[ { "key": "5A7WUTQM", "version": 4, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/5A7WUTQM", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/5A7WUTQM", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Elliott", "numChildren": 0 }, "data": { "key": "5A7WUTQM", "version": 4, "itemType": "journalArticle", "title": "State of ELN: Current Perceptions and New Paths", "creators": [ { "creatorType": "author", "firstName": "Michael H.", "lastName": "Elliott" } ], "abstractNote": "", "publicationTitle": "", "publisher": "", "place": "", "date": "", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.scientificcomputing.com/sites/scientificcomputing.com/files/SC_HPC1403_IN_Elliott.pdf", "accessDate": "2015-01-21T15:46:47Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "State of ELN", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T15:47:11Z", "dateModified": "2015-01-21T15:47:11Z" } }, { "key": "D4UQIWQX", "version": 3, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/D4UQIWQX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/D4UQIWQX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Badiola et al.", "parsedDate": "2014-10-20", "numChildren": 0 }, "data": { "key": "D4UQIWQX", "version": 3, "itemType": "journalArticle", "title": "Experiences with a researcher-centric ELN", "creators": [ { "creatorType": "author", "firstName": "Katrina A.", "lastName": "Badiola" }, { "creatorType": "author", "firstName": "Colin", "lastName": "Bird" }, { "creatorType": "author", "firstName": "William S.", "lastName": "Brocklesby" }, { "creatorType": "author", "firstName": "John", "lastName": "Casson" }, { "creatorType": "author", "firstName": "Richard T.", "lastName": "Chapman" }, { "creatorType": "author", "firstName": "Simon J.", "lastName": "Coles" }, { "creatorType": "author", "firstName": "James R.", "lastName": "Cronshaw" }, { "creatorType": "author", "firstName": "Adam", "lastName": "Fisher" }, { "creatorType": "author", "firstName": "Jeremy G.", "lastName": "Frey" }, { "creatorType": "author", "firstName": "Danmar", "lastName": "Gloria" }, { "creatorType": "author", "firstName": "Martin C.", "lastName": "Grossel" }, { "creatorType": "author", "firstName": "D. Brynn", "lastName": "Hibbert" }, { "creatorType": "author", "firstName": "Nicola", "lastName": "Knight" }, { "creatorType": "author", "firstName": "Lucy K.", "lastName": "Mapp" }, { "creatorType": "author", "firstName": "Luke", "lastName": "Marazzi" }, { "creatorType": "author", "firstName": "Brian", "lastName": "Matthews" }, { "creatorType": "author", "firstName": "Andy", "lastName": "Milsted" }, { "creatorType": "author", "firstName": "Russell S.", "lastName": "Minns" }, { "creatorType": "author", "firstName": "Karl T.", "lastName": "Mueller" }, { "creatorType": "author", "firstName": "Kelly", "lastName": "Murphy" }, { "creatorType": "author", "firstName": "Tim", "lastName": "Parkinson" }, { "creatorType": "author", "firstName": "Rosanne", "lastName": "Quinnell" }, { "creatorType": "author", "firstName": "John S.", "lastName": "Robinson" }, { "creatorType": "author", "firstName": "Murray N.", "lastName": "Robertson" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Robins" }, { "creatorType": "author", "firstName": "Emma", "lastName": "Springate" }, { "creatorType": "author", "firstName": "Graham", "lastName": "Tizzard" }, { "creatorType": "author", "firstName": "Matthew H.", "lastName": "Todd" }, { "creatorType": "author", "firstName": "Alice E.", "lastName": "Williamson" }, { "creatorType": "author", "firstName": "Cerys", "lastName": "Willoughby" }, { "creatorType": "author", "firstName": "Erica", "lastName": "Yang" }, { "creatorType": "author", "firstName": "Paul M.", "lastName": "Ylioja" } ], "abstractNote": "", "publicationTitle": "Chem. Sci.", "publisher": "", "place": "", "date": "2014-10-20", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1039/C4SC02128B", "citationKey": "", "url": "http://xlink.rsc.org/?DOI=C4SC02128B", "accessDate": "2015-01-21T13:52:39Z", "PMID": "", "PMCID": "", "ISSN": "2041-6520, 2041-6539", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:52:44Z", "dateModified": "2015-01-21T13:52:44Z" } }, { "key": "FVRC5VC5", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/FVRC5VC5", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/FVRC5VC5", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Willighagen and Brändle", "parsedDate": "2011", "numChildren": 0 }, "data": { "key": "FVRC5VC5", "version": 2, "itemType": "journalArticle", "title": "Resource description framework technologies in chemistry.", "creators": [ { "creatorType": "author", "firstName": "Egon L.", "lastName": "Willighagen" }, { "creatorType": "author", "firstName": "Martin P.", "lastName": "Brändle" } ], "abstractNote": "The Resource Description Framework (RDF) is provid- ing the life sciences with new standards around data and knowledge management. The uptake in the life sciences is significantly higher than the uptake of the eXtensible Markup Language (XML) and even relational databases, as was recently shown by Splendiani et al. [1] Chemistry is adopting these methods too. For example, Murray-Rust and co-workers used RDF already in 2004 to distribute news items where chemical structures were embedded using RDF Site Summary 1.0 [2]. Frey imple- mented a system which would now be referred to as an electronic lab notebook (ELN) [3]. The use of the SPARQL query language goes back to 2007 where it was used in a system to annotate crystal structures [4].", "publicationTitle": "J. Cheminformatics", "publisher": "", "place": "", "date": "2011", "volume": "3", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "15", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.biomedcentral.com/content/pdf/1758-2946-3-15.pdf", "accessDate": "2014-12-07T23:34:44Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "RKQKZ3TA" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "SFG54MMH", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/SFG54MMH", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/SFG54MMH", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Bachler et al.", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "SFG54MMH", "version": 2, "itemType": "journalArticle", "title": "Collaborative tools in the semantic grid", "creators": [ { "creatorType": "author", "firstName": "Michelle", "lastName": "Bachler" }, { "creatorType": "author", "firstName": "Simon", "lastName": "Buckingham Shum" }, { "creatorType": "author", "firstName": "Jessica", "lastName": "Chen-Burger" }, { "creatorType": "author", "firstName": "Jeff", "lastName": "Dalton" }, { "creatorType": "author", "firstName": "David", "lastName": "De Roure" }, { "creatorType": "author", "firstName": "Marc", "lastName": "Eisenstadt" }, { "creatorType": "author", "firstName": "Jiri", "lastName": "Komzak" }, { "creatorType": "author", "firstName": "Danius", "lastName": "Michaelides" }, { "creatorType": "author", "firstName": "Kevin", "lastName": "Page" }, { "creatorType": "author", "firstName": "Stephen", "lastName": "Potter" }, { "creatorType": "author", "name": "others" } ], "abstractNote": "The