对应序列上传时间",
allow: "",
index: false,
level: "D5"
},
related_articles: {
type: "string",
desc: "与样本相关的相关文献",
allow: "",
index: false,
level: "D5"
},
sequence_result: [
{
frame_type: {
type: "string",
desc: "序列类型",
allow: [
"in-frame",
"out-frame"
],
index: false,
level: "D5"
},
v_ref: {
type: "string",
desc: "对比到的V基因",
allow: "",
index: false,
level: "D5"
},
d_ref: {
type: "string",
desc: "对比到的D基因",
allow: "",
index: false,
level: "D5"
},
j_ref: {
type: "string",
desc: "对比到的J基因",
allow: "",
index: false,
level: "D5"
},
cdr3_start: {
type: "int",
desc: "CDR3起始位置",
allow: "",
index: false,
level: "D5"
},
cdr3_end: {
type: "int",
desc: "CDR3终止位置",
allow: "",
index: false,
level: "D5"
},
cdr3_nt: {
type: "string",
desc: "CDR3碱基序列",
allow: "",
index: false,
level: "D5"
},
chr3_aa: {
type: "string",
desc: "CDR3氨基酸序列",
allow: "",
index: false,
level: "D5"
},
3v_del: {
type: "string",
desc: "保存插入删除信息",
allow: "",
index: false,
level: "D5"
},
5d_del: {
type: "string",
desc: "保存插入删除信息",
allow: "",
index: false,
level: "D5"
},
3d_del: {
type: "string",
desc: "保存插入删除信息",
allow: "",
index: false,
level: "D5"
},
5j_del: {
type: "string",
desc: "保存插入删除信息",
allow: "",
index: false,
level: "D5"
},
vd_ins: {
type: "string",
desc: "保存插入删除信息",
allow: "",
index: false,
level: "D5"
},
dj_ins: {
type: "string",
desc: "保存插入删除信息",
allow: "",
index: false,
level: "D5"
},
vj_ins: {
type: "string",
desc: "保存插入删除信息",
allow: "",
index: false,
level: "D5"
},
strand: {
type: "string",
desc: "序列的方向",
allow: "",
index: false,
level: "D5"
},
sequence: {
type: "string",
desc: "碱基序列",
allow: "",
index: false,
level: "D5"
},
amino_acid: {
type: "string",
desc: "氨基酸序列",
allow: "",
index: false,
level: "D5"
},
v_comparison_info: {
type: "string",
desc: "V区比对信息",
allow: "",
index: false,
level: "D5"
},
v_comparison_rate: {
type: "float",
desc: "V区比对率",
allow: "",
index: false,
level: "D5"
},
v_comparison_length: {
type: "int",
desc: "V区比对长度",
allow: "",
index: false,
level: "D5"
},
v_comparison_mis: {
type: "int",
desc: "V区比对mismatch数",
allow: "",
index: false,
level: "D5"
},
v_comparison_start: {
type: "int",
desc: "V基因比对起始位置",
allow: "",
index: false,
level: "D5"
},
v_comparison_end: {
type: "int",
desc: "V基因比对终止位置",
allow: "",
index: false,
level: "D5"
},
seq_comp_V_start: {
type: "int",
desc: "序列比对到ref起始位置",
allow: "",
index: false,
level: "D5"
},
seq_comp_V_end: {
type: "int",
desc: "序列比对到ref终止位置",
allow: "",
index: false,
level: "D5"
},
v_comp_p: {
type: "float",
desc: "检验值",
allow: "",
index: false,
level: "D5"
},
v_comp_grade: {
type: "float",
desc: "评分",
allow: "",
index: false,
level: "D5"
},
d_comparison_info: {
type: "string",
desc: "D区比对信息",
allow: "",
index: false,
level: "D5"
},
d_comparison_rate: {
type: "float",
desc: "D区比对率",
allow: "",
index: false,
level: "D5"
},
d_comparison_length: {
type: "int",
desc: "D区比对长度",
allow: "",
index: false,
level: "D5"
},
d_comparison_mis: {
type: "int",
desc: "D区比对mismatch数",
allow: "",
index: false,
level: "D5"
},
d_comparison_start: {
type: "int",
desc: "D基因比对起始位置",
allow: "",
index: false,
level: "D5"
},
d_comparison_end: {
type: "int",
desc: "D基因比对终止位置",
allow: "",
index: false,
level: "D5"
},
seq_comp_d_start: {
type: "int",
desc: "序列比对到ref起始位置",
allow: "",
index: false,
level: "D5"
},
seq_comp_d_end: {
type: "int",
desc: "序列比对到ref终止位置",
allow: "",
index: false,
level: "D5"
},
d_comp_p: {
type: "float",
desc: "检验值",
allow: "",
index: false,
level: "D5"
},
d_comp_grade: {
type: "float",
desc: "评分",
allow: "",
index: false,
level: "D5"
},
j_comparison_info: {
type: "string",
desc: "J区比对信息",
allow: "",
index: false,
level: "D5"
},
j_comparison_rate: {
type: "float",
desc: "J区比对率",
allow: "",
index: false,
level: "D5"
},
j_comparison_length: {
type: "int",
desc: "J区比对长度",
allow: "",
index: false,
level: "D5"
},
j_comparison_mis: {
type: "int",
desc: "J区比对mismatch数",
allow: "",
index: false,
level: "D5"
},
j_comparison_start: {
type: "int",
desc: "J基因比对起始位置",
allow: "",
index: false,
level: "D5"
},
j_comparison_end: {
type: "int",
desc: "J基因比对终止位置",
allow: "",
index: false,
level: "D5"
},
seq_comp_j_start: {
type: "int",
desc: "序列比对到ref起始位置",
allow: "",
index: false,
level: "D5"
},
seq_comp_j_end: {
type: "int",
desc: "序列比对到ref终止位置",
allow: "",
index: false,
level: "D5"
},
j_comp_p: {
type: "float",
desc: "检验值",
