-
Notifications
You must be signed in to change notification settings - Fork 73
/
biolink-model.yaml
12382 lines (11484 loc) · 394 KB
/
biolink-model.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
---
id: https://w3id.org/biolink/biolink-model
name: Biolink-Model
description: Entity and association taxonomy and datamodel for life-sciences data
license: https://creativecommons.org/publicdomain/zero/1.0/
# Version should be kept in sync with primary Git repository release tag
version: 4.2.5
## ------------
##
## PREFIXES
## ------------
# CURIE namespaces (prefixes/base URI's) mappings of prefixes used in the body of the Biolink Model specification
# are resolved using a specific precedence order, for use in the generation of the Biolink Model context.jsonld
# mappings to namespaces. Any prefixes encountered in the Biolink Model but not resolved by the following
# precedence sources, are anonymously declared by linkml as http://example.org/UNKNOWN/ rooted base URI's
# which should ideally be repaired in one of the precedence lists.
#
# 1. The following 'prefixes:' delimited list has first precedence in resolution.
#
prefixes:
AGRKB: 'https://www.alliancegenome.org/'
apollo: 'https://github.com/GMOD/Apollo'
AspGD: 'http://www.aspergillusgenome.org/cgi-bin/locus.pl?dbid='
biolink: 'https://w3id.org/biolink/vocab/'
bioschemas: 'https://bioschemas.org/'
linkml: 'https://w3id.org/linkml/'
CAID: 'http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid='
# Placeholder: just points to GMOD Chado wiki
CHADO: 'http://gmod.org/wiki/Chado/'
# Placeholders: not sure how 'chembio'and CHEMBL.MECHANISM really resolve
ChemBank: 'http://chembank.broadinstitute.org/chemistry/viewMolecule.htm?cbid='
CHEMBL.MECHANISM: 'https://www.ebi.ac.uk/chembl/mechanism/inspect/'
CID: 'http://pubchem.ncbi.nlm.nih.gov/compound/'
CLINVAR: 'http://identifiers.org/clinvar'
COAR_RESOURCE: 'http://purl.org/coar/resource_type/'
COG: 'https://www.ncbi.nlm.nih.gov/research/cog-project/'
ComplexPortal: 'https://www.ebi.ac.uk/complexportal/complex/'
CPT: 'https://www.ama-assn.org/practice-management/cpt/'
CTD.CHEMICAL: 'http://ctdbase.org/detail.go?type=chem&acc='
CTD.DISEASE: 'http://ctdbase.org/detail.go?type=disease&db=MESH&acc='
CTD.GENE: 'http://ctdbase.org/detail.go?type=gene&acc='
CTD: 'http://ctdbase.org/'
DGIdb: 'https://www.dgidb.org/interaction_types'
dcat: 'http://www.w3.org/ns/dcat#'
dct: 'http://purl.org/dc/terms/'
dcid: 'https://datacommons.org/browser/'
doi: 'https://doi.org/'
DOID-PROPERTY: 'http://purl.obolibrary.org/obo/doid#'
DrugCentral: 'http://drugcentral.org/drugcard/'
ECTO: 'http://purl.obolibrary.org/obo/ECTO_'
EDAM-DATA: 'http://edamontology.org/data_'
EDAM-FORMAT: 'http://edamontology.org/format_'
EDAM-OPERATION: 'http://edamontology.org/operation_'
EDAM-TOPIC: 'http://edamontology.org/topic_'
EFO: 'http://www.ebi.ac.uk/efo/EFO_'
ExO: 'http://purl.obolibrary.org/obo/ExO_'
fabio: 'http://purl.org/spar/fabio/'