CoAKTinG project aims to advance the state of the art in collaborative mediated spaces for distributed e-Science. The project is integrating several knowledge based and hypertext tools into existing col- laborative environments, and through use of a shared ontology to exchange structure, promotes enhanced process tracking and navigation of resources before, after, and while a meeting occurs. This paper provides an overview of the CoAKTinG tools, the ontology that connects them, and current research activities.", "publicationTitle": "", "publisher": "", "place": "", "date": "2004", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://eprints.ecs.soton.ac.uk/9439", "accessDate": "2014-12-07T23:39:22Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DHFR3F6X" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "8D5UJDIQ", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/8D5UJDIQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/8D5UJDIQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Taylor et al.", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "8D5UJDIQ", "version": 2, "itemType": "journalArticle", "title": "The Semantic Grid and Chemistry: Experiences with CombeChem", "creators": [ { "creatorType": "author", "firstName": "K", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "J", "lastName": "Essex" }, { "creatorType": "author", "firstName": "J", "lastName": "Frey" }, { "creatorType": "author", "firstName": "H", "lastName": "Mills" }, { "creatorType": "author", "firstName": "G", "lastName": "Hughes" }, { "creatorType": "author", "firstName": "E", "lastName": "Zaluska" } ], "abstractNote": "The CombeChem e-Science project has demonstrated the advantages of using Semantic Web technology, in particular RDF and the associated triplestores, to describe and link diverse and complex chemical information, covering the whole process of the generation of chemical knowledge from inception in the synthetic chemistry laboratory, through analysis of the materials made which generates physical measurements, computations based on this data to develop interpretations, and the subsequent dissemination of the knowledge gained. The RDF descriptions employed allow for a uniform description of chemical data in a wide variety of forms including multimedia, and of the chemical processes both in the laboratory and in model building. The project successfully adopted a strategy of capturing semantic annotations ‘at source’ and establishing schema and ontologies based closely on current operational practice in order to facilitate implementation and adoption. We illustrate this in the contexts of the synthetic organic chemistry laboratory with chemists at the bench, computational chemistry for modelling data, and the linking of chemical publications to the underlying results and data to provide the appropriate provenance. The resulting ‘Semantic Data Grid’ comprises tens of millions of RDF triples across multiple stores representing complex chains of derived data with associated provenance.", "publicationTitle": "Web Semantics: Science, Services and Agents on the World Wide Web", "publisher": "", "place": "", "date": "06/2006", "volume": "4", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "84-101", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.websem.2006.03.003", "citationKey": "", "url": "http://linkinghub.elsevier.com/retrieve/pii/S1570826806000072", "accessDate": "2014-10-10T13:17:33Z", "PMID": "", "PMCID": "", "ISSN": "15708268", "archive": "", "archiveLocation": "", "shortTitle": "The Semantic Grid and chemistry", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DHFR3F6X" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "VEHGBVMS", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/VEHGBVMS", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/VEHGBVMS", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Heery et al.", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "VEHGBVMS", "version": 2, "itemType": "journalArticle", "title": "Integrating Research Data into the Publication Workflow: the eBank UK Experience", "creators": [ { "creatorType": "author", "firstName": "Rachel", "lastName": "Heery" }, { "creatorType": "author", "firstName": "Monica", "lastName": "Duke" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Day" }, { "creatorType": "author", "firstName": "Liz", "lastName": "Lyon" }, { "creatorType": "author", "firstName": "Michael B.", "lastName": "Hursthouse" }, { "creatorType": "author", "firstName": "Jeremy G.", "lastName": "Frey" }, { "creatorType": "author", "firstName": "Simon J.", "lastName": "Coles" }, { "creatorType": "author", "firstName": "Christopher J.", "lastName": "Gutteridge" }, { "creatorType": "author", "firstName": "Leslie A.", "lastName": "Carr" } ], "abstractNote": "E-science has the potential to enrich scholarly communication from the perspective of both research and learning. This paper will explore emerging infrastructure that will enable effective curation of data to deliver this potential. The exponential growth in digital data arising from e-science requires new modes of data curation. The large volume of digital data now being created calls for new modes of publication, discovery, re-use and preservation. New patterns of publication, ‘publication at source’, are required, embedding the publication of data into the research scientist’s work patterns. Curation of digital data must support discovery services, building new service models on traditional library and publishing practice. There are opportunities for re-use of the increasing amount of digital data being produced, whether re-use takes place as part of research activity or in the development of course materials. In addition, secure archiving is necessary to ensure preservation of digital data.", "publicationTitle": "", "publisher": "", "place": "", "date": "2004", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://eprints.soton.ac.uk/9705/1/PV2004-heery.pdf", "accessDate": "2014-10-10T13:17:42Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Integrating research data into the publication workflow", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DHFR3F6X" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "J68FVSTI", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/J68FVSTI", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/J68FVSTI", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Frey et al.", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "J68FVSTI", "version": 2, "itemType": "bookSection", "title": "Combechem: A Case Study in Provenance and Annotation using the Semantic Web", "creators": [ { "creatorType": "author", "firstName": "Jeremy", "lastName": "Frey" }, { "creatorType": "author", "firstName": "David", "lastName": "De