-
Notifications
You must be signed in to change notification settings - Fork 3
/
DataStandardOrTool.yaml
16717 lines (16717 loc) · 667 KB
/
DataStandardOrTool.yaml
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
---
data_standardortools_collection:
- id: B2AI_STANDARD:1
name: .ACE format
category: B2AI_STANDARD:BiomedicalStandard
description: .ACE format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
The ACE file format is a specification for storing data about genomic
contigs. The original ACE format was developed for use with Consed, a program
for viewing, editing, and finishing DNA sequence assemblies. ACE files are generated
by various assembly programs, including Phrap, CAP3, Newbler, Arachne, AMOS (sequence
assembly) (more specifically Minimo) and Tigr Assembler v2.
is_open: true
requires_registration: false
url: https://en.wikipedia.org/wiki/ACE_(genomic_file_format)
formal_specification: https://web.archive.org/web/20100609072313/http://bcr.musc.edu/manuals/CONSED.txt
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:2
name: DMS
category: B2AI_STANDARD:BiomedicalStandard
description: 2023 NIH Data Management and Sharing Policy
collection:
- policy
has_relevant_organization:
- B2AI_ORG:67
purpose_detail:
NIH has issued the Data Management and Sharing (DMS) policy (effective
January 25, 2023) to promote the sharing of scientific data. Sharing scientific
data accelerates biomedical research discovery, in part, by enabling validation
of research results, providing accessibility to high-value datasets, and promoting
data reuse for future research studies. Under the DMS policy, NIH expects that
investigators and institutions do the following. Plan and budget for the managing
and sharing of data, Submit a DMS plan for review when applying for funding, Comply
with the approved DMS plan.
is_open: true
requires_registration: false
url: https://sharing.nih.gov/data-management-and-sharing-policy/about-data-management-and-sharing-policy/data-management-and-sharing-policy-overview
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:3
name: ABCD
category: B2AI_STANDARD:BiomedicalStandard
description: Access to Biological Collections Data Schema
collection:
- datamodel
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:1
has_relevant_organization:
- B2AI_ORG:93
purpose_detail:
The Access to Biological Collections Data (ABCD) Schema is an evolving
comprehensive standard for the access to and exchange of data about specimens
and observations (a.k.a. primary biodiversity data). The ABCD Schema attempts
to be comprehensive and highly structured, supporting data from a wide variety
of databases. It is compatible with several existing data standards. Parallel
structures exist so that either (or both) atomised data and free-text can be accommodated.
Version 1.2 is currently in use with the GBIF (Global Biodiversity Information
Facility) and BioCASE (Biological Collection Access Service for Europe) networks.
Apart from the GBIF and BioCASE networks, the potential for the application of
ABCD extends to internal networks, or in-house legacy data access (e.g. datasets
from external sources that shall not be converted and integrated into an institution's
own data, but be kept separately, though easily accessible). By defining relations
between terms, ABCD is a step towards an ontology for biological collections.
is_open: true
requires_registration: false
url: https://abcd.tdwg.org/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:4
name: AGP
category: B2AI_STANDARD:BiomedicalStandard
description: AGP format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
AGP format describes the assembly of a larger sequence object from
smaller objects. The large object can be a contig, a scaffold (supercontig), or
a chromosome. Each line (row) of the AGP file describes a different piece of the
object, and has the column entries defined below. Extended comments follow. It
does not serve for either a description of how sequence reads were assembled,
or a description of the alignments between components used to construct a larger
object. Not all of the information in proprietary assembly files can be represented
in the AGP format. It is also not for recording the spans of features like repeats
or genes.
is_open: true
requires_registration: false
url: https://www.ncbi.nlm.nih.gov/assembly/agp/AGP_Specification/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:5
name: AnIML
category: B2AI_STANDARD:BiomedicalStandard
description: Analytical Information Markup Language
collection:
- markuplanguage
concerns_data_topic:
- B2AI_TOPIC:3
has_relevant_organization:
- B2AI_ORG:8
purpose_detail:
The Analytical Information Markup Language (AnIML) is the emerging
ASTM XML standard for analytical chemistry data. It is currently in pre-release
form. It is a combination of a highly flexible core schema that defines XML tagging
for any kind of analytical information; A set of technique definition documents.
