{ "access": { "embargo": { "active": false, "reason": null }, "files": "public", "record": "public", "status": "open" }, "created": "2018-12-05T10:57:39.260619+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "files": { "count": 1, "enabled": true, "entries": { "CWLProv.pdf": { "checksum": "md5:a3f5abeeeff1a7c81b26edc54b009c0f", "ext": "pdf", "id": "d3ccdddb-a999-4d2a-954f-5061543c1426", "key": "CWLProv.pdf", "metadata": null, "mimetype": "application/pdf", "size": 6214005 } }, "order": [], "total_bytes": 6214005 }, "id": "1966881", "is_draft": false, "is_published": true, "links": { "access": "https://zenodo.org/api/records/1966881/access", "access_links": "https://zenodo.org/api/records/1966881/access/links", "access_request": "https://zenodo.org/api/records/1966881/access/request", "access_users": "https://zenodo.org/api/records/1966881/access/users", "archive": "https://zenodo.org/api/records/1966881/files-archive", "archive_media": "https://zenodo.org/api/records/1966881/media-files-archive", "communities": "https://zenodo.org/api/records/1966881/communities", "communities-suggestions": "https://zenodo.org/api/records/1966881/communities-suggestions", "doi": "https://doi.org/10.5281/zenodo.1966881", "draft": "https://zenodo.org/api/records/1966881/draft", "files": "https://zenodo.org/api/records/1966881/files", "latest": "https://zenodo.org/api/records/1966881/versions/latest", "latest_html": "https://zenodo.org/records/1966881/latest", "media_files": "https://zenodo.org/api/records/1966881/media-files", "parent": "https://zenodo.org/api/records/1208477", "parent_doi": "https://zenodo.org/doi/10.5281/zenodo.1208477", "parent_html": "https://zenodo.org/records/1208477", "requests": "https://zenodo.org/api/records/1966881/requests", "reserve_doi": "https://zenodo.org/api/records/1966881/draft/pids/doi", "self": "https://zenodo.org/api/records/1966881", "self_doi": "https://zenodo.org/doi/10.5281/zenodo.1966881", "self_html": "https://zenodo.org/records/1966881", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:1966881/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:1966881/sequence/default", "versions": "https://zenodo.org/api/records/1966881/versions" }, "media_files": { "count": 0, "enabled": false, "entries": {}, "order": [], "total_bytes": 0 }, "metadata": { "additional_descriptions": [ { "description": "Submitted to GigaScience (GIGA-D-18-00483)", "type": { "id": "notes", "title": { "de": "Anmerkungen", "en": "Notes" } } } ], "contributors": [ { "affiliations": [ { "name": "Curoverse; Common Workflow Language" } ], "person_or_org": { "family_name": "Peter Amstutz", "identifiers": [ { "identifier": "0000-0003-3566-7705", "scheme": "orcid" } ], "name": "Peter Amstutz", "type": "personal" }, "role": { "id": "other", "title": { "de": "Andere", "en": "Other" } } }, { "affiliations": [ { "name": "EMBL-EBI" } ], "person_or_org": { "family_name": "Pau Ruiz Safont", "identifiers": [ { "identifier": "0000-0002-1827-331X", "scheme": "orcid" } ], "name": "Pau Ruiz Safont", "type": "personal" }, "role": { "id": "other", "title": { "de": "Andere", "en": "Other" } } }, { "person_or_org": { "family_name": "Pjotr Prins", "identifiers": [ { "identifier": "0000-0002-8021-9162", "scheme": "orcid" } ], "name": "Pjotr Prins", "type": "personal" }, "role": { "id": "other", "title": { "de": "Andere", "en": "Other" } } }, { "affiliations": [ { "name": "Harvard School of Public Health" } ], "person_or_org": { "family_name": "Brad Chapman", "identifiers": [ { "identifier": "0000-0002-3026-1856", "scheme": "orcid" } ], "name": "Brad Chapman", "type": "personal" }, "role": { "id": "other", "title": { "de": "Andere", "en": "Other" } } }, { "affiliations": [ { "name": "RTI