Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers
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...
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| Veröffentlicht in: | Journal of cheminformatics 2015-08, Vol.7 (1), p.37-37, Article 37 |
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| container_title | Journal of cheminformatics |
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| creator | Harvey, Matthew J Mason, Nicholas J McLean, Andrew Rzepa, Henry S |
| description | 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.
Graphical abstract
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| doi_str_mv | 10.1186/s13321-015-0081-7 |
| format | Article |
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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.
Graphical abstract
:</description><identifier>ISSN: 1758-2946</identifier><identifier>EISSN: 1758-2946</identifier><identifier>DOI: 10.1186/s13321-015-0081-7</identifier><identifier>PMID: 26257829</identifier><language>eng</language><publisher>Cham: Springer International Publishing</publisher><subject>Chemistry ; Chemistry and Materials Science ; Computational Biology/Bioinformatics ; Computer Applications in Chemistry ; Documentation and Information in Chemistry ; Jean-Claude Bradley Memorial Series ; Research Article ; Theoretical and Computational Chemistry</subject><ispartof>Journal of cheminformatics, 2015-08, Vol.7 (1), p.37-37, Article 37</ispartof><rights>Harvey et al. 2015</rights><rights>Journal of Cheminformatics is a copyright of Springer, 2015.</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c503t-a0896665f02242816cbd3ff602ac65daf17925c835579f53a98fffe47aa616563</citedby><cites>FETCH-LOGICAL-c503t-a0896665f02242816cbd3ff602ac65daf17925c835579f53a98fffe47aa616563</cites><orcidid>0000-0002-1653-7430 ; 0000-0003-1797-3186 ; 0000-0001-9475-0328 ; 0000-0002-8635-8390</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528360/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4528360/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,864,885,27924,27925,41120,41488,42189,42557,51319,51576,53791,53793</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/26257829$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Harvey, Matthew J</creatorcontrib><creatorcontrib>Mason, Nicholas J</creatorcontrib><creatorcontrib>McLean, Andrew</creatorcontrib><creatorcontrib>Rzepa, Henry S</creatorcontrib><title>Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers</title><title>Journal of cheminformatics</title><addtitle>J Cheminform</addtitle><addtitle>J Cheminform</addtitle><description>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.
Graphical abstract
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Mason, Nicholas J ; McLean, Andrew ; Rzepa, Henry S</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c503t-a0896665f02242816cbd3ff602ac65daf17925c835579f53a98fffe47aa616563</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2015</creationdate><topic>Chemistry</topic><topic>Chemistry and Materials Science</topic><topic>Computational Biology/Bioinformatics</topic><topic>Computer Applications in Chemistry</topic><topic>Documentation and Information in Chemistry</topic><topic>Jean-Claude Bradley Memorial Series</topic><topic>Research Article</topic><topic>Theoretical and Computational Chemistry</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Harvey, Matthew J</creatorcontrib><creatorcontrib>Mason, Nicholas J</creatorcontrib><creatorcontrib>McLean, Andrew</creatorcontrib><creatorcontrib>Rzepa, Henry S</creatorcontrib><collection>Springer Nature OA Free Journals</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Biotechnology Research Abstracts</collection><collection>Health & Medical Collection</collection><collection>ProQuest Central (purchase pre-March 2016)</collection><collection>ProQuest Pharma Collection</collection><collection>Technology Research Database</collection><collection>ProQuest SciTech Collection</collection><collection>ProQuest Technology Collection</collection><collection>ProQuest Natural Science Collection</collection><collection>Hospital Premium Collection</collection><collection>Hospital Premium Collection (Alumni Edition)</collection><collection>ProQuest Central (Alumni) (purchase pre-March 2016)</collection><collection>Materials Science & Engineering Collection</collection><collection>ProQuest Central (Alumni Edition)</collection><collection>ProQuest One Sustainability</collection><collection>ProQuest Central UK/Ireland</collection><collection>Advanced Technologies & Aerospace Collection</collection><collection>ProQuest Central Essentials</collection><collection>Biological Science Collection</collection><collection>ProQuest Central</collection><collection>Technology Collection</collection><collection>Natural Science Collection</collection><collection>ProQuest One Community College</collection><collection>ProQuest Materials Science Collection</collection><collection>ProQuest Central Korea</collection><collection>Engineering Research Database</collection><collection>Health Research Premium Collection</collection><collection>Health Research Premium Collection (Alumni)</collection><collection>ProQuest Central Student</collection><collection>SciTech Premium Collection</collection><collection>ProQuest Health & Medical Complete (Alumni)</collection><collection>Materials Science Database</collection><collection>ProQuest Biological Science Collection</collection><collection>Health & Medical Collection (Alumni Edition)</collection><collection>Biological Science Database</collection><collection>Advanced Technologies & Aerospace Database</collection><collection>ProQuest Advanced Technologies & Aerospace Collection</collection><collection>Biotechnology and BioEngineering Abstracts</collection><collection>Materials Science Collection</collection><collection>Publicly Available Content Database</collection><collection>ProQuest One Academic Eastern Edition (DO NOT USE)</collection><collection>ProQuest One Academic</collection><collection>ProQuest One Academic UKI Edition</collection><collection>ProQuest Central China</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Journal of cheminformatics</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Harvey, Matthew J</au><au>Mason, Nicholas J</au><au>McLean, Andrew</au><au>Rzepa, Henry S</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers</atitle><jtitle>Journal of cheminformatics</jtitle><stitle>J Cheminform</stitle><addtitle>J Cheminform</addtitle><date>2015-08-08</date><risdate>2015</risdate><volume>7</volume><issue>1</issue><spage>37</spage><epage>37</epage><pages>37-37</pages><artnum>37</artnum><issn>1758-2946</issn><eissn>1758-2946</eissn><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.
Graphical abstract
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| source | DOAJ Directory of Open Access Journals; PubMed Central Open Access; Springer Nature OA Free Journals; BioMedCentral; EZB-FREE-00999 freely available EZB journals; PubMed Central; Free Full-Text Journals in Chemistry; SpringerLink Journals - AutoHoldings |
| subjects | Chemistry Chemistry and Materials Science Computational Biology/Bioinformatics Computer Applications in Chemistry Documentation and Information in Chemistry Jean-Claude Bradley Memorial Series Research Article Theoretical and Computational Chemistry |
| title | Standards-based metadata procedures for retrieving data for display or mining utilizing persistent (data-DOI) identifiers |
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