These XML files, one per analytical technique, apply tight constraints to the
flexible core and in turn are defined by the Technique Schema; Extensions to Technique
Definitions are possible to accommodate vendor- and institution-specific data
fields. Mission Statement Our goal is to serve as the open-source development
platform for a new XML standard for Analytical Chemistry Information. The project
is a collaborative effort between many groups and individuals and is sanctioned
by the ASTM subcommittee E13.15. http://animl.cvs.sourceforge.net/viewvc/animl/schema/animl-core.xsd
is_open: true
requires_registration: false
url: https://www.animl.org/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:6
name: ARRIVE
category: B2AI_STANDARD:BiomedicalStandard
description: Animal Research Reporting In Vivo Experiments
collection:
- guidelines
purpose_detail: Guidelines intended to improve the reporting of animal experiments.
is_open: true
requires_registration: false
url: https://arriveguidelines.org/
publication: doi:10.1371/journal.pbio.3000411
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:7
name: aECG
category: B2AI_STANDARD:BiomedicalStandard
description: Annotated ECG standard
concerns_data_topic:
- B2AI_TOPIC:37
has_relevant_organization:
- B2AI_ORG:40
purpose_detail:
Provides a common means of electronically storing both the ECG wave
form and associated annotations.
is_open: true
requires_registration: false
formal_specification: https://www.hl7.org/implement/standards/product_brief.cfm?product_id=70
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:8
name: AIM
category: B2AI_STANDARD:BiomedicalStandard
description: Annotation and Image Markup schema
collection:
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:9
- B2AI_TOPIC:15
has_training_resource:
- B2AI_STANDARD:849
has_relevant_organization:
- B2AI_ORG:71
purpose_detail:
The Annotation and Image Markup project provides a standardized
schema for capturing the results of medical imaging exams, primarily radiology,
using controlled terminologies/ontologies. AIM captures results in terms of the
region within an image in which areas of interest are located, the semantic descriptions
of those regions, inferences about them, calculations on them, and quantitative
features derived by computer programs run on them. AIM is interoperable with DICOM-SR
and HL7-CDA, other standards for image metadata, but it provides unique advantages
by providing an explicit semantic model of imaging results.
is_open: true
requires_registration: false
formal_specification: https://github.com/NCIP/annotation-and-image-markup
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:9
name: ANSI/CTA-2090
category: B2AI_STANDARD:BiomedicalStandard
description:
ANSI/CTA Standard - The Use of Artificial Intelligence in Health Care
Trustworthiness
collection:
- guidelines
- has_ai_application
has_relevant_organization:
- B2AI_ORG:4
purpose_detail:
AI in healthcare; three major expressions of how trust is created
and maintained - Human Trust, Technical Trust, and Regulatory Trust.
is_open: false
requires_registration: false
url: https://shop.cta.tech/collections/standards/products/the-use-of-artificial-intelligence-in-healthcare-trustworthiness-cta-2090
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:10
name: AB1
category: B2AI_STANDARD:BiomedicalStandard
description: Applied Biosystems sequence read binary format file
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
A binary version of raw DNA sequence reads from Applied Biosystems
sequencing analysis software. Also known as ABIF.
is_open: false
requires_registration: false
formal_specification: https://projects.nfstc.org/workshops/resources/articles/ABIF_File_Format.pdf
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:11
name: ABI
category: B2AI_STANDARD:BiomedicalStandard
description: Applied Biosystems sequence read binary format file
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
A binary version of raw DNA sequence reads from Applied Biosystems
sequencing analysis software.
is_open: false
requires_registration: false
formal_specification: https://tools.thermofisher.com/content/sfs/manuals/4346366_DNA_Sequenc_Analysis_5_1_UG.pdf
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:12
name: ARB
category: B2AI_STANDARD:BiomedicalStandard
description: ARB software binary alignment format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail: A binary alignment format used by the ARB package.
is_open: true
requires_registration: false
url: http://www.arb-home.de/documentation.html
publication: doi:10.1093/nar/gkh293
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:13
name: ADL
category: B2AI_STANDARD:BiomedicalStandard
description: Archetype Definition Language
concerns_data_topic:
- B2AI_TOPIC:9
has_relevant_organization:
- B2AI_ORG:79
purpose_detail:
ADL is designed as an abstract human-readable and computer-processible
syntax. ADL archetypes can be hand-edited using a normal text editor. The intended
audience includes standards bodies producing health informatics standards; Academic
groups using openEHR; The open source healthcare community; Solution vendors;
Medical informaticians and clinicians interested in health information.
