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For reproducibility criteria to be met in a scientific context an increasing number of conditions need to be fulfilled. These conditions, explicited by the FAIR principle include traceability, reusability and data/methods permanent availability (findable). The challenge is not only to keep the right elements bundled together, but also to keep track of each component individual history (including individual updates) while associating every computational analysis with a transparent source. This issue, known as provenance, is the one we have been addressing in the context of this proposal. It is increasingly critical, at a time when a growing number of computational procedures are used to assess medical risks and take therapeutic decision. Our solution involves using the Research Object (RO) specification that have allowed us to implement a method that enables the creation of a package collecting all provenance metadata of a computational experiment, so that it can be easily shared, archived and reproduced when needed
", "languages": [ { "id": "eng", "title": { "en": "English" } } ], "publication_date": "2018-07-30", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "10.5281/zenodo.1215611", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" }, { "identifier": "10.1038/nbt.3820", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" }, { "identifier": "10.1016/j.websem.2015.01.003", "relation_type": { "id": "cites", "title": { "de": "Zitiert", "en": "Cites" } }, "scheme": "doi" } ], "resource_type": { "id": "publication-conferencepaper", "title": { "de": "Konferenzbeitrag", "en": "Conference paper" } }, "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": "nextflow" }, { "subject": "research object" }, { "subject": "reproducibility" }, { "subject": "provenance" } ], "title": "Nextflow integration for the Research Object Specification", "version": "2" }, "parent": { "access": { "owned_by": { "user": 49427 } }, "communities": { "default": "23d53652-d7fb-467a-9e6e-3c0714cc35c9", "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.