Motivation BBMRI-ERIC mission is to construct a pan-European biobanking infrastructure, building on existing infrastructure, resources and technologies, specifically complemented with innovative components and properly embedded into European ethical, legal and societal frameworks. BBMRI.it is the national node member of the BBMRI-ERIC infrastructures involving the majority biobanks and biological resource centers located in Italy. The Italian node is actually composed by more than 18 universities, 23 IRCCS, 40 hospitals, associations of patients. The activities of BBMRI.it are aimed at harmonizing the standard operating procedures (SOPs) of biobanks, implementing the quality management system and encouraging public/private partnerships. For this purpose and in collaboration with the BBMRI.it partners we have developed a dedicated web portal (http://www.bbmri.it) to construct and operate a sustainable infrastructure for biological information in Italy to support biomedical research and its translation to medicine in Italy. Methods The BBMRI.it web portal [1] has been developed in order to collect the data and to ensure the easiest way to interact with the central node of BBMRI-ERIC infrastructures. For the development of this portal we have using the Liferay community Web Portal [2]. Based on the Liferay services, we have organized a public area of the portal for publishing all the information regarding the activities of the BBMRI.it node in Italy and Europe. The portal provide also a private area, only available via Login for the registered user in order to perform these specific services: A) To collect the initial information from the Biobank's we have developed the Survey for Biobank's accreditation using the Java Vaadin Framework [3] (Version 7.1.15). By means of this service users can add all Biobanks information online and submit to the evaluation committee the formal request to be accredited in the BBMRI.it network. All the information are stored into a specific database managed by a dedicate middleware developed with the Hibernate Framework [3]. B) The BBMRI.it Directory Service has been developed in order to allow the users to search on-line the public information regarding all the Biobanks in Italy and in Europe by the Directory 3.1 based on the MIABIS standard. This Service is realized using the Java PrimeFaces Framework [4] (Version 5.2). Thought this application is it possible to store and retrieve the information, based on the biobanks accepted in the Italian Network. This system is able to collect the data and to share the information with the BBMRI-ERIC Directory 3.1. This application is divided in 4 categories: Biobanks Networks, Biobanks, Collections and Contacts. A specific middleware for management of data has been implemented in order to manage the data with a RDBMS interconnection locally and with the BBMRI-ERIC Directory; this allow the utilization of multiple data connectors for sharing information with an unique user interface. C) The BBMRI.it Biobank Manager service, is available for the users administration in order to validate the submitted data; this operation consist in different steps: Step 1) The registered Biobank after the admission in BBMRI.it Network is granted with the permission for access to the BBMRI.it Directory Service in order to complete the information requested. Step 2) The data already present in the survey are automatically added into the BBMRI.it Directory Structure in order to simplify the process of share the information with the BBMRI-ERIC Directory. Step 3) Finally the biobanks owner is informed via email about the final acceptance in BBMRI.it. All the services described have been integrated into the portal as a portlets and can be utilized by the users in according with their role in the portal. Results We have developed the BBMRI.it Portal to facilitate the collection of data and the collaboration among the biobanks. This portal represent the centralize resource for the storage and the analysis of the information related the biobanks. By using the Directory application is possible to interact and share the information with the central European directory server. Actually the BBMRI.it Directory stores total information about more than 70 biobanks. Finally for the bioinformatics analysis of the Omics data generated from the Biobanks samples we have also developed a platform hosted on a computer cluster at the Institute of Biomedical Technologies (ITB/CNR) in Milan able to combines several Bioinformatics and Systems Biology tools. References [1] BBMRI.it Project web Site: http://www.bbmri.it [2] Liferay Portal Site: http://www.liferay.com [3] Vaadin Site: https://vaadin.com/home [3] Hibernate Site: http://www.hibernate.org [4] Primefaces: http://www.primefaces.org
Web infrastructure for the management of the "bbmri.it" Italian Biobank Network