is_open: true
requires_registration: false
formal_specification: https://specifications.openehr.org/releases/AM/latest/ADL1.4.html
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:14
name: StructureDefinition-argo-careplan
category: B2AI_STANDARD:BiomedicalStandard
description: Argonaut Data Query Implementation Guide
has_training_resource:
- B2AI_STANDARD:845
- B2AI_STANDARD:846
- B2AI_STANDARD:847
- B2AI_STANDARD:850
collection:
- datamodel
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:4
has_relevant_organization:
- B2AI_ORG:40
purpose_detail:
Specifications for sharing single sets of patient care plans. Based
on FHIR R2.
is_open: true
requires_registration: false
url: http://www.fhir.org/guides/argonaut/r2/StructureDefinition-argo-careplan.html
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:15
name: AMIS
category: B2AI_STANDARD:BiomedicalStandard
description: Article Minimum Information Standard
collection:
- minimuminformationschema
concerns_data_topic:
- B2AI_TOPIC:16
purpose_detail:
The curation process is significantly slowed down by missing information
in the articles analyzed. The identity of the clones used to generate ISH probes
and the precise sequences tested in reporter assays constituted the most frequent
omissions. To help authors ensure in the future that necessary information is
present in their article, the Article Minimum Information Standard (AMIS) guidelines
have been defined. The guideline describes the mandatory (and useful) information
that should be mentioned in literature articles to facilitate the curation process.
These guidelines extend the minimal information defined by the MISFISHIE format
(Deutsch at al. 2008, Nature Biotechnology).
is_open: true
requires_registration: false
publication: doi:10.1038/npre.2010.5054.1
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:16
name: Axt
category: B2AI_STANDARD:BiomedicalStandard
description: Axt Alignment Format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail: A format for sequence alignments.
is_open: true
requires_registration: false
url: https://genome.ucsc.edu/goldenPath/help/axt.html
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:17
name: BAI
category: B2AI_STANDARD:BiomedicalStandard
description: BAM indexing format file
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail: A file containing the index for a Binary Alignment Map (BAM) file.
is_open: true
requires_registration: false
url: https://www.ncbi.nlm.nih.gov/tools/gbench/tutorial6/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:18
name: BEDgraph
category: B2AI_STANDARD:BiomedicalStandard
description: BEDgraph format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
The bedGraph format allows display of continuous-valued data in
track format.
is_open: true
requires_registration: false
url: http://genome.ucsc.edu/goldenPath/help/bedgraph.html
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:19
name: bigBED
category: B2AI_STANDARD:BiomedicalStandard
description: Big Browser Extensible Data Format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
The bigBed format stores annotation items that can be either a simple
or a linked collection of exons, much as BED files do.
is_open: true
requires_registration: false
url: https://genome.ucsc.edu/goldenPath/help/bigBed.html
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:20
name: bigWig
category: B2AI_STANDARD:BiomedicalStandard
description: Big Wiggle Format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
The bigWig format is for display of dense, continuous data that
will be displayed in the Genome Browser as a graph.
is_open: true
requires_registration: false
url: https://genome.ucsc.edu/goldenPath/help/bigWig.html
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:21
name: BAM/CRAM
category: B2AI_STANDARD:BiomedicalStandard
description: Binary Alignment Map / Compressed Reference-oriented Alignment Map
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail: sequencing alignment
is_open: true
requires_registration: false
url: https://samtools.github.io/hts-specs/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:22
name: BAM
category: B2AI_STANDARD:BiomedicalStandard
description: Binary Alignment Map format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail: A BAM file (.bam) is the binary version of a SAM file.
is_open: true
requires_registration: false
url: https://en.wikipedia.org/wiki/Binary_Alignment_Map
formal_specification: https://samtools.github.io/hts-specs/SAMv1.pdf
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:23
name: 2bit
category: B2AI_STANDARD:BiomedicalStandard
description: Binary sequence information Format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
A .2bit file stores multiple DNA sequences (up to 4 Gb total) in
a compact randomly-accessible format. The file contains masking information as
well as the DNA itself.