Roure" }, { "creatorType": "author", "firstName": "Kieron", "lastName": "Taylor" }, { "creatorType": "author", "firstName": "Jonathan", "lastName": "Essex" }, { "creatorType": "author", "firstName": "Hugo", "lastName": "Mills" }, { "creatorType": "author", "firstName": "Ed", "lastName": "Zaluska" } ], "abstractNote": "The CombeChem e-Science project has demonstrated the advantages of using Semantic Web technology, in particular RDF and triplestores, to de- scribe and link diverse and complex chemical information, covering the whole process of the generation of chemical knowledge from inception in the syn- thetic chemistry laboratory, through analysis of the materials made which gen- erates physical measurements, computations based on this data to develop in- terpretations, and the subsequent dissemination of the knowledge gained. The project successfully adopted a strategy of capturing semantic annotations ‘at source’ and establishing schema and ontologies based closely on current opera- tional practice in order to facilitate implementation and adoption. The resulting ‘Semantic Data Grid’ comprises around 45 million RDF triples across multiple stores.", "bookTitle": "Provenance and Annotation of Data", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2006", "publisher": "Springer", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "270–277", "ISBN": "", "DOI": "", "citationKey": "", "url": "http://link.springer.com/chapter/10.1007/11890850_27", "accessDate": "2014-10-10T13:17:30Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Combechem", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DHFR3F6X" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "4SUDXVMT", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/4SUDXVMT", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/4SUDXVMT", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Coles et al.", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "4SUDXVMT", "version": 2, "itemType": "journalArticle", "title": "An E-Science Environment for Service Crystallography from Submission to Dissemination", "creators": [ { "creatorType": "author", "firstName": "Simon J.", "lastName": "Coles" }, { "creatorType": "author", "firstName": "Jeremy G.", "lastName": "Frey" }, { "creatorType": "author", "firstName": "Michel B.", "lastName": "Hursthouse" }, { "creatorType": "author", "firstName": "Mark E.", "lastName": "Light" }, { "creatorType": "author", "firstName": "Andrew J.", "lastName": "Milsted" }, { "creatorType": "author", "firstName": "Leslie A.", "lastName": "Carr" }, { "creatorType": "author", "firstName": "David", "lastName": "DeRoure" }, { "creatorType": "author", "firstName": "Christopher J.", "lastName": "Gutteridge" }, { "creatorType": "author", "firstName": "Hugo R.", "lastName": "Mills" }, { "creatorType": "author", "firstName": "Ken E.", "lastName": "Meacham" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Surridge" }, { "creatorType": "author", "firstName": "Elizabeth", "lastName": "Lyon" }, { "creatorType": "author", "firstName": "Rachel", "lastName": "Heery" }, { "creatorType": "author", "firstName": "Monica", "lastName": "Duke" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Day" } ], "abstractNote": "The U.K. National Crystallography Service (NCS) has developed a prototype e-science infrastructure for the provision of a small molecule crystallography service from sample receipt to results dissemination. This paper outlines the two strands of this service, which (a) enable a user to contribute in the conduction of an experiment and (b) provide an effective route for the archival and dissemination of the arising results. Access to use the NCS facilities and expertise and a mechanism to submit samples is granted through a secure Grid infrastructure, which seamlessly provides instantaneous feedback and the ability to remotely monitor and guide diffraction experiments and stage the diffraction data to a securely accessible location. Publication of all the data and results generated during the course of the experiment, from processed data to analyzed structures, is then enabled by means of an open access data repository. The repository publishes its content through established digital libraries’ protocols, which enable harvester and aggregator services to make the data searchable and accessible.", "publicationTitle": "Journal of Chemical Information and Modeling", "publisher": "", "place": "", "date": "05/2006", "volume": "46", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "1006-1016", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1021/ci050362w", "citationKey": "", "url": "http://pubs.acs.org/doi/abs/10.1021/ci050362w", "accessDate": "2014-10-10T13:17:36Z", "PMID": "", "PMCID": "", "ISSN": "1549-9596, 1549-960X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DHFR3F6X" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "4I4VE83R", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/4I4VE83R", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/4I4VE83R", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Frey et al.", "parsedDate": "2003", "numChildren": 0 }, "data": { "key": "4I4VE83R", "version": 2, "itemType": "bookSection", "title": "Combinatorial Chemistry and the Grid", "creators": [ { "creatorType": "author", "firstName": "Jeremy G.", "lastName": "Frey" }, { "creatorType": "author", "firstName": "Mark", "lastName": "Bradley" }, { "creatorType": "author", "firstName": "Jonathan W.", "lastName": "Essex" }, { "creatorType": "author", "firstName": "Michael B.", "lastName": "Hursthouse" }, { "creatorType": "author", "firstName": "Susan, M.", "lastName": "Lewis" }, { "creatorType": "author", "firstName": "Michael, M.", "lastName": "Luck" }, { "creatorType": "author", "firstName": "Luc", "lastName": "Moreau" }, { "creatorType": "author", "firstName": "David, C.", "lastName": "De Roure" }, { "creatorType": "author", "firstName": "Michael", "lastName": "Surridge" }, { "creatorType": "author", "firstName": "Alan, H.", "lastName": "Welsh" } ], "abstractNote": "Chemistry has always made extensive use of the developing computing technology\nand available computing power though activities such as modelling, simulation and chemical structure interpretational - activities conveniently summarised as computational chemistry. Developing procedures in chemical synthesis and characterisation, particularly in the arena of parallel and combinatorial methodology, have generated ever increasing demands on both Computational Chemistry and Computer Technology. Significantly, the way in which networked services are being conceived to assist collaborative research pushes the use of data acquisition, remote interaction & control, computation, and visualisation, well beyond the traditional computational chemistry programmes, towards the basic issue of handling chemical information and knowledge. The rate at which new chemical data can now be generated in Combinatorial and Parallel