02156nas a2200241   4500008004100000020001400041245009200055210007100147260000900218300001600227490000700243520143800250100002101688700001901709700001801728700002201746700001501768700002001783700002601803700002001829700002501849856004001874       2018                        eng d  a0305-104800aPlanMine 3.0—improvements to a mineable resource of flatworm biology and biodiversity0 aPlanMine 30—improvements to a mineable resource of flatworm biol  c2018  aD812 - D8200 v473 aFlatworms (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.1 aRozanski, Andrei1 aBrandl, Holger1 aMoon, HongKee1 aGrohme, Markus, A1 aHenry, Ian1 aRink, Jochen, C1 aMartin-Duran, Jose, M1 aHüttner, Katja1 aBartscherer, Kerstin  uhttps://doi.org/10.1093/nar/gky107002142nas a2200205   4500008004100000020002300041245007500064210006900139260004000208300001600248490000700264520149300271100001901764700001801783700002401801700001901825700001501844700002001859856005701879       2016                        eng d  a0305-10481362-496200aPlanMine – a mineable resource of planarian biology and biodiversity0 aPlanMine a mineable resource of planarian biology and biodiversi  bOxford University Pressc2016/01/04  aD764 - D7730 v443 a<p>Planarian flatworms are in the midst of a renaissance as a model system for regeneration and stem cells. Besides two well-studied model species, hundreds of species exist worldwide that present a fascinating diversity of regenerative abilities, tissue turnover rates, reproductive strategies and other life history traits. PlanMine (http://planmine.mpi-cbg.de/) aims to accomplish two primary missions: First, to provide an easily accessible platform for sharing, comparing and value-added mining of planarian sequence data. Second, to catalyze the comparative analysis of the phenotypic diversity amongst planarian species. Currently, PlanMine houses transcriptomes independently assembled by our lab and community contributors. Detailed assembly/annotation statistics, a custom-developed BLAST viewer and easy export options enable comparisons at the contig and assembly level. Consistent annotation of all transcriptomes by an automated pipeline, the integration of published gene expression information and inter-relational query tools provide opportunities for mining planarian gene sequences and functions. For inter-species comparisons, we include transcriptomes of, so far, six planarian species, along with images, expert-curated information on their biology and pre-calculated cross-species sequence homologies. PlanMine is based on the popular InterMine system in order to make the rich biology of planarians accessible to the general life sciences research community.</p>
1 aBrandl, Holger1 aMoon, HongKee1 aVila-Farré, Miquel1 aLiu, Shang-Yun1 aHenry, Ian1 aRink, Jochen, C  uhttp://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702831/