is_open: true
requires_registration: false
url: http://genome.ucsc.edu/FAQ/FAQformat.html#format7
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:24
name: BCF
category: B2AI_STANDARD:BiomedicalStandard
description: Binary variant call format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail: A binary version of the variant call format (VCF).
is_open: true
requires_registration: false
url: https://samtools.github.io/bcftools/bcftools.html
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:25
name: BioCompute
category: B2AI_STANDARD:BiomedicalStandard
description: BioCompute Object standard
concerns_data_topic:
- B2AI_TOPIC:1
has_relevant_organization:
- B2AI_ORG:44
purpose_detail:
Because of the many different ways to organize data, a major goal
of the BioCompute project is to build and maintain a formal standard through recognized,
accredited standards setting organizations like the Institute for Electrical and
Electronics Engineers (IEEE) and the International Standards Organization (ISO).
A formal, consensus-based standard builds predictability and even more stability
into the way in which bioinformatic methods are communicated. The standard, officially
known as 2791-2020, has two parts, the standards document and the schema, which
is maintained in an open source repository.
is_open: true
requires_registration: false
url: https://docs.biocomputeobject.org/user_guide/
publication: doi:10.5731/pdajpst.2016.006734
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:26
name: Biolink
category: B2AI_STANDARD:BiomedicalStandard
description: Biolink Model
collection:
- datamodel
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:20
has_relevant_organization:
- B2AI_ORG:70
purpose_detail:
A high level datamodel of biological entities (genes, diseases,
phenotypes, pathways, individuals, substances, etc) and their associations.
is_open: true
requires_registration: false
url: https://biolink.github.io/biolink-model/
publication: doi:10.1111/cts.13302
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:27
name: BEL
category: B2AI_STANDARD:BiomedicalStandard
description: Biological Expression Language
collection:
- markuplanguage
purpose_detail:
A language for representing scientific findings in the life sciences
in a computable form.
is_open: true
requires_registration: false
url: https://bel.bio/
formal_specification: https://language.bel.bio/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:28
name: BRIDG Model
category: B2AI_STANDARD:BiomedicalStandard
description: Biomedical Research Integrated Domain Group Model
has_relevant_organization:
- B2AI_ORG:15
- B2AI_ORG:31
- B2AI_ORG:40
- B2AI_ORG:71
purpose_detail:
The Biomedical Research Integrated Domain Group (BRIDG) Model is
a collaborative effort engaging stakeholders from the Clinical Data Interchange
Standards Consortium (CDISC), the HL7 BRIDG Work Group, the US National Cancer
Institute (NCI), and the US Food and Drug Administration (FDA). The goal of the
BRIDG Model is to produce a shared view of the dynamic and static semantics for
the domain of basic, pre-clinical, clinical, and translational research and its
associated regulatory artifacts.
is_open: true
requires_registration: false
url: https://bridgmodel.nci.nih.gov/
publication: doi:10.1093/jamia/ocx004
formal_specification: https://github.com/CBIIT/bridg-model/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:29
name: BioPAX
category: B2AI_STANDARD:BiomedicalStandard
description: BioPAX standard
collection:
- markuplanguage
concerns_data_topic:
- B2AI_TOPIC:21
purpose_detail:
BioPAX is a standard language that aims to enable integration, exchange,
visualization and analysis of biological pathway data. Specifically, BioPAX supports
data exchange between pathway data groups and thus reduces the complexity of interchange
between data formats by providing an accepted standard format for pathway data.
By offering a standard, with well-defined semantics for pathway representation,
BioPAX allows pathway databases and software to interact more efficiently. In
addition, BioPAX enables the development of pathway visualization from databases
and facilitates analysis of experimentally generated data through combination
with prior knowledge. The BioPAX effort is coordinated closely with that of other
pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in
order to deliver a compatible standard in the areas where they overlap.
is_open: true
requires_registration: false
url: http://www.biopax.org/
publication: doi:10.1038/nbt.1666
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:30
name: Bioschemas
category: B2AI_STANDARD:BiomedicalStandard
description: Bioschemas
concerns_data_topic:
- B2AI_TOPIC:1
has_relevant_organization:
- B2AI_ORG:28
purpose_detail:
Bioschemas aims to improve the Findability on the Web of life sciences
resources such as datasets, software, and training materials.
