comparison test-data/simple_test_case_v2.json @ 11:f803a68fc9e5 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/ena_upload commit c7f54e6e3b1ffad5631ff7c150449cb79bd3686d
author iuc
date Sat, 23 Mar 2024 22:06:45 +0000
parents
children
comparison
equal deleted inserted replaced
10:480d9e9d156b 11:f803a68fc9e5
1 {
2 "identifier": "",
3 "title": "Test Case ENA upload tool",
4 "description": "This investigation matches the test case of the ENA upload tool",
5 "submissionDate": "",
6 "publicReleaseDate": "",
7 "ontologySourceReferences": [],
8 "filename": "Test Case ENA upload tool.txt",
9 "comments": [
10 {
11 "name": "ISAjson export time",
12 "value": "2023-11-08T16:27:49Z"
13 },
14 {
15 "name": "SEEK Project name",
16 "value": "Test Project ENA upload Tool"
17 },
18 {
19 "name": "SEEK Project ID",
20 "value": "http://localhost:3000/single_pages/16"
21 },
22 {
23 "name": "SEEK Investigation ID",
24 "value": "27"
25 }
26 ],
27 "publications": [],
28 "people": [
29 {
30 "@id": "#people/4",
31 "lastName": "De Pelseneer",
32 "firstName": "Kevin",
33 "midInitials": "",
34 "email": "kevin.depelseneer@psb.ugent.be",
35 "phone": "",
36 "fax": "",
37 "address": "",
38 "affiliation": "",
39 "roles": [
40 {
41 "termAccession": "",
42 "termSource": "",
43 "annotationValue": ""
44 }
45 ],
46 "comments": [
47 {
48 "@id": "",
49 "value": "",
50 "name": ""
51 }
52 ]
53 }
54 ],
55 "studies": [
56 {
57 "identifier": "",
58 "title": "Study - Test Case ENA",
59 "description": "",
60 "submissionDate": "",
61 "publicReleaseDate": "",
62 "filename": "Study - Test Case ENA.txt",
63 "comments": [
64 {
65 "@id": "#study_comment/25_13_49",
66 "name": "ena_sample_alias_prefix",
67 "value": "sample_alias_"
68 },
69 {
70 "@id": "#study_comment/25_ae7461a0-6081-013c-9ed3-7a163e608de1",
71 "name": "SEEK Study ID",
72 "value": "25"
73 },
74 {
75 "@id": "#study_comment/25_ae7467e0-6081-013c-9ed4-7a163e608de1",
76 "name": "SEEK creation date",
77 "value": "2023-10-20T11:12:23Z"
78 }
79 ],
80 "publications": [],
81 "people": [
82 {
83 "@id": "#people/4",
84 "lastName": "De Pelseneer",
85 "firstName": "Kevin",
86 "midInitials": "",
87 "email": "kevin.depelseneer@psb.ugent.be",
88 "phone": "",
89 "fax": "",
90 "address": "",
91 "affiliation": "",
92 "roles": [
93 {
94 "termAccession": "",
95 "termSource": "",
96 "annotationValue": ""
97 }
98 ],
99 "comments": [
100 {
101 "@id": "",
102 "value": "",
103 "name": ""
104 }
105 ]
106 }
107 ],
108 "studyDesignDescriptors": [],
109 "characteristicCategories": [
110 {
111 "@id": "#characteristic_category/geographic_location_(country_and/or_sea)_657",
112 "characteristicType": {
113 "annotationValue": "geographic location (country and/or sea)",
114 "termAccession": "",
115 "termSource": ""
116 }
117 },
118 {
119 "@id": "#characteristic_category/taxon_id_658",
120 "characteristicType": {
121 "annotationValue": "taxon_id",
122 "termAccession": "",
123 "termSource": ""
124 }
125 },
126 {
127 "@id": "#characteristic_category/title_662",
128 "characteristicType": {
129 "annotationValue": "title",
130 "termAccession": "",
131 "termSource": ""
132 }
133 },
134 {
135 "@id": "#characteristic_category/sample_description_663",
136 "characteristicType": {
137 "annotationValue": "sample_description",
138 "termAccession": "",
139 "termSource": ""
140 }
141 },
142 {
143 "@id": "#characteristic_category/collection_date_664",
144 "characteristicType": {
145 "annotationValue": "collection date",
146 "termAccession": "",
147 "termSource": ""
148 }
149 },
150 {
151 "@id": "#characteristic_category/accession_665",
152 "characteristicType": {
153 "annotationValue": "accession",
154 "termAccession": "",
155 "termSource": ""
156 }
157 },
158 {
159 "@id": "#characteristic_category/submission_date_666",
160 "characteristicType": {
161 "annotationValue": "submission date",
162 "termAccession": "",
163 "termSource": ""
164 }
165 },
166 {
