1 Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection University of Lodz, Pilarskiego St. 14/16, 90-237 Åódź, ...
Big Data Lab Management Systems Katarzyna Janik-Superson1, Marta Sobalska-Kwapis1,2, Marcin Słomka1,2, Błażej Marciniak1,2, Dominik Strapagiel1,2 1
Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection University of Lodz, Pilarskiego St. 14/16, 90-237 Łódź, Poland, www.biobank.uni.lodz.pl
2
BBMRI.pl Consortium, Wroclaw Research Centre EIT+, ul. Stabłowicka 147, 54-066 Wrocław
SMS Sample Management System
BBMS BioBank Management System
(TESTOPLEK, 2010)
(LabMind, 2013)
We work on a huge amount of data. We still collect and process thousands of genotypic and phenotypic information about one patient for use in extensive genetic and medical research. In 2010 we have created the Sample Management System (SMS) to collect and manage biological samples and phenotype data in the TESTOPLEK project, then in Biobank Lodz Laboratory of University of Lodz. We have already collected samples from over 10 000 Polish adults and also children, people suffering from cancers, endometriosis etc. We have created unique questionnaires, in which personal data were irreversibly anonymized, contained very detailed questions about appearance phenotype, living environment, family, ethnicity, education, addictions, diseases and treatment. All information and procedures for collecting material, conducted experiments, research results, genotypes, created vector constructs, warehouse and reagents were introduced into the SMS system. This made it very easy to work on a huge amount of material and the system is still used today to generate a test sample for GWAS and other studies. Collected genetic data will be available on platform e-czlowiek.pl as a part of the POPC Project (Operational Programme Digital Poland for 2014-2020).
We are helped by the biobanking system, which we are currently improving in Poland as a part of the European Research Infrastructure Consortium BBMRI-ERIC (Biobanking and BioMolecular resources Research Infrastructure European Research Infrastructure Consortium). As a member of BBMRI.pl consortium, we comprehensively tested freeware software BBMS for management of Biobanks (BioBank Management System), available online on the manufacturer's website (LabMind). The purpose of BBMS is to manage of sample storage and track all of the experimental procedures. This homogeneous system makes possibilities to unify data collection and management procedures for broad sharing and learning others, cooperation and information exchange between other scientific units and medical centers. BBMS, in addition to the registry functionality, is compatible with LIMS (Laboratory Information Management System), BIMS (Biobank Information Management System) and DMS (Document Management System) systems, enables the implementation of automated biobank maintenance processes and laboratory tests. EDES system (Electronic Data Exchange System) enables the implementation of cooperation between biobanks or between a biobank and a research and development facility.
Figure 8. BBMS system page with the division of access level and database administration.
Figure 9. BBMS system page with the history of the sample from collection to banking.
All information and procedures for collecting material Figure 1. SMS system page to search for a sample.
Medical history
Different types of biological samples
Figure 3. SMS system page for catalog of sample types.
Polling volunteers
History of family diseases
Phenotype data
Personal data anonymization
Polling patients
DNA samples
Sample’s lab history
Entering declarative data
Location of sample storage
Laboratory technicians authorization
Monitoring
Orders
Permissions
Lab rules
Figure 10. BBMS system page with researche projects.
Figure 11. BBMS system means.
Projects
Organizer
Repository
Lab equipment
Reagents
Experiments
Forms
Code base, e.g. ICD-10, AJCC
Figure 4. SMS system page with results of completed research.
Figure 2. SMS system page for entering data from the survey and information about the sample donor.
Collect and manage biological samples and phenotype data
Inspection and registration
Figure 11. Sample registration in BBMS system.
SYSTEM
Figure 6. SMS system page with vector construct markers.
Figure 5. SMS system page with laboratory history of the sample.
Reports
Results
Statistics
Alerts
Figure 7. Scheme of functions and organization of the sample and research results management system – a golden standard in every Biobank Lab.
„Digital sharing of biomolecular and descriptive resources of Biobank and Department of Anthropology, University of Lodz - characteristics of populations living in present-day Poland through the ages. Information platform e-Czlowiek.pl” (Operational Programme Digital Poland for 2014-2020) POPC.02.03.01-00-0012/17
Figure 12. Lab work organizer in BBMS system.
Project was financed by the Polish POIG Grant 01.01.0210-005/08 TESTOPLEK from the European Regional Development Fund.
Figure 13. Raport generator in BBMS system.
