An adaptable XML based approach for scientific data management and integration

Int. J. Semantic Computing

Pan

et al. 2013

Self Cite

XML is ubiquitously used as an information exchange platform for web-based applications in healthcare, life sciences, and many other domains. Proliferating XML data are now managed through latest native XML database technologies. XML data sources conforming to common XML schemas could be shared and integrated with syntactic interoperability. Semantic interoperability can be achieved through semantic annotations of data models using common data elements linked to concepts from ontologies. In this paper, we present a framework and software system to support the development of semantic interoperable XML based data sources that can be shared through a Grid infrastructure. We also present our work on supporting semantic validated XML data through semantic annotations for XML Schema, semantic validation and semantic authoring of XML data. We demonstrate the use of the system for a biomedical database of medical image annotations and markups.

Section: Use Case: Nci Tcga Aim Data Servicesmentioning

confidence: 99%

Semantically Interoperable XML Data

Vergara-Niedermayr

Int. J. Semantic Computing

Pan

et al. 2013

Self Cite

“…For example, XML database has been used in25 to manage biological pathway datasets. SciPort26, 27, 28 provides an XML based approach for modeling, managing and integrating scientific experiments and data. XML is also used to integrate heterogeneous bio-molecular data 29…”

Section: Related Workmentioning

confidence: 99%

Managing and querying image annotation and markup in XML

Medical Imaging 2010: Advanced PACS-based Imaging Informatics and Therapeutic Applications

Pan

Sharma

et al. 2010

Self Cite

Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid.

“…SciPort takes an XML based approach for data modeling, schema representation, and storage and queries, 1, 2, 3 and is supported by a backend native XML database. In SciPort, scientific data are represented as XML modeled documents, and documents are also organized into a hierarchy way for convenient browsing.…”

Section: Overview Of Scientific Data Management With Sciportmentioning

confidence: 99%

“…Privileges can be summarized with three major categories: i) Authoring : create, delete, update, and upload on resources; ii) Reading : read and download a resource; and iii) Publishing : publish a resource to a Central Server. 1 We propose to use roles to simplify the management of privileges.…”

Section: The Space and Role Based Security Modelmentioning

confidence: 99%

Securely and flexibly sharing a biomedical data management system

Medical Imaging 2009: Advanced PACS-based Imaging Informatics and Therapeutic Applications

Hussels

Liu

2009

Self Cite

Biomedical database systems need not only to address the issues of managing complex data, but also to provide data security and access control to the system. These include not only system level security, but also instance level access control such as access of documents, schemas, or aggregation of information. The latter is becoming more important as multiple users can share a single scientific data management system to conduct their research, while data have to be protected before they are published or IP-protected. This problem is challenging as users’ needs for data security vary dramatically from one application to another, in terms of who to share with, what resources to be shared, and at what access level. We develop a comprehensive data access framework for a biomedical data management system SciPort. SciPort provides fine-grained multi-level space based access control of resources at not only object level (documents and schemas), but also space level (resources set aggregated in a hierarchy way). Furthermore, to simplify the management of users and privileges, customizable role-based user model is developed. The access control is implemented efficiently by integrating access privileges into the backend XML database, thus efficient queries are supported. The secure access approach we take makes it possible for multiple users to share the same biomedical data management system with flexible access management and high data security.