1. IBIS, A Framework For the Interoperability Of Bio-repository Information System In Africa
Presented by : Mosaku Abayomi and Akanle Boladele
Covenant University – Nigeria
WACREN e-Research Hackfest – Lagos (Nigeria)
Authors: Johnmark O. Erigbe, Dr. Daramola Olawande, Mosaku Abayomi, Prof. Adebiyi Ezekiel, Prof. Omotosho, O.J., Prof. Goga, N., Boladale Akanle

2. Outline Research Background Scientific problem
Inter-operability Problems
Aim and Objectives
Justification
Use Case
Brief User Work Flow
Implementation strategy

3. Research Background
A bio-repository (bio-bank) is a resource centre that collects and stores samples of biomaterials such as tissues, urine, cells, Deoxyribonucleic acid( DNA), Ribonucleic acid( RNA ), protein and blood - International Society for Biological and Environmental Repositories (ISBER, 2008).
These biological materials could be taken from human beings, plants or animals for laboratory research purposes.
Bio-repositories play a significant role in clinical research because they provide the platform for sharing critical resources in translational medicine.
There is, the current challenge to evolve an inter-connectivity and inter-accessibility methodology for bio-repository systems that will provide information on the availability of bio-genetic species in other bio-banks (Mills and Brooks, 2010).

4. Research Background

5. Research Background
"Interoperability is the ability of multiple systems with different hardware and software platforms, data structures, and interfaces to exchange data with minimal loss of content and functionality" [NISO, 2004].

6. Scientific Problem
Bio-repositories have been developed for specific projects in local institutions, but most of such bio-repositories are often not interoperable.
This inadequacy makes it difficult for researchers to share data conveniently from a common centre (Kim, 2010).
The absence of Interoperable bio-repository information system in Nigeria/Africa has made it difficult for researchers to obtain needed data for their research into diseases .
Accessibility to repositories through such search tools as Specimen Resource Locator, and tissue Expediter among several others has provided indication that further improvement can be made through research efforts.
Observations (Krestyaninova, 2010; Tupasela, 2009) have shown that most database systems rely on database administrators to design and maintain database architecture and this process imposes constraints on database users when non-standardized input formats and parameters are set.
This inconsistency is generally a problem in addition to the loss of flexibility and control by individual databases to a central authority. These are obvious problems to which interoperability of biorepository systems could be a viable solution.

7. Other Problems We Are Solving
Inter-operability Problems
Schema Inter-operability Problems
Semantic Inter-operability Problems
Linguistic Inter-operability Problems

8. Aim and Objectives AIM The specific objectives of the research are:
The aim of this research is to develop a platform for interoperability of biorepository information systems in Africa.
The specific objectives of the research are:
Develop a computational framework that will facilitate the interoperability of biorepository information systems
To create a prototype virtual platform ( proof of concept) that allows retrieval and exchange of information across multiple biorepository databases
To integrate a data mining technique that will ensure knowledge discovery from multiple databases
To integrate Web 3.0 techniques to achieve semantic interoperability
Test and evaluate the usability and efficiency of the proposed framework

9. JUSTIFICATION
There is the argument that specimen queries across repositories will promote intra and inter program collaboration (Anderson, 2012; Morgan, 2011).
Eliminating the challenges of collaboration, exchange of data and absence of a system that provides real-time access to connected bio-repositories
Enhancing the genomic analysis of biopsies which will further allow researchers to develop new diagnostic tests, personalize treatment options, and new treatment methods
Providing rapid access to bio-repositories irrespective of geographic limitation will improve societal Health and wellbeing
In the presence of extensive databases, mining biospecimen data helps to extract useful knowledge from datasets.

10. Use Case

11. Brief User Work Flow
The main users of the system are: LABORATORY OR BIOBANK SPECIALIST at different locations who collects and stores samples of biomaterials [tissues, urine, cells, Deoxyribonucleic acid( DNA), Ribonucleic acid(RNA), protein, blood e.t.c ], updates their Cloud base Biobank Information Management System using the unique biomaterial Standard PREanalytical Code (SPREC).
The next user level is the META DATABASE ADMINSITRATOR: who connects biobanks to the Network (on request) via the admin section of the Framework (as described above) to make locally stored bio samples searchable from anywhere in the world
The third set of user are MEMBERS OF THE RESEARCH COMMUNITY who needs the bio samples for experiments and research purposes or to carry out genomic analysis of the samples towards the development of new diagnostic tests, personalize treatment options, and develop new treatment methods

18. Implementation Strategy
Implement SAML (Security Assertion Markup Language) or OAuth for Federated Authentication, and develop Java Servlets & Java API for RESTful Web Services (JAX-RS)
Develop Meta database store using OAR
Implement back end using Java Enterprise Programming Technologies (JSP, Servlet, JSTL, JDBC)
Develop mini-ontology using Protege and the Ontology Web Language
Build Internationalization engine using Java Server Pages (JSP) as a wrapper that connects the system to the Microsoft Bing Language API
Incorporate Java weka library to implement data mining algorithms for real time knowledge discovery from multiple databases.
Coding D3.js (Data Document) for real time visualization of data mining outputs
Develop JSP that will auto generate Attribute-Relation File Format (ARFF) to complete the KDD
Develop Java API for HL7 (Health Level 7).
Implement Java JENA library to connect to the Ontology

19. Implementation Strategy
Incorporate SPARQL Protocol and RDF Query Language
USER INTERFACE DESIGN PLAN
Develop User Interface and user interactivity using Hypertext Mark-up Language (HTML) and Java scripting
Style the interface using Cascading Style Sheet (CSS)
Accomplish mobile responsiveness using the CSS Query
Develop angularjs & javascript modules to ensure input data integrity and enforcing client side user validation
Implement twitter bootstrap, FontAwesome, Gritter Notifications, Data Tables , Bootstrap Growl, jQuery Backstretch, Excanvas, jQuery Idle Timeout for the U.I.

20. Thank you! Authors Johnmark O. Erigbe Prof. Adebiyi Ezekiel
Dr. Daramola Olawande
Mosaku Abayomi
Prof. Omotosho, O.J.
Prof. Goga, N.
Boladale Akanle