international" } ], "person_or_org": { "family_name": "Christopher Ball", "identifiers": [ { "identifier": "0000-0003-3523-5312", "scheme": "orcid" } ], "name": "Christopher Ball", "type": "personal" }, "role": { "id": "other", "title": { "de": "Andere", "en": "Other" } } }, { "affiliations": [ { "name": "University of California, Santa Cruz" } ], "person_or_org": { "family_name": "Lon Blauvelt", "identifiers": [ { "identifier": "0000-0001-8352-873X", "scheme": "orcid" } ], "name": "Lon Blauvelt", "type": "personal" }, "role": { "id": "other", "title": { "de": "Andere", "en": "Other" } } } ], "creators": [ { "affiliations": [ { "name": "The University of Melbourne; Common Workflow Language project" } ], "person_or_org": { "family_name": "Farah Zaib Khan", "identifiers": [ { "identifier": "0000-0002-6337-3037", "scheme": "orcid" } ], "name": "Farah Zaib Khan", "type": "personal" } }, { "affiliations": [ { "name": "The University of Manchester; Common Workflow Language project" } ], "person_or_org": { "family_name": "Stian Soiland-Reyes", "identifiers": [ { "identifier": "0000-0001-9842-9718", "scheme": "orcid" } ], "name": "Stian Soiland-Reyes", "type": "personal" } }, { "affiliations": [ { "name": "The University of Melbourne" } ], "person_or_org": { "family_name": "Richard O. Sinnott", "identifiers": [ { "identifier": "0000-0001-5998-222X", "scheme": "orcid" } ], "name": "Richard O. Sinnott", "type": "personal" } }, { "affiliations": [ { "name": "The University of Melbourne" } ], "person_or_org": { "family_name": "Andrew Lonie", "identifiers": [ { "identifier": "0000-0002-2006-3856", "scheme": "orcid" } ], "name": "Andrew Lonie", "type": "personal" } }, { "affiliations": [ { "name": "The University of Manchester" } ], "person_or_org": { "family_name": "Carole Goble", "identifiers": [ { "identifier": "0000-0003-1219-2137", "scheme": "orcid" } ], "name": "Carole Goble", "type": "personal" } }, { "affiliations": [ { "name": "Common Workflow Language project" } ], "person_or_org": { "family_name": "Michael R. Crusoe", "identifiers": [ { "identifier": "0000-0002-2961-9670", "scheme": "orcid" } ], "name": "Michael R. Crusoe", "type": "personal" } } ], "description": "
Background: The automation of data analysis in the form of scientific workflows has become a widely adopted practice in many fields of research. Computationally driven data-intensive experiments using workflows enable Automation, Scaling, Adaption and Provenance support (ASAP). However, there are still several challenges associated with the effective sharing, publication and reproducibility of such workflows due to the incomplete capture of provenance and lack of interoperability between different technical (software) platforms.
\n\nResults: Based on best practice recommendations identified from literature on workflow design, sharing and publishing, we define a hierarchical provenance framework to achieve uniformity in the provenance and support comprehensive and fully re-executable workflows equipped with domain-specific information. To realise this framework, we present CWLProv, a standard-based format to represent any workflow-based computational analysis to produce workflow output artefacts that satisfy the various levels of provenance. We utilise open source community-driven standards; interoperable workflow definitions in Common Workflow Language (CWL), structured provenance representation using the W3C PROV model, and resource aggregation and sharing as workflow-centric Research Objects (RO) generated along with the final outputs of a given workflow enactment. We demonstrate the utility of this approach through a practical implementation of CWLProv and evaluation using real-life genomic workflows developed by independent groups.