foaf: 'http://xmlns.com/foaf/0.1/'
foodb.compound: 'http://foodb.ca/compounds/'
foodb.food: 'http://foodb.ca/foods/'
FYECO: 'https://www.pombase.org/term/'
FYPO: 'http://purl.obolibrary.org/obo/FYPO_' # Fission Yeast Phenotype Ontology
gff3: 'https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md#'
GOREL: 'http://purl.obolibrary.org/obo/GOREL_'
# GOP: Gene Ontology Property (not really a GO term but an associated metadatum)
GOP: 'http://purl.obolibrary.org/obo/go#'
gpi: 'https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#'
GSID: 'https://scholar.google.com/citations?user='
GTEx: 'https://www.gtexportal.org/home/gene/'
GTOPDB: 'https://www.guidetopharmacology.org/GRAC/LigandDisplayForward?ligandId='
gtpo: 'https://rdf.guidetopharmacology.org/ns/gtpo#'
HANCESTRO: 'http://www.ebi.ac.uk/ancestro/ancestro_'
HCPCS: 'http://purl.bioontology.org/ontology/HCPCS/'
HsapDv: 'http://purl.obolibrary.org/obo/HsapDv_'
ICD10: 'https://icd.codes/icd9cm/'
ICD9: 'http://translator.ncats.nih.gov/ICD9_'
interpro: 'https://www.ebi.ac.uk/interpro/entry/'
INO: 'http://purl.obolibrary.org/obo/INO_'
isbn: 'https://www.isbn-international.org/identifier/' # note: a resolvable base URI not available from isbn-international
isni: 'https://isni.org/isni/'
issn: 'https://portal.issn.org/resource/ISSN/'
ncats.drug: 'https://drugs.ncats.io/drug/'
KEGG.BRITE: 'https://bioregistry.io/kegg.brite:'
KEGG: 'http://www.kegg.jp/entry/'
KEGG.GENES: 'https://bioregistry.io/kegg.genes:bsu:'
KEGG.PATHWAY: 'https://bioregistry.io/kegg.pathway:'
KEGG.RCLASS: 'https://www.genome.jp/dbget-bin/www_bget?rc:'
LOINC: 'http://loinc.org/rdf/'
MAXO: 'http://purl.obolibrary.org/obo/MAXO_'
medgen: 'https://www.ncbi.nlm.nih.gov/medgen/'
metacyc.reaction: 'http://identifiers.org/metacyc.reaction:'
METANETX.REACTION: 'https://www.metanetx.org/equa_info/'
MESH: 'http://id.nlm.nih.gov/mesh/'
MI: 'http://purl.obolibrary.org/obo/MI_'
mirbase: 'http://identifiers.org/mirbase'
mmmp.biomaps: 'https://bioregistry.io/mmmp.biomaps:'
MmusDv: 'http://purl.obolibrary.org/obo/MMUSDV_'
MSigDB: 'https://www.gsea-msigdb.org/gsea/msigdb/'
NBO-PROPERTY: 'http://purl.obolibrary.org/obo/nbo#'
ncats.bioplanet: 'https://tripod.nih.gov/bioplanet/detail.jsp?pid='
NCBIGene: 'http://identifiers.org/ncbigene/'
NCIT-OBO: 'http://purl.obolibrary.org/obo/ncit#'
NDDF: 'http://purl.bioontology.org/ontology/NDDF/'
NLMID: 'https://www.ncbi.nlm.nih.gov/nlmcatalog/?term='
OBAN: 'http://purl.org/oban/'
OMIM.PS: 'https://www.omim.org/phenotypicSeries/'
ORCID: 'https://orcid.org/'
orphanet: 'http://www.orpha.net/ORDO/Orphanet_'
os: 'https://github.com/cmungall/owlstar/blob/master/owlstar.ttl'
PANTHER.FAMILY: 'http://www.pantherdb.org/panther/family.do?clsAccession='
PathWhiz: 'http://smpdb.ca/pathways/#' # See also https://smpdb.ca/pathwhiz/
pav: 'http://purl.org/pav/'
PHARMGKB.DRUG: 'https://www.pharmgkb.org/chemical/'
PHARMGKB.DISEASE: 'https://www.pharmgkb.org/disease/'
PHARMGKB.GENE: 'https://www.pharmgkb.org/gene/'