167 "@id": "#characteristic_category/status_667",
168 "characteristicType": {
169 "annotationValue": "status",
170 "termAccession": "",
171 "termSource": ""
172 }
173 }
174 ],
175 "materials": {
176 "sources": [
177 {
178 "@id": "#source/223",
179 "name": "Source 1",
180 "characteristics": [
181 {
182 "category": {
183 "@id": "#characteristic_category/geographic_location_(country_and/or_sea)_657"
184 },
185 "value": {
186 "annotationValue": "Argentina",
187 "termSource": "",
188 "termAccession": ""
189 },
190 "unit": {
191 "termSource": "",
192 "termAccession": "",
193 "comments": []
194 }
195 },
196 {
197 "category": {
198 "@id": "#characteristic_category/taxon_id_658"
199 },
200 "value": {
201 "annotationValue": "9606",
202 "termSource": "",
203 "termAccession": ""
204 },
205 "unit": {
206 "termSource": "",
207 "termAccession": "",
208 "comments": []
209 }
210 }
211 ]
212 },
213 {
214 "@id": "#source/226",
215 "name": "Source 2",
216 "characteristics": [
217 {
218 "category": {
219 "@id": "#characteristic_category/geographic_location_(country_and/or_sea)_657"
220 },
221 "value": {
222 "annotationValue": "Belgium",
223 "termSource": "",
224 "termAccession": ""
225 },
226 "unit": {
227 "termSource": "",
228 "termAccession": "",
229 "comments": []
230 }
231 },
232 {
233 "category": {
234 "@id": "#characteristic_category/taxon_id_658"
235 },
236 "value": {
237 "annotationValue": "646099",
238 "termSource": "",
239 "termAccession": ""
240 },
241 "unit": {
242 "termSource": "",
243 "termAccession": "",
244 "comments": []
245 }
246 }
247 ]
248 }
249 ],
250 "samples": [
251 {
252 "@id": "#sample/224",
253 "name": "Sample 1",
254 "derivesFrom": [
255 {
256 "@id": "#source/223"
257 }
258 ],
259 "characteristics": [
260 {
261 "category": {
262 "@id": "#characteristic_category/title_662"
263 },
264 "value": {
265 "annotationValue": "sample_title_1",
266 "termSource": "",
267 "termAccession": ""
268 },
269 "unit": {
270 "termSource": "",
271 "termAccession": "",
272 "comments": []
273 }
274 },
275 {
276 "category": {
277 "@id": "#characteristic_category/sample_description_663"
278 },
279 "value": {
280 "annotationValue": "sample_description_1",
281 "termSource": "",
282 "termAccession": ""
283 },
284 "unit": {
285 "termSource": "",
286 "termAccession": "",
287 "comments": []
288 }
289 },
290 {
291 "category": {
292 "@id": "#characteristic_category/collection_date_664"
293 },
294 "value": {
295 "annotationValue": "2020-10-11",
296 "termSource": "",
297 "termAccession": ""
298 },
299 "unit": {
300 "termSource": "",
301 "termAccession": "",
302 "comments": []
303 }
304 },
305 {
306 "category": {
307 "@id": "#characteristic_category/accession_665"
308 },
309 "value": {
310 "annotationValue": "",
311 "termSource": "",
312 "termAccession": ""
313 },
314 "unit": {
315 "termSource": "",
316 "termAccession": "",
317 "comments": []
318 }
319 },
320 {
321 "category": {
322 "@id": "#characteristic_category/submission_date_666"
323 },
324 "value": {
325 "annotationValue": "",
326 "termSource": "",
327 "termAccession": ""
328 },
329 "unit": {
330 "termSource": "",
331 "termAccession": "",
332 "comments": []
333 }
334 },
335 {
336 "category": {
337 "@id": "#characteristic_category/status_667"
338 },
339 "value": {
340 "annotationValue": "add",
341 "termSource": "",
342 "termAccession": ""
343 },
344 "unit": {
345 "termSource": "",
346 "termAccession": "",
347 "comments": []
348 }
349 }
350 ],
351 "factorValues": [
352 {
353 "category": {
354 "@id": ""
355 },
356 "value": {
357 "annotationValue": "",
358 "termSource": "",
359 "termAccession": ""
360 },
361 "unit": {
362 "termSource": "",
363 "termAccession": "",
364 "comments": []
365 }
366 }
367 ]
368 },
369 {
370 "@id": "#sample/225",
371 "name": "Sample 2",
372 "derivesFrom": [
373 {
374 "@id": "#source/226"
375 }
376 ],
377 "characteristics": [
378 {
379 "category": {
380 "@id": "#characteristic_category/title_662"