synthesis and screening processes, means that the data can only realistically be handled efficiently by increased automation of the data analysis as well as the experimentation and collection. Without this automation we run the risk of generating information without the ability to understand it.", "bookTitle": "", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2003", "publisher": "", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "945-962", "ISBN": "", "DOI": "", "citationKey": "", "url": "http://eprints.soton.ac.uk/260963/1/hey_book_for_e-prints.pdf", "accessDate": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "DHFR3F6X" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "RWGHUKSW", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/RWGHUKSW", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/RWGHUKSW", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Frey", "parsedDate": "2009", "numChildren": 0 }, "data": { "key": "RWGHUKSW", "version": 2, "itemType": "journalArticle", "title": "The Value of the Semantic Web in the Laboratory", "creators": [ { "creatorType": "author", "firstName": "Jeremy G.", "lastName": "Frey" } ], "abstractNote": "The Semantic Web is beginning to impact on the wider chemical and physical sciences, beyond the earlier adopted bio-informatics. While useful in large-scale data driven science with automated processing, these technologies can also help integrate the work of smaller scale laboratories producing diverse data. The semantics aid the discovery, reliable re-use of data, provide improved provenance and facilitate automated processing by increased resilience to changes in presentation and reduced ambiguity. The Semantic Web, its tools and collections are not yet competitive with well-established solutions to current problems. It is in the reduced cost of instituting solutions to new problems that the versatility of Semantic Web- enabled data and resources will make their mark once the more general- purpose tools are more available.", "publicationTitle": "Drug Discovery Today", "publisher": "", "place": "", "date": "6/2009", "volume": "14", "issue": "11-12", "section": "", "partNumber": "", "partTitle": "", "pages": "552-561", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.drudis.2009.03.007", "citationKey": "", "url": "http://linkinghub.elsevier.com/retrieve/pii/S1359644609000737", "accessDate": "2014-10-13T13:50:50Z", "PMID": "", "PMCID": "", "ISSN": "13596446", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "ZAAKWVFP" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "D5CXAXJX", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/D5CXAXJX", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/D5CXAXJX", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Hawizy et al.", "parsedDate": "2011", "numChildren": 0 }, "data": { "key": "D5CXAXJX", "version": 2, "itemType": "journalArticle", "title": "ChemicalTagger: A Tool for Semantic Text-Mining in Chemistry", "creators": [ { "creatorType": "author", "firstName": "Lezan", "lastName": "Hawizy" }, { "creatorType": "author", "firstName": "David M.", "lastName": "Jessop" }, { "creatorType": "author", "firstName": "Nico", "lastName": "Adams" }, { "creatorType": "author", "firstName": "Peter", "lastName": "Murray-Rust" } ], "abstractNote": "The primary method for scientific communication is in the form of published scientific articles and theses which use natural language combined with domain-specific terminology. As such, they contain free owing unstructured text. Given the usefulness of data extraction from unstructured literature, we aim to show how this can be achieved for the discipline of chemistry. The highly formulaic style of writing most chemists adopt make their contributions well suited to high-throughput Natural Language Processing (NLP) approaches.", "publicationTitle": "Journal of cheminformatics", "publisher": "", "place": "", "date": "2011", "volume": "3", "issue": "1", "section": "", "partNumber": "", "partTitle": "", "pages": "17", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.biomedcentral.com/1758-2946/3/17", "accessDate": "2014-10-13T13:50:44Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "ChemicalTagger", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "ZAAKWVFP" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "X39KFQ2X", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/X39KFQ2X", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/X39KFQ2X", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "De Jong et al.", "parsedDate": "2013", "numChildren": 0 }, "data": { "key": "X39KFQ2X", "version": 2, "itemType": "journalArticle", "title": "From Data to Analysis: Linking NWChem and Avogadro with the Syntax and Semantics of Chemical Markup Language.", "creators": [ { "creatorType": "author", "firstName": "Wibe A.", "lastName": "De Jong" }, { "creatorType": "author", "firstName": "Andrew M.", "lastName": "Walker" }, { "creatorType": "author", "firstName": "Marcus D.", "lastName": "Hanwell" } ], "abstractNote": "Multidisciplinary integrated research requires the ability to couple the diverse sets of data obtained from a range of complex experiments and computer simulations. Integrating data requires semantically rich information. In this paper an end-to-end use of semantically rich data in computational chemistry is demonstrated utilizing the Chemical Markup Language (CML) framework. Semantically rich data is generated by the NWChem computational chemistry software with the FoX library and utilized by the Avogadro molecular editor for analysis and visualization.", "publicationTitle": "J. Cheminformatics", "publisher": "", "place": "", "date": "2013", "volume": "5", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "25", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.biomedcentral.com/content/pdf/1758-2946-5-25.pdf", "accessDate": "2014-10-13T13:50:47Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "From data to analysis", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "ZAAKWVFP" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "VPXCDF5I", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/VPXCDF5I", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/VPXCDF5I", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Gil et al.", "parsedDate": "2011", "numChildren": 0 }, "data": { "key": "VPXCDF5I", "version": 2, "itemType": "bookSection", "title": "Mind your Metadata: Exploiting Semantics for Configuration, Adaptation, and Provenance in Scientific Workflows", "creators": [ { "creatorType": "author", "firstName": "Yolanda", "lastName": "Gil" }, { "creatorType": "author", "firstName": "Pedro", "lastName": "Szekely" }, { "creatorType": "author", "firstName": "Sandra", "lastName": "Villamizar" }, { "creatorType": "author", "firstName": "Thomas