BioGuide - example
   

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Example

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Context
   
  Let us consider the following question:
Which information may I get about genetic sleep disorders such as narcolepsy and the genes related to these diseases?
.

In this question the user expresses the need for getting information about the correlation between diseases and sets of genes.

Note: This example uses the BioGuideSRS version.
 
 
First step: express the query
   
  - Select entities:
The user has first to select the two entities in the graph of entities as shown in the figure (double-click on the entities).
- Add a filter for Narcolepsy:
Then she can use the pop-up menu to create a SRS filter (screen capture 1).
She can then specify "narcolepsy" as a keyword to be searched for the Disease entity (screen capture 2).
Consequently, Disease appears in yellow type font (screen capture 3).
 
View screen captures

 
 
Second step: Preferences and strategy
   
  Assume that the user specifies some preference-filters:
  • (i) no more than 3 cross-references must be followed per path,
  • (ii) only very reliable sources should be consulted,
  • (iii) concerning the gene entity, only complete sources should be consulted, and
  • (iv) the EMBLRelease source (the full EMBL source) should not be considered.
- (i) Filter on path length:
  • Use the Filters menu (screen capture 1), select the item Filter on path length
  • Enter the limits for path length: number of cross-references must lay between 1 and 3 (screen capture 2)
- (ii) Limit queries to very reliable sources:
  • Use the Filters menu (screen capture 1), select the item Sources-Entities filters
  • The user wants to use only sources with a reliability preference value lying between 7 and 10; regardless of the entity queried.
    Thus she will use the Global filter slider, which will automatically set the filter value for all entities queried. (screen capture 3).
- (iii) Force a good completeness for sources providing gene data:
  • In the same window as the one used for the previous step; the user can select the tab Completeness
  • She wants to force a good completeness for the entity Gene only, thus she will use the Gene slider (screen capture 4) to set the completeness interval as [4, 10].
    Note: She could then use the red cross (on the right) to reset this filter to the general filter.
- (iv)  Exclude the source EMBLRelease for the result paths:
  • First of all the user has to visualize the sources providing Gene data, thus she will click on the Gene entity in the entities graph (left-hand side of the main window)
  • Then she can exclude EMBLRelease_Gene by using a right click on this source, and choosing the menu item Exclude/Include.
    -> The source will then appear grey-color and struck out (screen capture 5)

View screen capturess

 
 
Last step: Run the query
   
  - Run the query:
Run the query with the button .
- Understand the results:
As a result, BioGuideSRS provides five paths as five alternative ways to get data.
The results are ordered according to the user's preferences (screen capture 1)

- From BioGuide paths to SRS data instances:
For each path the corresponding instances of data can be accessed by clicking on the "View in SRS" link. The screen capture 2 shows the results obtained for the first path.

View screen capturess

 
 

 

 

 

 


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Laboratoire de Recherche en Informatique, University of Pennsylvania

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