\n\nConclusions: The underlying principles of the standards utilised by CWLProv enable semantically-rich and executable Research Objects that capture computational workflows with retrospective provenance such that any platform supporting CWL will be able to understand the analysis, re-use the methods for partial re-runs, or reproduce the analysis to validate the published findings.
", "funding": [ { "award": { "acronym": "IBISBA 1.0", "id": "00k4n6c32::730976", "identifiers": [ { "identifier": "https://cordis.europa.eu/projects/730976", "scheme": "url" } ], "number": "730976", "program": "H2020", "title": { "en": "Industrial Biotechnology Innovation and Synthetic Biology Accelerator" } }, "funder": { "id": "00k4n6c32", "name": "European Commission" } }, { "award": { "acronym": "BioExcel", "id": "00k4n6c32::675728", "identifiers": [ { "identifier": "https://cordis.europa.eu/projects/675728", "scheme": "url" } ], "number": "675728", "program": "H2020", "title": { "en": "Centre of Excellence for Biomolecular Research" } }, "funder": { "id": "00k4n6c32", "name": "European Commission" } } ], "publication_date": "2018-12-04", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.1109/BigData.2016.7840618", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" }, { "identifier": "10.5281/zenodo.592090", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" }, { "identifier": "10.5281/zenodo.51314", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" }, { "identifier": "https://zenodo.org/record/1304969", "relation_type": { "id": "isdocumentedby", "title": { "de": "Wird dokumentiert von", "en": "Is documented by" } }, "scheme": "url" }, { "identifier": "10.17632/xnwncxpw42.1", "relation_type": { "id": "issupplementedby", "title": { "de": "Wird erg\u00e4nzt durch", "en": "Is supplemented by" } }, "scheme": "doi" }, { "identifier": "10.17632/6wtpgr3kbj.1", "relation_type": { "id": "issupplementedby", "title": { "de": "Wird erg\u00e4nzt durch", "en": "Is supplemented by" } }, "scheme": "doi" }, { "identifier": "10.17632/97hj93mkfd.3", "relation_type": { "id": "issupplementedby", "title": { "de": "Wird erg\u00e4nzt durch", "en": "Is supplemented by" } }, "scheme": "doi" }, { "identifier": "10.5281/zenodo.1471376", "relation_type": { "id": "haspart", "title": { "de": "Umfasst folgenden Teil", "en": "Has part" } }, "scheme": "doi" }, { "identifier": "10.5281/zenodo.1471585", "relation_type": { "id": "haspart", "title": { "de": "Umfasst folgenden Teil", "en": "Has part" } }, "scheme": "doi" }, { "identifier": "10.5281/zenodo.1471589", "relation_type": { "id": "haspart", "title": { "de": "Umfasst folgenden Teil", "en": "Has part" } }, "scheme": "doi" } ], "resource_type": { "id": "publication-preprint", "title": { "de": "Preprint", "en": "Preprint" } }, "rights": [ { "description": { "en": "The Creative Commons Attribution license allows re-distribution and re-use of a licensed work on the condition that the creator is appropriately credited." }, "icon": "cc-by-icon", "id": "cc-by-4.0", "props": { "scheme": "spdx", "url": "https://creativecommons.org/licenses/by/4.0/legalcode" }, "title": { "en": "Creative Commons Attribution 4.0 International" } } ], "subjects": [ { "subject": "Provenance" }, { "subject": "Common Workflow Language" }, { "subject": "CWL" }, { "subject": "Research Object" }, { "subject": "RO" }, { "subject": "BagIt" }, { "subject": "Interoperability" }, { "subject": "Scientific Workflows" }, { "subject": "Containers" } ], "title": "Sharing interoperable workflow provenance: A review of best practices and their practical application in CWLProv" }, "parent": { "access": { "owned_by": { "user": 4363 } }, "communities": { "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2018-02-26T13:21:51.113075+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "23d53652-d7fb-467a-9e6e-3c0714cc35c9", "links": {}, "metadata": { "curation_policy": "This Zenodo community welcomes submissions of preprints, Open Access articles and presentation and any FAIR Research Data packing formats (e.g. Research Objects, RO-Crate, BagIt, COMBINE archive), covering topics including, but not limited to:
Research Object publication, archiving and curation
Research Object creation and manipulation
Research Object exploration and visualization
Research Object evolution, derivation and provenance
Handling Big Data in Research Objects
Data Archive packaging and formats
Rich metadata of research data and software
Alignments with community efforts
Citation and attribution of research data and software
Annotation and peer review of research data
Distributed data publication (blockchain, nanopublication)
Driving adoption within current scholarly communications ecosystem
Research Object model domain extensions
Research Object granular access control approaches
Research Object social impact metrics
Self-contained executable Research Objects (i.e., including execution environment description)
Submissions must use an open license, if you are not sure use Creative Commons Attribution 4.0 (for text, figures, data, metadata) or Apache License 2.0 (for software, workflows, scripts).