381 },
382 "value": {
383 "annotationValue": "sample_title_2",
384 "termSource": "",
385 "termAccession": ""
386 },
387 "unit": {
388 "termSource": "",
389 "termAccession": "",
390 "comments": []
391 }
392 },
393 {
394 "category": {
395 "@id": "#characteristic_category/sample_description_663"
396 },
397 "value": {
398 "annotationValue": "sample_description_2",
399 "termSource": "",
400 "termAccession": ""
401 },
402 "unit": {
403 "termSource": "",
404 "termAccession": "",
405 "comments": []
406 }
407 },
408 {
409 "category": {
410 "@id": "#characteristic_category/collection_date_664"
411 },
412 "value": {
413 "annotationValue": "2008-01-24",
414 "termSource": "",
415 "termAccession": ""
416 },
417 "unit": {
418 "termSource": "",
419 "termAccession": "",
420 "comments": []
421 }
422 },
423 {
424 "category": {
425 "@id": "#characteristic_category/accession_665"
426 },
427 "value": {
428 "annotationValue": "",
429 "termSource": "",
430 "termAccession": ""
431 },
432 "unit": {
433 "termSource": "",
434 "termAccession": "",
435 "comments": []
436 }
437 },
438 {
439 "category": {
440 "@id": "#characteristic_category/submission_date_666"
441 },
442 "value": {
443 "annotationValue": "",
444 "termSource": "",
445 "termAccession": ""
446 },
447 "unit": {
448 "termSource": "",
449 "termAccession": "",
450 "comments": []
451 }
452 },
453 {
454 "category": {
455 "@id": "#characteristic_category/status_667"
456 },
457 "value": {
458 "annotationValue": "add",
459 "termSource": "",
460 "termAccession": ""
461 },
462 "unit": {
463 "termSource": "",
464 "termAccession": "",
465 "comments": []
466 }
467 }
468 ],
469 "factorValues": [
470 {
471 "category": {
472 "@id": ""
473 },
474 "value": {
475 "annotationValue": "",
476 "termSource": "",
477 "termAccession": ""
478 },
479 "unit": {
480 "termSource": "",
481 "termAccession": "",
482 "comments": []
483 }
484 }
485 ]
486 }
487 ]
488 },
489 "protocols": [
490 {
491 "@id": "#protocol/_25",
492 "name": "sample collection",
493 "protocolType": {
494 "annotationValue": "sample collection",
495 "termAccession": "",
496 "termSource": ""
497 },
498 "description": "",
499 "uri": "",
500 "version": "",
501 "parameters": [],
502 "components": [
503 {
504 "componentName": "",
505 "componentType": {
506 "annotationValue": "",
507 "termSource": "",
508 "termAccession": ""
509 }
510 }
511 ]
512 },
513 {
514 "@id": "#protocol/_48",
515 "name": "library construction",
516 "protocolType": {
517 "annotationValue": "library construction",
518 "termAccession": "",
519 "termSource": ""
520 },
521 "description": "",
522 "uri": "",
523 "version": "",
524 "parameters": [
525 {
526 "@id": "#parameter/672",
527 "parameterName": {
528 "annotationValue": "design_description",
529 "termAccession": "",
530 "termSource": ""
531 }
532 },
533 {
534 "@id": "#parameter/674",
535 "parameterName": {
536 "annotationValue": "library_source",
537 "termAccession": "",
538 "termSource": ""
539 }
540 },
541 {
542 "@id": "#parameter/675",
543 "parameterName": {
544 "annotationValue": "library_strategy",
545 "termAccession": "",
546 "termSource": ""
547 }
548 },
549 {
550 "@id": "#parameter/676",
551 "parameterName": {
552 "annotationValue": "library_selection",
553 "termAccession": "",
554 "termSource": ""
555 }
556 },
557 {
558 "@id": "#parameter/677",
559 "parameterName": {
560 "annotationValue": "library_layout",
561 "termAccession": "",
562 "termSource": ""
563 }
564 },
565 {
566 "@id": "#parameter/678",
567 "parameterName": {
568 "annotationValue": "insert_size",
569 "termAccession": "",
570 "termSource": ""
571 }
572 },
573 {
574 "@id": "#parameter/679",
575 "parameterName": {
576 "annotationValue": "platform",
577 "termAccession": "",
578 "termSource": ""
579 }
580 },
581 {
582 "@id": "#parameter/680",
583 "parameterName": {
584 "annotationValue": "instrument_model",
585 "termAccession": "",
586 "termSource": ""
587 }
588 }
