Draft 1, BeeSpace Navigator V. 3.5 User Documentation
Brant Chee and Jim Buell, 11/7/07, p. 1 of 36
User Documentation for BeeSpace Navigator Version
3.5
(Draft Version)
CONTENTS
[Click on a line to jump to the section]
Conceptual Overview of BeeSpace Navigator 3.5 ............................................................. 2
Navigator v. 3.5 Screen Shots and Function Descriptions.................................................. 4
Login page .......................................................................................................................... 4
Getting Started: The main BeeSpace Navigator screen .................................................. 5
Core Functions .................................................................................................................... 7
Concept Browse of a Space ............................................................................................ 7
Concept Browse of a Region in Space ............................................................................ 8
The Gene functions: Find, Annotate, and Summarize .................................................. 10
‘Finding’ a gene ........................................................................................................ 10
Annotating a gene ..................................................................................................... 11
Summarizing a gene .................................................................................................. 14
Browsing functions ........................................................................................................... 15
View .............................................................................................................................. 15
Save ............................................................................................................................... 16
Steerable Map/Natural Map/Build (mapping functions) .............................................. 18
Extract ........................................................................................................................... 20
Space management functions ............................................................................................ 22
Edit/delete/browse......................................................................................................... 22
Merge ............................................................................................................................ 23
Intersect ..................................................................................................................... 23
Union......................................................................................................................... 24
Difference ................................................................................................................. 25
Top ............................................................................................................................ 26
Region management functions .......................................................................................... 27
Use/Edit/Delete ............................................................................................................. 28
Editing a Region ....................................................................................................... 28
Deleting a Region ..................................................................................................... 28
Using a Region .......................................................................................................... 29
Merge ............................................................................................................................ 30
Intersect ..................................................................................................................... 31
Union......................................................................................................................... 32
Difference ................................................................................................................. 33
Build .............................................................................................................................. 33
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Conceptual Overview of BeeSpace Navigator 3.5
The BeeSpace Navigator is a next-generation tool for helping research scientists search
and save online collections of biological literature. It is being developed by the BeeSpace
Project at the University of Illinois, with five-year funding (2004-2009) from the
National Science Foundation. The latest version of the BeeSpace Navigator, v. 3.5, offers
unique functionality for Concept Navigation and Gene Navigation within and across data
stores of biological literature.
Our core users are biological scientists seeking a better way to explore and manage the
professional literatures of their own and related fields of study. In the genomic age,
scientists who specialize in a particular species are increasingly required to navigate the
literatures of other organisms, for instance to seek insights about how the same genetic
sequences might serve different but related functions in different species. The BeeSpace
Navigator is being developed with direct assistance from honey bee genomics researchers
affiliated with the laboratory of Gene Robinson, a co-investigator on the project.
Additional users of our prototype are bee scientists affiliated with other bee laboratories
around the world, and researchers exploring the genomics of other organisms at the
University of Illinois’ Institute for Genomic Biology and elsewhere around the world.
BeeSpace Navigator is built around the metaphor of "Search Spaces." A Space is a
collection of article abstracts and metadata from the scientific literature having a
particular focus. The Navigator software is set up with several Spaces that are of primary
interest to different scholarly communities. Users of the software can easily generate
additional Spaces and share them with other members of the user community. Prespecified 'System' Spaces exist for several organisms including bee, bird, fruit fly, fish,
mosquito, wasp, and yeast. There are also pre-specified System Spaces for crossorganism constructs such as plant genetics, maturation, and social behavior. An
additional System Space includes all 17 million literature records from the Medline
PubMed collection. Users can construct their own unique Spaces as well, by casting their
own search terms, or “Region” definitions, across an existing Space.
Running on a high-speed server computer operated by our Project, the BeeSpace software
uses best-of-breed text-mining algorithms to navigate through these Spaces on the fly, in
order to find and highlight literature that has special relevance to users' particular
information needs. The software offers two main function sets: Browse functions, which
operate across article abstracts in a general fashion, and Gene functions, which optimize
navigation to highlight gene-related information from literature.
The Browse functions provide an overview of the literature contained in a Space; a user
may Browse an entire space, or may specify Region key words to restrict or re-order the
literature contained in a Space. The Browse functions are View, Steerable Map, Natural
Map, Build, Extract, and Save. The 'View' function brings up a list of search results
similar to one that a traditional search-engine search would generate, but operates only on
the documents within a particular Space rather than across an entire universe of
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documents. Besides 'View,' the Browse functions include 'Save', three Mapping functions
(called Steerable Map, Natural Map, and Build), and 'Extract'. 'Save' enables users to save
Spaces they find relevant, to their own personal data store. Each of the Mapping
functions splits the Space into coherent subspaces: ‘Steerable Map’ takes a partitioning
approach, while 'Natural Map' takes a hierarchical merging approach, and 'Build' utilizes
user-specified input in constructing the subspaces. We encourage our users to try out and
become familiar with all three Mapping functions, as one approach might work better
than another for meeting their information needs on a particular occasion. 'Extract'
identifies the primary Region (set of search terms) from a particular Space; the extracted
theme is immediately saved into the user's data store, available for potential use in
subsequent Concept Navigation.