Gnocchi M;Moscatelli M;Manconi A;Milanesi L
2017
Abstract
Motivation BBMRI-ERIC mission is to construct a pan-European biobanking infrastructure, building on existing infrastructure, resources and technologies, specifically complemented with innovative components and properly embedded into European ethical, legal and societal frameworks. BBMRI.it is the national node member of the BBMRI-ERIC infrastructures involving the majority biobanks and biological resource centers located in Italy. The Italian node is actually composed by more than 18 universities, 23 IRCCS, 40 hospitals, associations of patients. The activities of BBMRI.it are aimed at harmonizing the standard operating procedures (SOPs) of biobanks, implementing the quality management system and encouraging public/private partnerships. For this purpose and in collaboration with the BBMRI.it partners we have developed a dedicated web portal (http://www.bbmri.it) to construct and operate a sustainable infrastructure for biological information in Italy to support biomedical research and its translation to medicine in Italy. Methods The BBMRI.it web portal [1] has been developed in order to collect the data and to ensure the easiest way to interact with the central node of BBMRI-ERIC infrastructures. For the development of this portal we have using the Liferay community Web Portal [2]. Based on the Liferay services, we have organized a public area of the portal for publishing all the information regarding the activities of the BBMRI.it node in Italy and Europe. The portal provide also a private area, only available via Login for the registered user in order to perform these specific services: A) To collect the initial information from the Biobank's we have developed the Survey for Biobank's accreditation using the Java Vaadin Framework [3] (Version 7.1.15). By means of this service users can add all Biobanks information online and submit to the evaluation committee the formal request to be accredited in the BBMRI.it network. All the information are stored into a specific database managed by a dedicate middleware developed with the Hibernate Framework [3]. B) The BBMRI.it Directory Service has been developed in order to allow the users to search on-line the public information regarding all the Biobanks in Italy and in Europe by the Directory 3.1 based on the MIABIS standard. This Service is realized using the Java PrimeFaces Framework [4] (Version 5.2). Thought this application is it possible to store and retrieve the information, based on the biobanks accepted in the Italian Network. This system is able to collect the data and to share the information with the BBMRI-ERIC Directory 3.1. This application is divided in 4 categories: Biobanks Networks, Biobanks, Collections and Contacts. A specific middleware for management of data has been implemented in order to manage the data with a RDBMS interconnection locally and with the BBMRI-ERIC Directory; this allow the utilization of multiple data connectors for sharing information with an unique user interface. C) The BBMRI.it Biobank Manager service, is available for the users administration in order to validate the submitted data; this operation consist in different steps: Step 1) The registered Biobank after the admission in BBMRI.it Network is granted with the permission for access to the BBMRI.it Directory Service in order to complete the information requested. Step 2) The data already present in the survey are automatically added into the BBMRI.it Directory Structure in order to simplify the process of share the information with the BBMRI-ERIC Directory. Step 3) Finally the biobanks owner is informed via email about the final acceptance in BBMRI.it. All the services described have been integrated into the portal as a portlets and can be utilized by the users in according with their role in the portal. Results We have developed the BBMRI.it Portal to facilitate the collection of data and the collaboration among the biobanks. This portal represent the centralize resource for the storage and the analysis of the information related the biobanks. By using the Directory application is possible to interact and share the information with the central European directory server. Actually the BBMRI.it Directory stores total information about more than 70 biobanks. Finally for the bioinformatics analysis of the Omics data generated from the Biobanks samples we have also developed a platform hosted on a computer cluster at the Institute of Biomedical Technologies (ITB/CNR) in Milan able to combines several Bioinformatics and Systems Biology tools. References [1] BBMRI.it Project web Site: http://www.bbmri.it [2] Liferay Portal Site: http://www.liferay.com [3] Vaadin Site: https://vaadin.com/home [3] Hibernate Site: http://www.hibernate.org [4] Primefaces: http://www.primefaces.orgI documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