589 ],
590 "components": [
591 {
592 "componentName": "",
593 "componentType": {
594 "annotationValue": "",
595 "termSource": "",
596 "termAccession": ""
597 }
598 }
599 ]
600 },
601 {
602 "@id": "#protocol/_49",
603 "name": "nucleic acid sequencing",
604 "protocolType": {
605 "annotationValue": "nucleic acid sequencing",
606 "termAccession": "",
607 "termSource": ""
608 },
609 "description": "",
610 "uri": "",
611 "version": "",
612 "parameters": [],
613 "components": [
614 {
615 "componentName": "",
616 "componentType": {
617 "annotationValue": "",
618 "termSource": "",
619 "termAccession": ""
620 }
621 }
622 ]
623 }
624 ],
625 "processSequence": [
626 {
627 "@id": "#process/sample_collection/224",
628 "name": "",
629 "executesProtocol": {
630 "@id": "#protocol/_25"
631 },
632 "parameterValues": [],
633 "performer": "",
634 "date": "",
635 "inputs": [
636 {
637 "@id": "#source/223"
638 }
639 ],
640 "outputs": [
641 {
642 "@id": "#sample/224"
643 }
644 ]
645 },
646 {
647 "@id": "#process/sample_collection/225",
648 "name": "",
649 "executesProtocol": {
650 "@id": "#protocol/_25"
651 },
652 "parameterValues": [],
653 "performer": "",
654 "date": "",
655 "inputs": [
656 {
657 "@id": "#source/226"
658 }
659 ],
660 "outputs": [
661 {
662 "@id": "#sample/225"
663 }
664 ]
665 }
666 ],
667 "assays": [
668 {
669 "@id": "#assay/48_49",
670 "filename": "a_ena_stream_1.txt",
671 "measurementType": {
672 "annotationValue": "",
673 "termSource": "",
674 "termAccession": ""
675 },
676 "technologyType": {
677 "annotationValue": "",
678 "termSource": "",
679 "termAccession": ""
680 },
681 "comments": [
682 {
683 "@id": "#assay_comment/25_48_49_14_50",
684 "name": "ena_study_title",
685 "value": "study_title_1"
686 },
687 {
688 "@id": "#assay_comment/25_48_49_14_51",
689 "name": "study_type",
690 "value": "Transcriptome Analysis"
691 },
692 {
693 "@id": "#assay_comment/25_48_49_14_52",
694 "name": "new_study_type",
695 "value": "This should not be submitted!"
696 },
697 {
698 "@id": "#assay_comment/25_48_49_14_53",
699 "name": "ena_study_abstract",
700 "value": "study_abstract_1"
701 },
702 {
703 "@id": "#assay_comment/25_48_49_14_54",
704 "name": "assay_stream",
705 "value": "Ena stream 1"
706 },
707 {
708 "@id": "#assay_comment/25_48_49_14_55",
709 "name": "ena_study_alias_prefix",
710 "value": "study_alias_"
711 },
712 {
713 "@id": "#assay_comment/25_48_49_14_56",
714 "name": "ena_experiment_alias_prefix",
715 "value": "experiment_alias_"
716 },
717 {
718 "@id": "#assay_comment/25_48_49_14_57",
719 "name": "ena_run_alias_prefix",
720 "value": "run_alias_"
721 },
722 {
723 "@id": "#assay_comment/48_49",
724 "name": "linked_assays",
725 "value": "[{\"id\":48,\"title\":\"Assay 1 - Test case ENA upload tool\"},{\"id\":49,\"title\":\"Assay 2 - Test case ENA upload tool\"}]"
726 }
727 ],
728 "technologyPlatform": "",
729 "characteristicCategories": [
730 {
731 "@id": "#characteristic_category/title_671",
732 "characteristicType": {
733 "annotationValue": "title",
734 "termAccession": "",
735 "termSource": ""
736 }
737 },
738 {
739 "@id": "#characteristic_category/library_name_673",
740 "characteristicType": {
741 "annotationValue": "library_name",
742 "termAccession": "",
743 "termSource": ""
744 }
745 },
746 {
747 "@id": "#characteristic_category/accession_681",
748 "characteristicType": {
749 "annotationValue": "accession",
750 "termAccession": "",
751 "termSource": ""
752 }
753 },
754 {
755 "@id": "#characteristic_category/submission_date_682",
756 "characteristicType": {
757 "annotationValue": "submission date",
758 "termAccession": "",
759 "termSource": ""
760 }
761 },
762 {
763 "@id": "#characteristic_category/status_683",
764 "characteristicType": {
765 "annotationValue": "status",
766 "termAccession": "",
767 "termSource": ""
768 }
769 }
770 ],
771 "materials": {
772 "samples": [],
773 "otherMaterials": [
774 {
775 "@id": "#other_material/227",