PHARMGKB.PATHWAYS: 'https://www.pharmgkb.org/pathway/'
PHARMGKB.VARIANT: 'https://www.pharmgkb.org/variant/'
PHAROS: 'http://pharos.nih.gov'
PomBase: 'https://www.pombase.org/gene/'
prov: 'http://www.w3.org/ns/prov#'
qud: 'http://qudt.org/1.1/schema/qudt#'
REPODB: 'http://apps.chiragjpgroup.org/repoDB/'
ResearchID: 'https://publons.com/researcher/'
RO: 'http://purl.obolibrary.org/obo/RO_'
RXNORM: 'http://purl.bioontology.org/ontology/RXNORM/'
RXCUI: 'https://mor.nlm.nih.gov/RxNav/search?searchBy=RXCUI&searchTerm='
schema: 'http://schema.org/'
ScopusID: 'https://www.scopus.com/authid/detail.uri?authorId='
SEED.REACTION: 'https://modelseed.org/biochem/reactions/'
SEMMEDDB: 'https://skr3.nlm.nih.gov/SemMedDB'
SIO: 'http://semanticscience.org/resource/SIO_'
SNOMEDCT: 'http://snomed.info/id/'
SPDI: 'https://api.ncbi.nlm.nih.gov/variation/v0/spdi/'
UBERGRAPH: 'http://translator.renci.org/ubergraph-axioms.ofn#'
UBERON_CORE: 'http://purl.obolibrary.org/obo/uberon/core#'
UBERON_NONAMESPACE: 'http://purl.obolibrary.org/obo/core#'
STY: 'http://purl.bioontology.org/ontology/STY/'
UMLSSG: 'https://lhncbc.nlm.nih.gov/semanticnetwork/download/sg_archive/SemGroups-v04.txt'
UniProtKB: 'http://purl.uniprot.org/uniprot/'
UNIPROT.ISOFORM: 'http://purl.uniprot.org/isoforms/'
VANDF: 'https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/VANDF/'
UO-PROPERTY: 'http://purl.obolibrary.org/obo/uo#'
VMC: 'https://github.com/ga4gh/vr-spec/'
WBls: 'http://purl.obolibrary.org/obo/WBls_'
WBbt: 'http://purl.obolibrary.org/obo/WBbt_'
WBVocab: 'http://bio2rdf.org/wormbase_vocabulary'
WIKIDATA: 'https://www.wikidata.org/entity/' # Wikidata Entity
WIKIDATA_PROPERTY: 'https://www.wikidata.org/prop/'
wgs: 'http://www.w3.org/2003/01/geo/wgs84_pos'
XPO: 'http://purl.obolibrary.org/obo/XPO_' # Xenopus Phenotype Ontology
Xenbase: 'http://www.xenbase.org/gene/showgene.do?method=display&geneId='
PMC: 'http://europepmc.org/articles/PMC'
default_prefix: biolink
default_range: string
default_curi_maps:
- obo_context
- idot_context
- monarch_context
- semweb_context
emit_prefixes:
- rdf
- rdfs
- xsd
- skos
- oboInOwl
- BIOGRID
- SO
## ------------
## SUBSETS
## ------------
subsets:
model_organism_database:
description: >-
Subset that is relevant for a typical Model Organism Database (MOD)
translator_minimal:
description: >-
Minimum subset of translator work
samples:
description: >-
Sample/biosample datamodel
testing:
description: >-
TBD
## ------------
## TYPES
## ------------
imports:
- linkml:types
types:
chemical formula value:
uri: xsd:string
base: str
description: A chemical formula
notes:
- Should be implemented as a stronger type
iri type:
uri: xsd:string
typeof: uriorcurie
description: >-
An IRI
label type:
uri: xsd:string
typeof: string
description: >-
A string that provides a human-readable name for an entity
predicate type:
uri: xsd:string
typeof: uriorcurie
description: >-
A CURIE from the biolink related_to hierarchy.
