{ "types" : { "Bookmark" : { "pluralLabel" : "Bookmarks" }, "Publication" : { "pluralLabel" : "Publications" }, "GoldStandardPublication" : { "pluralLabel" : "GoldStandardPublications" }, "GoldStandardBookmark" : { "pluralLabel" : "GoldStandardBookmarks" }, "Tag" : { "pluralLabel" : "Tags" }, "User" : { "pluralLabel" : "Users" }, "Group" : { "pluralLabel" : "Groups" }, "Sphere" : { "pluralLabel" : "Spheres" } }, "properties" : { "count" : { "valueType" : "number" }, "date" : { "valueType" : "date" }, "changeDate" : { "valueType" : "date" }, "url" : { "valueType" : "url" }, "id" : { "valueType" : "url" }, "tags" : { "valueType" : "item" }, "user" : { "valueType" : "item" } }, "items" : [ { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/efc785e0e1d42b64c99e71ed046f2191/diglezakis", "tags" : [ "forschungsdaten","metadata","researchObjects","tools" ], "intraHash" : "efc785e0e1d42b64c99e71ed046f2191", "label" : "Core Software Libraries", "user" : "diglezakis", "description" : "", "date" : "2020-02-01 13:10:40", "changeDate" : "2020-02-01 12:10:40", "count" : 1, "url" : "https://frictionlessdata.io/software/" } , { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/52ac3b69b0b591470c4ef0145d167f64/diglezakis", "tags" : [ "forschungsdaten","computing","researchObjects","platform" ], "intraHash" : "52ac3b69b0b591470c4ef0145d167f64", "label" : "GitHub - whole-tale/whole-tale: The Whole Tale - Merging Science and Cyberinfrastructure Pathway", "user" : "diglezakis", "description" : "The Whole Tale - Merging Science and Cyberinfrastructure Pathway - whole-tale/whole-tale", "date" : "2019-10-23 13:23:42", "changeDate" : "2019-10-23 11:23:42", "count" : 1, "url" : "https://github.com/whole-tale/whole-tale" } , { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/0d127d75c80d297edf38fc8f1e6e5d61/diglezakis", "tags" : [ "forschungsdaten","researchObjects" ], "intraHash" : "0d127d75c80d297edf38fc8f1e6e5d61", "label" : "Developing, Packaging and Sharing Reproducible Research Objects: The Whole Tale Approach | DataONE", "user" : "diglezakis", "description" : "", "date" : "2019-10-23 13:09:27", "changeDate" : "2019-10-23 11:09:27", "count" : 1, "url" : "https://www.dataone.org/webinars/developing-packaging-and-sharing-reproducible-research-objects-whole-tale-approach" } , { "type" : "Bookmark", "id" : "https://puma.ub.uni-stuttgart.de/url/7b3acbad11e534852a0dc31c0db61d1f/diglezakis", "tags" : [ "bagit","forschungsdaten","metadata","researchObjects" ], "intraHash" : "7b3acbad11e534852a0dc31c0db61d1f", "label" : "datacrate/data_crate_specification_v0.2.md at new_draft/0.2 · UTS-eResearch/datacrate · GitHub", "user" : "diglezakis", "description" : "This document specifies a method of organising file-based data with associated metadata, known as DataCrate in both human and machine readable formats, based on the schema.org linked-data vocabularly, supplemented with terms from the SPAR ontologies and [PCDM] where schema.org does not have coverage. The motivation for this work comes from the research domain.\r\n\r\nA DataCrate is a dataset a set of files contained in a single directory. There are two ways of organizing a DataCrate.\r\n\r\n For working data or data that does not need to be distributed with checksums, a Working DataCrate is a plain-old directory containing payload data files, with two metadata files at the root; one for humans and one for machines.\r\n\r\n For distribution, or archiving; where integrity is important, a Bagged DataCrate is a BagIt bag conforming to the DataCrate BagIt profile with the payload files in the /data directory. 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Wilkinson","Finn Bacall","Stian Soiland-Reyes","Simone Leo","Luca Pireddu","Stuart Owen","Nick Juty","José M. Fernández","Tom Brown","Hervé Ménager","Björn Grüning","Salvador Capella-Gutierrez","Frederik Coppens","Carole Goble" ], "authors": [ {"first" : "Ove Johan Ragnar", "last" : "Gustafsson"}, {"first" : "Sean R.", "last" : "Wilkinson"}, {"first" : "Finn", "last" : "Bacall"}, {"first" : "Stian", "last" : "Soiland-Reyes"}, {"first" : "Simone", "last" : "Leo"}, {"first" : "Luca", "last" : "Pireddu"}, {"first" : "Stuart", "last" : "Owen"}, {"first" : "Nick", "last" : "Juty"}, {"first" : "José