IBM Semea Sud IBM Business Consulting Services FIRBLIBI

IBM Semea Sud – Life Sciences Services Team IBM Semea Sud (ISS) is part of BCS Italy and has the mission to operate on innovative and challenging e-business integration projects both in traditional and emerging areas § ISS is part of the IBM BCS organization and consists of 5 Innovation Technology Centers covering the majority of needed capabilities to develop innovative e-business projects. § ISS demonstrated its experience in developing “mission critical” e-business integration projects, today in production with hundreds thousands users. § ISS was formed in 1992 in South Italy with the aim to operate also on applied research projects by providing a strong link between the worldwide IBM research and emerging areas divisions and the local market. 2 FIRB-LIBI project © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team ISS directed part of its investment around the new Life Sciences emerging area creating a dedicated team and targeting business opportunities in the data, information and application integration services § In December 2001 a dedicated Life Sciences Team, within the ISS Java Technology Center, was created with the aim provide to the Life Sciences & Pharma area data, information and application integration services. § Thanks to strong competencies of Enterprise Application Integration (EAI) based on the standard J 2 EE integration platform and advanced areas such as Wireless, Knowledge Mining, Knowledge Management, Web Mining and Artificial Intelligence the team shortly acquired and developed specific Life Sciences services project in Italy. § The ISS Life Sciences team strategy try to leverage customer solutions by proposing both IBM Life Sciences integration technology with addedvalue services supplied also by IBM research stuff and/or specific research works realized internally jointly with academic partners 3 FIRB-LIBI project © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team ISS team concentrates its research efforts to attack a number of significant “complex problems” (pressures) that are impacting the effectiveness of traditional business process in the Life Sciences domain Inhibition and difficulty in sharing data and information! Capabilities Need a structured way to manage, integrate, analyze and act on data, information regardless of the source Data Management & Integration FIRB-LIBI project Process Optimization & Integration Knowledge Management & Mining Need to develop knowledge value & transfer culture and improve the external sources knowledge acquiring process 4 Inhibition to integrate internal and external applications! Need a way to manage, integrate, analyze and act on application services Data and Information overloading! © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team ISS activities within the LIBI project (WP 4) will be focused on two main complex problems (which are also “pressures” of the laboratory as well as for our customers): ability of data/database integration/federation and search on both structured and unstructured data and integrate also specialized mining capabilities on unstructured biological literature data. In particular, ISS is aspecting to coordinate and bring ahead (by collaborating with other partners) three main research activity streams § Task 1. Work to propose an overall data/database integration and search model for the laboratory (potentially with all partners) § Task 2. Work to integrate into the model above also information mined from “unstructured” data coming from the biomedical literature in order to set-up automatic/semi-automatic structure biological databases (Univ. of Bari – Dip. Infomatica, CNR, and other partners that should be defined) § Task 3. Experiment the data integration models on a specific application scenario supplied by a vertical application able to store and analyze complete mitochondria genomes (Univ. of Bari – Dip. Biologia, and other partners that should be defined) 5 FIRB-LIBI project © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team Task 1. This task will investigate within the main issue to extract data from multiple, heterogeneous biological data sources with the aim to provide both a “single query” modality and services and work to have a shared “semantic” concerning all data managed into the laboratory Main activities and results: 6 - Contribute to analyze and define the schema/content (and semantic) of the different databases to be integrated in the laboratory - Analysis of the Laboratory needs concerning the extraction of structured and unstructured information from the available databases - Design of a model for the effective integration of the Laboratory databases - Implementation of the integration system for at least half of the laboratory databases - Definition of services and API shown in the Laboratory platform for the query and retrieval of information from databases FIRB-LIBI project © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team Task 2. This task aims to investigates how to improve the data integration model also with information mined from “unstructured” data coming from the biomedical literature in order to set-up automatic/semiautomatic structure biological databases Main activities and results: 7 - Analysis of the Laboratory needs concerning the extraction of relevant information from unstructured textual data from the available databases - Design of a model for the effective integration structured and unstructured information - Design and implementation of the mining and retrieval functionalities of unstructured information - Define a services API shown in the Laboratory platform for the query also on mined data - Experiment the services of data query and retrieval FIRB-LIBI project © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team Task 3. This work aims to experiment the services of data query and retrieval on a specific application scenario supplied by a vertical application able to store and analyze complete mitochondria genomes Main activities and results: 8 - Analysis of the needs concerning in terms of data integration and extraction of relevant information from unstructured textual data from the available databases for the considered application - Design and implementation of the component application able to search integration API the mitochondria genomes application - Experiment the services of data query and retrieval with the context of the mitochondria genomes application FIRB-LIBI project © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team Back-up 9 FIRB-LIBI project © 2005

IBM Semea Sud – Life Sciences Services Team Invest in applied research projects to provide “added-value” services and assets to our customers § Leverage customer solutions by proposing both IBM Life Sciences integration technology, software and services jointly with “advanced” capability and assets by exploiting works matured into research activities § Integrate and extend IBM Research works § Integrate and extend works from Research partners § Work locally on “challenging and complex” problems 10 FIRB-LIBI project © 2005 IBM Corporation IBM Confidential

IBM Semea Sud – Life Sciences Services Team ISS is aspecting to bring ahead (by collaborating with other partners) tthree main research activity streams § MS 1: - Analysis of the schema and content of the different databases to be integrated in the platform - Analysis of the Laboratory needs concerning the extraction of structured and unstructured information from the available databases § MS 2: - Design of a model for the effective integration of the Laboratory databases - Implementation of the integration system for at least half of the laboratory databases - Design and implementation of the mining and retrieval functionalities of unstructured information - Definition of services and API shown in the Laboratory platform for the query and retrieval of information from databases § MS 3: - Completion of the integration phases of the laboratory databases - Release and integration test of the services of data query and retrieval with the other services and applications of the laboratory 11 FIRB-LIBI project © 2005 IBM Corporation IBM Confidential