{ "access": { "embargo": { "active": false, "reason": null }, "files": "public", "record": "public", "status": "open" }, "created": "2015-02-02T16:48:36+00:00", "custom_fields": { "journal:journal": { "pages": "1678\u20131695", "title": "The ISME Journal", "volume": "7" } }, "deletion_status": { "is_deleted": false, "status": "P" }, "files": { "count": 1, "enabled": true, "entries": { "ismej201359a.pdf": { "checksum": "md5:f4c5acced65d9853d1b1e8aa0499ed42", "ext": "pdf", "id": "aebeeac0-a9a1-4939-8f5e-b5c05a7408a5", "key": "ismej201359a.pdf", "metadata": null, "mimetype": "application/pdf", "size": 1401414 } }, "order": [], "total_bytes": 1401414 }, "id": "7123", "is_draft": false, "is_published": true, "links": { "access": "https://zenodo.org/api/records/7123/access", "access_links": "https://zenodo.org/api/records/7123/access/links", "access_request": "https://zenodo.org/api/records/7123/access/request", "access_users": "https://zenodo.org/api/records/7123/access/users", "archive": "https://zenodo.org/api/records/7123/files-archive", "archive_media": "https://zenodo.org/api/records/7123/media-files-archive", "communities": "https://zenodo.org/api/records/7123/communities", "communities-suggestions": "https://zenodo.org/api/records/7123/communities-suggestions", "doi": "https://doi.org/10.1038/ismej.2013.59", "draft": "https://zenodo.org/api/records/7123/draft", "files": "https://zenodo.org/api/records/7123/files", "latest": "https://zenodo.org/api/records/7123/versions/latest", "latest_html": "https://zenodo.org/records/7123/latest", "media_files": "https://zenodo.org/api/records/7123/media-files", "parent": "https://zenodo.org/api/records/641989", "parent_doi": "https://zenodo.org/doi/", "parent_html": "https://zenodo.org/records/641989", "requests": "https://zenodo.org/api/records/7123/requests", "reserve_doi": "https://zenodo.org/api/records/7123/draft/pids/doi", "self": "https://zenodo.org/api/records/7123", "self_doi": "https://zenodo.org/doi/10.1038/ismej.2013.59", "self_html": "https://zenodo.org/records/7123", "self_iiif_manifest": "https://zenodo.org/api/iiif/record:7123/manifest", "self_iiif_sequence": "https://zenodo.org/api/iiif/record:7123/sequence/default", "versions": "https://zenodo.org/api/records/7123/versions" }, "media_files": { "count": 0, "enabled": false, "entries": {}, "order": [], "total_bytes": 0 }, "metadata": { "creators": [ { "affiliations": [ { "name": "CNRS, Aix-Marseille Universit\u00e9, Laboratoire Information G\u00e9nomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France" } ], "person_or_org": { "family_name": "Hingamp", "given_name": "Pascal", "name": "Hingamp, Pascal", "type": "personal" } }, { "affiliations": [ { "name": "CNRS and Universit\u00e9 Pierre et Marie (Paris 06), UMR 7232, Observatoire Oc\u00e9anologique, Banyuls-sur-Mer, France" } ], "person_or_org": { "family_name": "Grimsley", "given_name": "Nigel", "name": "Grimsley, Nigel", "type": "personal" } }, { "affiliations": [ { "name": "Institute of Marine Science (ICM), CSIC,Barcelona, Spain" } ], "person_or_org": { "family_name": "Acinas", "given_name": "Silvia G.", "name": "Acinas, Silvia G.", "type": "personal" } }, { "affiliations": [ { "name": "CNRS and Universit\u00e9 Pierre et Marie (Paris 06), UMR 7232, Observatoire Oc\u00e9anologique, Banyuls-sur-Mer, France" } ], "person_or_org": { "family_name": "Clerissi", "given_name": "Camille", "name": "Clerissi, Camille", "type": "personal" } }, { "affiliations": [ { "name": "CNRS and Universit\u00e9 Pierre et Marie (Paris 06), UMR 7232, Observatoire Oc\u00e9anologique, Banyuls-sur-Mer, France" } ], "person_or_org": { "family_name": "Subirana", "given_name": "Lucie", "name": "Subirana, Lucie", "type": "personal" } }, { "affiliations": [ { "name": "CEA, Institut de G\u00e9nomique, Genoscope, Evry, France" } ], "person_or_org": { "family_name": "Poulain", "given_name": "Julie", "name": "Poulain, Julie", "type": "personal" } }, { "affiliations": [ { "name": "Institute of Marine Science (ICM), CSIC, Spain, Departament de Gen\u00e8tica i de Microbiologia, Universitat Aut\u00f2noma de Barcelona, Bellaterra ES-08193, Spain." } ], "person_or_org": { "family_name": "Ferrera", "given_name": "Isabel", "name": "Ferrera, Isabel", "type": "personal" } }, { "affiliations": [ { "name": "Institute of Marine Science (ICM), CSIC, Barcelona, Spain" } ], "person_or_org": { "family_name": "Sarmento", "given_name": "Hugo", "name": "Sarmento, Hugo", "type": "personal" } }, { "affiliations": [ { "name": "CNRS, Aix-Marseille Universit\u00e9, Laboratoire Information G\u00e9nomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France" } ], "person_or_org": { "family_name": "Villar", "given_name": "Emilie", "name": "Villar, Emilie", "type": "personal" } }, { "affiliations": [ { "name": "Department of Structural Biology, VIB, Brussel, Belgium" } ], "person_or_org": { "family_name": "Lima-Medez", "given_name": "Gipsi", "name": "Lima-Medez, Gipsi", "type": "personal" } }, { "person_or_org": { "family_name": "Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium", "name": "Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium", "type": "personal" } }, { "affiliations": [ { "name": "Department of Structural Biology, VIB, Brussel, Belgium" } ], "person_or_org": { "family_name": "Faust", "given_name": "Karoline", "name": "Faust, Karoline", "type": "personal" } }, { "person_or_org": { "family_name": "Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium", "name": "Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium", "type": "personal" } }, { "affiliations": [ { "name": "European Molecular Biology Laboratory, Heidelberg, Germany" } ], "person_or_org": { "family_name": "Sunagawa", "given_name": "Shinichi", "name": "Sunagawa, Shinichi", "type": "personal" } }, { "affiliations": [ { "name": "CNRS, Aix-Marseille Universit\u00e9, Laboratoire Information G\u00e9nomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France" } ], "person_or_org": { "family_name": "Claverie", "given_name": "Jean-Michel", "name": "Claverie, Jean-Michel", "type": "personal" } }, { "affiliations": [ { "name": "CNRS and Universit\u00e9 Pierre et Marie (Paris 06), UMR 7232, Observatoire Oc\u00e9anologique, Banyuls-sur-Mer, France" } ], "person_or_org": { "family_name": "Moreau", "given_name": "Herv\u00e9", "name": "Moreau, Herv\u00e9", "type": "personal" } }, { "affiliations": [ { "name": "CNRS and Universit\u00e9 Pierre et Marie (Paris 06), UMR 7232, Observatoire Oc\u00e9anologique, Banyuls-sur-Mer, France" } ], "person_or_org": { "family_name": "Desdevises", "given_name": "Yves", "name": "Desdevises, Yves", "type": "personal" } }, { "affiliations": [ { "name": "European Molecular Biology Laboratory, Heidelberg, Germany" } ], "person_or_org": { "family_name": "Bork", "given_name": "Peer", "name": "Bork, Peer", "type": "personal" } }, { "affiliations": [ { "name": "Department of Structural Biology, VIB, Brussel, Belgium" } ], "person_or_org": { "family_name": "Raes", "given_name": "Jeroen", "name": "Raes, Jeroen", "type": "personal" } }, { "person_or_org": { "family_name": "Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium", "name": "Department of Applied Biological Sciences (DBIT), Vrije Universiteit Brussel, Brussels, Belgium", "type": "personal" } }, { "affiliations": [ { "name": "CNRS, Universit\u00e9 Pierre et Marie Curie (Paris 06), UMR 7144, Station Biologique de Roscoff, Roscoff, France" } ], "person_or_org": { "family_name": "de Vargas", "given_name": "Colomban", "name": "de Vargas, Colomban", "type": "personal" } }, { "affiliations": [ { "name": "European Molecular Biology Laboratory, Heidelberg, Germany" } ], "person_or_org": { "family_name": "Karsenti", "given_name": "Eric", "name": "Karsenti, Eric", "type": "personal" } }, { "affiliations": [ { "name": "European Molecular Biology Laboratory, Heidelberg, Germany" } ], "person_or_org": { "family_name": "Kandels-Lewis", "given_name": "Stefanie", "name": "Kandels-Lewis, Stefanie", "type": "personal" } }, { "affiliations": [ { "name": "CEA, Institut de G\u00e9nomique, Genoscope, Evry, France" } ], "person_or_org": { "family_name": "Jaillon", "given_name": "Olivier", "name": "Jaillon, Olivier", "type": "personal" } }, { "affiliations": [ { "name": "CNRS, Universit\u00e9 Pierre et Marie Curie (Paris 06), UMR 7144, Station Biologique de Roscoff, Roscoff, France" } ], "person_or_org": { "family_name": "Not", "given_name": "Fabrice", "name": "Not, Fabrice", "type": "personal" } }, { "affiliations": [ { "name": "MARUM\u2014Center for Marine Environmental Sciences, Universit\u00e4t Bremen, Bremen, Germany" } ], "person_or_org": { "family_name": "Pesant", "given_name": "St\u00e9phane", "name": "Pesant, St\u00e9phane", "type": "personal" } }, { "affiliations": [ { "name": "CEA, Institut de G\u00e9nomique, Genoscope, Evry, France" } ], "person_or_org": { "family_name": "Wincker", "given_name": "Patrick", "name": "Wincker, Patrick", "type": "personal" } }, { "affiliations": [ { "name": "CNRS, Aix-Marseille Universit\u00e9, Laboratoire Information G\u00e9nomique et Structurale (UMR 7256), Mediterranean Institute of Microbiology (FR 3479), Marseille, France, Education Academy of Computational Life Sciences, Tokyo Institute of Technology, Tokyo, Japan, These authors contributed equally to this work." } ], "person_or_org": { "family_name": "Ogata", "given_name": "Hiroyuki", "name": "Ogata, Hiroyuki", "type": "personal" } } ], "description": "Nucleo-cytoplasmic large DNA viruses (NCLDVs) constitute a group of eukaryotic viruses that can have crucial ecological roles in the sea by accelerating the turnover of their unicellular hosts or by causing diseases in animals. To better characterize the diversity, abundance and biogeography of marine NCLDVs, we analyzed 17 metagenomes derived from microbial samples (0.2\u20131.6\u2009\u03bcm size range) collected during the Tara Oceans Expedition. The sample set includes ecosystems under-represented in previous studies, such as the Arabian Sea oxygen minimum zone (OMZ) and Indian Ocean lagoons. By combining computationally derived relative abundance and direct prokaryote cell counts, the abundance of NCLDVs was found to be in the order of 104\u2013105 genomes\u2009ml\u22121 for the samples from the photic zone and 102\u2013103 genomes\u2009ml\u22121 for the OMZ. The Megaviridae and Phycodnaviridae dominated the NCLDV populations in the metagenomes, although most of the reads classified in these families showed large divergence from known viral genomes. Our taxon co-occurrence analysis revealed a potential association between viruses of the Megaviridae family and eukaryotes related to oomycetes. In support of this predicted association, we identified six cases of lateral gene transfer between Megaviridae and oomycetes. Our results suggest that marine NCLDVs probably outnumber eukaryotic organisms in the photic layer (per given water mass) and that metagenomic sequence analyses promise to shed new light on the biodiversity of marine viruses and their interactions with potential hosts.", "funding": [ { "award": { "acronym": "MICRO B3", "id": "00k4n6c32::287589", "identifiers": [ { "identifier": "https://cordis.europa.eu/projects/287589", "scheme": "url" } ], "number": "287589", "program": "FP7", "title": { "en": "Marine Microbial Biodiversity, Bioinformatics and Biotechnology" } }, "funder": { "id": "00k4n6c32", "name": "European Commission" } } ], "publication_date": "2013-04-11", "publisher": "Zenodo", "resource_type": { "id": "publication-article", "title": { "de": "Zeitschriftenartikel", "en": "Journal article" } }, "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": "eukaryotic viruses" }, { "subject": "marine NCLDVs" }, { "subject": "taxon co-occurrence" }, { "subject": "oomycetes" } ], "title": "Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes" }, "parent": { "access": { "owned_by": {}, "settings": { "accept_conditions_text": null, "allow_guest_requests": false, "allow_user_requests": false, "secret_link_expiration": 0 } }, "communities": { "entries": [ { "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/.
", "title": "EU Open Research Repository (Pilot)", "type": { "id": "organization" }, "website": "https://research-and-innovation.ec.europa.eu" }, "revision_id": 16, "slug": "eu", "theme": { "brand": "horizon", "enabled": true, "style": { "font": { "family": "Arial, sans-serif", "size": "16px", "weight": 600 }, "mainHeaderBackgroundColor": "#FFFFFF", "primaryColor": "#004494", "primaryTextColor": "#FFFFFF", "secondaryColor": "#FFD617", "secondaryTextColor": "#000000", "tertiaryColor": "#e3eefd", "tertiaryTextColor": "#1c5694" } }, "updated": "2024-03-20T06:47:47.577483+00:00" } ], "ids": [ "f0a8b890-f97a-4eb2-9eac-8b8a712d3a6c" ] }, "id": "641989", "pids": {} }, "pids": { "doi": { "identifier": "10.1038/ismej.2013.59", "provider": "external" }, "oai": { "identifier": "oai:zenodo.org:7123", "provider": "oai" } }, "revision_id": 11, "stats": { "all_versions": { "data_volume": 155556954.0, "downloads": 111, "unique_downloads": 106, "unique_views": 221, "views": 227 }, "this_version": { "data_volume": 155556954.0, "downloads": 111, "unique_downloads": 106, "unique_views": 218, "views": 224 } }, "status": "published", "updated": "2020-01-20T16:41:39.026443+00:00", "versions": { "index": 1, "is_latest": true } }