M.", "last" : "Fernández"}, {"first" : "Tom", "last" : "Brown"}, {"first" : "Hervé", "last" : "Ménager"}, {"first" : "Björn", "last" : "Grüning"}, {"first" : "Salvador", "last" : "Capella-Gutierrez"}, {"first" : "Frederik", "last" : "Coppens"}, {"first" : "Carole", "last" : "Goble"} ], "volume": "12","number": "1","pages": "837--","abstract": "The rising popularity of computational workflows is driven by the need for repetitive and scalable data processing, sharing of processing know-how, and transparent methods. As both combined records of analysis and descriptions of processing steps, workflows should be reproducible, reusable, adaptable, and available. Workflow sharing presents opportunities to reduce unnecessary reinvention, promote reuse, increase access to best practice analyses for non-experts, and increase productivity. In reality, workflows are scattered and difficult to find, in part due to the diversity of available workflow engines and ecosystems, and because workflow sharing is not yet part of research practice. WorkflowHub provides a unified registry for all computational workflows that links to community repositories, and supports both the workflow lifecycle and making workflows findable, accessible, interoperable, and reusable (FAIR). By interoperating with diverse platforms, services, and external registries, WorkflowHub adds value by supporting workflow sharing, explicitly assigning credit, enhancing FAIRness, and promoting workflows as scholarly artefacts. The registry has a global reach, with hundreds of research organisations involved, and more than 800 workflows registered.", "issn" : "20524463", "refid" : "Gustafsson2025", "doi" : "10.1038/s41597-025-04786-3", "bibtexKey": "gustafsson2025workflowhub" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/290b2c8f8aab0ac6dff4ae2c7d9bf47d8/diglezakis", "tags" : [ "forschungsdaten","metadata","useCases","researchObjects" ], "intraHash" : "90b2c8f8aab0ac6dff4ae2c7d9bf47d8", "interHash" : "3d842eaea164685fae9c9bd99b33c5c8", "label" : "Using a suite of ontologies for preserving workflow-centric research objects", "user" : "diglezakis", "description" : "Using a suite of ontologies for preserving workflow-centric research objects - ScienceDirect", "date" : "2020-09-24 13:53:56", "changeDate" : "2020-09-24 11:55:20", "count" : 2, "pub-type": "article", "journal": "Journal of Web Semantics", "year": "2015", "url": "http://www.sciencedirect.com/science/article/pii/S1570826815000049", "author": [ "Khalid Belhajjame","Jun Zhao","Daniel Garijo","Matthew Gamble","Kristina Hettne","Raul Palma","Eleni Mina","Oscar Corcho","José Manuel Gómez-Pérez","Sean Bechhofer","Graham Klyne","Carole Goble" ], "authors": [ {"first" : "Khalid", "last" : "Belhajjame"}, {"first" : "Jun", "last" : "Zhao"}, {"first" : "Daniel", "last" : "Garijo"}, {"first" : "Matthew", "last" : "Gamble"}, {"first" : "Kristina", "last" : "Hettne"}, {"first" : "Raul", "last" : "Palma"}, {"first" : "Eleni", "last" : "Mina"}, {"first" : "Oscar", "last" : "Corcho"}, {"first" : "José Manuel", "last" : "Gómez-Pérez"}, {"first" : "Sean", "last" : "Bechhofer"}, {"first" : "Graham", "last" : "Klyne"}, {"first" : "Carole", "last" : "Goble"} ], "volume": "32","pages": "16 - 42","abstract": "Scientific workflows are a popular mechanism for specifying and automating data-driven in silico experiments. A significant aspect of their value lies in their potential to be reused. Once shared, workflows become useful building blocks that can be combined or modified for developing new experiments. However, previous studies have shown that storing workflow specifications alone is not sufficient to ensure that they can be successfully reused, without being able to understand what the workflows aim to achieve or to re-enact them. To gain an understanding of the workflow, and how it may be used and repurposed for their needs, scientists require access to additional resources such as annotations describing the workflow, datasets used and produced by the workflow, and provenance traces recording workflow executions. In this article, we present a novel approach to the preservation of scientific workflows through the application of research objects\u2014aggregations of data and metadata that