", "description": "For and about Research Objects using the RO-Crate standard, classic RO ontologies and other related work on scholarly communication.", "organizations": [ { "id": "027m9bs27" }, { "id": "00rqy9422" } ], "page": "Scholarly Communication has evolved significantly in recent years, with an increasing focus on Open Research, data sharing and community-developed open source methods. The concepts of authorship and citation are changing, as researchers are increasingly reusing and evolving common software tools and datasets. Yet with a growing amount of cloud compute power and open platforms available, reproducibility of computational analyses becomes more challenging, and often overlooked in peer review. While recent advances in scientific workflows and provenance capture systems have improved on this situation, a question remains on how to publish, archive and explore digital research outputs, as academic authors and publishers remain focused on PDFs and the occasional CSV file, with the Web and Open Research often left to \"best effort\" rather than being the expected norm.
To this mean the community initiative Research Object (RO) have been proposed as a way to package and describe research outputs, data, methods, workflows, provenance and structured metadata, reusing existing Web standards and formats.
Accepting published peer-reviewed publications; recommendations and standards; open source software; vocabularies and ontologies; linked data datasets; theses and student reports.
\r\n", "page": "Linked Data is a way to publish structured information on the Web, using well-defined properties with links related resources, all identified with accessible URIs.
\r\n\r\nLinked Data builds on (and includes) Semantic Web technologies like RDF, HTTP, REST and JSON-LD, and has a strong emphasis on openess and reuse of identifiers. Interoperability and ease of use has higher priority than reaching ideal semantic clarity.
\r\n\r\nLinked Data is also an important part of the Open Data movement, as it standardizes how to structure data and merging multiple disparate data sets is made possible using common identifiers and vocabularies.
\r\n\r\nThis community's logo is adapted from the Linking Open Data cloud diagram 2014, by Max Schmachtenberg, Christian Bizer, Anja Jentzsch and Richard Cyganiak. http://lod-cloud.net/
", "title": "Linked Data" }, "revision_id": 0, "slug": "linkeddata", "updated": "2018-03-07T16:51:40.482257+00:00" }, { "access": { "member_policy": "open", "members_visibility": "restricted", "record_policy": "open", "review_policy": "closed", "visibility": "public" }, "children": { "allow": true }, "created": "2022-11-23T15:53:29.436323+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "f0a8b890-f97a-4eb2-9eac-8b8a712d3a6c", "links": {}, "metadata": { "curation_policy": "The EU Open Research Repository serves as a repository for research outputs (data, software, posters, presentations, publications, etc) which have been funded under an EU research funding programme such as Horizon Europe, Euratom or earlier Framework Programmes.
\nThe community is managed by CERN on behalf of the European Commission.
\nZenodo’s general policies and Terms of Use apply to all content.
\nThe EU Open Research Repository accepts all digital research objects which is a research output stemming from one of EU’s research and innovation funding programmes. The funding programmes currently include:
\nHorizon Europe (including ERC, MSCA), earlier Framework Programmes (eg Horizon 2020) as well as Euratom.