776 "name": "library_construction_protocol_1",
777 "type": "library_construction_protocol",
778 "characteristics": [
779 {
780 "category": {
781 "@id": "#characteristic_category/title_671"
782 },
783 "value": {
784 "annotationValue": "experiment_title_1",
785 "termSource": "",
786 "termAccession": ""
787 },
788 "unit": {
789 "termSource": "",
790 "termAccession": "",
791 "comments": []
792 }
793 },
794 {
795 "category": {
796 "@id": "#characteristic_category/library_name_673"
797 },
798 "value": {
799 "annotationValue": "library_name_1",
800 "termSource": "",
801 "termAccession": ""
802 },
803 "unit": {
804 "termSource": "",
805 "termAccession": "",
806 "comments": []
807 }
808 },
809 {
810 "category": {
811 "@id": "#characteristic_category/accession_681"
812 },
813 "value": {
814 "annotationValue": "",
815 "termSource": "",
816 "termAccession": ""
817 },
818 "unit": {
819 "termSource": "",
820 "termAccession": "",
821 "comments": []
822 }
823 },
824 {
825 "category": {
826 "@id": "#characteristic_category/submission_date_682"
827 },
828 "value": {
829 "annotationValue": "",
830 "termSource": "",
831 "termAccession": ""
832 },
833 "unit": {
834 "termSource": "",
835 "termAccession": "",
836 "comments": []
837 }
838 },
839 {
840 "category": {
841 "@id": "#characteristic_category/status_683"
842 },
843 "value": {
844 "annotationValue": "add",
845 "termSource": "",
846 "termAccession": ""
847 },
848 "unit": {
849 "termSource": "",
850 "termAccession": "",
851 "comments": []
852 }
853 }
854 ],
855 "derivesFrom": [
856 {
857 "@id": "#sample/224"
858 }
859 ]
860 },
861 {
862 "@id": "#other_material/228",
863 "name": "library_construction_protocol_2",
864 "type": "library_construction_protocol",
865 "characteristics": [
866 {
867 "category": {
868 "@id": "#characteristic_category/title_671"
869 },
870 "value": {
871 "annotationValue": "experiment_title_2",
872 "termSource": "",
873 "termAccession": ""
874 },
875 "unit": {
876 "termSource": "",
877 "termAccession": "",
878 "comments": []
879 }
880 },
881 {
882 "category": {
883 "@id": "#characteristic_category/library_name_673"
884 },
885 "value": {
886 "annotationValue": "library_name_2",
887 "termSource": "",
888 "termAccession": ""
889 },
890 "unit": {
891 "termSource": "",
892 "termAccession": "",
893 "comments": []
894 }
895 },
896 {
897 "category": {
898 "@id": "#characteristic_category/accession_681"
899 },
900 "value": {
901 "annotationValue": "",
902 "termSource": "",
903 "termAccession": ""
904 },
905 "unit": {
906 "termSource": "",
907 "termAccession": "",
908 "comments": []
909 }
910 },
911 {
912 "category": {
913 "@id": "#characteristic_category/submission_date_682"
914 },
915 "value": {
916 "annotationValue": "",
917 "termSource": "",
918 "termAccession": ""
919 },
920 "unit": {
921 "termSource": "",
922 "termAccession": "",
923 "comments": []
924 }
925 },
926 {
927 "category": {
928 "@id": "#characteristic_category/status_683"
929 },
930 "value": {
931 "annotationValue": "add",
932 "termSource": "",
933 "termAccession": ""
934 },
935 "unit": {
936 "termSource": "",
937 "termAccession": "",
938 "comments": []
939 }
940 }
941 ],
942 "derivesFrom": [
943 {
944 "@id": "#sample/225"
945 }
946 ]
947 },
948 {
949 "@id": "#other_material/229",
950 "name": "library_construction_protocol_2",
951 "type": "library_construction_protocol",
952 "characteristics": [
953 {
954 "category": {
955 "@id": "#characteristic_category/title_671"
956 },
957 "value": {
958 "annotationValue": "experiment_title_3",
959 "termSource": "",
960 "termAccession": ""
961 },
962 "unit": {
963 "termSource": "",
964 "termAccession": "",
965 "comments": []
966 }
967 },
968 {
969 "category": {
970 "@id": "#characteristic_category/library_name_673"
971 },
972 "value": {
973 "annotationValue": "library_name_2",
974 "termSource": "",
975 "termAccession": ""
976 },
977 "unit": {
978 "termSource": "",
