User Manual for Dragon Exploratory System on Hepatitis C Virus
(DESHCV)
Section A
A typical user query interface showing the various utility components. DESHCV is free for academic and non-profit users via http://apps.sanbi.ac.za/DESHCV/ and its mirror site http://cbrc.kaust.edu.sa/deshcv/
Figure 1. DESHCV user Interface
1. For Abstract and Concept queries
[For further details consult sections B, C and D of this manual]
2. Help
Click on help menu for detailed explanations of concepts and help manual on DESHCV usage.
Section B: Abstract query
Figure 2. Displays the simplified abstract query interface A typical Analysis Flow
Type any keyword for example: hypervariability -> check abstract radio button -> click on search -> a display of PubMed abstracts with tagged colour-coded concepts
Section C: Concept query
Figure 3. Displays the simplified concept query interface A typical Analysis Flow
Type any concept name for example: “F protein” -> check concept radio button -> click on search -> a graphical display of colour-coded concept
Concept Search Output and Analysis Flow
Figure 4. Textual display of concept search output
1. Concept query term “F protein”
2. Type: F protein -> click on either display as dictionary or table -> click on concepts search button ->concept lists output
Note: do not re-type F protein if it has been queried already (this is an illustration)
3. Lists of the various color-coded concepts assigned to their respective dictionaries. Users can retrieve cross-referenced annotations by clicking on any of the concepts.
Green: Human proteins and genes Light pink: Metabolites and enzymes Blue: Pathways
Yellow: Chemicals with Pharmacological effects Purple: Diseases concepts
4. Visualization
Network generator: click on draw network -> generates a network of interconnected concepts
Hypothesis Generator: click on show hypothesis -> generates correlated concepts in a graphical format as hypothesis
Download: click on table download -> retrieves a list of concepts in a CSV format Interactive Association Map
Figure 5. Graphical display of interacting concepts
5. Association Map Analysis flow
Click on any of the specified dictionaries (For example: metabolites and enzymes) -> click on draw graph -> redraws the graph with the newly defined concepts.
Buttons
Ignore links less than: enable the user to display the network according to the number of links.
Paper size: enables the user to resize the map by choosing from a range of A0 to A5. Details [%]: enable the user to enhance the visualization clarity by varying the detail slider.
6. Indicates the number of occurrences of the selected concept in PubMed abstracts. Clicking on the link retrieves the related PubMed abstracts.
Note: The network consist of proposed correlations and the user is required to manually verify the abstract to either reject or accept the suggested association
Hypothesis Generator
Generate implicit relationships between disjunct literatures associated with concepts. This proposed hypothesis must be manually verified by consulting the linked PubMed abstracts
Figure 6. Graphical display of generated hypothesis
7. Buttons:
Frequency Sort: enable users to sort the generated hypothesis according to the frequency of occurrence of the concepts.
Name Sort: enable users to retrieve the generated hypothesis in an alphabetical order. Graph: enables users to visualize the generated hypothesis in an interactive map Text: displays the hypothesis in a textual format
Manual Test: by checking on this button, users are required to manually verify the abstract to ascertain the veracity of the proposed hypothesis.
Auto test: automatically verifies the abstracts to ascertain whether the proposed
8. This drop down menu enables users to select dictionaries and associated concepts with which to generate the hypothesis. This concept is known as the linking term since it links the starting and the targets terms respectively.
According to Figure 6:
Starting term: F protein belongs to the human proteins and genes dictionary Linking term: Hepatocellular Carcinoma belongs to the disease dictionary Target term: Any Concept in the pharmacological chemicals dictionary
9. Click on Get hypothesis -> generates hypothesis according to specified dictionary concepts
10. Allow browsing of hypothesis by page
11. Displays the number of PubMed abstracts reporting the association
12. Indicate whether the displayed correlation has been reported
Not confirmed: Hypothesis has not been reported which could mean a novel discovery Found: 68, means 68 abstracts have reported the hypothesis
Section D: Simulated concept query examples 1. Concept query: “Thalidomide”
Figure 7. A screenshot montage of thalidomide concept query. This displays both the
2. Thalidomide-Chronic Hepatitis C Association
Generate concept query for “thalidomide” -> Click on Get hypothesis -> generates hypothesis -> Specify the dictionaries as indicated in figure 8 and re-generate hypothesis. -> Click on the linked abstract to verify the hypothesis. -> Explore results for potential novel insights.
Figure 8. A screenshot montage showing thalidomide-chronic hepatitis C hypothesis. This displays the implicit relationship existing between the two concepts. The red arrow linking the hypothesis and PubMed abstract displays the verification of the hypothesis. The yellow dash lines and the white question mark sign displays the implicit relationship existing between the two concepts.
3. Thalidomide-Amantadine Association
Generate concept query for “thalidomide” -> Click on Get hypothesis -> generates hypothesis -> Specify the dictionaries as indicated in figure 9 and re-generate hypothesis. -> Explore results for potential novel insights.
Appendix II (Chapter 2)
Frequently asked questions (FAQ)
1. What is DESHCV?
Dragon Exploratory System on Hepatitis C Virus (DESHCV) is the first reported comprehensive Hepatitis C Virus (HCV) customized biomedical text-mining based online web resource. A list of abstracts retrieved via PubMed database using specific keywords searches related to HCV were processed based on concept recognition of concepts from several dictionaries. It is a tool with the potential to assist in discovering associations between biomedical concepts and could lead to new research focus and possible novel discoveries.
2. What are the benefits of using DESHCV?
The web query interface enables retrieval of information using specified concepts, keywords and phrases, generating text-derived association networks and hypotheses which could be tested to identify potentially novel relationship between different concepts.
3. Which dictionaries can be retrieved from DESHCV?
Biomedical concepts related to HCV are retrieved from the following dictionaries: "Human genes and proteins", "Metabolites and Enzymes", "Pathways", "Chemicals with pharmacological effects", and "Disease concepts".
4. What makes DESHCV unique?
DESHCV contains pre-compiled dictionaries enriched with biomedical concepts pertaining to HCV proteins, their name variants and symbols to make it suitable for targeted information exploration and knowledge extraction as focused on HCV.
5. Can I download the query results retrieved from the DESHCV?
Yes, you can download the concept list and pair list spreadsheet. And also the user has the option of downloading the retrieved table of concepts for further analysis. The user may right-click on the images or figures generated to download.
6. Are there any limitations in the usage of DESHCV?
Yes, associations generated between paired concepts are inferred from co-occurrences and may not necessarily relate to any molecular functionality. Users are required to manually confirm the text accompanying the hypothesis to either accept or reject the suggested hypothesis.
7. Are there any future updates or modification in the pipeline?
Yes, we would like to integrate Blast and identifier queries to enhance querying capabilities of DESHCV. The possibility of integrating full text document is currently being explored and could be added to the database as a separate feature. The database would be updated every six months to meet the demands of ever increasing PubMed records related to HCV
8. Is there a help manual on DESHCV?
Yes, a help manual has been developed to ease the exploration of this database and can be accessed by clicking the help menu on index page (http://apps.sanbi.ac.za/DESHCV/) or via http://apps.sanbi.ac.za/DESHCV/help.pdf/.
9. To whom can I report a bug or discrepancy? Please refer all queries via:
http://apps.sanbi.ac.za/DESHCV/Contact.php