C.", "lastName": "Harmon" }, { "creatorType": "author", "firstName": "Varun", "lastName": "Ratnakar" }, { "creatorType": "author", "firstName": "Shubham", "lastName": "Gupta" }, { "creatorType": "author", "firstName": "Maria", "lastName": "Muslea" }, { "creatorType": "author", "firstName": "Fabio", "lastName": "Silva" }, { "creatorType": "author", "firstName": "Craig A.", "lastName": "Knoblock" } ], "abstractNote": "Scientific metadata containing semantic descriptions of scientific data is expensive to capture and is typically not used across entire data analytic processes. We present an approach where semantic metadata is generated as scientific data is being prepared, and then subsequently used to configure models and to customize them to the data. The metadata captured includes sensor descriptions, data characteristics, data types, and process documentation. This metadata is then used in a workflow system to select analytic models dynamically and to set up model parameters automatically. In addition, all aspects of data processing are documented, and the system is able to generate extensive provenance records for new data products based on the metadata. As a result, the system can dynamically select analytic models based on the metadata properties of the data it is processing, generating more accurate results. We show results in analyzing stream metabolism for watershed ecosystem management.", "bookTitle": "The Semantic Web–ISWC 2011", "series": "", "seriesNumber": "", "volume": "", "numberOfVolumes": "", "edition": "", "date": "2011", "publisher": "Springer", "place": "", "originalDate": "", "originalPublisher": "", "originalPlace": "", "format": "", "pages": "65–80", "ISBN": "", "DOI": "", "citationKey": "", "url": "http://link.springer.com/chapter/10.1007/978-3-642-25093-4_5", "accessDate": "2014-10-13T13:50:59Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Mind your metadata", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "ZAAKWVFP" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "8HU5HK8N", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/8HU5HK8N", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/8HU5HK8N", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Hanwell et al.", "parsedDate": "2012", "numChildren": 0 }, "data": { "key": "8HU5HK8N", "version": 2, "itemType": "journalArticle", "title": "Avogadro: An Advanced Semantic Chemical Editor, Visualization, and Analysis Platform.", "creators": [ { "creatorType": "author", "firstName": "Marcus D.", "lastName": "Hanwell" }, { "creatorType": "author", "firstName": "Donald Ephraim", "lastName": "Curtis" }, { "creatorType": "author", "firstName": "David C.", "lastName": "Lonie" }, { "creatorType": "author", "firstName": "Tim", "lastName": "Vandermeersch" }, { "creatorType": "author", "firstName": "Eva", "lastName": "Zurek" }, { "creatorType": "author", "firstName": "Geoffrey R.", "lastName": "Hutchison" } ], "abstractNote": "The Avogadro project has developed anadvanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.", "publicationTitle": "J. Cheminformatics", "publisher": "", "place": "", "date": "2012", "volume": "4", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "17", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.biomedcentral.com/content/pdf/1758-2946-4-17.pdf", "accessDate": "2014-10-13T13:50:40Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Avogadro", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "ZAAKWVFP" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "R2IJVCGJ", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/R2IJVCGJ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/R2IJVCGJ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Caeiro et al.", "parsedDate": "2011", "numChildren": 0 }, "data": { "key": "R2IJVCGJ", "version": 2, "itemType": "conferencePaper", "title": "A Chemical Model for Dynamic Workflow Coordination", "creators": [ { "creatorType": "author", "firstName": "Manuel", "lastName": "Caeiro" }, { "creatorType": "author", "firstName": "Zsolt", "lastName": "Nemeth" }, { "creatorType": "author", "firstName": "Thierry", "lastName": "Priol" } ], "abstractNote": "This paper investigates a chemical workflow enact- ment model that is intended to coordinate workflows of large set of activities on a large number of resources in a self-evolving nature, based on a chemical analogy. The concept of chemical workflow engine is introduced for a concurrent, self-coordinating enactment exploiting as much parallelism as inherently present. The concept is aimed at supporting a generalized workflow lan- guage without any restrictions, modeling most workflow patterns, separating data and control flow, supporting dynamic changes by multiple versions and instances. The paper presents the notion and model of the chemical based coordination.", "proceedingsTitle": "", "conferenceName": "", "publisher": "IEEE", "place": "", "date": "02/2011", "eventPlace": "", "volume": "", "issue": "", "numberOfVolumes": "", "pages": "215-222", "series": "", "seriesNumber": "", "DOI": "10.1109/PDP.2011.93", "ISBN": "978-1-4244-9682-2", "citationKey": "", "url": "http://ieeexplore.ieee.org/lpdocs/epic03/wrapper.htm?arnumber=5739004", "accessDate": "2014-10-13T13:50:37Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "ZAAKWVFP" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "8MGGGQJ9", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/8MGGGQJ9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/8MGGGQJ9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Rudolphi and Goossen", "parsedDate": "2012-02-27", "numChildren": 0 }, "data": { "key": "8MGGGQJ9", "version": 2, "itemType": "journalArticle", "title": "Electronic Laboratory Notebook: The Academic Point of View", "creators": [ { "creatorType": "author", "firstName": "Felix", "lastName": "Rudolphi" }, { "creatorType": "author", "firstName": "Lukas J.", "lastName": "Goossen" } ], "abstractNote": "Based on a requirement analysis and alternative design considerations, a platform-independent electronic laboratory notebook (ELN) has been developed that specifi- cally targets academic users. Its intuitive design and numerous productivity features motivate chemical researchers and stu- dents to record their data electronically. The data are stored in a highly structured form that offers substantial benefits over laboratory notebooks written on paper with regard to data retrieval, data mining, and exchange of results.", "publicationTitle": "Journal of Chemical Information and Modeling", "publisher": "", "place": "", "date": "2012-02-27", "volume": "52", "issue": "2", "section": "", "partNumber": "", "partTitle": "", "pages": "293-301", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1021/ci2003895", "citationKey": "", "url": "http://pubs.acs.org/doi/abs/10.1021/ci2003895", "accessDate": "2015-01-10T14:18:11Z", "PMID": "", "PMCID": "", "ISSN": "1549-9596, 1549-960X", "archive": "", "archiveLocation": "", "shortTitle": "Electronic Laboratory