979 "termAccession": "",
980 "comments": []
981 }
982 },
983 {
984 "category": {
985 "@id": "#characteristic_category/accession_681"
986 },
987 "value": {
988 "annotationValue": "",
989 "termSource": "",
990 "termAccession": ""
991 },
992 "unit": {
993 "termSource": "",
994 "termAccession": "",
995 "comments": []
996 }
997 },
998 {
999 "category": {
1000 "@id": "#characteristic_category/submission_date_682"
1001 },
1002 "value": {
1003 "annotationValue": "",
1004 "termSource": "",
1005 "termAccession": ""
1006 },
1007 "unit": {
1008 "termSource": "",
1009 "termAccession": "",
1010 "comments": []
1011 }
1012 },
1013 {
1014 "category": {
1015 "@id": "#characteristic_category/status_683"
1016 },
1017 "value": {
1018 "annotationValue": "add",
1019 "termSource": "",
1020 "termAccession": ""
1021 },
1022 "unit": {
1023 "termSource": "",
1024 "termAccession": "",
1025 "comments": []
1026 }
1027 }
1028 ],
1029 "derivesFrom": [
1030 {
1031 "@id": "#sample/225"
1032 }
1033 ]
1034 }
1035 ]
1036 },
1037 "processSequence": [
1038 {
1039 "@id": "#process/library_construction/227",
1040 "name": "",
1041 "executesProtocol": {
1042 "@id": "#protocol/_48"
1043 },
1044 "parameterValues": [
1045 {
1046 "category": {
1047 "@id": "#parameter/672"
1048 },
1049 "value": {
1050 "annotationValue": "design_description_1",
1051 "termSource": "",
1052 "termAccession": ""
1053 },
1054 "unit": {
1055 "termSource": "",
1056 "termAccession": "",
1057 "comments": []
1058 }
1059 },
1060 {
1061 "category": {
1062 "@id": "#parameter/674"
1063 },
1064 "value": {
1065 "annotationValue": "GENOMIC",
1066 "termSource": "",
1067 "termAccession": ""
1068 },
1069 "unit": {
1070 "termSource": "",
1071 "termAccession": "",
1072 "comments": []
1073 }
1074 },
1075 {
1076 "category": {
1077 "@id": "#parameter/675"
1078 },
1079 "value": {
1080 "annotationValue": "WGA",
1081 "termSource": "",
1082 "termAccession": ""
1083 },
1084 "unit": {
1085 "termSource": "",
1086 "termAccession": "",
1087 "comments": []
1088 }
1089 },
1090 {
1091 "category": {
1092 "@id": "#parameter/676"
1093 },
1094 "value": {
1095 "annotationValue": "RANDOM",
1096 "termSource": "",
1097 "termAccession": ""
1098 },
1099 "unit": {
1100 "termSource": "",
1101 "termAccession": "",
1102 "comments": []
1103 }
1104 },
1105 {
1106 "category": {
1107 "@id": "#parameter/677"
1108 },
1109 "value": {
1110 "annotationValue": "PAIRED",
1111 "termSource": "",
1112 "termAccession": ""
1113 },
1114 "unit": {
1115 "termSource": "",
1116 "termAccession": "",
1117 "comments": []
1118 }
1119 },
1120 {
1121 "category": {
1122 "@id": "#parameter/678"
1123 },
1124 "value": {
1125 "annotationValue": "250",
1126 "termSource": "",
1127 "termAccession": ""
1128 },
1129 "unit": {
1130 "termSource": "",
1131 "termAccession": "",
1132 "comments": []
1133 }
1134 },
1135 {
1136 "category": {
1137 "@id": "#parameter/679"
1138 },
1139 "value": {
1140 "annotationValue": "LS454",
1141 "termSource": "",
1142 "termAccession": ""
1143 },
1144 "unit": {
1145 "termSource": "",
1146 "termAccession": "",
1147 "comments": []
1148 }
1149 },
1150 {
1151 "category": {
1152 "@id": "#parameter/680"
1153 },
1154 "value": {
1155 "annotationValue": "454 GS 20",
1156 "termSource": "",
1157 "termAccession": ""
1158 },
1159 "unit": {
1160 "termSource": "",
1161 "termAccession": "",
1162 "comments": []
1163 }
1164 }
1165 ],
1166 "performer": "",
1167 "date": "",
1168 "inputs": [
1169 {
1170 "@id": "#sample/224"
1171 }
1172 ],
1173 "outputs": [
1174 {
1175 "@id": "#other_material/227"
1176 }
1177 ],
1178 "previousProcess": {
1179 "@id": "#process/sample_collection/227"
1180 },
1181 "nextProcess": {
1182 "@id": "#process/nucleic_acid_sequencing/227"
1183 }
1184 },
1185 {
1186 "@id": "#process/library_construction/228",
1187 "name": "",
1188 "executesProtocol": {
1189 "@id": "#protocol/_48"
1190 },
1191 "parameterValues": [
1192 {
1193 "category": {
1194 "@id": "#parameter/672"
