The Experts below are selected from a list of 6027 Experts worldwide ranked by ideXlab platform

Haruki Nakamura - One of the best experts on this subject based on the ideXlab platform.

  • Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
    Nucleic Acids Research, 2016
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Yasuyo Ikegawa, Gert-jan Bekker, Yuko Tsuchiya, Takeshi Kawabata, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the resource description framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

  • protein data bank japan pdbj maintaining a structural data archive and resource description framework format
    Nucleic Acids Research, 2012
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Daron M Standley, Atsushi Nakagawa, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the resource description framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

Akira R Kinjo - One of the best experts on this subject based on the ideXlab platform.

  • Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
    Nucleic Acids Research, 2016
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Yasuyo Ikegawa, Gert-jan Bekker, Yuko Tsuchiya, Takeshi Kawabata, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the resource description framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

  • protein data bank japan pdbj maintaining a structural data archive and resource description framework format
    Nucleic Acids Research, 2012
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Daron M Standley, Atsushi Nakagawa, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the resource description framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

Bhavani Thuraisingham - One of the best experts on this subject based on the ideXlab platform.

  • geospatial resource description framework grdf and security constructs
    International Conference on Data Engineering, 2008
    Co-Authors: Ashraful Alam, Latifur Khan, Bhavani Thuraisingham
    Abstract:

    The semantic Web enables an automated, ontology based information aggregation mechanism. In geographic domain, automatic aggregation is a particularly important task in light of the over-abundance of data formats and types. Because the formats and types are not necessarily uniform or adhere to a particular information structure, aggregating geospatial data with differing formats is a challenging task. The aggregation is extremely useful in many areas such as business, academic, homeland security and public awareness. In this paper, we propose a set of geospatial constructs written in Web ontology language (OWL) and collectively referred to as geographic resource description framework (GRDF).Our goal is to propose a broad, semantics-aware and expressive language for geospatial domain. The most important advantage GRDF has over other geospatial languages is the ability to use logical inference and dynamic content aggregation. We also publish our work on security constructs for GRDF that allows domain experts and software developers to address the security concerns as part of the core development process instead of an ad-hoc course of action.

  • ICDE Workshops - Geospatial resource description framework (GRDF) and security constructs
    2008 IEEE 24th International Conference on Data Engineering Workshop, 2008
    Co-Authors: Ashraful Alam, Latifur Khan, Bhavani Thuraisingham
    Abstract:

    The semantic Web enables an automated, ontology based information aggregation mechanism. In geographic domain, automatic aggregation is a particularly important task in light of the over-abundance of data formats and types. Because the formats and types are not necessarily uniform or adhere to a particular information structure, aggregating geospatial data with differing formats is a challenging task. The aggregation is extremely useful in many areas such as business, academic, homeland security and public awareness. In this paper, we propose a set of geospatial constructs written in Web ontology language (OWL) and collectively referred to as geographic resource description framework (GRDF).Our goal is to propose a broad, semantics-aware and expressive language for geospatial domain. The most important advantage GRDF has over other geospatial languages is the ability to use logical inference and dynamic content aggregation. We also publish our work on security constructs for GRDF that allows domain experts and software developers to address the security concerns as part of the core development process instead of an ad-hoc course of action.

Hirofumi Suzuki - One of the best experts on this subject based on the ideXlab platform.

  • Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
    Nucleic Acids Research, 2016
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Yasuyo Ikegawa, Gert-jan Bekker, Yuko Tsuchiya, Takeshi Kawabata, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the resource description framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

  • protein data bank japan pdbj maintaining a structural data archive and resource description framework format
    Nucleic Acids Research, 2012
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Daron M Standley, Atsushi Nakagawa, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the resource description framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.

Yasuyo Ikegawa - One of the best experts on this subject based on the ideXlab platform.

  • Protein Data Bank Japan (PDBj): updated user interfaces, resource description framework, analysis tools for large structures
    Nucleic Acids Research, 2016
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Yasuyo Ikegawa, Gert-jan Bekker, Yuko Tsuchiya, Takeshi Kawabata, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org), a member of the worldwide Protein Data Bank (wwPDB), accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins. We herein outline the updated web user interfaces together with RESTful web services and the backend relational database that support the former. To enhance the interoperability of the PDB data, we have previously developed PDB/RDF, PDB data in the resource description framework (RDF) format, which is now a wwPDB standard called wwPDB/RDF. We have enhanced the connectivity of the wwPDB/RDF data by incorporating various external data resources. Services for searching, comparing and analyzing the ever-increasing large structures determined by hybrid methods are also described.

  • protein data bank japan pdbj maintaining a structural data archive and resource description framework format
    Nucleic Acids Research, 2012
    Co-Authors: Akira R Kinjo, Hirofumi Suzuki, Reiko Yamashita, Yasuyo Ikegawa, Takahiro Kudou, Reiko Igarashi, Yumiko Kengaku, Daron M Standley, Atsushi Nakagawa, Haruki Nakamura
    Abstract:

    The Protein Data Bank Japan (PDBj, http://pdbj.org) is a member of the worldwide Protein Data Bank (wwPDB) and accepts and processes the deposited data of experimentally determined macromolecular structures. While maintaining the archive in collaboration with other wwPDB partners, PDBj also provides a wide range of services and tools for analyzing structures and functions of proteins, which are summarized in this article. To enhance the interoperability of the PDB data, we have recently developed PDB/RDF, PDB data in the resource description framework (RDF) format, along with its ontology in the Web Ontology Language (OWL) based on the PDB mmCIF Exchange Dictionary. Being in the standard format for the Semantic Web, the PDB/RDF data provide a means to integrate the PDB with other biological information resources.