is_open: true
requires_registration: false
url: https://bioschemas.org/
formal_specification: https://github.com/BioSchemas/specifications
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:31
name: BRISQ
category: B2AI_STANDARD:BiomedicalStandard
description: Biospecimen Reporting for Improved Study Quality
collection:
- guidelines
concerns_data_topic:
- B2AI_TOPIC:1
has_relevant_organization:
- B2AI_ORG:72
purpose_detail:
Human biospecimens are subject to a number of different collection,
processing, and storage factors that can significantly alter their molecular composition
and consistency. These biospecimen preanalytical factors, in turn, influence experimental
outcomes and the ability to reproduce scientific results. Currently, the extent
and type of information specific to the biospecimen preanalytical conditions reported
in scientific publications and regulatory submissions varies widely. To improve
the quality of research utilizing human tissues, it is critical that information
regarding the handling of biospecimens be reported in a thorough, accurate, and
standardized manner. The Biospecimen Reporting for Improved Study Quality (BRISQ)
recommendations outlined herein are intended to apply to any study in which human
biospecimens are used. The purpose of reporting these details is to supply others,
from researchers to regulators, with more consistent and standardized information
to better evaluate, interpret, compare, and reproduce the experimental results.
The BRISQ guidelines are proposed as an important and timely resource tool to
strengthen communication and publications around biospecimen-related research
and help reassure patient contributors and the advocacy community that the contributions
are valued and respected
is_open: true
requires_registration: false
publication: doi:10.1002/cncy.20147
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:32
name: BioXSD
category: B2AI_STANDARD:BiomedicalStandard
description: BioXSD
collection:
- datamodel
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:20
has_relevant_organization:
- B2AI_ORG:28
purpose_detail:
Data model and exchange formats for basic bioinformatics types of
data - sequences, alignments, feature records with associated data and metadata.
is_open: true
requires_registration: false
url: http://bioxsd.org/
publication: doi:10.1093/bioinformatics/btq391
formal_specification: https://github.com/bioxsd/bioxsd
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:33
name: BIDS
category: B2AI_STANDARD:BiomedicalStandard
description: Brain Imaging Data Structure
collection:
- datamodel
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:22
purpose_detail:
The Brain Imaging Data Structure (BIDS) is a simple and intuitive
way to organize and describe data. This document defines the BIDS specification,
which provides many details to help implement the standard. It includes the core
specification as well as many extensions to specific brain imaging modalities,
and increasingly also to other kinds of data.
is_open: true
requires_registration: false
url: https://bids-specification.readthedocs.io/en/stable/
publication: doi:10.1038/sdata.2016.44
formal_specification: https://github.com/bids-standard/bids-specification
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:34
name: BFI
category: B2AI_STANDARD:BiomedicalStandard
description: Brief Fatigue Inventory
collection:
- diagnosticinstrument
concerns_data_topic:
- B2AI_TOPIC:9
purpose_detail:
The Brief Fatigue Inventory (BFI) is used to rapidly assess the
severity and impact of cancer-related fatigue. An increasing focus on cancer-related
fatigue emphasized the need for sensitive tools to assess this most frequently
reported symptom. The six interference items correlate with standard quality-of-life
measures.
is_open: true
requires_registration: false
url: https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/symptom-research/symptom-assessment-tools/brief-fatigue-inventory.html
formal_specification: http://www.npcrc.org/files/news/brief_fatigue_inventory.pdf
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:35
name: BPI
category: B2AI_STANDARD:BiomedicalStandard
description: Brief Pain Inventory
collection:
- diagnosticinstrument
concerns_data_topic:
- B2AI_TOPIC:9
purpose_detail:
The Brief Pain Inventory (BPI) rapidly assesses the severity of
pain and its impact on functioning. The BPI has been translated into dozens of
languages, and it is widely used in both research and clinical settings.
is_open: true
requires_registration: false
url: https://www.mdanderson.org/research/departments-labs-institutes/departments-divisions/symptom-research/symptom-assessment-tools/brief-pain-inventory.html
formal_specification: http://www.npcrc.org/files/news/briefpain_short.pdf
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:36
name: BED
category: B2AI_STANDARD:BiomedicalStandard
description: Browser Extensible Data Format
collection:
- fileformat
concerns_data_topic:
- B2AI_TOPIC:12
- B2AI_TOPIC:13
purpose_detail:
BED (Browser Extensible Data) format provides a flexible way to
define the data lines that are displayed in an annotation track. BED lines have
three required fields and nine additional optional fields. The number of fields
per line must be consistent throughout any single set of data in an annotation
track. The order of the optional fields is binding. Lower-numbered fields must
always be populated if higher-numbered fields are used.