1195 },
1196 "value": {
1197 "annotationValue": "design_description_2",
1198 "termSource": "",
1199 "termAccession": ""
1200 },
1201 "unit": {
1202 "termSource": "",
1203 "termAccession": "",
1204 "comments": []
1205 }
1206 },
1207 {
1208 "category": {
1209 "@id": "#parameter/674"
1210 },
1211 "value": {
1212 "annotationValue": "TRANSCRIPTOMIC",
1213 "termSource": "",
1214 "termAccession": ""
1215 },
1216 "unit": {
1217 "termSource": "",
1218 "termAccession": "",
1219 "comments": []
1220 }
1221 },
1222 {
1223 "category": {
1224 "@id": "#parameter/675"
1225 },
1226 "value": {
1227 "annotationValue": "RNA-Seq",
1228 "termSource": "",
1229 "termAccession": ""
1230 },
1231 "unit": {
1232 "termSource": "",
1233 "termAccession": "",
1234 "comments": []
1235 }
1236 },
1237 {
1238 "category": {
1239 "@id": "#parameter/676"
1240 },
1241 "value": {
1242 "annotationValue": "repeat fractionation",
1243 "termSource": "",
1244 "termAccession": ""
1245 },
1246 "unit": {
1247 "termSource": "",
1248 "termAccession": "",
1249 "comments": []
1250 }
1251 },
1252 {
1253 "category": {
1254 "@id": "#parameter/677"
1255 },
1256 "value": {
1257 "annotationValue": "SINGLE",
1258 "termSource": "",
1259 "termAccession": ""
1260 },
1261 "unit": {
1262 "termSource": "",
1263 "termAccession": "",
1264 "comments": []
1265 }
1266 },
1267 {
1268 "category": {
1269 "@id": "#parameter/678"
1270 },
1271 "value": {
1272 "annotationValue": "None",
1273 "termSource": "",
1274 "termAccession": ""
1275 },
1276 "unit": {
1277 "termSource": "",
1278 "termAccession": "",
1279 "comments": []
1280 }
1281 },
1282 {
1283 "category": {
1284 "@id": "#parameter/679"
1285 },
1286 "value": {
1287 "annotationValue": "Illumina",
1288 "termSource": "",
1289 "termAccession": ""
1290 },
1291 "unit": {
1292 "termSource": "",
1293 "termAccession": "",
1294 "comments": []
1295 }
1296 },
1297 {
1298 "category": {
1299 "@id": "#parameter/680"
1300 },
1301 "value": {
1302 "annotationValue": "Illumina Genome Analyzer",
1303 "termSource": "",
1304 "termAccession": ""
1305 },
1306 "unit": {
1307 "termSource": "",
1308 "termAccession": "",
1309 "comments": []
1310 }
1311 }
1312 ],
1313 "performer": "",
1314 "date": "",
1315 "inputs": [
1316 {
1317 "@id": "#sample/225"
1318 }
1319 ],
1320 "outputs": [
1321 {
1322 "@id": "#other_material/228"
1323 }
1324 ],
1325 "previousProcess": {
1326 "@id": "#process/sample_collection/228"
1327 },
1328 "nextProcess": {}
1329 },
1330 {
1331 "@id": "#process/library_construction/229",
1332 "name": "",
1333 "executesProtocol": {
1334 "@id": "#protocol/_48"
1335 },
1336 "parameterValues": [
1337 {
1338 "category": {
1339 "@id": "#parameter/672"
1340 },
1341 "value": {
1342 "annotationValue": "design_description_3",
1343 "termSource": "",
1344 "termAccession": ""
1345 },
1346 "unit": {
1347 "termSource": "",
1348 "termAccession": "",
1349 "comments": []
1350 }
1351 },
1352 {
1353 "category": {
1354 "@id": "#parameter/674"
1355 },
1356 "value": {
1357 "annotationValue": "TRANSCRIPTOMIC",
1358 "termSource": "",
1359 "termAccession": ""
1360 },
1361 "unit": {
1362 "termSource": "",
1363 "termAccession": "",
1364 "comments": []
1365 }
1366 },
1367 {
1368 "category": {
1369 "@id": "#parameter/675"
1370 },
1371 "value": {
1372 "annotationValue": "RNA-Seq",
1373 "termSource": "",
1374 "termAccession": ""
1375 },
1376 "unit": {
1377 "termSource": "",
1378 "termAccession": "",
1379 "comments": []
1380 }
1381 },
1382 {
1383 "category": {
1384 "@id": "#parameter/676"
1385 },
1386 "value": {
1387 "annotationValue": "repeat fractionation",
1388 "termSource": "",
1389 "termAccession": ""
1390 },
1391 "unit": {
1392 "termSource": "",
1393 "termAccession": "",
1394 "comments": []
1395 }
1396 },
1397 {
1398 "category": {
1399 "@id": "#parameter/677"
1400 },
1401 "value": {
1402 "annotationValue": "SINGLE",
1403 "termSource": "",
1404 "termAccession": ""
1405 },
1406 "unit": {
