Version 6.1 by maaike on 2022/06/23 16:33
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maaike 1.1 1 == Programmatic access (API) ==
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3 The EBRAINS Knowledge Graph provides convenient tools and APIs for the implementation of queries into your scripts.
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5 **Request permission**
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7 To be able to access the Knowledge Graph (KG) programmatically, you require:
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9 1. An EBRAINS account. Register for an account here: [[https:~~/~~/ebrains.eu/register/>>https://ebrains.eu/register/]]
10 1. Register and request credentials for your KG client by emailing support@ebrains.eu
11
12 === Query Builder ===
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14 The query builder allows you to make, save, and reuse complex queries without any knowledge of graph query languages.
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16 Go to the Query Builder: [[https:~~/~~/query.kg.ebrains.eu>>https://query.kg.ebrains.eu/#state=6a41dd5b-3cf9-4263-8a65-83d41f27677a&session_state=638c33f5-4551-4d70-8b1d-a5c900aa62d0&code=300f25d8-caac-4576-9a21-195ccc93fd31.638c33f5-4551-4d70-8b1d-a5c900aa62d0.4214dba9-b6d0-4331-9837-3e75a10cda14]]
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18 ==== Select a category ====
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20 A query for the Knowledge Graph is always executed against a specific data structure (e.g. a "Dataset version"). First select the data structure for your query.
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22 [[image:QB1.png||alt="Step 1: Select a category" height="520" width="700"]]
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24 ==== Select an experimental approach ====
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26 Similar to the facetted filters in the Knowledge Graph Search UI, we can refine our query by defining the experimental approach of our interest, for example electrophysiology.
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28 To ensure that all dataset versions with electrophysiology are queried, and none of the dataset versions without electrophysiology, we make this property required and we apply a filter to the label we are searching for (i.e. electrophysiology).
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30 [[image:QBstep2.png||alt="Step 2: Select modality" height="541" width="700"]]
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32 ==== Select species ====
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34 Similarly, we can refine our query for mice only.
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36 [[image:QBstep3.png||alt="Step 3: Select species" height="543" width="700"]]
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maaike 5.2 38
maaike 1.1 39 ==== Access detailed metadata ====
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maaike 5.2 41 (% class="wikigeneratedid" id="H" %)
42 Following
maaike 1.1 43
maaike 5.2 44 ==== [[image:QB4.png||alt="Step 4: Access detailed metadata" height="432" width="700"]] ====
maaike 1.1 45
maaike 5.2 46 ==== ====
47
48 The above query in the Query Builder is written below:
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maaike 1.1 50 {{code language="python"}}
maaike 5.2 51 {
52 "@context": {
53 "@vocab": "https://core.kg.ebrains.eu/vocab/query/",
54 "query": "https://schema.hbp.eu/myQuery/",
55 "propertyName": {
56 "@id": "propertyName",
57 "@type": "@id"
58 },
59 "path": {
60 "@id": "path",
61 "@type": "@id"
62 }
63 },
64 "meta": {
65 "type": "https://openminds.ebrains.eu/core/DatasetVersion",
66 "responseVocab": "https://schema.hbp.eu/myQuery/"
67 },
68 "structure": [
69 {
70 "propertyName": "query:experimentalApproach",
71 "path": "https://openminds.ebrains.eu/vocab/experimentalApproach",
72 "required": true,
73 "structure": {
74 "propertyName": "query:name",
75 "path": "https://openminds.ebrains.eu/vocab/name",
76 "required": true,
77 "filter": {
78 "op": "CONTAINS",
79 "value": "electrophysiology"
80 }
81 }
82 },
83 {
84 "propertyName": "query:studiedSpecimen",
85 "path": "https://openminds.ebrains.eu/vocab/studiedSpecimen",
86 "structure": [
87 {
88 "propertyName": "query:species",
89 "path": "https://openminds.ebrains.eu/vocab/species",
90 "required": true,
91 "structure": [
92 {
93 "propertyName": "query:name",
94 "path": "https://openminds.ebrains.eu/vocab/name"
95 },
96 {
97 "propertyName": "query:species",
98 "path": "https://openminds.ebrains.eu/vocab/species",
99 "required": true,
100 "structure": {
101 "propertyName": "query:name",
102 "path": "https://openminds.ebrains.eu/vocab/name",
103 "required": true,
104 "filter": {
105 "op": "CONTAINS",
106 "value": "mus musculus"
107 }
108 }
109 }
110 ]
111 },
112 {
113 "propertyName": "query:lookupLabel",
114 "path": "https://openminds.ebrains.eu/vocab/lookupLabel"
115 },
116 {
117 "propertyName": "query:biologicalSex",
118 "path": "https://openminds.ebrains.eu/vocab/biologicalSex",
119 "structure": {
120 "propertyName": "query:name",
121 "path": "https://openminds.ebrains.eu/vocab/name",
122 "required": true,
123 "filter": {
124 "op": "CONTAINS",
125 "value": "male"
126 }
127 }
128 },
129 {
130 "propertyName": "query:studiedState",
131 "path": "https://openminds.ebrains.eu/vocab/studiedState",
132 "structure": [
133 {
134 "propertyName": "query:lookupLabel",
135 "path": "https://openminds.ebrains.eu/vocab/lookupLabel"
136 },
137 {
138 "propertyName": "query:age",
139 "path": "https://openminds.ebrains.eu/vocab/age",
140 "structure": [
141 {
142 "propertyName": "query:value",
143 "path": "https://openminds.ebrains.eu/vocab/value"
144 },
145 {
146 "propertyName": "query:unit",
147 "path": "https://openminds.ebrains.eu/vocab/unit",
148 "structure": {
149 "propertyName": "query:name",
150 "path": "https://openminds.ebrains.eu/vocab/name"
151 }
152 }
153 ]
154 },
155 {
156 "propertyName": "query:ageCategory",
157 "path": "https://openminds.ebrains.eu/vocab/ageCategory",
158 "structure": {
159 "propertyName": "query:name",
160 "path": "https://openminds.ebrains.eu/vocab/name"
161 }
162 },
163 {
164 "propertyName": "query:attribute",
165 "path": "https://openminds.ebrains.eu/vocab/attribute",
166 "structure": {
167 "propertyName": "query:name",
168 "path": "https://openminds.ebrains.eu/vocab/name"
169 }
170 }
171 ]
172 }
173 ]
174 }
175 ]
176 }
maaike 1.1 177 {{/code}}
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