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deepakunni3deepakunni3
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Regenerate artifacts from biolink-model.yaml
1 parent 54813c3 commit 8b5ca35

13 files changed

+1437
-957
lines changed

‎biolink-model.graphql

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -548,7 +548,7 @@ type ChemicalExposure implements ExposureEvent
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timepoint: TimeType
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}
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551-
interface ChemicalOrDrugOrTreatement
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interface ChemicalOrDrugOrTreatment
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{
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}
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@@ -1103,7 +1103,7 @@ type DiseaseToPhenotypicFeatureAssociation implements EntityToPhenotypicFeatureA
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sexQualifier: BiologicalSex
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}
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1106-
type Drug implements Mixture, ChemicalOrDrugOrTreatement, OntologyClass
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type Drug implements Mixture, ChemicalOrDrugOrTreatment, OntologyClass
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{
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id: String!
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iri: IriType
@@ -3353,7 +3353,7 @@ type TranscriptToGeneRelationship
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object: Gene!
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}
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3356-
type Treatment implements ExposureEvent, ChemicalOrDrugOrTreatement
3356+
type Treatment implements ExposureEvent, ChemicalOrDrugOrTreatment
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{
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id: String!
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iri: IriType

‎biolink-model.owl.ttl

Lines changed: 925 additions & 471 deletions
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‎biolink-model.shex

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Original file line numberDiff line numberDiff line change
@@ -481,9 +481,9 @@ linkml:Nodeidentifier NONLITERAL
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} OR @<ComplexChemicalExposure>
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)
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<ChemicalOrDrugOrTreatement> {
485-
( $<ChemicalOrDrugOrTreatement_tes> rdf:type . * ;
486-
rdf:type [ <ChemicalOrDrugOrTreatement> ] ?
484+
<ChemicalOrDrugOrTreatment> {
485+
( $<ChemicalOrDrugOrTreatment_tes> rdf:type . * ;
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rdf:type [ <ChemicalOrDrugOrTreatment> ] ?
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)
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}
489489

@@ -859,8 +859,8 @@ linkml:Nodeidentifier NONLITERAL
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rdf:type [ <MolecularEntity> ] ? ;
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&<Mixture_tes> ;
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rdf:type [ <Mixture> ] ? ;
862-
&<ChemicalOrDrugOrTreatement_tes> ;
863-
rdf:type [ <ChemicalOrDrugOrTreatement> ] ? ;
862+
&<ChemicalOrDrugOrTreatment_tes> ;
863+
rdf:type [ <ChemicalOrDrugOrTreatment> ] ? ;
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&<OntologyClass_tes> ;
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rdf:type [ <OntologyClass> ] ? ;
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<has_constituent> @<ChemicalSubstance> *
@@ -2564,8 +2564,8 @@ linkml:Nodeidentifier NONLITERAL
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rdf:type [ <NamedThing> ] ? ;
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&<ExposureEvent_tes> ;
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rdf:type [ <ExposureEvent> ] ? ;
2567-
&<ChemicalOrDrugOrTreatement_tes> ;
2568-
rdf:type [ <ChemicalOrDrugOrTreatement> ] ? ;
2567+
&<ChemicalOrDrugOrTreatment_tes> ;
2568+
rdf:type [ <ChemicalOrDrugOrTreatment> ] ? ;
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<has_drug> @<Drug> * ;
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<has_device> @<Device> * ;
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<has_procedure> @<Procedure> * ;

‎biolink-model.ttl

Lines changed: 183 additions & 184 deletions
Large diffs are not rendered by default.

‎biolink/model.py

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
# Auto generated from biolink-model.yaml by pythongen.py version: 0.9.0
2-
# Generation date: 2021-04-05 18:38
2+
# Generation date: 2021-04-12 17:09
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# Schema: Biolink-Model
44
#
55
# id: https://w3id.org/biolink/biolink-model
@@ -1269,13 +1269,13 @@ def __post_init__(self, *_: List[str], **kwargs: Dict[str, Any]):
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super().__post_init__(**kwargs)
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12711271

1272-
class ChemicalOrDrugOrTreatement(YAMLRoot):
1272+
class ChemicalOrDrugOrTreatment(YAMLRoot):
12731273
_inherited_slots: ClassVar[List[str]] = []
12741274