For example, biolink:related_to, biolink:causes, biolink:treats.
narrative text:
uri: xsd:string
typeof: string
description: >-
A string that provides a human-readable description of something
symbol type:
uri: xsd:string
typeof: string
frequency value:
typeof: string
uri: UO:0000105
percentage frequency value:
typeof: double
uri: UO:0000187
quotient:
aliases: ['ratio']
typeof: double
uri: UO:0010006
unit:
typeof: string
uri: UO:0000000
id_prefixes:
- UO
exact_mappings:
- qud:Unit
time type:
uri: xsd:time
typeof: time
biological sequence:
uri: xsd:string
typeof: string
## ------------
## SLOTS
## ------------
slots:
has attribute:
description: >-
connects any entity to an attribute
domain: entity
range: attribute
multivalued: true
in_subset:
- samples
close_mappings:
# RTX term meaning 'specifies value of' tagged as inverse of 'biolink:has attribute'
- OBI:0001927
exact_mappings:
- SIO:000008
narrow_mappings:
# if 'has attribute' annotates a NamedThing as subject or
# object of an association, these OBAN mappings may apply
- OBAN:association_has_subject_property
- OBAN:association_has_object_property
- CPT:has_possibly_included_panel_element
- DRUGBANK:category
# RTX contributed terms. Could perhaps review for more semantically precise mappings?
- EFO:is_executed_in
- HANCESTRO:0301
- LOINC:has_action_guidance
- LOINC:has_adjustment
- LOINC:has_aggregation_view
- LOINC:has_approach_guidance
- LOINC:has_divisor
- LOINC:has_exam
- LOINC:has_method
- LOINC:has_modality_subtype
- LOINC:has_object_guidance
- LOINC:has_scale
- LOINC:has_suffix
- LOINC:has_time_aspect
- LOINC:has_time_modifier
- LOINC:has_timing_of
# disease is stage
- NCIT:R88
- NCIT:eo_disease_has_property_or_attribute
- NCIT:has_data_element
- NCIT:has_pharmaceutical_administration_method
- NCIT:has_pharmaceutical_basic_dose_form
- NCIT:has_pharmaceutical_intended_site
- NCIT:has_pharmaceutical_release_characteristics
- NCIT:has_pharmaceutical_state_of_matter
- NCIT:has_pharmaceutical_transformation
- NCIT:is_qualified_by
- NCIT:qualifier_applies_to
- NCIT:role_has_domain
- NCIT:role_has_range
- INO:0000154
- HANCESTRO:0308
- OMIM:has_inheritance_type
- orphanet:C016
- orphanet:C017
- RO:0000053
# RTX tagged a few RO terms as 'biolink:related_to' but semantics suggest a better mapping here
- RO:0000086
- RO:0000087
- SNOMED:has_access
- SNOMED:has_clinical_course
- SNOMED:has_count_of_base_of_active_ingredient
- SNOMED:has_dose_form_administration_method
- SNOMED:has_dose_form_release_characteristic
- SNOMED:has_dose_form_transformation
- SNOMED:has_finding_context
- SNOMED:has_finding_informer
- SNOMED:has_inherent_attribute
- SNOMED:has_intent
- SNOMED:has_interpretation
- SNOMED:has_laterality
- SNOMED:has_measurement_method
- SNOMED:has_method
- SNOMED:has_priority
- SNOMED:has_procedure_context
- SNOMED:has_process_duration
- SNOMED:has_property
- SNOMED:has_revision_status
- SNOMED:has_scale_type
- SNOMED:has_severity
- SNOMED:has_specimen
- SNOMED:has_state_of_matter
- SNOMED:has_subject_relationship_context
- SNOMED:has_surgical_approach
- SNOMED:has_technique
- SNOMED:has_temporal_context
- SNOMED:has_time_aspect
- SNOMED:has_units
- UMLS:has_structural_class
- UMLS:has_supported_concept_property
- UMLS:has_supported_concept_relationship
- UMLS:may_be_qualified_by
has attribute type:
description: >-
connects an attribute to a class that describes it
domain: attribute
range: ontology class
multivalued: false
required: true
in_subset:
- samples
narrow_mappings:
- LOINC:has_modality_type
- LOINC:has_view_type
# TRAPI Attribute schema alignment:
# value: NamedThing.name
# value_type: NamedThing.category
# value_type_name: quantity_value.NamedThing.name
has qualitative value:
description: >-
connects an attribute to a value
domain: attribute
range: named thing
multivalued: false
in_subset:
- samples
# TRAPI Attribute schema alignment:
# value: quantity_value.has_numeric_value[double] - may be a vector?
# value_type: quantity_value.has_unit.unit.uri
# value_type_name: quantity_value.has_unit.unit.name[string]
has quantitative value:
description: >-
connects an attribute to a value
domain: attribute
range: quantity value
multivalued: true
exact_mappings:
- qud:quantityValue
narrow_mappings:
- SNOMED:has_concentration_strength_numerator_value
- SNOMED:has_presentation_strength_denominator_value
- SNOMED:has_presentation_strength_numerator_value
in_subset:
- samples
has numeric value:
description: >-
connects a quantity value to a number
domain: quantity value
range: double
multivalued: false
exact_mappings:
- qud:quantityValue
in_subset:
- samples
has unit:
description: >-
connects a quantity value to a unit
domain: quantity value
range: unit
multivalued: false
close_mappings:
# These RTX contributed terms mean "is unit of" which is the semantic inverse of this biolink:has_unit term
- EFO:0001697
- UO-PROPERTY:is_unit_of
exact_mappings:
- qud:unit
- IAO:0000039
narrow_mappings:
- SNOMED:has_concentration_strength_denominator_unit
- SNOMED:has_concentration_strength_numerator_unit
- SNOMED:has_presentation_strength_denominator_unit
- SNOMED:has_presentation_strength_numerator_unit
- SNOMED:has_unit_of_presentation
in_subset:
- samples
base coordinate:
is_a: sequence localization attribute
aliases: ['one-based', 'fully-closed']
description: >-
A position in the base coordinate system. Base coordinates start at position 1 instead of position 0.
range: integer
## --------------------
## NODE PROPERTY SLOTS
## --------------------
node property:
description: >-
A grouping for any property that holds between a node and a value
domain: named thing
id:
identifier: true
domain: entity
description: >-
A unique identifier for an entity.
Must be either a CURIE shorthand for a URI or a complete URI
in_subset:
- translator_minimal
required: true
exact_mappings:
- AGRKB:primaryId
- gff3:ID
- gpi:DB_Object_ID
iri:
description: >-
An IRI for an entity. This is determined by the id using expansion rules.
range: iri type
in_subset:
- translator_minimal
- samples
exact_mappings:
- WIKIDATA_PROPERTY:P854
type:
slot_uri: rdf:type
domain: entity
exact_mappings:
- gff3:type
- gpi:DB_Object_Type
multivalued: true
category:
is_a: type
domain: entity
range: uriorcurie
designates_type: true
description: >-
Name of the high level ontology class in which this entity is categorized. Corresponds to the label for the
biolink entity type class. In a neo4j database this MAY correspond to the neo4j label tag. In an RDF database it should be a biolink model class URI.
This field is multi-valued. It should include values for ancestors of the biolink class; for example,
a protein such as Shh would have category values `biolink:Protein`, `biolink:GeneProduct`, `biolink:MolecularEntity`.