allow: "",
index: false,
level: "D5"
},
j_comp_grade: {
type: "float",
desc: "评分",
allow: "",
index: false,
level: "D5"
},
mutation: {
type: "float",
desc: "突变率",
allow: "",
index: false,
level: "D5"
},
isotype: {
type: "string",
desc: "",
allow: [
"IGHA",
"IGHD",
"IGHE",
"IGHG",
"IGHM",
"unknown"
],
index: false,
level: "D5"
},
},
],
disease: {
name: {
type: "string",
desc: "疾病名称",
allow: "",
index: false,
level: "D5"
},
pathogenic_clone: {
type: "string",
desc: "疾病相关克隆",
allow: "",
index: false,
level: "D5"
},
related_articles: {
type: "string",
desc: "相关报导文件",
allow: "",
index: false,
level: "D5"
}
},
phenotype: {
inform: {
type: "string",
desc: "是否有知情同意书",
allow: "",
index: false,
level: "D5"
},
date: {
type: "date",
desc: "采样时间",
allow: "",
index: false,
level: "D5"
},
sample_type: {
type: "string",
desc: "样本类型",
allow: "",
index: false,
level: "D5"
},
gender: {
type: "string",
desc: "性别",
allow: "",
index: false,
level: "D5"
},
age: {
type: "int",
desc: "年龄",
allow: "",
index: false,
level: "D5"
},
race: {
type: "string"desc: "民族",
allow: "",
index: false,
level: "D5"
},
height: {
type: "float",
desc: "身高",
allow: "",
index: false,
level: "D5"
},
weight: {
type: "float",
desc: "体重",
allow: "",
index: false,
level: "D5"
},
BMI: {
type: "float",
desc: "身高体重指数",
allow: "",
index: false,
level: "D5"
},
waist: {
type: "float",
desc: "腰围",
allow: "",
index: false,
level: "D5"
},
hip: {
type: "float",
desc: "臀围",
allow: "",
index: false,
level: "D5"
},
whr: {
type: "float",
desc: "腰臀比",
allow: "",
index: false,
level: "D5"
},
blood_pressure: {
type: "float",
desc: "血压",
allow: "",
index: false,
level: "D5"
},
fast_glucose: {
type: "float",
desc: "空腹血糖",
allow: "",
index: false,
level: "D5"
},
blood_lipids: {
type: "float",
desc: "血脂",
allow: "",
index: false,
level: "D5"
},
t2d: {
type: "bool",
desc: "是否有二型糖尿病",
allow: [
true,
false
],
index: false,
level: "D5"
}
}
}
|
cdr3_aa
格式如下:
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 | {
sample_id: {
type: "string",
desc: "样本id",
allow: "",
index: false,
level: "D5"
},
seq: {
type: "string",
desc: "CDR3氨基酸序列",
allow: "",
index: false,
level: "D5"
},
num: {
type: "int",
desc: "CDR3序列数目",
allow: "",
index: false,
level: "D5"
},
freq: {
type: "float",
desc: "CDR3丰度",
allow: "0-100",
index: false,
level: "D5"
}
}
|
cdr3_nt
格式如下:
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 | {
sample_id: {
type: "string",
desc: "样本id",
allow: "",
index: false,
level: "D5"
},
seq: {
type: "string",
desc: "CDR3氨基酸序列",
allow: "",
index: false,
level: "D5"
},
num: {
type: "int",
desc: "CDR3序列数目",
allow: "",
index: false,
level: "D5"
},
freq: {
type: "float",
desc: "CDR3丰度",
allow: "0-100",
index: false,
level: "D5"
}
}
|
v
格式如下:
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 | {
sample_id: {
type: "string",
desc: "样本id",
allow: "",
index: false,
level: "D5"
},
species: {
type: "string",
desc: "物种名称",
allow: "",
index: false,
level: "D5"
},
name: {
type: "string",
desc: "V基因名称",
allow: "",
index: false,
level: "D5"
},
seq: {
type: "string",
desc: "V参考基因碱基序列",
allow: "",
index: false,
level: "D5"
},
num: {
type: "int",
desc: "V基因使用具体数目",
allow: "",
index: false,
level: "D5"
},
freq: {
type: "float",
desc: "V基因使用频率",
allow: "0-100",
index: false,
level: "D5"
}
}
|
j
格式如下:
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 | {
sample_id: {
type: "string",
desc: "样本id",
allow: "",
index: false,
level: "D5"
},
species: {
type: "string",
desc: "物种名称",
allow: "",
index: false,
level: "D5"
},
name: {
type: "string",
desc: "J基因名称",
allow: "",
index: false,
level: "D5"
},
seq: {
type: "string",
desc: "J参考基因碱基序列",
allow: "",
index: false,
level: "D5"
},
num: {
type: "int",
desc: "J基因使用具体数目",
allow: "",
index: false,
level: "D5"
},
freq: {
type: "float",
desc: "J基因使用频率",
allow: "0-100",
index: false,
level: "D5"
}
}
|
vj
格式如下:
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 | {
sample_id: {
type: "string",
desc: "样本id",
allow: "",
index: false,
level: "D5"
},
name_v: {
type: "string",
desc: "V基因名称",
allow: "",
index: false,
level: "D5"
},
name_j: {
type: "string",
desc: "J基因名称",
allow: "",
index: false,
level: "D5"
},
num: {
type: "int",
desc: "VJ基因使用具体数目",
allow: "",
index: false,
level: "D5"
},
freq: {
type: "float",
desc: "VJ基因使用频率",
allow: "0-100",
index: false,
level: "D5"
}
}
|