The Gene functions of BeeSpace Navigator use text-mining algorithms that are optimized
to highlight gene-related information from literature. To use these Gene functions, a user
selects a Space and types the name of one or more genes in the Region text area, then
clicks either the ‘Find,’ ‘Annotate,’ or ‘Summarize’ button. ‘Find’ is similar to the
Browse View function but utilizes query expansion to retrieve article abstracts that are
most relevant to the user-specified gene. ‘Annotate’ takes a user-provided list of
GenBank gene IDs and uses a text-mining approach to find the most representative
concepts from it. ‘Summarize’ uses a text-mining approach to build a summary
description for a particular gene, out of multiple article abstracts.
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Navigator v. 3.5 Screen Shots and Function Descriptions
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. 3.5 Login Page. Users may log in as ‘guest’ or may
register to create a private login and password.
Figure: Registering to create a unique user login.
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Figure: Logging in with your own username and password.
Getting Started: The main BeeSpace Navigator screen
To use the Navigator, begin by choosing a Space to operate on. Optionally, you may also
type search terms into the “Describe Region” text area, to guide navigation of the space
you choose. You then click one of the “Choose Action” buttons to run the navigation.
Figure: The main BeeSpace Navigator screen.
The main areas of functionality are “Choose Space,” “Describe Region,” and “Choose
Action.” “Choose Space” provides a pulldown menu where the user can select a
particular Space, or literature collection, upon which to perform Navigator operations.
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Individual users’ Spaces and general System Spaces are available. The “Manage” link
leads to a screen where the user can manipulate Spaces.
Figure: The “Choose Space” section of the main BeeSpace Navigator screen.
“Describe Region” provides a text area in which the user can type a set of search terms to
guide navigation of the selected Space. This may be left blank if the user wishes to
navigate through the entire Space. The “Manage” link leads to a screen where the user
can manipulate Regions.
Figure: The “Describe Region” section of the main BeeSpace Navigator screen.
“Choose Action” provides buttons that link to the various Concept Browse functions and
to the individual Gene functions (Find, Annotate, and Summarize).
Figure: the “Choose Action” section of the main BeeSpace Navigator screen.
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Core Functions
Concept Browse of a 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.
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Concept Browse of a 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 ‘juvenile hormone’ within the Apis
mellifera Space yielded 2112 documents, down from the 12144 documents in the entire
Apis mellifera Space.
Figure: Browsing the user-specified ‘foraging gene’ Region within the Apis mellifera
Space.
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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.
The “Switch Space” section of the Browse Results screen enables the user to cast the
Region of interest (“juvenile hormone,” in this example) across another Space, e.g.
Drosophila melanogaster instead of Apis mellifera.
Figure: The “Switch Space” section of the Browse Results screen.
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The Gene functions: Find, Annotate, and Summarize
‘Finding’ a gene
The purpose of the Gene functions is to bring up documents within a Space that contain
information about genes and proteins. Algorithms tuned for finding gene-related
information are built into the Gene functions ‘Find,’ ‘Annotate,’ and ‘Summarize.’ Each
of these functions is triggered by a button on the main screen of the BeeSpace Navigator
interface. ‘Find’ operates similarly to the Concept Browse function, but performs gene
synonym expansion before executing the query. In some instances, the results of
‘Browse’ and ‘Find’ will vary little if at all; in others, they may be quite different.
A Concept Browse of the Region term “eag” within the Drosophila Space, for instance,
brings up 118 matching articles.
Figure: Concept Browse of “eag” within Drosophila Space.
On the other hand, a Gene Find for the Region term “eag” within the Drosophila Space
brings up 306 matching articles.
Figure: Gene Find of “eag” within Drosophila Space.
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Using the gene Find feature can be especially useful when the Region term of interest
happens to be an especially common word in the English language. For example, “for”
can denote the foraging gene in both Drosophila melanogaster and Apis mellifera.
However, “for” is such a common word in English that it is desirable to specifically
exclude it from general searches. Thus, a Concept Browse of the term “for” in the Apis
mellifera Space brings up no articles at all.
Figure: Concept Browse of “for” within Apis mellifera Space.
However, a Gene Find of the term “for” in the Apis mellifera Space brings up 1402
matching records.
Figure: Gene Find of “for” within Apis mellifera Space.
Annotating a gene
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 a user choosing an already created
gene list to provide to the Annotate function, and then running the function to annotate
the gene list.
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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.
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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.
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Summarizing a gene
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: Summarizing a gene.