1407 "termSource": "",
1408 "termAccession": "",
1409 "comments": []
1410 }
1411 },
1412 {
1413 "category": {
1414 "@id": "#parameter/678"
1415 },
1416 "value": {
1417 "annotationValue": "None",
1418 "termSource": "",
1419 "termAccession": ""
1420 },
1421 "unit": {
1422 "termSource": "",
1423 "termAccession": "",
1424 "comments": []
1425 }
1426 },
1427 {
1428 "category": {
1429 "@id": "#parameter/679"
1430 },
1431 "value": {
1432 "annotationValue": "Illumina",
1433 "termSource": "",
1434 "termAccession": ""
1435 },
1436 "unit": {
1437 "termSource": "",
1438 "termAccession": "",
1439 "comments": []
1440 }
1441 },
1442 {
1443 "category": {
1444 "@id": "#parameter/680"
1445 },
1446 "value": {
1447 "annotationValue": "Illumina Genome Analyzer",
1448 "termSource": "",
1449 "termAccession": ""
1450 },
1451 "unit": {
1452 "termSource": "",
1453 "termAccession": "",
1454 "comments": []
1455 }
1456 }
1457 ],
1458 "performer": "",
1459 "date": "",
1460 "inputs": [
1461 {
1462 "@id": "#sample/225"
1463 }
1464 ],
1465 "outputs": [
1466 {
1467 "@id": "#other_material/229"
1468 }
1469 ],
1470 "previousProcess": {
1471 "@id": "#process/sample_collection/229"
1472 },
1473 "nextProcess": {
1474 "@id": "#process/nucleic_acid_sequencing/229"
1475 }
1476 },
1477 {
1478 "@id": "#process/nucleic_acid_sequencing/233_234",
1479 "name": "",
1480 "executesProtocol": {
1481 "@id": "#protocol/_49"
1482 },
1483 "parameterValues": [],
1484 "performer": "",
1485 "date": "",
1486 "inputs": [
1487 {
1488 "@id": "#other_material/227"
1489 }
1490 ],
1491 "outputs": [
1492 {
1493 "@id": "#data_file/233"
1494 },
1495 {
1496 "@id": "#data_file/234"
1497 }
1498 ],
1499 "previousProcess": {
1500 "@id": "#process/library_construction/233"
1501 },
1502 "nextProcess": {}
1503 },
1504 {
1505 "@id": "#process/nucleic_acid_sequencing/235",
1506 "name": "",
1507 "executesProtocol": {
1508 "@id": "#protocol/_49"
1509 },
1510 "parameterValues": [],
1511 "performer": "",
1512 "date": "",
1513 "inputs": [
1514 {
1515 "@id": "#other_material/229"
1516 }
1517 ],
1518 "outputs": [
1519 {
1520 "@id": "#data_file/235"
1521 }
1522 ],
1523 "previousProcess": {
1524 "@id": "#process/library_construction/235"
1525 },
1526 "nextProcess": {}
1527 }
1528 ],
1529 "dataFiles": [
1530 {
1531 "@id": "#data_file/233",
1532 "name": "RD file 1a",
1533 "type": "Raw Data File",
1534 "comments": [
1535 {
1536 "name": "file_name",
1537 "value": "ENA_TEST2.R1.fastq.gz"
1538 },
1539 {
1540 "name": "file_type",
1541 "value": "fastq"
1542 },
1543 {
1544 "name": "file checksum",
1545 "value": ""
1546 },
1547 {
1548 "name": "accession",
1549 "value": ""
1550 },
1551 {
1552 "name": "submission date",
1553 "value": ""
1554 },
1555 {
1556 "name": "status",
1557 "value": "add"
1558 }
1559 ]
1560 },
1561 {
1562 "@id": "#data_file/234",
1563 "name": "RD file 1b",
1564 "type": "Raw Data File",
1565 "comments": [
1566 {
1567 "name": "file_name",
1568 "value": "ENA_TEST2.R2.fastq.gz"
1569 },
1570 {
1571 "name": "file_type",
1572 "value": "fastq"
1573 },
1574 {
1575 "name": "file checksum",
1576 "value": ""
1577 },
1578 {
1579 "name": "accession",
1580 "value": ""
1581 },
1582 {
1583 "name": "submission date",
1584 "value": ""
1585 },
1586 {
1587 "name": "status",
1588 "value": "add"
1589 }
1590 ]
1591 },
1592 {
1593 "@id": "#data_file/235",
1594 "name": "RD file 3",
1595 "type": "Raw Data File",
1596 "comments": [
1597 {
1598 "name": "file_name",
1599 "value": "ENA_TEST1.R1.fastq.gz"
1600 },
1601 {
1602 "name": "file_type",
1603 "value": "fastq"
1604 },
1605 {
1606 "name": "file checksum",
1607 "value": ""
1608 },
1609 {
1610 "name": "accession",
1611 "value": ""
1612 },
1613 {
1614 "name": "submission date",
1615 "value": ""
1616 },
1617 {
1618 "name": "status",
1619 "value": "add"
1620 }
1621 ]
1622 }
1623 ],
1624 "unitCategories": []
1625 }
1626 ],
1627 "factors": [],
1628 "unitCategories": []
1629 }
1630 ]
1631 }