The Experts below are selected from a list of 3879 Experts worldwide ranked by ideXlab platform

Matt Huculak - One of the best experts on this subject based on the ideXlab platform.

Henry S. Rzepa - One of the best experts on this subject based on the ideXlab platform.

  • Standards-based curation of a decade-old digital repository dataset of molecular information
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa, Peter Murray-rust, James J P Stewart
    Abstract:

    Background The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. Results The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite Persistent Identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. Conclusions We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the “supporting information”) should be conducted in a manner that facilitates automatic periodic curation. Graphical abstract: Standards and metadata-based curation of a decade-old digital repository dataset of molecular information.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers.
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type. Results The procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories. Conclusions Our methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data.

Matthew J. Harvey - One of the best experts on this subject based on the ideXlab platform.

  • Standards-based curation of a decade-old digital repository dataset of molecular information
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa, Peter Murray-rust, James J P Stewart
    Abstract:

    Background The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. Results The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite Persistent Identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. Conclusions We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the “supporting information”) should be conducted in a manner that facilitates automatic periodic curation. Graphical abstract: Standards and metadata-based curation of a decade-old digital repository dataset of molecular information.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers.
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type. Results The procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories. Conclusions Our methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data.

Andrew Mclean - One of the best experts on this subject based on the ideXlab platform.

  • Standards-based curation of a decade-old digital repository dataset of molecular information
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa, Peter Murray-rust, James J P Stewart
    Abstract:

    Background The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. Results The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite Persistent Identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. Conclusions We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the “supporting information”) should be conducted in a manner that facilitates automatic periodic curation. Graphical abstract: Standards and metadata-based curation of a decade-old digital repository dataset of molecular information.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers.
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type. Results The procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories. Conclusions Our methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data.

Nicholas J. Mason - One of the best experts on this subject based on the ideXlab platform.

  • Standards-based curation of a decade-old digital repository dataset of molecular information
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa, Peter Murray-rust, James J P Stewart
    Abstract:

    Background The desirable curation of 158,122 molecular geometries derived from the NCI set of reference molecules together with associated properties computed using the MOPAC semi-empirical quantum mechanical method and originally deposited in 2005 into the Cambridge DSpace repository as a data collection is reported. Results The procedures involved in the curation included annotation of the original data using new MOPAC methods, updating the syntax of the CML documents used to express the data to ensure schema conformance and adding new metadata describing the entries together with a XML schema transformation to map the metadata schema to that used by the DataCite organisation. We have adopted a granularity model in which a DataCite Persistent Identifier (DOI) is created for each individual molecule to enable data discovery and data metrics at this level using DataCite tools. Conclusions We recommend that the future research data management (RDM) of the scientific and chemical data components associated with journal articles (the “supporting information”) should be conducted in a manner that facilitates automatic periodic curation. Graphical abstract: Standards and metadata-based curation of a decade-old digital repository dataset of molecular information.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers.
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type.

  • Standards-based metadata procedures for retrieving data for display or mining utilizing Persistent (data-DOI) Identifiers
    Journal of Cheminformatics, 2015
    Co-Authors: Matthew J. Harvey, Nicholas J. Mason, Andrew Mclean, Henry S. Rzepa
    Abstract:

    Background We describe three different procedures based on metadata standards for enabling automated retrieval of scientific data from digital repositories utilising the Persistent Identifier of the dataset with optional specification of the attributes of the data document such as filename or media type. Results The procedures are demonstrated using the JSmol molecular visualizer as a component of a web page and Avogadro as a stand-alone modelling program. We compare our methods for automated retrieval of data from a standards-compliant data repository with those currently in operation for a selection of existing molecular databases and repositories. Conclusions Our methods illustrate the importance of adopting a standards-based approach of using metadata declarations to increase access to and discoverability of repository-based data.