In this example, the Gene Summarize function has constructed a summary for the gene
“for” in Drosophila melanogaster. The 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: Result of Gene Summary of “for” in Drosophila melanogaster Space.
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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 Apis mellifera Space. (‘Check all’ was selected, then
‘View’).
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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.
Figure: Saving a Space relevant to a user’s 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. The Space
may be saved for the user’s private use, or shared with others through selecting the
“Shared?” checkbox.
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Figure: Giving the newly created Space a Description to aid later reference.
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Steerable Map/Natural Map/Build (mapping functions)
The mapping functions split the Space into coherent subspaces. ‘Steerable Map’ takes a
deep clustering approach to splitting the Space into subspaces, while ‘Natural Map’ uses
a shallow clustering approach to constructing subspaces. The ‘Build’ function utilizes
user-specified input in constructing the subspaces.
Figure: Generating a Steerable Map of the “juvenile hormone” Region in Apis
mellifera Space
Figure: A Steerable Map of the “juvenile hormone” Region of the Apis mellifera Space
identifying six Subspaces.
Figure: Viewing the Subspace. Mousing over the Region description will display the
full list of words comprising the Region.
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Natural Map creates an alternative mapping of the searched Space, through application of
a different search algorithm. A Natural Map of our “juvenile hormone Apis mellifera”
Space identifies 36 subspaces (the top 12 of which appear in the screenshot below).
Figure: Natural Map of subspaces.
The ‘Build’ mapping function permits the user to provide terms that will be used to direct
a Steerable Mapping of the information Space. In this example, a Steerable Map of the
“juvenile hormone Apis mellifera” Space is being organized around three regions:
worker, queen, and drone.
Figure: Region Builder, with which user can guide the Steerable Map clustering.
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The Build function constructs a Steerable Map of the information Space, with the
uppermost Subspaces organized around the user’s specified Region definitions (worker,
queen, and drone in this example).
Figure: Result of Building a Steerable Map of the Apis mellifera Space, using
‘worker,’ ‘queen,’ and ‘drone’ as top three regions.
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.
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Figure: Extracting, editing, and updating the Region.
Generating a Region list of terms with the Extract function brings up a Region Manager
screen, where buttons enable the user to Use the Region in a new query, Edit details of a
Region, or Delete a Region. The Region Manager screen also links to features for
Manipulating Regions and Building Regions.
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Space management functions
As explained above, Spaces are the specialized collections of literature that the BeeSpace
Navigator’s various Browse and Gene functions operate upon, and Regions are sets of
user-provided search terms that are used to generate Spaces. The BeeSpace Navigator’s
System Spaces – which themselves are generated from searches of the PubMed and
Biosis biological literature databases. To create additional Spaces, users cast Region
definitions across existing Spaces and save the custom-generated collection as a new
Space. The BeeSpace Navigator’s User functions allow for managing both Spaces and
Regions.
When beginning a new session, users of the BeeSpace Navigator may choose to Log In
under their own names, or using the generic “guest” login. The username selected for the
session determines the default User for the Space Manager and Region Manager screens;
through Switch User pull-down menu on each Manager screen, users may access other
users’ shared Spaces and Regions of other users.
From the initial Space Control screen, the Space Manager is accessed by clicking the link
labeled ‘Manage,’ next to the “Choose Space” area of the screen.
Figure: Accessing the Space Manager.
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.
The Space Manager looks like this. Its key features are a ‘Switch User’ pull-down menu,
a ‘Save’ area for new Spaces (with an option to share the space with others or not),
buttons for ‘Use,’ ‘Browse,’ ‘Edit,’ and ‘Delete’ of existing Spaces, the option to
Manipulate Spaces by merging them with others, and an area for Displaying Spaces of
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the selected user (as determined initially at session login, and within this screen by use of
the ‘Switch User’ pull-down menu).
Figure: The Space Manager.
Merge
Clicking on the link labeled “Manipulate Spaces” brings up the ‘Space Merge’ functions.
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: The Space Merge screen provides set operations over spaces.
Intersect
‘Intersect’ generates a new Space that contains documents found in both the input spaces.
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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.
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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.
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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.
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Figure: Saving of a ‘Top’ Space with 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.
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Use/Edit/Delete
Editing a Region
A user may edit the Label, Description, and content of a selected Region, and may select
whether the Region is to be shared with other BeeSpace Navigator users or kept private.
Figure: Selecting ‘Edit’ in the Region Manager.
Figure: Using the ‘Edit’ feature to update the Label and Description of a Region.
Deleting a Region
‘Delete’ may be used for removing a Region from the user’s personal data store.
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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.
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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.
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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 Apis mellifera
Space.
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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.
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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 is accessed from the Region Manager, by clicking the
link labeled “Build Regions.”
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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.
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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 “Steerable
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).
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From this Subspace screen, Space functions (Save, Steerable Map, Natural Map, 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.