\nIn line with the principle as open as possible, as closed as necessary both public and restricted content is accepted. See note on how Zenodo handles restricted content.
\nEU programme beneficiaries are eligible to submit content to the community. The community supports three types of content submissions:
\nSubmission via an EU Project Community (through user interface or programmatic APIs).
\nSubmission directly to the EU Open Research Repository.
\nAutomated harvesting from existing Zenodo content.
\nA representative of an EU project may request an EU Project Community and invite other project participants as members of the community. The project community is linked to one or more European Commission grants. All records in the project community are automatically integrated into the EU Open Research Repository immediately upon acceptance into the project community.
\nAny user may submit a record directly to the EU Open Research Repository. The submission will be moderated by Zenodo staff for compliance with the minimal required metadata requirements and its correctness.
\nRecords found among Zenodo’s existing content will on a regular basis automatically be integrated if they are found to comply with the requirements. The submissions through this method are integrated into the EU Open Research Repository with delay in a fully automated way.
\nRecords in the EU Open Research Repository are required to comply with the following minimal metadata requirements:
\nVisibility: Both public and restricted (with or without embargo and/or access request)
\nResource types: All resource types.
\nLicenses: Public and embargoed records MUST specify a license.
\nFunding information: Records MUST specify at least one grant from the European Commission.
\nCreators: Creators SHOULD be identified with a persistent identifier (e.g. ORCID, GND, …), and affiliations SHOULD be identified with a persistent identifier (e.g. ROR, ISNI, …)
\nSubjects: Records SHOULD specify one or more fields of science from the European Science Vocabulary.
\nAll submissions will undergo automated curation checks for compliance with the policy. Submissions through project communities are reviewed by the project community. Submission directly to the EU Open Research Repository is reviewed by Zenodo staff.
\nCommunity curators may at any point edit metadata of the records in the community without notice through human or automated processing. The curators may at their sole discretion remove records from the community that are deemed not to comply with the content and curation policy or which are deemed of insufficient quality.
\nThe content and curation policy is subject to change by the community owner at any time and without notice, other than through updating this page.
", "description": "Open repository for EU-funded research outputs from Horizon Europe, Euratom and earlier Framework Programmes.", "organizations": [ { "id": "00k4n6c32" } ], "page": "The EU Open Research Repository is a Zenodo-community dedicated to fostering open science and enhancing the visibility and accessibility of research outputs funded by the European Union. The community is managed by CERN on behalf of the European Commission.
\nThe mission of the repository is to support the implementation of the EU's open science policy, providing a trusted and comprehensive space for researchers to share their research outputs such as data, software, reports, presentations, posters and more. The EU Open Research Repository simplifies the process of complying with open science requirements, ensuring that research outputs from Horizon Europe, Euratom, and earlier Framework Programmes are freely accessible, thereby accelerating scientific discovery and innovation.
\nThe EU Open Research Repository serves as a complementary platform to the Open Research Europe (ORE) publishing platform. Open Research Europe focuses on providing a publishing venue for peer-reviewed articles, ensuring that research meets rigorous academic standards. The EU Open Research Repository provides a space for all the other research outputs including data sets, software, posters, and presentations that are out of scope for ORE. This holistic approach enables researchers to not only publish their findings but also share the underlying data and materials that support their work, fostering transparency and reproducibility in the scientific process.
\nCurrently in its pilot phase and set to be fully operational during autumn 2024, the EU Open Research Repository is constantly evolving. Efforts are committed to integrating cutting-edge features, including automated curation checks and FAIR (Findable, Accessible, Interoperable, and Reusable) assistance, to further support the research community. The goal is to provide researchers with a simple goto solution for making their publicly funded research open and as FAIR as possible.
\nThe EU Open Research Repository is funded by the European Union under grant agreement no. 101122956(HORIZON-ZEN). For more information about the project see https://about.zenodo.org/projects/horizon-zen/.
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