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  • HumanData.png
  • SoftwareSearch.png

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1		-XWiki.oschmid
	1	+XWiki.maaike

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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	+[[Log in to your EBRAINS account and try running the examples yourself!>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/Practical%20Guide%20to%20Using%20the%20EBRAINS%20Knowledge%20Graph%20in%20(your)%20Research%20-%20User%20Examples/query.ipynb]]
	10	+
9	9	=== Example 1 - How many datasets used human subjects? ===
10	10
11	11	==== **Search UI** ====
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12	12
13	13	In the filter function, select "Homo Sapiens" under species. This filters the available datasets in the Knowledge Graph for human subjects only.
14	14
15		-[[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]]
	17	+[[[[image:HumanData.png]]>>https://search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_speciesFilter[0]=Homo%20sapien&category=Dataset&species[0]=Homo%20sapiens]]
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	19	+[[https:~~/~~/search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_speciesFilter[0]=Homo%20sapien&category=Dataset&species[0]=Homo%20sapiens>>https://search.kg.ebrains.eu/?facet_type[0]=Dataset&facet_Dataset_speciesFilter[0]=Homo%20sapien&category=Dataset&species[0]=Homo%20sapiens]]
	20	+
17	17	==== **Query Builder** ====
18	18
19	19	To search for datasets containing human subjects only, you can first declare the id (to get the involved instances) as well as a link to the "studied specimen" (you can add a type filter and restrict it to "Subject" and "Subject group" only since we are not interested in "Tissue samples" and "Tissue sample collections" in this moment). From "studied specimen", we're interested in the "Species" (here you can - again add a type filter to exclude "Strain" since this is irrelevant for human subjects). For the "Species", we want the "label" to contain "homo sapiens" which is why we add a filter "contains" with the value "homo sapiens".  We might want to simplify the deeply nested structure by "flattening" both, the "Studied specimen" as well as the "Species". Once we go to the "execute query" section (the play button on the left) and we run the query, we can see the total number of dataset versions.
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80	80
81	81	==== **Search UI** ====
82	82
83		-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.
	87	+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. When searching for "male adult" subjects in the search UI, we find datasets that have these keywords in any of the text summarised on the dataset card (it is a 'fuzzy search' : [[https:~~/~~/search.kg.ebrains.eu/?category=Dataset&q=male%20and%20adult>>https://search.kg.ebrains.eu/?category=Dataset&q=male%20and%20adult]]). To ensure we only look for the any specimen (subjects or samples) originating from male adult mice, we need to write a query and extract the metadata programmatically.
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85	85	==== **Query Builder** ====
86	86
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295	295
296	296	==== **Search UI** ====
297	297
	302	+To find software that can open a particular file format like the Spike2 file format (.smr), we can select the category "software" and then filter based on "input format". We select "application/vnd.spike2.sonpy.son" to ensure we only get software for this file format.
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	304	+[[[[image:SoftwareSearch.png||alt="Software Search"]]>>https://search.kg.ebrains.eu/?category=Software&inputFormats[0]=application%2Fvnd.spike2.sonpy.so]]
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299	299	[[https:~~/~~/search.kg.ebrains.eu/?category=Software&inputFormats[0]=application%2Fvnd.spike2.sonpy.son>>https://search.kg.ebrains.eu/?category=Software&inputFormats[0]=application%2Fvnd.spike2.sonpy.son]]
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301	301
302	302	==== **Query Builder** ====
303	303
	311	+For this question, we will execute the query against the "softwareVersion data structure. We ask for the name, version and input type of the software. We further refine our query by restricting the result to software that can open files with the file extension ".smr". We get the same 3 software types as in the search, and we immediately see that one of the software types has multiple versions that can open this kind of files.
	312	+
304	304	{{code language="json" layout="LINENUMBERS"}}
305	305	{
306	306	"@context": {

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