Notebook", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "F5VMMMRC", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/F5VMMMRC", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/F5VMMMRC", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Voegele et al.", "parsedDate": "2013-07-01", "numChildren": 0 }, "data": { "key": "F5VMMMRC", "version": 2, "itemType": "journalArticle", "title": "A Universal Open-Source Electronic Laboratory Notebook", "creators": [ { "creatorType": "author", "firstName": "C.", "lastName": "Voegele" }, { "creatorType": "author", "firstName": "B.", "lastName": "Bouchereau" }, { "creatorType": "author", "firstName": "N.", "lastName": "Robinot" }, { "creatorType": "author", "firstName": "J.", "lastName": "McKay" }, { "creatorType": "author", "firstName": "P.", "lastName": "Damiecki" }, { "creatorType": "author", "firstName": "L.", "lastName": "Alteyrac" } ], "abstractNote": "Laboratory notebooks remain crucial to the activities of research communities. With the increase in generation of electronic data within both wet and dry analytical laboratories and new technolo- gies providing more efficient means of communication, Electronic Laboratory Notebooks (ELN) offer equivalent record keeping to paper-based laboratory notebooks (PLN). They additionally allow more efficient mechanisms for data sharing and retrieval, which explains the growing number of commercial ELNs available varying in size and scope but all are increasingly accepted and used by the sci- entific community. The International Agency for Research on Cancer (IARC) having already an LIMS and a Biobank Management System for respectively laboratory workflows and sample management, we have developed a free multidisciplinary ELN specifically dedicated to work notes that will be flexible enough to accommodate different types of data.", "publicationTitle": "Bioinformatics", "publisher": "", "place": "", "date": "2013-07-01", "volume": "29", "issue": "13", "section": "", "partNumber": "", "partTitle": "", "pages": "1710-1712", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1093/bioinformatics/btt253", "citationKey": "", "url": "http://bioinformatics.oxfordjournals.org/cgi/doi/10.1093/bioinformatics/btt253", "accessDate": "2015-01-10T14:18:08Z", "PMID": "", "PMCID": "", "ISSN": "1367-4803, 1460-2059", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "J7AF2382", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/J7AF2382", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/J7AF2382", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Kihlén", "parsedDate": "2005", "numChildren": 0 }, "data": { "key": "J7AF2382", "version": 2, "itemType": "journalArticle", "title": "Electronic lab notebooks–do they work in reality?", "creators": [ { "creatorType": "author", "firstName": "Mats", "lastName": "Kihlén" } ], "abstractNote": "In most organizations any new IT system is carefully scrutinized with regards to return on investment and how the system fits within corporate strategy. There have been extensive discussions about the legal validity and practical feasibility of electronic laboratory notebooks (ELN). Would they really work in the laboratory? What about electronic archiving? Usually it is assumed that the current practice is satisfactory, albeit slightly inefficient, and that any new system needs to justify its existence.", "publicationTitle": "Drug Discovery Today", "publisher": "", "place": "", "date": "2005", "volume": "10", "issue": "18", "section": "", "partNumber": "", "partTitle": "", "pages": "1205–1207", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.sciencedirect.com/science/article/pii/S1359644605035762", "accessDate": "2015-01-10T14:18:02Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "W6VRXB79", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/W6VRXB79", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/W6VRXB79", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Mohd Zaki et al.", "parsedDate": "2013", "numChildren": 0 }, "data": { "key": "W6VRXB79", "version": 2, "itemType": "journalArticle", "title": "Architecture Design of a User-Orientated Electronic Laboratory Notebook: A Case Study Within An Atmospheric Chemistry Community", "creators": [ { "creatorType": "author", "firstName": "Zulkifly", "lastName": "Mohd Zaki" }, { "creatorType": "author", "firstName": "Peter M.", "lastName": "Dew" }, { "creatorType": "author", "firstName": "Lydia M.S.", "lastName": "Lau" }, { "creatorType": "author", "firstName": "Andrew R.", "lastName": "Rickard" }, { "creatorType": "author", "firstName": "Jenny C.", "lastName": "Young" }, { "creatorType": "author", "firstName": "Tahir", "lastName": "Farooq" }, { "creatorType": "author", "firstName": "Michael J.", "lastName": "Pilling" }, { "creatorType": "author", "firstName": "Chris J.", "lastName": "Martin" } ], "abstractNote": "Data is particularly valuable to scientists when details of its provenance are known. This research concerned deploying a user-orientated electronic laboratory notebook (ELN) system within a scientific community. The ELN system supported the capture and retrieval of semantic metadata describing the provenance of the modelling activities of scientists within that community. The research was grounded within the atmospheric chemistry community but has applicability to other communities using an iterative model development process. The ELN system involved the automatic capture of metadata concerning the modelling process together with inline annotations added by the modeller explaining the reasoning for modelling decisions at each step of the process. A full realisation of the ELN system was built and evaluated by members of the atmospheric chemistry community. In order to promote reusability the ELN system architecture had domain-independent as well as domain-dependent elements. An ontology (in OWL) was used to ensure that the specific terminology of the community was used within the provenance metadata and also that it was used consistently. Other domain-independent elements of the architecture included a dynamic graphic interface that allowed the modeller to view his/her modelling history. This was recorded as a set of nodes each pointing to the stored provenance metadata associated with a specific simulation run. In addition, there was an innovative mechanism that enabled the modeller to navigate through the various nodes. The navigation process supported making comparisons between different nodes: a facility that users found particularly valuable. Members of the atmospheric chemistry community took part in a two-day summative evaluation of the ELN system. This confirmed its value to the modellers and it is now being introduced more widely across the modelling community. In addition, the research proposes a methodology for transferring this ELN system to other modelling communities making use of the domain-independent elements of the architecture.", "publicationTitle": "Future Generation Computer