User Documentation for BeeSpace Navigator Version 3
Login page
Users of the BeeSpace Navigator must log in to use the resource. Registration is available to anyone who would like to manage their own data store within the Navigator. A ‘Guest’ login is available for anyone who would like to try out the system without registering.
Figure: The BeeSpace Navigator v. 3 Login Page
Core Functions
Browse Space
The user may select a Space and click ‘Browse’ to view the Space. The user is shown a list of documents that comprise a Space, with the most relevant documents listed first.
Figure: Selecting a Space to browse.
Figure: Browsing a Space.
Browse Region in Space
The user may describe a Region of interest in the Space and click ‘Browse’ to view the Subspace most relevant to their described Region.
Figure: Describing a Region (‘foraging gene’) and browsing it in the Bee Space.
The user is shown a list of documents that comprise the Region, with the most relevant documents listed first. In this example, browsing ‘foraging gene’ within the Bee Space yielded 3407 documents, down from the 24062 documents in the entire Bee Space.
Figure: Browsing the user-specified ‘foraging gene’ Region within the Bee Space.
Within a Browse Results page, holding the mouse pointer over the name of the Space shows header information about the Region being viewed, as well as how many documents were found relevant in the selected Space
Figure: Mousing over the name of the Space shows header information.
Gene annotation
The Annotate function takes a user-provided list of gene IDs and uses a text-mining approach to find the most representative concepts from it, relative to the background Space that was selected. The three screens below show user choosing an already-created gene list to provide to the Annotate function, and then running the function to annotate the gene list.
Figure: Clicking ‘Manage’ to access the ‘Region Manager’ screen.
Figure: Within the Region Manager, choosing a gene list (previously saved by a user as a Region) to provide to the Annotate function.
Figure: Running the Annotate function on a list of genes.
The Gene Annotation Results page provides multiple ways of filtering and sorting the returned concepts. ‘Filter Genes’ allows one to include or exclude gene names from the result set. ‘Filter Phrases’ allows one to include or exclude multi-word descriptive phrases from the result set. ‘Sort By’ allows one to select sorting by Significance (the likelihood ratio score of the concept) (default), Ratio (proportion of genes in the input list that the concept is associated with), or Concept (an alphabetized listing).
Figure: Gene Annotation Results.
Gene summarization
The Summarization function uses a text mining approach to provide a Flybase-like summarization of the user-provided genes. This function currently operates on gene names, such as “SHH” or “juvenile hormone”.
Figure: Running the Summarize function on a gene name (‘jh’) in the Honey Bee Space.
The Gene Summarization function displays a list of sentences found relevant for the gene, categorized by Gene Product (GP), Expression Location (EL), Sequence Information (SI), Wild-Type Function & Phenotypic Information (WFPI), Mutant Phenotype (MP), and Genetical Interaction (GI).
Figure: Gene Summary of ‘jh’ from the Honey Bee Space.
Browsing functions
View
The View function displays the documents with the Region words highlighted in light blue, and ‘found’ genes highlighted in light green.‘Found’ refers to genes recognized by a Named Entity Recognition program
Figure: Viewing a Region in BeeSpace. (‘Check all’ was selected, then ‘View’).
Figure: Viewed documents with user’s Region words in blue, and ‘found’ genes in green.
Save
Users can save spaces that they find relevant, to their own personalized data store. The default Label, which includes a timestamp, also be changed by the user to a more meaningful label. The user can also create a Description in addition to Label.
Figure: Saving a Space relevant to a user’s personalized data store.
Figure: Giving the newly created Space a Description to aid later reference.
Map/map2/build (mapping functions)
The mapping functions split the Space into coherent subspaces. ‘Map’ takes a partitioning approach to splitting the Space into subspaces, while ‘Map2’ uses a hierarchical merging approach to constructing subspaces. The ‘Build’ function utilizes user-specified input in constructing the subspaces.
Figure: Generating a map
Figure: Saving a Space relevant to a user’s personalized data store
Figure: Viewing the Subspace. Mousing over the Region description will display the full list of words comprising the Region.
Extract
Figure: Selecting the ‘Extract’ function.
‘Extract’ extracts out the primary Region from this Space. The extracted theme is immediately saved into the user’s data store, and the user is taken to the Region Manager page, which enables editing and annotating the extracted Region.
Figure: Extracting, editing, and updating the Region.
Figure: Result of extracting, editing and updating the Region
Space management functions
Edit/delete/browse
When editing information about a Space, the user may provide a Label (the default includes a timestamp) and Description. The Space Manager also provides functions for browsing a Space and deleting a Space.
Figure: Editing information about a Space in the Space Manager.
Figure: Result of editing Space information in the Space Manager.
Merge
The ‘Intersect,’ ‘Union,’ and ‘Difference’ Merge functions provide Boolean set operations (AND, OR, NOT) over spaces. The ‘Top’ function provides a way of selecting the top documents in a Space, constructing a new Space from the most relevant documents in the selected Space. The ‘Limit’ box provides a mechanism for controlling the number of results generated from the operation. The default Limit is currently 100,000 documents.