is_open: true
requires_registration: false
url: https://genome.ucsc.edu/FAQ/FAQformat.html#format1
formal_specification: https://github.com/samtools/hts-specs/blob/master/BEDv1.pdf
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:37
name: BPMN
category: B2AI_STANDARD:BiomedicalStandard
description: Business Process Modeling Notation
concerns_data_topic:
- B2AI_TOPIC:5
has_relevant_organization:
- B2AI_ORG:10
purpose_detail:
A graphical notation that depicts the steps in a business process.
BPMN depicts the end-to-end flow of a business process. The notation has been
specifically designed to coordinate the sequence of processes and the messages
that flow between different process participants in a related set of activities.
is_open: true
requires_registration: false
url: https://www.omg.org/bpmn/index.htm
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:38
name: CMMN
category: B2AI_STANDARD:BiomedicalStandard
description: Case Management Model and Notation
concerns_data_topic:
- B2AI_TOPIC:4
has_relevant_organization:
- B2AI_ORG:10
purpose_detail:
A common meta- model and notation for modeling and graphically expressing
a case as well as an interchange format for exchanging case models among different
tools.
is_open: true
requires_registration: false
url: https://www.omg.org/cmmn/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:39
name: CARE
category: B2AI_STANDARD:BiomedicalStandard
description: Case Report guidelines
collection:
- guidelines
concerns_data_topic:
- B2AI_TOPIC:4
purpose_detail:
The CARE guidelines provide a framework that supports transparency
and accuracy in the publication of case reports and the reporting of information
from patient encounters.
is_open: true
requires_registration: false
url: https://www.care-statement.org/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:40
name: Define
category: B2AI_STANDARD:BiomedicalStandard
description: CDISC Case Report Tabulation Data Definition Specification
concerns_data_topic:
- B2AI_TOPIC:4
has_relevant_organization:
- B2AI_ORG:15
purpose_detail:
The CDISC Case Report Tabulation Data Definition Specification (define.xml)
Version 1.0 reflects changes from a comment period through the Health Level 7
(HL7) Regulated Clinical Research Information Management Technical Committee (RCRIM)
in December 2003 (www.hl7.org) and CDISC's website in September 2004 as well as
the work done by the define.xml team in conjunction with the CDISC ODM team to
add functionality, features, and additional documentation. This document specifies
the standard for providing Case Report Tabulations Data Definitions in an XML
format for submission to regulatory authorities (e.g., FDA). The XML schema used
to define the expected structure for these XML files is based on an extension
to the CDISC Operational Data Model (ODM). The 1999 FDA electronic submission
(eSub) guidance and the electronic Common Technical Document (eCTD) documents
specify that a document describing the content and structure of the included data
should be provided within a submission. This document is known as the Data Definition
Document (e.g., define.pdf in the 1999 guidance). The Data Definition Document
provides a list of the datasets included in the submission along with a detailed
description of the contents of each dataset. To increase the level of automation
and improve the efficiency of the Regulatory Review process, define.xml can be
used to provide the Data Definition Document in a machine-readable format.
is_open: true
requires_registration: true
url: https://www.cdisc.org/standards/data-exchange/define-xml
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:41
name: CDISC ADaM
category: B2AI_STANDARD:BiomedicalStandard
description: CDISC Controlled Terminology for Analysis Dataset Model
concerns_data_topic:
- B2AI_TOPIC:5
has_relevant_organization:
- B2AI_ORG:15
purpose_detail: Controlled terminology for data analysis and assessments.
is_open: true
requires_registration: false
url: https://evs.nci.nih.gov/ftp1/CDISC/ADaM/ADaM%20Terminology.html
formal_specification: https://evs.nci.nih.gov/ftp1/CDISC/ADaM/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:42
name: CDISC Protocol
category: B2AI_STANDARD:BiomedicalStandard
description: CDISC Controlled Terminology for Data Collection for Protocol
concerns_data_topic:
- B2AI_TOPIC:5
has_relevant_organization:
- B2AI_ORG:15
purpose_detail: Controlled terminology for biomedical protocols.