1275-
class_class_uri: ClassVar[URIRef] = BIOLINK.ChemicalOrDrugOrTreatement
1276-
class_class_curie: ClassVar[str] = "biolink:ChemicalOrDrugOrTreatement"
1277-
class_name: ClassVar[str] = "chemical or drug or treatement"
1278-
class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalOrDrugOrTreatement
1275+
class_class_uri: ClassVar[URIRef] = BIOLINK.ChemicalOrDrugOrTreatment
1276+
class_class_curie: ClassVar[str] = "biolink:ChemicalOrDrugOrTreatment"
1277+
class_name: ClassVar[str] = "chemical or drug or treatment"
1278+
class_model_uri: ClassVar[URIRef] = BIOLINK.ChemicalOrDrugOrTreatment
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@dataclass

‎context.jsonld

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
{
2-
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-04-05 18:38\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
2+
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-04-12 17:09\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
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"@context": {
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"APO": {
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"@id": "http://purl.obolibrary.org/obo/APO_",

‎contextn.jsonld

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,5 +1,5 @@
11
{
2-
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-04-05 18:38\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
2+
"_comments": "Auto generated from biolink-model.yaml by jsonldcontextgen.py version: 0.1.1\n Generation date: 2021-04-12 17:09\n Schema: Biolink-Model\n \n id: https://w3id.org/biolink/biolink-model\n description: Entity and association taxonomy and datamodel for life-sciences data\n license: https://creativecommons.org/publicdomain/zero/1.0/\n ",
33
"@context": {
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"APO": {
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"@id": "http://purl.obolibrary.org/obo/APO_",

‎graphviz/chemical_or_drug_or_treatment.gv

Lines changed: 8 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,8 @@
1+
digraph {
2+
graph [bb="0,0,302.87,36"];
3+
node [label="\N"];
4+
"chemical or drug or treatment" [height=0.5,
5+
label="chemical or drug or treatment",
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pos="151.44,18",
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width=4.2066];
8+
}