enrich the workflow specifications. Our approach is realised as a suite of ontologies that support the creation of workflow-centric research objects. Their design was guided by requirements elicited from previous empirical analyses of workflow decay and repair. The ontologies developed make use of and extend existing well known ontologies, namely the Object Reuse and Exchange (ORE) vocabulary, the Annotation Ontology (AO) and the W3C PROV ontology (PROVO). We illustrate the application of the ontologies for building Workflow Research Objects with a case-study that investigates Huntington\u2019s disease, performed in collaboration with a team from the Leiden University Medial Centre (HG-LUMC). Finally we present a number of tools developed for creating and managing workflow-centric research objects.", "issn" : "1570-8268", "doi" : "https://doi.org/10.1016/j.websem.2015.01.003", "bibtexKey": "BELHAJJAME201516" } , { "type" : "Publication", "id" : "https://puma.ub.uni-stuttgart.de/bibtex/294a0c5222ce8a6c7729e068ede08e314/diglezakis", "tags" : [ "forschungsdaten","metadata","researchObjects" ], "intraHash" : "94a0c5222ce8a6c7729e068ede08e314", "interHash" : "e0b0e6d2b15177175520ffe539b5ab39", "label" : "Using a suite of ontologies for preserving workflow-centric research objects", "user" : "diglezakis", "description" : "", "date" : "2017-10-24 10:41:17", "changeDate" : "2017-12-30 08:58:31", "count" : 1, "pub-type": "article", "journal": "Web Semantics: Science, Services and Agents on the World Wide Web", "year": "2015", "url": "https://doi.org/10.1016/j.websem.2015.01.003", "author": [ "Khalid Belhajjame","Jun Zhao","Daniel Garijo","Matthew Gable","Kristina Hettne","Raul Palma","Eleni Mina","Oscar Corcho","José Manuel Gómez-Pérez","Sean Bechofer","Graham Klyne","Carole Goble" ], "authors": [ {"first" : "Khalid", "last" : "Belhajjame"}, {"first" : "Jun", "last" : "Zhao"}, {"first" : "Daniel", "last" : "Garijo"}, {"first" : "Matthew", "last" : "Gable"}, {"first" : "Kristina", "last" : "Hettne"}, {"first" : "Raul", "last" : "Palma"}, {"first" : "Eleni", "last" : "Mina"}, {"first" : "Oscar", "last" : "Corcho"}, {"first" : "José Manuel", "last" : "Gómez-Pérez"}, {"first" : "Sean", "last" : "Bechofer"}, {"first" : "Graham", "last" : "Klyne"}, {"first" : "Carole", "last" : "Goble"} ], "volume": "32","pages": "16-42","abstract": "Scientific workflows are a popular mechanism for specifying and automating data-driven in silico experiments. A significant aspect of their value lies in their potential to be reused. Once shared, workflows become useful building blocks that can be combined or modified for developing new experiments. However, previous studies have shown that storing workflow specifications alone is not sufficient to ensure that they can be successfully reused, without being able to understand what the workflows aim to achieve or to re-enact them. To gain an understanding of the workflow, and how it may be used and repurposed for their needs, scientists require access to additional resources such as annotations describing the workflow, datasets used and produced by the workflow, and provenance traces recording workflow executions.\r\n\r\nIn this article, we present a novel approach to the preservation of scientific workflows through the application of research objects\u2014aggregations of data and metadata that enrich the workflow specifications. Our approach is realised as a suite of ontologies that support the creation of workflow-centric research objects. Their design was guided by requirements elicited from previous empirical analyses of workflow decay and repair. The ontologies developed make use of and extend existing well known ontologies, namely the Object Reuse and Exchange (ORE) vocabulary, the Annotation Ontology (AO) and the W3C PROV ontology (PROVO). We illustrate the application of the ontologies for building Workflow Research Objects with a case-study that investigates Huntington\u2019s disease, performed in collaboration with a team from the Leiden University Medial Centre (HG-LUMC). Finally we present a number of tools developed for creating and managing workflow-centric research objects.", "doi" : "10.1016/j.websem.2015.01.003", "bibtexKey": "belhajjame2015using" } ] }