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A generic online database for clinical data collec1on
Marc Bonin Department of Rheumatology and Clinical Immunology Charité University Hospital Charitéplatz 1 D-‐10117 Berlin Germany Tel: +49(0) 30 450 513 296 Fax: +49(0) 30 450 513 968 E-‐Mail: [email protected] Web: www.charite-‐bioinformaXk.de
Contacts:
Background and Objec1ve: Materials and Methods:
Results:
Conclusion:
www.charite-‐bioinformaXk.de
Programming was based on a web framework in Ruby on Rails. SQLite was used as database system. The complete so^ware package is running on a Linux or Mac OSX, which acts as a normal server.
With the new so^ware, users can generate in a standard browser tables by defining the names of rows and columns and enter a type of data corresponding to each field of the table. The possible data types include funcXon, images, files, string, numbers, dates, enumeraXon with the possibility of adding default values to each of them. (Fig. 1) The interface is divided into administraXve work for creaXng or deleXng the tables, rows and columns, specifying advanced view parameters of the tables, and into data collecXon for entering new paXents, visits as well as data values. (Fig. 2 and Fig. 3) For storage of clinical informaXon, two tables were defined. The first table contains all data in structured format, the second table harbors all informaXon about the structure for each type of parameter (Fig. 4). The database is currently applied for collecXng informaXon in the mulX-‐center biomarker research project ArthoMark. To provide data policy, different levels of rights were generated for reading, wriXng and sharing data as well as administraXng the structure of tables. Any changes applied to the data and tables are tracked in the log file. For example, a data structure for clinical informaXon from paXents with arthriXs was established.
Any kind of informaXon can be stored in the new database. Every new parameter can be added without programming knowledge. The database is simultaneously accessible from the Internet. Thus the database enables to collect data in the clinics, to share these with scienXsts, to perform biobanking or sample tracking. The database is currently part of the BMBF funded naXonal research network ArthoMark and the EU funded network BTCure.
The demand for a generic structural collecXon and opXmal sharing of clinical data is increasing due to the large amount of data and constantly changing requirements. The system should offer the flexibility in adding new parameters as well as criteria, to perform new analysis without extra programming effort. It should also provide the collecXon, processing and sharing of the data in agreements according to data privacy regulaXons and at the same Xme be accessible through the intranet/internet.
Acknowledgement: BTCure IMI grant agreement no. 115142
Figure 1
ArthroMark grant no 01EC1009A
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Figure 1: AdministraXve modul. Columns and rows can be defined by a user without any programming knowledge. The paXent‘s and visit‘s specific tables can be generated and listed as well under corresponding categories. a. Any type of data including String, Number with Unit, Date, URL, EnumeraXon etc can be selected. b. Default value can be entered for any type of data as well as specific values for a fix value or enumeraXon.
a.
b.
Figure 2: Data collecXon modul. By choosing a paXent and a visit, the filled visit‘s specific tables can be viewed. The same preview is provided for paXent‘s specific tables. The color of the tables‘ names idenXfy whether if the table is filled (grey), some data has to be entered (red) or if the table is empty (blue).
Figure 3: Data collecXon modul. While ediXng the data in a table, it is possible to add rows defined in the administraXve modul. If the data did not correspond to the specific type defined by the field, the verificaXon process will not allow to save the table and will throw an error noXce.
Figure 1
Figure 3
Figure 2
Table name
Beginn of symptoms
Date of diagnos1cs End of disease
rheumatoid arthri1s 02/2008 06/2008 diabetes mellitus 06/2009 12/2009 arterial hypertonia 12/2010 12/2010
pneumonia 03/2011 03/2011 04/2011
value (date)
Row name (Parameterkey 2)
Column name (Parameterkey 3)
Masterkey 1
for storing paXent specific data (common data about paXent)
for storing paXent and visit specific data (visit dependent data about paXent)
Parameterkey 2 Parameterkey 3 Parameterkey 1
Value Unit Standard Value
CrP 0.7 mg/dl 0.5 ESR 1h 30 mm/1h 15 ESR 2h 50 mm/2h 30 white blood cells (WBC) 7.3 /nl 4..10
value (number,string)
+
PaXents (PaXent-‐ID)
Masterkey 2 Visits (visit date)
Masterkey 1 PaXents (PaXent-‐ID)
Figure 4: DefiniXon of masterkeys and parameterkeys. The masterkeys define the paXent idenXty (paXent-‐ID) and the Xme point of the visit. The parameter keys define the structure of tables (names of the tables, the rows, and the columns), which can be generated by the user to store clinical informaXon.
Figure 4 Parameterkey 2 Parameterkey 3 Parameterkey 1
Laboratory
Diagnos1cs
Department of Rheumatology and Clinical Immunology, Charité University Hospital, Berlin, Germany
Jekaterina Kokatjuhha, Marc Bonin, Sascha Johannes, Florian Heyl, Irene Ziska, Pascal Schendel, Karsten Mans, Biljana Smiljanovic, Till Sörensen, Thomas Häupl
