Advanced Search Manual
Created on 2023/11/07, Revised on 2024/05/01

1About Advanced Search• https://knowledge.brc.riken.jp/advanced• Features of Advanced Search• Allows selection of search keywords while confirming theontology hierarchy (e.g., diseases) to search for relatedbioresources.
• Enables search by category. Currently, categories include genes,
literature (PubMed ID), viruses (virus name, viral infection name,biological process, related molecules, anatomical site, case).
Users can enter or select search keywords for each category.
• During the search process, users can confirm the number of hit
bioresources and proceed with the search.
• Users can combine multiple search conditions (OR search, AND
search) with some limitations.

• Contact for inquiries about issues• E-mail: brcqa@brc.riken.jp• Questionnaire page: https://krs2.riken.jp/m/questionnaire_en• FAX: +81-29-836-9077

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Future Tasks (Including Functions Under
Development)• Display of data sources and search paths that support search
results.
• Implementation of NOT search.
• Addition of ontology data (ontology search). Example: Human
Phenotype Ontology (HPO).

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Screen Description
Keyword input window (e.g., RBRC06342, APOE)

Search condition buttons

Figure 1. There are two main methods of searching in Advanced Search.
1. Searching from the keyword input window (effective for free word searches,e.g., RBRC06342, APOE).
2. Searching by selecting search condition buttons (effective when narrowing
down search by ontology terms, gene names, literature, virus categories).

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Search Methods• Basic Operation 1: Keyword Search• Basic Operation 2: Ontology Search• Basic Operation 3: Gene Search• Basic Operation 4: Literature Search• Basic Operation 5: Virus Search• Applied Operation 1: AND/OR Search• Applied Operation 2: Combining Multiple Search
Conditions

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Basic Operation 1: Keyword Search 1/5

Search box

Figure 2. Enter the search term in the search box. When entering a term with four or morecharacters, candidate terms are displayed. Select a candidate term or press the enter key
without selecting to start the search. For search terms with three characters or less, add ahalf-width space at the end of the search term before selecting a candidate word or pressing
the enter key to start the search.

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Basic Operation 1: Keyword Search 2/5
The search results are displayed byresource type.

bioresource number (ID)Figure 3a. The search results are displayed by resource types, namely
mouse, plant, cell, and microbe. Selecting the desired bioresource
number (ID) will display individual resource pages.

7Basic Operation 1: Keyword Search 3/5

To start a new search, click "x"on the Set Filters.

Figure 3b. To start a new search, click "x" on the Set Filters to delete theprevious search term, then enter a new search term to start the search. To add asearch term to the previous search, enter the search term in the search window
without clicking "x".

8Basic Operation 1: Keyword Search 4/5

Enter the first search term (e.g., lung)

Figure 4a. In the advanced search (current version), search terms
separated by spaces are treated as phrases (e.g., lung cancer). To performan AND search with multiple search terms (e.g., lung AND cancer), enter9
the first search term (e.g., lung) and press the enter key.

Basic Operation 1: Keyword Search 5/5

Next, enter the next search term (e.g., cancer)

The conditions of the AND search can be
confirmed under "Set Filter."Figure 4b. After entering the next search term (e.g., cancer), press
the enter key to perform an AND search (e.g., lung AND cancer). The
conditions of the AND search can be confirmed under "Set Filter" below
the input window. Note that OR search is not supported.

10Basic Operation 2: Ontology Search 1/7

Ontology Search button

Figure 5. Select the Ontology button.
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Basic Operation 2: Ontology Search 2/7

Currently, there are 9 types of
ontologies available for search.

Figure 6. Pressing the Ontology button opens the ontology searchwindow. Currently, there are 9 types of ontologies available forsearch.

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Basic Operation 2: Ontology Search 3/7
Candidate terms are displayed whenentering a search term with four ormore characters.

Figure 7. Enter the search term in the input window of the ontology search window.
Similar to Basic Operation 1, candidate terms are displayed when entering a searchterm with four or more characters. Select a candidate term to start the search. For
search terms with three characters or less, add a space at the end to display
candidate terms. Note that in ontology search, you cannot start a search without
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selecting a candidate term.

Basic Operation 2: Ontology Search 4/7

Check the ontology term you want to search for

The superclass panel displays theupper terms you want to search for.
The subclass panel displays
the lower terms you want tosearch for.
Click the OK button

Figure 8. Check the ontology term you want to search for and click
the OK button at the bottom of the screen.

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Basic Operation 2: Ontology Search 5/7
The search results are displayed byresource type.

To start a new search, click "x" on
the Set Filters.

Figure 9. The search results are displayed by the number of hits foreach type of bioresource: experimental animals, plants, cells, genematerials, and microbes.

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Basic Operation 2: Ontology Search 6/7

Put search term in the
Current term panel

Click the arrow button to move thesearch term to the Current term panel.

Figure 10. To search for terms in the upper or lower hierarchy of theterm (e.g., Alzheimer disease) in the central panel (Current term panel),click the arrow button to move the term to the Current term panel.

16Basic Operation 2: Ontology Search 7/7

Move "familial Alzheimer disease” in the
Subclass panel to the Current term panel.

By checking "familial Alzheimer
disease", you can search for
related bioresources.

Figure 11. Check the term you want to search for (e.g., familial
Alzheimer disease) and click the OK button at the bottom of the screen.

