Last modified by maaike on 2022/07/05 20:42
From version 23.3
edited by maaike
on 2022/06/23 14:06
Change comment: There is no comment for this version
To version 19.1
edited by maaike
on 2022/06/23 11:16
Change comment: There is no comment for this version

Summary

Details

Page properties
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28 28  
29 29  The Knowledge Graph search user inferface is a user-friendly interface for accessing and extracting data and metadata. Use of the Knowledge Graph search is free and most datasets are open to the public. Human datasets with identifiable information can only be accessed with an EBRAINS account.
30 30  
31 -Go to the Search UI: [[https:~~/~~/search.kg.ebrains.eu/>>https://search.kg.ebrains.eu/]]
31 +Go to the Search UI: https:~/~/search.kg.ebrains.eu.
32 32  
33 33  ==== Refine search ====
34 34  
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40 40  
41 41  [[image:SearchStep1-3.png||alt="Steps 1-3: Refine search" height="398" width="700"]]
42 42  
43 -You can refine you search even further by using the free text search. Based on your search criteria, you get a number of hits. ([[https:~~/~~/search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_modalityForFilter[0]=electrophysiology&facet_Dataset_speciesFilter[0]=Mus%20musculus>>https://search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_modalityForFilter[0]=electrophysiology&facet_Dataset_speciesFilter[0]=Mus%20musculus]])
43 +You can refine you search even further by using the free text search. Based on your search criteria, you get a number of hits.
44 44  
45 45  ==== Select a dataset ====
46 46  
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50 50  
51 51  ==== Access detailed metadata ====
52 52  
53 -In the side panel, you can find an overview of the metadata that is available for this dataset ([[https:~~/~~/search.kg.ebrains.eu/instances/7866daf2-7064-4fa0-b6a2-0b1c899ba35f>>https://search.kg.ebrains.eu/instances/7866daf2-7064-4fa0-b6a2-0b1c899ba35f]]). For example:
53 +In the side panel, you can find an overview of the metadata that is available for this dataset. For example:
54 54  
55 55  1. The data descriptor is a pdf text file with detailed information about the dataset, including the methods, technical validation, usage notes and data organisation.
56 56  1. Detailed subject metadata can be found in a separate tab (see below).
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59 59  
60 60  In this dataset, a number of subjects were used with a C57BL/6J (wildtype) genotype. These were 4-9 months old (adult mice) with a weight between 38 - 47 gram. They were tested three times under aneasthesia, which is captured by the "studied states" of the subject. Additional details regarding the tests is stored under additional remarks (currently not visible in the image).
61 61  
62 -= Programmatic access (API) =
62 += Knowledge Graph Query Builder =
63 63  
64 -The EBRAINS Knowledge Graph provides convenient tools and APIs for the implementation of queries into your scripts.
64 += =
65 65  
66 -=== Request permission ===
67 -
68 -To be able to access the Knowledge Graph (KG) programmatically, you require:
69 -
70 -1. An EBRAINS account. Register for an account here: [[https:~~/~~/ebrains.eu/register/>>https://ebrains.eu/register/]]
71 -1. Register and request credentials for your KG client by emailing support@ebrains.eu
72 -
73 -=== Query Builder ===
74 -
75 -The query builder allows you to make, save, and reuse complex queries without any knowledge of graph query languages.
76 -
77 -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]]
78 -
79 -
80 -==== Select a category ====
81 -
82 -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.
83 -
84 -[[image:QB1.png||alt="Step 1: Select a category" height="520" width="700"]]
85 -
86 -
87 -==== Select an experimental approach ====
88 -
89 -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.
90 -
91 -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).
92 -
93 -[[image:QBstep2.png||alt="Step 2: Select modality" height="541" width="700"]]
94 -
95 -
96 -==== Select species ====
97 -
98 -Similarly, we can refine our query for mice only.
99 -
100 -[[image:QBstep3.png||alt="Step 3: Select species" height="543" width="700"]]
101 -
102 102  = Who has access? =
103 103  
104 104  Describe the audience of this collab.
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