Systems", "publisher": "", "place": "", "date": "10/2013", "volume": "29", "issue": "8", "section": "", "partNumber": "", "partTitle": "", "pages": "2182-2196", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1016/j.future.2013.04.011", "citationKey": "", "url": "http://linkinghub.elsevier.com/retrieve/pii/S0167739X1300071X", "accessDate": "2015-01-10T14:13:08Z", "PMID": "", "PMCID": "", "ISSN": "0167739X", "archive": "", "archiveLocation": "", "shortTitle": "Architecture design of a user-orientated electronic laboratory notebook", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "JUEITV69", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/JUEITV69", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/JUEITV69", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Hughes et al.", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "JUEITV69", "version": 2, "itemType": "journalArticle", "title": "The Semantic Smart Laboratory: a System for Supporting the Chemical eScientist", "creators": [ { "creatorType": "author", "firstName": "Gareth", "lastName": "Hughes" }, { "creatorType": "author", "firstName": "Hugo", "lastName": "Mills" }, { "creatorType": "author", "firstName": "David", "lastName": "De Roure" }, { "creatorType": "author", "firstName": "Jeremy G.", "lastName": "Frey" }, { "creatorType": "author", "firstName": "Luc", "lastName": "Moreau" }, { "creatorType": "author", "firstName": "m. c.", "lastName": "schraefel" }, { "creatorType": "author", "firstName": "Graham", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Ed", "lastName": "Zaluska" } ], "abstractNote": "One goal of eScience is to enable the end-to-end publication of experiments and results. In the Combechem project we have developed an innovative human-centred system which captures the process of a chemistry experiment from plan to execution. The system comprises an electronic lab book replacement, which has been successfully trialled\nin a synthetic organic chemistry laboratory, and a flexible back-end storage system. Working closely with the users, we found that a light touch and a high degree of flexibility was required in the user interface. In this paper, we concentrate on the representation and storage of human-scale experiment metadata, introducing an ontology to describe the record of an experiment, and a storage system for the data from our lab book software. Just as the interfaces need to be flexible to cope with whatever a chemist wishes to record, so the back end solutions need\nto be similarly flexible to store any metadata that may be created. The storage system is based on Semantic Web technologies, such as RDF, and Web Services. It gives a much higher degree of flexibility to the type of metadata it can store, compared to the use of rigid relational databases.", "publicationTitle": "Organic & Biomolecular Chemistry", "publisher": "", "place": "", "date": "2004", "volume": "2", "issue": "22", "section": "", "partNumber": "", "partTitle": "", "pages": "3284", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1039/b410075a", "citationKey": "", "url": "http://xlink.rsc.org/?DOI=b410075a", "accessDate": "2014-10-10T13:02:38Z", "PMID": "", "PMCID": "", "ISSN": "1477-0520, 1477-0539", "archive": "", "archiveLocation": "", "shortTitle": "The semantic smart laboratory", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "ST_8" } ], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "RT9TXHP9", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/RT9TXHP9", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/RT9TXHP9", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Taylor", "parsedDate": "2006", "numChildren": 0 }, "data": { "key": "RT9TXHP9", "version": 2, "itemType": "journalArticle", "title": "The Status of Electronic Laboratory Notebooks for Chemistry and Biology", "creators": [ { "creatorType": "author", "firstName": "Keith T.", "lastName": "Taylor" } ], "abstractNote": "Documenting an experiment in a way that ensures that the record can act as evidence to support a patent claim or to demonstrate compliance with the US Food and Drug Administration's (FDA's) predicate rules, puts demands on an electronic laboratory notebook (ELN) that are not trivial. The 1996 General Agreement on Tariffs and Trade (GATT) allowed notebook records that were generated outside of the US to be used to claim precedence in US patent claims. This agreement spurred interest in the development of ELNs in Europe. The pharmaceutical research process became dependent on computer systems during the latter part of the 1990s, and this also led to a wider interest in ELNs. More recently, the FDA began to encourage submissions in an all- electronic form, leading to great interest in the use of ELNs in development and manufacturing. As a result of these influences, the pharmaceutical industry is now actively pursuing ELN evaluations and implementations. This article describes some of the early efforts and the recent drivers for ELN adoption. The state of the ELN market in 2005 is also described.", "publicationTitle": "Current Opinion in Drug Discovery and Development", "publisher": "", "place": "", "date": "2006", "volume": "9", "issue": "3", "section": "", "partNumber": "", "partTitle": "", "pages": "348", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://www.atriumresearch.com/library/Taylor_Electronic_laboratory_notebooks.pdf", "accessDate": "2014-10-13T12:56:08Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "ST_10" } ], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "WPDJP8ES", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/WPDJP8ES", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/WPDJP8ES", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Cooke and others", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "WPDJP8ES", "version": 2, "itemType": "journalArticle", "title": "Signature Flip and Clip: Virtually Flipping and Dog Earing Pages in a Digital Lab Book", "creators": [ { "creatorType": "author", "firstName": "Ray", "lastName": "Cooke" }, { "creatorType": "author", "name": "others" } ], "abstractNote": "Paper-based lab books have been used successfully by scientists for hundreds of years. The historic success of the lab book has much to do with the affordances of paper: ease of data entry, robustness of the media, rapid access to previous conent, ease of marking pages of interest. We describe Signature Flip and Clip, an interaction technique that provides the affordances of two of the attributes of a paper lab book: flipping through pages of experiments and dog earing information of current interest. We describe our approach, and its deployment within the Smarttea Lab Book system [5], and present the results of a design test of the system with chemists, and plans for generalizing the technique.", "publicationTitle": "", "publisher": "", "place": "", "date": "2004", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "", "citationKey": "", "url": "http://eprints.soton.ac.uk/259251/", "accessDate": "2014-10-10T13:02:35Z", "PMID": "", "PMCID": "", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Signature