‎graphviz/chemical_or_drug_or_treatment.svg

Lines changed: 19 additions & 0 deletions
Loading

‎graphviz/drug.gv

Lines changed: 55 additions & 55 deletions
Original file line numberDiff line numberDiff line change
@@ -1,151 +1,151 @@
11
digraph {
2-
graph [bb="0,0,2260.5,123"];
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graph [bb="0,0,2248.5,123"];
33
node [label="\N"];
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drug [height=0.5,
55
label=drug,
6-
pos="1163.1,105",
6+
pos="1151.1,105",
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width=0.9027];
88
"molecular entity" [height=0.5,
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pos="87.092,18",
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width=2.4192];
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drug -> "molecular entity" [label=is_a,
12-
lp="396.09,61.5",
13-
pos="e,146.12,31.257 1130.6,103.94 1023.5,103.45 671.29,99.468 382.09,69 304.2,60.794 215.73,44.91 156.16,33.238"];
12+
lp="394.09,61.5",
13+
pos="e,145.99,31.298 1118.3,103.93 1011.6,103.41 664.89,99.326 380.09,69 302.84,60.774 215.13,44.933 155.97,33.277"];
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mixture [height=0.5,
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pos="240.09,18",
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width=1.3179];
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drug -> mixture [label=uses,
18-
lp="525.59,61.5",
19-
pos="e,274.48,30.476 1130.5,104.01 1015.4,103.51 617.81,97.17 297.09,36 292.93,35.206 288.63,34.229 284.35,33.148"];
20-
"chemical or drug or treatement" [height=0.5,
21-
pos="463.09,18",
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width=4.3691];
23-
drug -> "chemical or drug or treatement" [label=uses,
24-
lp="835.59,61.5",
25-
pos="e,554.06,32.751 1131.3,101.17 1070.5,95.68 933.81,82.887 819.09,69 733.02,58.581 635.53,44.746 564.36,34.271"];
18+
lp="522.59,61.5",
19+
pos="e,274.48,30.463 1118.6,103.98 1004.6,103.35 612.96,96.63 297.09,36 292.93,35.201 288.63,34.22 284.36,33.138"];
20+
"chemical or drug or treatment" [height=0.5,
21+
pos="457.09,18",
22+
width=4.2066];
23+
drug -> "chemical or drug or treatment" [label=uses,
24+
lp="823.59,61.5",
25+
pos="e,545.43,32.629 1119.3,101.2 1058.5,95.747 921.8,83.023 807.09,69 722.02,58.6 625.62,44.67 555.57,34.154"];
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"ontology class" [height=0.5,
27-
pos="715.09,18",
27+
pos="703.09,18",
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width=2.1304];
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drug -> "ontology class" [label=uses,
30-
lp="941.59,61.5",
31-
pos="e,764.05,31.944 1131.4,100.23 1085.6,94.6 998.51,83.11 925.09,69 873.64,59.112 815.76,45.113 773.82,34.442"];
30+
lp="929.59,61.5",
31+
pos="e,752.05,31.944 1119.4,100.23 1073.6,94.6 986.51,83.11 913.09,69 861.64,59.112 803.76,45.113 761.82,34.442"];
3232
id [color=blue,
3333
height=0.5,
3434
label=string,
35-
pos="848.09,18",
35+
pos="836.09,18",
3636
width=1.0652];
3737
drug -> id [color=blue,
3838
label=id,
39-
lp="1020.1,61.5",
40-
pos="e,877.14,29.766 1133.6,97.418 1084.1,86.167 981.45,61.927 896.09,36 893,35.062 889.82,34.046 886.63,32.993",
39+
lp="1008.1,61.5",
40+
pos="e,865.14,29.766 1121.6,97.418 1072.1,86.167 969.45,61.927 884.09,36 881,35.062 877.82,34.046 874.63,32.993",
4141
style=solid];
4242
iri [color=blue,
4343
height=0.5,
4444
label="iri type",
45-
pos="949.09,18",
45+
pos="937.09,18",
4646
width=1.2277];
4747
drug -> iri [color=blue,
4848
label=iri,
49-
lp="1077.1,61.5",
50-
pos="e,979.84,31.211 1137.3,93.747 1100.5,79.133 1032.6,52.179 989.24,34.945",
49+
lp="1065.1,61.5",
50+
pos="e,967.84,31.211 1125.3,93.747 1088.5,79.133 1020.6,52.179 977.24,34.945",
5151
style=solid];
5252
type [color=blue,
5353
height=0.5,
5454
label=string,
55-
pos="1050.1,18",
55+
pos="1038.1,18",
5656
width=1.0652];
5757
drug -> type [color=blue,
5858
label=type,
59-
lp="1130.1,61.5",
60-
pos="e,1069.6,33.696 1144.7,90.154 1126.5,76.51 1098.6,55.491 1077.8,39.83",
59+
lp="1118.1,61.5",
60+
pos="e,1057.6,33.696 1132.7,90.154 1114.5,76.51 1086.6,55.491 1065.8,39.83",
6161
style=solid];
6262
name [color=blue,
6363
height=0.5,
6464
label="label type",
65-
pos="1163.1,18",
65+
pos="1151.1,18",
6666
width=1.5707];
6767
drug -> name [color=blue,
6868
label=name,
69-
lp="1183.1,61.5",
70-
pos="e,1163.1,36.175 1163.1,86.799 1163.1,75.163 1163.1,59.548 1163.1,46.237",
69+
lp="1171.1,61.5",
70+
pos="e,1151.1,36.175 1151.1,86.799 1151.1,75.163 1151.1,59.548 1151.1,46.237",
7171
