1. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
CHCDB & CHCDBWEB
Clinical Annotation Database and web interface
Thomas Burguiere
INSERM Unit´e 674
May 5th, 2011
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 1 / 35

2. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
1 Introduction
2 Relational Database
Principle
Benefits
Interface
3 Clinical Annotation data
Specificities
E.A.V.
4 CHCDB
5 CHCDBWEB
6 Conclusions
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 2 / 35

3. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
• 1500 liver tumor samples
• Malignant (HCC) and benign (HCA) tumors
• Normal Tissue
Existing Data
• Clinical Annotations of malignant tumors (4D)
• Excel files which contains :
• Clinical Annotations of malignant & benign tumors
• Other annotations (mutations, clinical studies, etc.)
• Tissue extractions listings (concentrations / quantities)
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 4 / 35

4. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Existing Data
• Clinical Annotations of malignant tumors (4D)
• Excel files which contains :
• Clinical Annotations of malignant & benign tumors
• Other annotations (mutations, clinical studies, etc.)
• Tissue extractions listings (concentrations / quantities)
Problems
• Clinical Annotations of malignant tumours can only be accessed on
single machine
• Redundant data among di↵erent files
• Duplicated files on di↵erent machines
,! Discrepancies between di↵erent files
,! Cross-checking data between the di↵erent data source is cumbersome
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 5 / 35

5. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
1 Introduction
2 Relational Database
Principle
Benefits
Interface
3 Clinical Annotation data
Specificities
E.A.V.
4 CHCDB
5 CHCDBWEB
6 Conclusions
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 6 / 35

6. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Principle
Relational Database : Software
• Relational Database Management System : software which contains
and organizes data (OracleTM
, MySQL, DB2TM
, SQL ServerTM
, etc.)
• Client Server architecture :
• Server software, which manages data, installed on a single machine
• Client software, which queries the server, installed on any machine used to
consult the database
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 7 / 35

7. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Principle
Client Server architecture
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 8 / 35

8. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Principle
Relational Database : Data
• The data is stored in a set of tables
• One can define a set of constraints regarding the data contained in
the tables
• The tables can be associated to one another by logical links : integrity
constraints
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 9 / 35

9. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Principle
Relational Database : Example
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Classical table (e.g. Excel sheet)
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 10 / 35

10. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Principle
Relational Database : Example
1 Breaking down
data
2 Typing
constraints
3 Unicity
constraints
4 Integrity
constraints
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8'*!"'* 9:&
9:&;<<=,': (=<'&8'*!"'*
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 11 / 35

11. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Benefits
Relational Database : Benefits
• Data centralisation on the server side
• Constraints allow, in some instances, to avoid data inconsistencies
,! Consistent data
• E cient : tables containing millions of rows can be easily manipulated
• Querying a correctly structured database allows one to cross-check
data very rapidly*
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 12 / 35

12. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Interface
A database requires graphical interface
• Data manipulation in a database is done exclusively with queries,
written in SQL (Structured Query Language)
•
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• SELECT t a b l e 1 . t i s s u e I D , t a b l e 1 . TumorType ,
t a b l e 1 . Sex , t a b l e 1 . Age , t a b l e 2 . S t e a t o s i s ,
t a b l e 2 . nb adenomas , t a b l e 2 .CRP
FROM t a b l e 1 INNER JOIN t a b l e 2
ON ( t a b l e 1 . t i s s u e I D = t a b l e 2 . t i s s u e I D )
WHERE t a b l e 1 . TissueID = ’CHC358T ’ ;
• Powerful language, albeit counterintuitive
,! A graphical interface must be associated to the database
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 13 / 35

13. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Interface
Graphical interface : principle
Mecanism
1 The interface receives instruction from the user, and transform them
into SQL queries sent to the server
2 The server receives the SQL queries, and sends back results
3 The interface receives the results from the server, and displays the
results to the user
Interface types
• 2 types of interface : desktop program or web interface
• In our case, we decided to develop a web interface
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 14 / 35

14. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Interface
Web interface
• Software installed on a single machine : the web server
• Accessing the interface only requires a web browser
,! Avoids installation and maintenance issues on the client machines
,! Avoids OS compatibility issues (Mac, Windows, Linux, etc. . .)
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 15 / 35

15. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Interface
Web client / server architecture
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 16 / 35

16. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
1 Introduction
2 Relational Database
Principle
Benefits
Interface
3 Clinical Annotation data
Specificities
E.A.V.
4 CHCDB
5 CHCDBWEB
6 Conclusions
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 17 / 35

17. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Specificities
Specific features of clinical annotation data
Specificities
• New variables are
frequently added
• Data regarding the same
variable can be input
di↵erently, depending of
sample provenance and
type (malignant or
benign tumor)
Consequences in a database
• Frequent addition of new
columns or sub-tables
• Tables contain a lot of columns,
with sparsely filled rows
,! Constant maintenance of the
database
Clinical annotation data must be stored in a specific database structure :
the E.A.V. structure
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 18 / 35

18. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
E.A.V.
Principle
• E.A.V. = Entity Attribute Value[?]
• An E.A.V. is a subset of tables in a relational database, with a
specific organization
• This data organization is particularly suitable of clinical annotation
data
• In the E.A.V., all clinical annotation data is stored in one 3-columns
table :
• Entity : contains the identifier of the entity for which an annotation is
stored (In our case, an entity is a tissue)
• Attribute : contains the identifier (e.g. the name) of the annotation variable
• Value : contains the value of the annotation, for a given entity
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 19 / 35

19. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
E.A.V.
Example
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!"!#$%& &012 - .3.
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 20 / 35

20. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
E.A.V.
Example
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256789
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?@AB>;9
?@AB>;9
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 20 / 35

21. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
E.A.V.
Example
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Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 20 / 35

22. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
E.A.V.
Pros & Cons
Pros
• New annotation = New line in
the table
• No structural modifications
• No sparsely filled tables
Cons
• A lot of lines in the table
• Very complex queries
• Columns are no longer typed
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Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 21 / 35

23. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
E.A.V.
Metadata
• Loosing
information
regarding variable
data types is
problematic
,! This data is
stored in an
ancillary table,
the metadata
table
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Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 22 / 35

24. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
1 Introduction
2 Relational Database
Principle
Benefits
Interface
3 Clinical Annotation data
Specificities
E.A.V.
4 CHCDB
5 CHCDBWEB
6 Conclusions
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 23 / 35

25. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
CHCDB
Software
• R.D.B.M.S. : MySQL
• Open source & free
• Most widely used open-source R.D.B.M.S.
,! Actively maintained
,! Lots of maintenance and development tools
• The machine hosting the R.D.B.M.S. has yet to be bought
Data
• CHCDB’s tables fall into one of three categories
• Tissue listings
• Clinical annotation data, in the E.A.V. structure
• Extraction data
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 24 / 35

26. Database structure

27. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
1 Introduction
2 Relational Database
Principle
Benefits
Interface
3 Clinical Annotation data
Specificities
E.A.V.
4 CHCDB
5 CHCDBWEB
6 Conclusions
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 26 / 35

28. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
A web interface
Peculiarities
• Installed on the server hosting the R.D.B.M.S.
• Can be reached from any machine on the CEPH network
Features
• Consultation and modificationof clinical annotations for a given tissue
• Listing of tissues and their annotations
• Listing of tissue extractions
• Management (add/modify/delete) of annotation variables
• Batch import of annotations
• Batch import of extraction data
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 27 / 35

29. Consultation & modification of the annotations of a given
tissue

30. Consultation & modification of the annotations of a given
tissue

31. Listing of tissues and annotations

32. Listing of tissue extractions

33. Annotation variables management

34. Annotation variables management

35. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
1 Introduction
2 Relational Database
Principle
Benefits
Interface
3 Clinical Annotation data
Specificities
E.A.V.
4 CHCDB
5 CHCDBWEB
6 Conclusions
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 33 / 35

36. Introduction Relational Database Clinical Annotation data CHCDB CHCDBWEB Conclusions
Missing features in CHCDBWEB
• The tissue management interface is not yet complete
• The batch import interface for annotations and extraction is missing
CHCDB
• Defining a starting set of variables
• Importing existing data into CHCDB
Material
• Acquiring a configuring the machine which will host the database and
the web server
CHCDB and CHCDBWEB should enter production phase in June 2011.
Thomas Burguiere (INSERM Unit´e 674) CHCDB & CHCDBWEB May 5th, 2011 34 / 35