is_open: true
requires_registration: false
url: https://evs.nci.nih.gov/ftp1/CDISC/Protocol/Protocol%20Terminology.html
formal_specification: https://evs.nci.nih.gov/ftp1/CDISC/Protocol/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:43
name: CDISC TAUGs
category: B2AI_STANDARD:BiomedicalStandard
description: CDISC Controlled Terminology for Therapeutic Area Standards
concerns_data_topic:
- B2AI_TOPIC:4
- B2AI_TOPIC:7
has_relevant_organization:
- B2AI_ORG:15
purpose_detail:
Disease-specific metadata, examples and guidance on implementing
CDISC standards.
is_open: true
requires_registration: false
url: https://www.cdisc.org/standards/therapeutic-areas
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:44
name: SDTM
category: B2AI_STANDARD:BiomedicalStandard
description:
CDISC Controlled Terminology Standards for Data Aggregation through
Study Data Tabulation Model (including QRS, Medical Device and Pharmacogenomics
Data)
concerns_data_topic:
- B2AI_TOPIC:4
has_relevant_organization:
- B2AI_ORG:15
purpose_detail:
A standard for organizing and formatting data to streamline processes
in collection, management, analysis and reporting.
is_open: true
requires_registration: false
url: https://www.cdisc.org/standards/foundational/sdtm
formal_specification: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:45
name: CDASH
category: B2AI_STANDARD:BiomedicalStandard
description:
CDISC Controlled Terminology Standards for Data Collection through
Clinical Data Acquisition Standards Harmonization
concerns_data_topic:
- B2AI_TOPIC:4
has_relevant_organization:
- B2AI_ORG:15
purpose_detail:
A standard way to collect data consistently across studies and sponsors
so that data collection formats and structures provide clear traceability of submission
data into the Study Data Tabulation Model (SDTM).
is_open: true
requires_registration: false
url: https://www.cdisc.org/standards/foundational/cdash
formal_specification: https://evs.nci.nih.gov/ftp1/CDISC/SDTM/
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:46
name: CDISC Dataset
category: B2AI_STANDARD:BiomedicalStandard
description: CDISC Dataset-XML
collection:
- markuplanguage
has_relevant_organization:
- B2AI_ORG:15
purpose_detail:
"CDISC Dataset-XML, which was released for comment under the name\
\ \u201CStudyDataSet-XML\u201D but was renamed to avoid confusion with the CDISC\
\ SDS team, is a new standard used to exchange study datasets in an XML format.\
\ The purpose of Dataset-XML is to support the interchange of tabular data for\
\ clinical research applications using ODM-based XML technologies. The Dataset-XML\
\ model is based on the CDISC Operational Data Model (ODM) standard and should\
\ follow the metadata structure defined in the CDISC Define-XML standard. Dataset-XML\
\ can represent any tabular dataset including SDTM, ADaM, SEND, or non-standard\
\ legacy datasets. Some noteworthy items relating to Dataset-XML v1.0 include\
\ alternative to SAS Version 5 Transport (XPT) format for datasets ODM-based model\
\ for representation of SEND, SDTM, ADaM or legacy datasets Capable of supporting\
\ CDISC regulatory data submissions Based on Define-XML v2 or v1 metadata, easy\
\ to reference Dataset-XML supports all language encodings supported by XML."
is_open: true
requires_registration: true
url: https://www.cdisc.org/standards/data-exchange/dataset-xml
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:47
name: CDISC LAB
category: B2AI_STANDARD:BiomedicalStandard
description: CDISC Laboratory Data Model
collection:
- datamodel
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:4
has_relevant_organization:
- B2AI_ORG:15
purpose_detail:
LAB provides a standard model for the acquisition and exchange of
laboratory data, primarily between labs and sponsors or CROs. The LAB standard
was specifically designed for the interchange of lab data acquired in clinical
trials.
is_open: true
requires_registration: true
url: https://www.cdisc.org/standards/data-exchange/lab
contributor_name: Harry Caufield
contributor_github_name: caufieldjh
contributor_orcid: ORCID:0000-0001-5705-7831
- id: B2AI_STANDARD:48
name: CDISC ODM
category: B2AI_STANDARD:BiomedicalStandard
description: CDISC Operational Data Model
collection:
- datamodel
- has_ai_application
concerns_data_topic:
- B2AI_TOPIC:4
has_relevant_organization:
- B2AI_ORG:15