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Basic Operation 3: Gene Search 1/7

Gene search button

Figure 12. Select the Gene search button.
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Basic Operation 3: Gene Search 2/7

遺伝⼦名（ラベル，例，APP, TP53）を⼊⼒
Enter the gene label (APP, TP53)

Figure 13. Enter the gene (protein) name or ID in the input field.
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Basic Operation 3: Gene Search 3/7

Check the gene name to search for.

Figure 14. Select the gene name to search for. Multiple checks may beavailable, resulting in an OR search.
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Basic Operation 3: Gene Search 4/7
Clicking on this marker at the
top right of the window will
display selected gene labels.

Click the OK button

Figure 15. Click the OK button to display the search results.
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Basic Operation 3: Gene Search 5/7
Select the bioresource you want to display.

Search condition will be displayed here.

Figure 16. Select the bioresource (mouse, plant, cell, gene,microbe) you want to display.

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Basic Operation 3: Gene Search 6/7

Paralog box

Figure 17a. Checking the Paralog box next to the input field will display
candidates including genes with an paralogous relationship to the entered
gene.

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Basic Operation 3: Gene Search 7/7

Ortholog box

Figure 17b. Checking the Ortholog box next to the input field will
display candidates including genes with an orthologous relationship tothe entered gene.

24Basic Operation 4: Literature Search 1/3

Article search button

Figure 18. Select the Article search button to display the literaturesearch screen.

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Basic Operation 4: Literature Search 2/3

Enter any keyword or PubMed ID

Select the literature

Click the OK button

Figure 19. Enter any keyword or PubMed ID in the input field, select theliterature from the candidate list, and click the OK button at the bottomof the screen.

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Basic Operation 4: Literature Search 3/3

Select the bioresource you want to search for.

To start a new search, click"x" on the Set Filters.

Figure 20. Select the resource to display the literature list.
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Basic Operation 5: Virus Search 1/3

Virus search button

Figure 21. Select the Virus search button to display the virus
search screen.

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Basic Operation 5: Virus Search 2/3

This suggests that 52 biological resources are
involved in viral attachment to host cells.

Click the OK button

Figure 22. Select categories such as virus name, viral infection name,biological process name (e.g., virion attachment to host cell), biologicalmolecule, anatomical site, symptoms/phenotypes/related diseases.

29Basic Operation 5: Virus Search 3/3
Select the bioresource youwant to search for

Search condition will be displayed here.

Figure 23. Select the bioresource to display the search results.

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 1/10

Select the Ontology
search button

Figure 24. Press the Ontology search button to display the ontology
search screen.

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 2/10

Enter "stomach cancer"

Figure 25. Enter "stomach cancer" in the input field and select stomach
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cancer from the human disease ontology DOID.

Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 3/10

Select stomach cancer

Enter the OK button

Figure 26. Select stomach cancer, click the OK button, and start
the search.

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 4/10
32 mice are found.

Click the "+" button in the
Set Filters to add additional
conditions in the disease
ontology DOID.

Figure 27. 32 mice related to stomach cancer are found. Then, click the"+" button in the Set Filters to add additional conditions in the disease
ontology DOID.

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 5/10

Enter "liver cancer"

Click the OK button

Figure 28. Enter "liver cancer" in the input field.
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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 6/10

Select "liver cancer"

Enter the OK button

Figure 29. Select "liver cancer," click the OK button, anddisplay the results.

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 7/10

63 mice are found.

Set the search condition"stomach cancer OR livercancer".

Figure 30. 63 mice are found under the search condition "stomach cancer
OR liver cancer".

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 8/10

Toggle button to switch the AND/OR
search condition

Figure 31. Switch the search condition to AND search using the toggle
button to display the search results for "stomach cancer AND livercancer".

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 9/10

If you press the Ontology button
without pressing the "+" button
in Set Filters to add a searchterm..

Figure 32. [Note] If you press the Ontology button without pressing the"+" button in Set Filters to add a search term, the following will happen.

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Applied Operation 1: AND/OR Search (e.g., stomach
cancer [AND/OR] liver cancer) 10/10

When adding search terms
within the same ontology,pressing the "+" button allows
selecting between OR and AND
search.

Figure 33. [Note] Only AND search can be performed. When adding
search terms within the same ontology, pressing the "+" button allows
selecting between OR and AND search.

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Applied Operation 2: Combining Multiple Search Conditions(e.g., gene and literature search, APP [AND] Alzheimer) 1/5

Gene search button

Figure 34. Press the Gene search button to display the gene search
screen.

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Applied Operation 2: Combining Multiple Search Conditions(e.g., gene and literature search, APP [AND] Alzheimer) 2/5

Enter "APP"Check the gene symbol to search for.

Click the OK button

Figure 35. Enter "APP" in the input field, check the gene symbol
to search for, and click the OK button.

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Applied Operation 2: Combining Multiple Search Conditions(e.g., gene and literature search, APP [AND] Alzheimer) 3/5

9 mice related to the APP geneare found.

Article search button

Figure 36. 9 mice related to the APP gene are found. Then, press the
Article search button to display the Article search screen.

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Applied Operation 2: Combining Multiple Search Conditions(e.g., gene and literature search, APP [AND] Alzheimer) 4/5

Enter "Alzheimer"

Click the mouse icon tosort in descending order

Check one or more articles

Click the OK button

Figure 37. Enter "Alzheimer" in the input field, click the mouse icon tosort in descending order, check one or more papers, and click the OK
button to display the results.

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Applied Operation 2: Combining Multiple Search Conditions(e.g., gene and literature search, APP [AND] Alzheimer) 5/5

Search conditions

Figure 38. 8 mice were found under the conditions "related to APP gene"and "articles describing Alzheimer's".
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