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Finding Our Way through Phenotypes

Andrew R. Deans, Suzanna E. Lewis, Eva Huala, Salvatore S. Anzaldo, Michael Ashburner, James P. Balhoff, David C. Blackburn, Judith A. Blake, J. Gordon Burleigh, Bruno Chanet, Laurel D. Cooper, Mélanie Courtot (+62 others)
<span title="2015-01-06">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tsaumnzpkvdmvdi3blhl5clb24" style="color: black;">PLoS Biology</a> </i> &nbsp;
We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support  ...  Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes.  ...  We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.1002033">doi:10.1371/journal.pbio.1002033</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25562316">pmid:25562316</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4285398/">pmcid:PMC4285398</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5reifkvhcnh53ab6cv44ewlrba">fatcat:5reifkvhcnh53ab6cv44ewlrba</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190427091044/https://uknowledge.uky.edu/cgi/viewcontent.cgi?article=1085&amp;context=entomology_facpub" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a6/cb/a6cb7df64991145870cd5795e9ac416e9ebb032d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.1002033"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285398" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computing on Phenotypic Descriptions for Candidate Gene Discovery and Crop Improvement

Ian R. Braun, Colleen F. Yanarella, Carolyn J. Lawrence-Dill
<span title="2020-05-20">2020</span> <i title="American Association for the Advancement of Science (AAAS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/45zzn4bvl5cd5ptvizrfz6emi4" style="color: black;">Plant Phenomics</a> </i> &nbsp;
Simultaneously, researchers in other domains have been working to enable computation on natural language.  ...  Here, we describe current and ongoing efforts to provide tools for the plant phenomics community to explore novel predictions that can be generated using these techniques.  ...  Acknowledgments We thank the Iowa State University Plant Science Institute Faculty Scholars and the Iowa State University Predictive Plant Phenomics graduate students for helpful discussions on the topics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.34133/2020/1963251">doi:10.34133/2020/1963251</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33313544">pmid:33313544</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7706311/">pmcid:PMC7706311</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ux7htcuzovhnhl3orocziai52m">fatcat:ux7htcuzovhnhl3orocziai52m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200521035105/http://downloads.spj.sciencemag.org/plantphenomics/2020/1963251.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/14/06/14068c89a2513e736e9a489249a49d5ad617aa71.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.34133/2020/1963251"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706311" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An ontology approach to comparative phenomics in plants

Anika Oellrich, Ramona L Walls, Ethalinda Cannon, Steven B Cannon, Laurel Cooper, Jack Gardiner, Georgios V Gkoutos, Lisa Harper, Mingze He, Robert Hoehndorf, Pankaj Jaiswal, Scott R Kalberer (+8 others)
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7g2xzafrze7jhzts3tizvsi7e" style="color: black;">Plant Methods</a> </i> &nbsp;
In addition, these tools should enhance future efforts to explore the relationships among phenotypic similarity, gene function, and sequence similarity in plants, and to make genotype-to-phenotype predictions  ...  We then compared ontology-based phenotypic descriptions with an existing classification system for plant phenotypes and evaluated our semantic similarity dataset for its ability to enhance predictions  ...  Acknowledgements The NSF Phenotype RCN supported this work by allowing plant and computational biologists to come together and develop a common vocabulary and supported the preliminary analysis of generated  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13007-015-0053-y">doi:10.1186/s13007-015-0053-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25774204">pmid:25774204</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4359497/">pmcid:PMC4359497</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2ts43o4iaffqvltwcse2zvpgyq">fatcat:2ts43o4iaffqvltwcse2zvpgyq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809103958/https://plantmethods.biomedcentral.com/track/pdf/10.1186/s13007-015-0053-y?site=plantmethods.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/72/9d/729d46468f4e24dba9ad7e9a93ae97b5e5d9fc96.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13007-015-0053-y"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4359497" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Time to change how we describe biodiversity

Andrew R. Deans, Matthew J. Yoder, James P. Balhoff
<span title="">2012</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/vrxa4vnzsbfw5omchmsoaaj3pa" style="color: black;">Trends in Ecology &amp; Evolution</a> </i> &nbsp;
Encyclopedia of Life, and in rigorous conversation with participants of the Phenotype RCN (http://www.phenotypercn.org).  ...  Acknowledgments The ideas presented herein were developed during meetings funded by the US National Science Foundation (NSF; grants DBI-0850223, DEB-0956049) and the Biodiversity Synthesis Center of the  ...  The natural language description remains available to the domain expert (i.e. taxonomy proceeds unabated), and the machine-readable annotation enters a system that facilitates computation across phenotypes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tree.2011.11.007">doi:10.1016/j.tree.2011.11.007</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22189359">pmid:22189359</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/baoxrnvs2jfpplax6ix6br4hge">fatcat:baoxrnvs2jfpplax6ix6br4hge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810043144/http://entocourses.tamu.edu/ento601/pdf/Deans_et_al_2012.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/b2/c8b2a07ecabc74e479f3071a848acbc150ccae70.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tree.2011.11.007"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Transforming the study of organisms: Phenomic data models and knowledge bases