In an RDF database, nodes will typically have an rdf:type triples. This can be to the most specific biolink
class, or potentially to a class more specific than something in biolink. For example, a sequence feature `f`
may have a rdf:type assertion to a SO class such as TF_binding_site,
which is more specific than anything in biolink. Here we would have categories {biolink:GenomicEntity,
biolink:MolecularEntity, biolink:NamedThing}
is_class_field: true
multivalued: true
in_subset:
- translator_minimal
publication type:
slot_uri: dct:type
description: >-
Ontology term for publication type may be drawn from
Dublin Core types (https://www.dublincore.org/specifications/dublin-core/dcmi-type-vocabulary/),
FRBR-aligned Bibliographic Ontology (https://sparontologies.github.io/fabio/current/fabio.html),
the MESH publication types (https://www.nlm.nih.gov/mesh/pubtypes.html),
the Confederation of Open Access Repositories (COAR) Controlled Vocabulary for Resource Type Genres
(http://vocabularies.coar-repositories.org/documentation/resource_types/),
Wikidata (https://www.wikidata.org/wiki/Wikidata:Publication_types), or
equivalent publication type ontology. When a given publication type ontology term
is used within a given knowledge graph, then the CURIE identified term must be
documented in the graph as a concept node of biolink:category biolink:OntologyClass.
values_from: # Not sure which takes precedence, if any...
- dctypes
- fabio
- MESH_PUB
- COAR_RESOURCE
- WIKIDATA
multivalued: true
name:
aliases: ['label', 'display name', 'title']
description: >-
A human-readable name for an attribute or entity.
domain: entity
range: label type
in_subset:
- translator_minimal
- samples
slot_uri: rdfs:label
exact_mappings:
- gff3:Name
- gpi:DB_Object_Name
narrow_mappings:
- dct:title
- WIKIDATA_PROPERTY:P1476
stoichiometry:
description: >-
the relationship between the relative quantities of substances taking part in a reaction or
forming a compound, typically a ratio of whole integers.
is_a: association slot
range: integer
reaction direction:
description: >-
the direction of a reaction as constrained by the direction enum (ie: left_to_right, neutral, etc.)
is_a: association slot
range: ReactionDirectionEnum
narrow_mappings:
- NCIT:C42677
reaction balanced:
is_a: association slot
range: boolean
reaction side:
description: >-
the side of a reaction being modeled (ie: left or right)
is_a: association slot
range: ReactionSideEnum
symbol:
is_a: node property
domain: named thing
description: >-
Symbol for a particular thing
exact_mappings:
- AGRKB:symbol
- gpi:DB_Object_Symbol
synonym:
is_a: node property
aliases: ['alias']
domain: named thing
range: label type
description: >-
Alternate human-readable names for a thing
multivalued: true
in_subset:
- translator_minimal
narrow_mappings:
# there is an interesting debate here: are these terms "narrower" a.k.a. more specialized instances of
# 'biolink:synonym' or should they be binned into their respective namesake class of mappings?
# namely, is 'oboInOwl:hasExactSynonym' an instance 'exact_mappings', etc.
- skos:altLabel
- gff3:Alias
- AGRKB:synonyms
- gpi:DB_Object_Synonyms
# TODO: RTX contributed terms mapped here... May need review?
- HANCESTRO:0330
- IAO:0000136
- RXNORM:has_tradename
exact synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasExactSynonym
broad synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasBroadSynonym
narrow synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasNarrowSynonym
related synonym:
is_a: synonym
exact_mappings:
- oboInOwl:hasRelatedSynonym
deprecated:
range: boolean
exact_mappings:
- oboInOwl:ObsoleteClass
description: >-
A boolean flag indicating that an entity is no longer considered current or valid.
has topic:
aliases: ['topic', 'descriptors']
is_a: node property
range: ontology class
exact_mappings:
- foaf:topic
description: >-
Connects a node to a vocabulary term or ontology class that describes some aspect of the entity. In general specific characterization is preferred.
