Changes for page 3 Try it yourself!

Last modified by maaike on 2022/07/06 10:08
From version 1.1
edited by maaike
on 2022/06/27 11:22
Change comment: There is no comment for this version
To version 2.3
edited by maaike
on 2022/06/28 10:10
Change comment: There is no comment for this version

Summary

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Content
... ... @@ -6,24 +6,163 @@
6 6  1. Find datasets that contain NIfTI files
7 7  1. Find the software that can be used to open .smr file formats?
8 8  
9 -=== ===
9 +=== ===
10 10  
11 11  ==== Example 1 - How many datasets used human subjects? ====
12 12  
13 -Search UI
13 +**Search UI**
14 14  
15 15  In the filter function, select "Homo Sapiens" under species. This filters the available datasets in the Knowledge Graph for human subjects only.
16 16  
17 17  [[https:~~/~~/search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_speciesFilter[0]=Homo%20sapiens>>https://search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_speciesFilter[0]=Homo%20sapiens]]
18 18  
19 -Query Builder
19 +**Query Builder**
20 20  
21 +
22 +==== Example 2 - Find datasets with male adult subjects ====
23 +
24 +**Search UI**
25 +
26 +All the metadata in the knowledge graph is represented by nodes and their relationships by the edges. Most of the "basic" metadata is visualised in the Search UI to make it easy for the user to find datasets that fit certain criteria without needing to know how to navigate and traverse a graph structure.
27 +
28 +**Query Builder**
29 +
21 21  {{code language="python"}}
22 -x = 1
23 -if x == 1:
24 - # indented four spaces
25 - print("x is 1.")
31 +query = {
32 + "@context": {
33 + "@vocab": "https://core.kg.ebrains.eu/vocab/query/",
34 + "query": "https://schema.hbp.eu/myQuery/",
35 + "propertyName": {
36 + "@id": "propertyName",
37 + "@type": "@id"
38 + },
39 + "path": {
40 + "@id": "path",
41 + "@type": "@id"
42 + }
43 + },
44 + "meta": {
45 + "type": "https://openminds.ebrains.eu/core/DatasetVersion",
46 + "responseVocab": "https://schema.hbp.eu/myQuery/"
47 + },
48 + "structure": [
49 + {
50 + "propertyName": "query:id",
51 + "path": "@id"
52 + },
53 + {
54 + "propertyName": "query:shortName",
55 + "path": "https://openminds.ebrains.eu/vocab/shortName"
56 + },
57 + {
58 + "propertyName": "query:studiedSpecimen",
59 + "path": "https://openminds.ebrains.eu/vocab/studiedSpecimen",
60 + "required": true,
61 + "structure": [
62 + {
63 + "propertyName": "query:id",
64 + "path": "@id"
65 + },
66 + {
67 + "propertyName": "query:biologicalSex",
68 + "path": "https://openminds.ebrains.eu/vocab/biologicalSex",
69 + "required": true,
70 + "structure": {
71 + "propertyName": "query:name",
72 + "path": "https://openminds.ebrains.eu/vocab/name",
73 + "required": true,
74 + "filter": {
75 + "op": "EQUALS",
76 + "value": "male"
77 + }
78 + }
79 + },
80 + {
81 + "propertyName": "query:studiedState",
82 + "path": "https://openminds.ebrains.eu/vocab/studiedState",
83 + "required": true,
84 + "structure": {
85 + "propertyName": "query:ageCategory",
86 + "path": "https://openminds.ebrains.eu/vocab/ageCategory",
87 + "required": true,
88 + "structure": {
89 + "propertyName": "query:name",
90 + "path": "https://openminds.ebrains.eu/vocab/name",
91 + "required": true,
92 + "filter": {
93 + "op": "EQUALS",
94 + "value": "adult"
95 + }
96 + }
97 + }
98 + }
99 + ]
100 + }
101 + ]
102 +}
26 26  {{/code}}
27 27  
28 -(% class="wikigeneratedid" id="HH4Won27tAppearinToC" %)
29 -
105 +==== Example 3 - Find datasets that contain NIfTI files ====
106 +
107 +**Search UI**
108 +
109 +Files are organised based on their file format (i.e. file extension) and the software that could be used to open these files. In openMINDS this is captured with the content type. In the filter function, select "application/vnd.nifti.1" under content types to select all the dataset with a NIfTI 1 file format.
110 +
111 +[[[[image:ContentTypes.png]]>>https://search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_contentTypes[0]=application%2Fvnd.nifti.1]]
112 +
113 +[[https:~~/~~/search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_contentTypes[0]=application%2Fvnd.nifti.1>>https://search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_contentTypes[0]=application%2Fvnd.nifti.1]]
114 +
115 +**Query Builder**
116 +
117 +{{code language="python"}}
118 +query = {
119 + "@context": {
120 + "@vocab": "https://core.kg.ebrains.eu/vocab/query/",
121 + "query": "https://schema.hbp.eu/myQuery/",
122 + "propertyName": {
123 + "@id": "propertyName",
124 + "@type": "@id"
125 + },
126 + "path": {
127 + "@id": "path",
128 + "@type": "@id"
129 + }
130 + },
131 + "meta": {
132 + "type": "https://openminds.ebrains.eu/core/DatasetVersion",
133 + "responseVocab": "https://schema.hbp.eu/myQuery/"
134 + },
135 + "structure": [
136 + {
137 + "propertyName": "query:shortName",
138 + "path": "https://openminds.ebrains.eu/vocab/shortName"
139 + },
140 + {
141 + "propertyName": "query:id",
142 + "path": "@id"
143 + },
144 + {
145 + "propertyName": "query:repository",
146 + "path": "https://openminds.ebrains.eu/vocab/repository",
147 + "required": true,
148 + "structure": {
149 + "propertyName": "query:fileRepository",
150 + "path": {
151 + "@id": "https://openminds.ebrains.eu/vocab/fileRepository",
152 + "reverse": true
153 + },
154 + "required": true,
155 + "structure": {
156 + "propertyName": "query:name",
157 + "path": "https://openminds.ebrains.eu/vocab/name",
158 + "required": true,
159 + "filter": {
160 + "op": "ENDS_WITH",
161 + "value": ".nii.gz"
162 + }
163 + }
164 + }
165 + }
166 + ]
167 +}
168 +{{/code}}
ContentTypes.png
Author
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1 +XWiki.maaike
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1 +120.6 KB
Content