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel (+1 others)
<span title="2020-11-24">2020</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their  ...  In this review, we will compare and contrast existing ontology and data models, focusing on nonhuman phenotypes and traits.  ...  Acknowledgments The authors would like to acknowledge the organizers and sponsors of the 2019 US2TS Conference held at Duke University who created space for this discussion.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008376">doi:10.1371/journal.pcbi.1008376</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33232313">pmid:33232313</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7685442/">pmcid:PMC7685442</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d36yhdezgnbblbj4sy62jiqw3m">fatcat:d36yhdezgnbblbj4sy62jiqw3m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201126164342/https://journals.plos.org/ploscompbiol/article/file?id=10.1371%2Fjournal.pcbi.1008376&amp;type=printable" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6a/58/6a58674367bc772f1b08308c33362fe42f5fb010.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1008376"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7685442" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bioinformatics in the plant genomic and phenomic domain: The German contribution to resources, services and perspectives

Thomas Schmutzer, Marie E. Bolger, Stephen Rudd, Jinbo Chen, Heidrun Gundlach, Daniel Arend, Markus Oppermann, Stephan Weise, Matthias Lange, Manuel Spannagl, Björn Usadel, Klaus F.X. Mayer (+1 others)
<span title="">2017</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/se63ciaet5axrek43i2fdqnqui" style="color: black;">Journal of Biotechnology</a> </i> &nbsp;
services that link genotypes and phenotypes.  ...  With this we provide several established solutions for the plant science community to accomplish genomics and phenomics tasks.  ...  Mayer and Björn Usadel acknowledge support from the German Ministry of Education and Research (BMBF) for grant 031A536 "de.NBI". Uwe Scholz and Klaus F.X.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbiotec.2017.07.006">doi:10.1016/j.jbiotec.2017.07.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28698099">pmid:28698099</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mvlhv6xkevdy5bz4zknuo436oa">fatcat:mvlhv6xkevdy5bz4zknuo436oa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719084455/http://juser.fz-juelich.de/record/848037/files/1-s2.0-S0168165617315183-main.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/33/cf/33cf4f7e0cbdc4d4a38666b2257fd01867471184.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbiotec.2017.07.006"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

Evolution of genome-phenome diversity under environmental stress

E. Nevo
<span title="2001-05-22">2001</span> <i title="Proceedings of the National Academy of Sciences"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nvtuoas5pbdsllkntnhizy4f4q" style="color: black;">Proceedings of the National Academy of Sciences of the United States of America</a> </i> &nbsp;
We advanced ecological genetics into ecological genomics and analyzed globally ecological, demographic, and life history variables in 1,200 diverse species across life, thousands of populations, and tens  ...  Our model organisms represent diverse taxa across life, from bacteria to mammals, in an attempt to unravel regularity, convergence, and divergence of genotypic and phenotypic patterns: Nostoc linckia (  ...  This intraspecific interslope divergence can be compared in many species across life from prokaryotic bacteria through eukaryotic lower and higher plants, fungi, and animals (7, 8) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.101109298">doi:10.1073/pnas.101109298</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11371642">pmid:11371642</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC33451/">pmcid:PMC33451</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2pmolxb6afaaxnsvqyews5o3de">fatcat:2pmolxb6afaaxnsvqyews5o3de</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160804055007/http://www.pnas.org:80/content/98/11/6233.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2e/c8/2ec8b51891aa3b364faf531bce94547542e5f118.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1073/pnas.101109298"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC33451" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cyberinfrastructure and resources to enable an integrative approach to studying forest trees

Jill L Wegrzyn, Taylor Falk, Emily Grau, Sean Buehler, Risharde Ramnath, Nic Herndon
<span title="2019-08-26">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hnstxxau2bbjhkazfbxx7sdac4" style="color: black;">Evolutionary Applications</a> </i> &nbsp;
Successful implementation of life science cyberinfrastructure is improving data standards, ontologies, analytic workflows, and integrated database platforms for both model and non-model plant species.  ...  To address questions related to forest health and productivity, cyberinfrastructure must keep pace with the magnitude of genomic and phenomic sampling of larger populations.  ...  | INTRODUC TI ON High-throughput technologies are enabling rapid data generation in the fields of genomics, proteomics, and phenomics.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/eva.12860">doi:10.1111/eva.12860</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31892954">pmid:31892954</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6935593/">pmcid:PMC6935593</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r2zcwfc7irdgdln4faunycp3ui">fatcat:r2zcwfc7irdgdln4faunycp3ui</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200509041543/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6935593&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/59/ac/59ac3294b61b112e6dcec418c4df9da14e5925d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/eva.12860"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6935593" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology

Joanna Friesner, Sarah M. Assmann, Ruth Bastow, Julia Bailey-Serres, Jim Beynon, Volker Brendel, C. Robin Buell, Alexander Bucksch, Wolfgang Busch, Taku Demura, Jose R. Dinneny, Colleen J. Doherty (+27 others)
<span title="">2017</span> <i title="American Society of Plant Biologists (ASPB)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lyouqq67dncvxgcbflq26svwta" style="color: black;">Plant Physiology</a> </i> &nbsp;
Basic knowledge in the specific domains of computer science, statistics, and mathematics that intersect with modern biology. 2.  ...  It is likely that many fundamental biological processes are conserved across plant species (McGary et al., 2010; Oellrich et al., 2015) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.17.01490">doi:10.1104/pp.17.01490</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29208732">pmid:29208732</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5717721/">pmcid:PMC5717721</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/diocyqmgbvdm7dpoanfwxnlc4y">fatcat:diocyqmgbvdm7dpoanfwxnlc4y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190207230914/http://www.plantphysiol.org/content/plantphysiol/175/4/1499.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e2/99/e29997b85b445c656ea8584c9f8f4ceec4721bed.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1104/pp.17.01490"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5717721" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Next-Generation Breeding Strategies for Climate-Ready Crops

Ali Razzaq, Parwinder Kaur, Naheed Akhter, Shabir Hussain Wani, Fozia Saleem
<span title="2021-07-21">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bbmitkj3efgeppizzjrx6w5emu" style="color: black;">Frontiers in Plant Science</a> </i> &nbsp;
the lost gene repertoire of a species.  ...  The integration of speed breeding with genomic and phenomic tools can allow rapid gene identifications and ultimately accelerate crop improvement programs.  ...  PK was supported by the University of Western Australia with additional computational resources and support from the Pawsey Supercomputing Centre with funding from the Australian Government and the Government  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2021.620420">doi:10.3389/fpls.2021.620420</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3lgi77owurcpdjmumlsueytef4">fatcat:3lgi77owurcpdjmumlsueytef4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220302092315/https://fjfsdata01prod.blob.core.windows.net/articles/files/620420/pubmed-zip/.versions/2/.package-entries/fpls-12-620420-r1/fpls-12-620420.pdf?sv=2018-03-28&amp;sr=b&amp;sig=xTPdXGaNo0Jhur7PEUDl7EqIe2PsegU2LeyUvyQG6tM%3D&amp;se=2022-03-02T09%3A23%3A44Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fpls-12-620420.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5d/e9/5de91d8d8ba524291e061e3b291641d85b8de20f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fpls.2021.620420"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a>

The Case for Retaining Natural Language Descriptions of Phenotypes in Plant Databases and a Web Application as Proof of Concept [article]

Ian R Braun, Diane C Bassham, Carolyn J Lawrence-Dill
<span title="2021-02-06">2021</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Results A wide variety of approaches from the natural language processing domain perform as well as similarity metrics over curated annotations for predicting shared phenotypes.  ...  Here we generate networks of phenotype similarity and share a web application for querying a dataset of associated plant genes using these text mining approaches.  ...  ACKNOWLEDGEMENTS The authors thank Carson Andorf, John Portwood, and Naama Menda for their assistance in obtaining the dataset of plant phenotype descriptions and annotations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.02.04.429796">doi:10.1101/2021.02.04.429796</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4d24vmcc7femfozz3viviebr5a">fatcat:4d24vmcc7femfozz3viviebr5a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210429060954/https://www.biorxiv.org/content/biorxiv/early/2021/02/06/2021.02.04.429796.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2f/49/2f49d37482ee50749600cc69ba17c11469f94cc5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2021.02.04.429796"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Directions for research and training in plant omics: Big Questions and Big Data