style=solid];
7272
description [color=blue,
7373
height=0.5,
7474
label="narrative text",
75-
pos="1313.1,18",
75+
pos="1301.1,18",
7676
width=2.0943];
7777
drug -> description [color=blue,
7878
label=description,
79-
lp="1287.6,61.5",
80-
pos="e,1285.1,34.852 1184.9,91.64 1208.8,78.096 1247.6,56.137 1276.2,39.903",
79+
lp="1275.6,61.5",
80+
pos="e,1273.1,34.852 1172.9,91.64 1196.8,78.096 1235.6,56.137 1264.2,39.903",
8181
style=solid];
8282
source [color=blue,
8383
height=0.5,
8484
label="label type",
85-
pos="1463.1,18",
85+
pos="1451.1,18",
8686
width=1.5707];
8787
drug -> source [color=blue,
8888
label=source,
89-
lp="1401.1,61.5",
90-
pos="e,1432,33.16 1187.5,92.716 1192.8,90.555 1198.6,88.501 1204.1,87 1259.5,71.877 1276.5,83.333 1332.1,69 1363.2,60.975 1397.1,47.916 \
91-
1422.6,37.156",
89+
lp="1389.1,61.5",
90+
pos="e,1420,33.16 1175.5,92.716 1180.8,90.555 1186.6,88.501 1192.1,87 1247.5,71.877 1264.5,83.333 1320.1,69 1351.2,60.975 1385.1,47.916 \
91+
1410.6,37.156",
9292
style=solid];
9393
"provided by" [color=blue,
9494
height=0.5,
9595
label=agent,
96-
pos="1575.1,18",
96+
pos="1563.1,18",
9797
width=1.0291];
9898
drug -> "provided by" [color=blue,
9999
label="provided by",
100-
lp="1524.6,61.5",
101-
pos="e,1546.4,29.767 1187,92.64 1192.5,90.427 1198.4,88.372 1204.1,87 1301.6,63.5 1330.8,88.86 1429.1,69 1475,59.735 1484.9,51.448 1529.1,\
102-
36 1531.6,35.109 1534.3,34.177 1536.9,33.229",
100+
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101+
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102+
36 1519.6,35.109 1522.3,34.177 1524.9,33.229",
103103
style=solid];
104104
"has attribute" [color=blue,
105105
height=0.5,
106106
label=attribute,
107-
pos="1682.1,18",
107+
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108108
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109109
drug -> "has attribute" [color=blue,
110110
label="has attribute",
111-
lp="1660.1,61.5",
112-
pos="e,1656.6,33.804 1186.9,92.51 1192.4,90.304 1198.4,88.284 1204.1,87 1363.4,51.197 1412.3,107.2 1571.1,69 1597.9,62.54 1626.3,49.648 \
113-
1647.6,38.574",
111+
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112+
pos="e,1644.6,33.804 1174.9,92.51 1180.4,90.304 1186.4,88.284 1192.1,87 1351.4,51.197 1400.3,107.2 1559.1,69 1585.9,62.54 1614.3,49.648 \
113+
1635.6,38.574",
114114
style=solid];
115115
category [height=0.5,
116-
pos="1803.1,18",
116+
pos="1791.1,18",
117117
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118118
drug -> category [color=blue,
119119
label=category,
120-
lp="1780.6,61.5",
121-
pos="e,1781.6,34.403 1186.9,92.452 1192.4,90.249 1198.4,88.245 1204.1,87 1314.3,63.028 1602.3,98.707 1711.1,69 1733.2,62.963 1755.8,50.752 \
122-
1773.1,39.909",
120+
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121+
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122+
1761.1,39.909",
123123
style=solid];
124124
"in taxon" [color=blue,
125125
height=0.5,
126126
label="organism taxon",
127-
pos="1956.1,18",
127+
pos="1944.1,18",
128128
width=2.3109];
129129
drug -> "in taxon" [color=blue,
130130
label="in taxon",
131-
lp="1901.1,61.5",
132-
pos="e,1922.1,34.533 1186.9,92.426 1192.4,90.225 1198.4,88.228 1204.1,87 1337.1,58.473 1682.4,94.19 1816.1,69 1849.6,62.695 1885.7,49.608 \
133-
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131+
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132+
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133+
1900.9,38.403",
134134
style=solid];
135135
"has constituent" [color=blue,
136136
height=0.5,
137137
label="chemical substance",
138-
pos="2159.1,18",
138+
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139139
width=2.8164];
140140
drug -> "has constituent" [color=blue,
141141
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142-
lp="2077.6,61.5",
143-
pos="e,2107.3,33.515 1186.9,92.406 1192.4,90.206 1198.4,88.214 1204.1,87 1362.8,53.355 1773,88.693 1934.1,69 1990,62.16 2052.5,47.711 \
144-
2097.4,36.097",
142+
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143+
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144+
2085.4,36.097",
145145
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146146
"named thing_category" [color=blue,
147147
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148148
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149-
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149+
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150150
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151151
}

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