See https://github.com/biolink/biolink-model/issues/238
xref:
aliases: ['dbxref', 'Dbxref', 'DbXref', 'record_url', 'source_record_urls']
domain: named thing
range: uriorcurie
description: >-
A database cross reference or alternative identifier for a NamedThing or edge between two
NamedThings. This property should point to a database record or webpage that supports the existence of the edge, or
gives more detail about the edge. This property can be used on a node or edge to provide multiple
URIs or CURIE cross references.
multivalued: true
in_subset:
- translator_minimal
narrow_mappings:
- gff3:Dbxref
- gpi:DB_Xrefs
url:
is_a: node property
description: >-
This slot holds a string representation of a URL for an external resource about the node it is
present on. Unlike an 'xref' that is primarily represented by a CURIE, this slot is intended to hold a full
URL that can be used to directly access a resource. When linking to an external resource that cannot be
represented by a unique CURIE, this slot should be used. However, when the intent is to link to the
default URI expansion of a CURIE related to the node it is present on, the xref slot should be used instead.
domain: entity
range: string
semmed agreement count:
is_a: association slot
range: integer
description: >-
The number of times this concept has been asserted in the SemMedDB literature database.
in_subset:
- translator_minimal
support graphs:
description: >-
A list of knowledge graphs that support the existence of this association.
multivalued: true
is_a: association slot
in_subset:
- translator_minimal
resource id:
is_a: node property
description: >-
The CURIE for an Information Resource that served as a source
of knowledge expressed in an Edge, or a source of data used to
generate this knowledge.
domain: retrieval source
range: uriorcurie
in_subset:
- translator_minimal
resource role:
is_a: node property
description: >-
The role played by the InformationResource in serving as a
source for an Edge. Note that a given Edge should have one
and only one 'primary' source, and may have any number of
'aggregator' or 'supporting data' sources.
domain: retrieval source
range: ResourceRoleEnum
in_subset:
- translator_minimal
retrieval source ids:
description: >-
A list of retrieval sources that served as a source of knowledge
expressed in an Edge, or a source of data used to generate this
knowledge.
multivalued: true
range: retrieval source
in_subset:
- translator_minimal
full name:
is_a: node property
domain: named thing
range: label type
description: >-
a long-form human readable name for a thing
upstream resource ids:
is_a: node property
description: >-
An upstream InformationResource from which the resource
being described directly retrieved a record of the knowledge
expressed in the Edge, or data used to generate this knowledge.
This is an array because there are cases where a merged Edge
holds knowledge that was retrieved from multiple sources. e.g.
an Edge provided by the ARAGORN ARA can expressing knowledge it
retrieved from both the automat-mychem-info and molepro KPs,
which both provided it with records of this single fact.
domain: retrieval source
range: uriorcurie
description:
aliases: ['definition']
range: narrative text
description: >-
a human-readable description of an entity
in_subset:
- translator_minimal
slot_uri: dct:description
exact_mappings:
- IAO:0000115
- skos:definitions
narrow_mappings:
- gff3:Description
systematic synonym:
is_a: node property
domain: named thing
range: label type
multivalued: true
slot_uri: GOP:systematic_synonym
description: >-
more commonly used for gene symbols in yeast
affiliation:
is_a: node property
description: >-
a professional relationship between one provider (often a person) within another provider (often an organization).
Target provider identity should be specified by a CURIE. Providers may have multiple affiliations.
domain: agent
range: uriorcurie
multivalued: true
address:
is_a: node property
description: >-
the particulars of the place where someone or an organization is situated. For now, this slot is a
simple text "blob" containing all relevant details of the given location for fitness of purpose.
For the moment, this "address" can include other contact details such as email and phone number(?).