Figure: Selecting ‘Manipulate Spaces’ from the Space Manager, to bring up the Space Merge screen.
Figure: The Space Merge screen provides set operations over spaces.
Intersect
‘Intersect’ generates a new Space that contains documents found in both the input spaces.
Figure: Selecting the ‘Intersect’ merge function.
Figure: Creation of new Space as the result of running the ‘Intersect’ merge function.
Figure: Saving of an ‘Intersect’ Space with a meaningful Label and Description.
Union
‘Union’ generates a new Space that contains documents found from either input Space.
Figure: Selecting the ‘Union’ merge function.
Figure: The saved Space resulting from operation of the ‘Union’ merge function (after user has provided a meaningful Label and Description).
Difference
‘Difference’ generates a new Space that contains documents found in input Space 1 that are not in input Space 2.
Figure: Selecting the ‘Difference’ merge function.
Figure: The saved Space resulting from operation of the ‘Difference’ merge function (after user has provided a meaningful Label and Description).
Top
‘Top’ generates a new Space from the most significant N documents from the input Space, where N is specified in the ‘Limit’ box.
Figure: Selecting the ‘Top’ merge function and specifying a Limit of 100 documents.
Figure: Saving of a ‘Top’ Space with a meaningful Label and Description.
Figure: The saved Space resulting from operation of the ‘Difference’ merge function (after user has provided a meaningful Label and Description).
Region management functions
Region management functions are accessible from the “Manage” link, next to “Describe Region:” on the main screen. The “Manage” link takes the user to the “Region Manager” screen, where a list of the user’s regions is displayed. The user can select an existing Region, and Edit, Delete, or Use it.
Figure: Click ‘Manage’ next to the “Describe Region:” label to go to the Region Manager screen.
Edit/delete/use
Editing a Region
A user may edit the Label, Description, and content of a selected Region.
Figure: Selecting ‘Edit’ in the Region Manager.
Figure: Using the ‘Edit’ feature to update the Label and Description of a Region.
Figure: After updating, the Region has an informative Label and Description.
Deleting a Region
‘Delete’ may be used for removing a Region from the user’s personal data store.
Figure: Using ‘Delete’ to remove a selected Region in the Region Manager.
Using a Region
To Use a Region, the user selects the Region’s radio button and clicks ‘Use.’ This brings up the Navigator’s main window, populated with the contents of the selected Region. From the main window, the user can choose a Space to navigate using the Region, and an action to apply (Browse, Annotate, or Summarize).
Figure: Selecting a Region and clicking ‘Use’ to load it into the main Navigator window.
Figure: The Region selected by the user is loaded into the main Navigator window.
Merge
The Region Merge functions are accessible by clicking the “Manipulate Regions” link in the Region Manager. Within the Region Merge screen, the user chooses two Regions to merge, chooses a Space on which to cast the merged regions, and chooses a function. The ‘Intersect,’ ‘Union,’ and ‘Difference’ functions provide the standard Boolean query operations of AND, OR, and NOT. The default limit is currently 100,000 documents.
Figure: Clicking ‘Manipulate Regions’ accesses the Region Merge functions.
Figure: Choosing Regions, a Space, and a function on the Region Merge screen.
Intersect
‘Intersect’ generates a new Region that contains documents found in both input Regions (Boolean AND).
Figure: Running the ‘Intersect’ function on two chosen regions over the Fly Space.
Figure: Browsing results of the Intersect function.
Union
‘Union’ generates a new Region that contains documents found from either input Region (Boolean OR).
Figure: Running the ‘Union’ function on two chosen regions over the Fly Space.
Figure: Browsing results of the ‘Union’ function.
Difference
‘Difference’ generates a new Region that contains documents found in either input Region but not in both (Boolean NOT).
Figure: Running the ‘Difference’ function on two chosen regions over the Fly Space.
Figure: Browsing results of the ‘Difference’ function.
Build
The ‘Build’ function utilizes user-specified input in extracting Subspaces from an input Space. The Region Builder screen [[why not Subspace Builder?? - jb]] is accessed from the Region Manager, by clicking the link labeled “Build Regions.”
Figure: Selecting ‘Build Regions’ from the Region Manager.
Within the Region Builder screen, the user may specify up to six Regions to map into a Space.
Figure: The Region Builder screen with Space for up to six user-provided regions.
Figure: Region Builder with four regions provided by the user, operating on the Social Behavior Space.
After entering terms for each Region and choosing a Space, the user clicks the “Map” button to build the Region. This returns a screen displaying subspaces built from the user-provided Regions.
Figure: Map of subspaces built from the user-provided regions on the Social Behavior Space.
Clicking on the line for any Subspace will return a listing of documents in the Subspace. The Subspace can be saved as a Region (set of terms) or a Space (set of documents). From this Subspace screen, Space functions (Save, Map, Map2, Build, Extract) can be applied to the Subspace, and individual documents or sets of documents can be Viewed.
Figure: A bee-related Subspace from the Map.