Cristiana T. Argueso, Sarah M. Assmann, Kenneth D. Birnbaum, Sixue Chen, José R. Dinneny, Colleen J. Doherty, Andrea L. Eveland, Joanna Friesner, Vanessa R. Greenlee, Julie A. Law, Amy Marshall-Colón, Grace Alex Mason (+8 others)
<span title="2019-04-23">2019</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a7p5unsuyff7bnvxtpt272ocfq" style="color: black;">Plant Direct</a> </i> &nbsp;
on the reference species Arabidopsis thaliana and other valuable plant systems.  ...  A first workshop focused on training needs for bioinformatic and computational approaches in plant biology was held in 2016, and recommendations from that workshop have been published (Friesner et al.,  ...  It is the meta-analysis across datasets and from the fine-to coarse-scales that will most strongly enable predictive capability to address pressing issues in plant biology across topics as diverse as engineering  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pld3.133">doi:10.1002/pld3.133</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31245771">pmid:31245771</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6589541/">pmcid:PMC6589541</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gwcnbgow3jcqlpzth7ufcotazi">fatcat:gwcnbgow3jcqlpzth7ufcotazi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210526223231/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6589541&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/77/83/7783562fd7b57888136ac3325a4072048b6e27ef.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/pld3.133"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6589541" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ASAS Centennial Paper: Future needs in animal breeding and genetics

R. D. Green
<span title="2009-02-01">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rpte5rjgn5hi3i37cwn2bhoioi" style="color: black;">Journal of Animal Science</a> </i> &nbsp;
sophisticated genetic prediction systems enabling industry genetic improvement.  ...  manage-ment of specific genotypes, all early in the life of the animal.  ...  large, highly resourced, and deeply phenotyped populations (i.e., phenomics) and in bioinformatics and computational biology.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2527/jas.2008-1406">doi:10.2527/jas.2008-1406</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18952735">pmid:18952735</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/orfm2tvr65azrd2ztx36vszvna">fatcat:orfm2tvr65azrd2ztx36vszvna</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303004652/http://pdfs.semanticscholar.org/ac73/5c80b8caa74c7d7c56f946d4ad9ccefb8cce.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/73/ac735c80b8caa74c7d7c56f946d4ad9ccefb8cce.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2527/jas.2008-1406"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Phenomics – technologies to relieve the phenotyping bottleneck

Robert T. Furbank, Mark Tester
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s7wj3rwofngddnaxae7vb54u3e" style="color: black;">Trends in Plant Science</a> </i> &nbsp;
The frequency with which the annotation 'no visible phenotype' occurs is symptomatic of, among other things, a lack of capacity for the plant community to analyze the subtle and sometimes complex phenotypic  ...  Plant phenomics offers a suite of new technologies to accelerate progress in understanding gene function and environmental responses.  ...  Acknowledgements We thank Drs Bettina Berger and Xavier Sirault for valuable comments on the manuscript, and the funding agencies who have allowed the establishment of the Australian Plant Phenomics Facility  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tplants.2011.09.005">doi:10.1016/j.tplants.2011.09.005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22074787">pmid:22074787</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mh5uwult7ncxbagimo5s2ljyta">fatcat:mh5uwult7ncxbagimo5s2ljyta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160228082658/http://plantphenomics.org.au/publications/2011TrendsFurbankTester.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a0/7a/a07a8874568532882e25f34dd247258f22669e53.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tplants.2011.09.005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Computer Vision, Machine Learning, and the Promise of Phenomics in Ecology and Evolutionary Biology

Moritz D. Lürig, Seth Donoughe, Erik I. Svensson, Arthur Porto, Masahito Tsuboi
<span title="2021-04-21">2021</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/sdhva7kh2febjl6ejo6uomjrhq" style="color: black;">Frontiers in Ecology and Evolution</a> </i> &nbsp;
This has proven to be an impediment to the growing field of phenomics – the study of many phenotypic dimensions together.  ...  For centuries, ecologists and evolutionary biologists have used images such as drawings, paintings and photographs to record and quantify the shapes and patterns of life.  ...  result of the combination of the predictions generated by each component. part, methodological choices in CV are highly domain-specific (see section "Practical Considerations for Computer Vision" and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fevo.2021.642774">doi:10.3389/fevo.2021.642774</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/br47precdzevbleph5zpyp2ina">fatcat:br47precdzevbleph5zpyp2ina</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210425200717/https://fjfsdata01prod.blob.core.windows.net/articles/files/642774/pubmed-zip/.versions/1/.package-entries/fevo-09-642774/fevo-09-642774.pdf?sv=2018-03-28&amp;sr=b&amp;sig=DGLdPmgBaeln4fwMRQM%2Fsc%2Fuw%2Bu%2BpOPZ0pDzd1G5pns%3D&amp;se=2021-04-25T20%3A07%3A46Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fevo-09-642774.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8e/90/8e907c33b124609c54b3cd507c57109f903fa6d2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fevo.2021.642774"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a>
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