PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity.
dc.contributor.author | Rozanski, A | en_US |
dc.contributor.author | Moon, H | en_US |
dc.contributor.author | Brandl, H | en_US |
dc.contributor.author | Martín-Durán, JM | en_US |
dc.contributor.author | Grohme, MA | en_US |
dc.contributor.author | Hüttner, K | en_US |
dc.contributor.author | Bartscherer, K | en_US |
dc.contributor.author | Henry, I | en_US |
dc.contributor.author | Rink, JC | en_US |
dc.date.accessioned | 2019-01-16T10:25:37Z | |
dc.date.available | 2018-11-26 | en_US |
dc.date.issued | 2019-01-08 | en_US |
dc.date.submitted | 2018-12-09T17:22:50.356Z | |
dc.identifier.uri | https://qmro.qmul.ac.uk/xmlui/handle/123456789/54688 | |
dc.description.abstract | Flatworms (Platyhelminthes) are a basally branching phylum that harbours a wealth of fascinating biology, including planarians with their astonishing regenerative abilities and the parasitic tape worms and blood flukes that exert a massive impact on human health. PlanMine (http://planmine.mpi-cbg.de/) has the mission objective of providing both a mineable sequence repository for planarians and also a resource for the comparative analysis of flatworm biology. While the original PlanMine release was entirely based on transcriptomes, the current release transitions to a more genomic perspective. Building on the recent availability of a high quality genome assembly of the planarian model species Schmidtea mediterranea, we provide a gene prediction set that now assign existing transcripts to defined genomic coordinates. The addition of recent single cell and bulk RNA-seq datasets greatly expands the available gene expression information. Further, we add transcriptomes from a broad range of other flatworms and provide a phylogeny-aware interface that makes evolutionary species comparisons accessible to non-experts. At its core, PlanMine continues to utilize the powerful InterMine framework and consistent data annotations to enable meaningful inter-species comparisons. Overall, PlanMine 3.0 thus provides a host of new features that makes the fascinating biology of flatworms accessible to the wider research community. | en_US |
dc.format.extent | D812 - D820 | en_US |
dc.language | eng | en_US |
dc.relation.ispartof | Nucleic Acids Res | en_US |
dc.rights | This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com | |
dc.rights | Attribution 3.0 United States | * |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/us/ | * |
dc.title | PlanMine 3.0-improvements to a mineable resource of flatworm biology and biodiversity. | en_US |
dc.type | Article | |
dc.rights.holder | © The Author(s) 2018 | |
dc.identifier.doi | 10.1093/nar/gky1070 | en_US |
pubs.author-url | https://www.ncbi.nlm.nih.gov/pubmed/30496475 | en_US |
pubs.issue | D1 | en_US |
pubs.notes | No embargo | en_US |
pubs.publication-status | Published | en_US |
pubs.volume | 47 | en_US |
dcterms.dateAccepted | 2018-11-26 | en_US |
rioxxterms.funder | Default funder | en_US |
rioxxterms.identifier.project | Default project | en_US |
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Except where otherwise noted, this item's license is described as This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com