Flip and Clip", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "ST_7" } ], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "GKCB7GEQ", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/GKCB7GEQ", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/GKCB7GEQ", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Harvey et al.", "parsedDate": "2014-08-29", "numChildren": 0 }, "data": { "key": "GKCB7GEQ", "version": 2, "itemType": "journalArticle", "title": "Digital data Repositories in Chemistry and their Integration with Journals and Electronic Notebooks", "creators": [ { "creatorType": "author", "firstName": "Matthew", "lastName": "Harvey" }, { "creatorType": "author", "firstName": "Nicholas", "lastName": "Mason" }, { "creatorType": "author", "firstName": "Henry S", "lastName": "Rzepa" } ], "abstractNote": "We discuss the concept of recasting the data- rich scientific journal article into two components, a narrative and separate data components, each of which is assigned a persistent digital object identifier. Doing so allows each of these components to exist in an environment optimized for purpose. We make use of a poorly-known feature of the handle system for assigning persistent identifiers that allows an individual data file from a larger file set to be retrieved according to its file name or its MIME type. The data objects allow facile visualization and retrieval for reuse of the data and facilitates other operations such as data mining. Examples from five recently published articles illustrate these concepts.", "publicationTitle": "Journal of Chemical Information and Modeling", "publisher": "", "place": "", "date": "2014-08-29", "volume": "", "issue": "", "section": "", "partNumber": "", "partTitle": "", "pages": "140829132040008", "series": "", "seriesTitle": "", "seriesText": "", "journalAbbreviation": "", "DOI": "10.1021/ci500302p", "citationKey": "", "url": "http://pubs.acs.org/doi/abs/10.1021/ci500302p", "accessDate": "2014-10-13T14:05:52Z", "PMID": "", "PMCID": "", "ISSN": "1549-9596, 1549-960X", "archive": "", "archiveLocation": "", "shortTitle": "", "language": "en", "libraryCatalog": "CrossRef", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "ST_13" } ], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "C65N9ZNE", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/C65N9ZNE", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/C65N9ZNE", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Smith and others", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "C65N9ZNE", "version": 2, "itemType": "conferencePaper", "title": "The Radial Scroll tool: Scrolling Support for Stylus-or Touch-Based Document Navigation", "creators": [ { "creatorType": "author", "firstName": "Gary M.", "lastName": "Smith" }, { "creatorType": "author", "name": "others" } ], "abstractNote": "We present radial scroll, an interface widget to support scrolling particularly on either small or large scale touch displays. Instead of dragging a elevator in a scroll bar, or using repetitive key presses to page up or down, users gesture anywhere on the document surface such that clockwise gestures advance the document; counter clockwise gestures reverse the document. We describe our prototype implementation and discuss the results of an initial user study.", "proceedingsTitle": "Proceedings of the 17th annual ACM symposium on User interface software and technology", "conferenceName": "", "publisher": "ACM", "place": "", "date": "2004", "eventPlace": "", "volume": "", "issue": "", "numberOfVolumes": "", "pages": "53–56", "series": "", "seriesNumber": "", "DOI": "", "ISBN": "", "citationKey": "", "url": "http://dl.acm.org/citation.cfm?id=1029641", "accessDate": "2014-10-10T13:02:32Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "The radial scroll tool", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "ST_6" } ], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } }, { "key": "96UQBK2V", "version": 2, "library": { "type": "group", "id": 321672, "name": "SamiPhD", "links": { "alternate": { "href": "https://www.zotero.org/groups/samiphd", "type": "text/html" } } }, "links": { "self": { "href": "https://api.zotero.org/groups/321672/items/96UQBK2V", "type": "application/json" }, "alternate": { "href": "https://www.zotero.org/groups/samiphd/items/96UQBK2V", "type": "text/html" } }, "meta": { "createdByUser": { "id": 1939229, "username": "skanza", "name": "Samantha Kanza", "links": { "alternate": { "href": "https://www.zotero.org/skanza", "type": "text/html" } } }, "creatorSummary": "Hughes et al.", "parsedDate": "2004", "numChildren": 0 }, "data": { "key": "96UQBK2V", "version": 2, "itemType": "conferencePaper", "title": "Breaking the Book: Translating the Chemistry Lab Book into a Pervasive Computing Lab Environment", "creators": [ { "creatorType": "author", "firstName": "Gareth V.", "lastName": "Hughes" }, { "creatorType": "author", "firstName": "Hugo R.", "lastName": "Mills" }, { "creatorType": "author", "firstName": "Graham", "lastName": "Smith" }, { "creatorType": "author", "firstName": "Terry R.", "lastName": "Payne" }, { "creatorType": "author", "firstName": "Jeremy", "lastName": "Frey" }, { "creatorType": "author", "name": "others" } ], "abstractNote": "The UK e-Science programme is relying on the evolution of the paper lab book into a pervasive data gathering lab system. To date take up of existing commercial or research lab book replacement systems has not been great. In this paper, we reconsider both the role of the lab book in the experimental cycle, as well as its affective and experiential properties as an artefact, in order to design an e-Science lab book that will be acceptable to the scientists who will use it. To this end we combined and extended existing design analysis models in order to assess the artefact functionally and experientially. We present the approach we developed, the prototype we designed based on our analysis, and the results of the formative study we performed of the artefact in real use. We show that our design elicitation method strongly contributed to the success of our prototype’s take up.", "proceedingsTitle": "Proceedings of the SIGCHI conference on Human factors in computing systems", "conferenceName": "", "publisher": "ACM", "place": "", "date": "2004", "eventPlace": "", "volume": "", "issue": "", "numberOfVolumes": "", "pages": "25–32", "series": "", "seriesNumber": "", "DOI": "", "ISBN": "", "citationKey": "", "url": "http://dl.acm.org/citation.cfm?id=985696", "accessDate": "2014-10-10T13:02:23Z", "ISSN": "", "archive": "", "archiveLocation": "", "shortTitle": "Breaking the book", "language": "", "libraryCatalog": "Google Scholar", "callNumber": "", "rights": "", "extra": "", "tags": [ { "tag": "ST_3" } ], "collections": [ "NINJ7FD3" ], "relations": {}, "dateAdded": "2015-01-21T13:50:41Z", "dateModified": "2015-01-21T13:50:41Z" } } ]