## Space
latitude:
is_a: node property
range: float
description: >-
latitude
exact_mappings:
- wgs:lat
longitude:
is_a: node property
range: float
description: >-
longitude
exact_mappings:
- wgs:long
## Time
timepoint:
aliases: ['duration']
range: time type
description: >-
a point in time
creation date:
is_a: node property
aliases: ['publication date']
range: date
description: >-
date on which an entity was created. This can be applied to nodes or edges
exact_mappings:
- dct:createdOn
- WIKIDATA_PROPERTY:P577
update date:
is_a: node property
range: date
description: >-
date on which an entity was updated. This can be applied to nodes or edges
## Statistics
aggregate statistic:
is_a: node property
abstract: true
has count:
description: >-
number of things with a particular property
is_a: aggregate statistic
range: integer
exact_mappings:
- LOINC:has_count
has total:
description: >-
total number of things in a particular reference set
is_a: aggregate statistic
range: integer
has quotient:
is_a: aggregate statistic
range: double
has percentage:
description: >-
equivalent to has quotient multiplied by 100
is_a: aggregate statistic
range: double
## Properties for Information Content Entity and Publication Nodes
has taxonomic rank:
is_a: node property
range: taxonomic rank
multivalued: false
mappings:
- WIKIDATA:P105
has dataset:
is_a: node property
domain: dataset version
range: dataset
broad_mappings:
- dct:source
source web page:
is_a: node property
domain: dataset summary
broad_mappings:
- dct:source
source logo:
is_a: node property
domain: dataset summary
slot_uri: schema:logo
retrieved on:
is_a: node property
domain: dataset
range: date
exact_mappings:
- pav:retrievedOn
version of:
is_a: node property
domain: dataset version
range: dataset summary
exact_mappings:
- dct:isVersionOf
version:
is_a: node property
domain: dataset
broad_mappings:
- pav:version
- owl:versionInfo
license:
is_a: node property
domain: information content entity
exact_mappings:
- dct:license
narrow_mappings:
- WIKIDATA_PROPERTY:P275
rights:
is_a: node property
domain: information content entity
exact_mappings:
- dct:rights
format:
is_a: node property
domain: information content entity
exact_mappings:
- dct:format
- WIKIDATA_PROPERTY:P2701
created with:
is_a: node property
domain: dataset
exact_mappings:
- pav:createdWith
download url:
is_a: node property
domain: information content entity
slot_uri: dcat:downloadURL
dataset download url:
is_a: node property
domain: dataset
slot_uri: dcat:downloadURL
distribution download url:
is_a: node property
domain: dataset distribution
exact_mappings:
- dcat:downloadURL
ingest date:
is_a: node property
domain: dataset version
broad_mappings:
- dct:issued
has distribution:
is_a: node property
domain: dataset version
range: dataset distribution
slot_uri: dct:distribution
published in:
is_a: node property
description: >-
CURIE identifier of a broader publication context within which the publication may be placed,
e.g. a specified book or journal.
domain: publication
range: uriorcurie
values_from:
- NLMID
- issn
- isbn
exact_mappings:
- WIKIDATA_PROPERTY:P1433
iso abbreviation:
is_a: node property
description: >-
Standard abbreviation for periodicals in the International Organization for Standardization (ISO) 4 system
See https://www.issn.org/services/online-services/access-to-the-ltwa/. If the 'published in' property is set,
then the iso abbreviation pertains to the broader publication context (the journal) within which the given
publication node is embedded, not the publication itself.
domain: publication
exact_mappings:
- WIKIDATA_PROPERTY:P1160
authors:
is_a: node property
description: >-
connects an publication to the list of authors who contributed to the publication.
This property should be a comma-delimited list of author names. It is recommended that an author's name
be formatted as "surname, firstname initial.". Note that this property is a node annotation expressing
the citation list of authorship which might typically otherwise be more completely documented in
biolink:PublicationToProviderAssociation defined edges which point to full details about an author
and possibly, some qualifiers which clarify the specific status of a given author in the publication.
multivalued: true
domain: publication
range: agent
volume: