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Araport: the Arabidopsis Information Portal

Vivek Krishnakumar, Matthew R. Hanlon, Sergio Contrino, Erik S. Ferlanti, Svetlana Karamycheva, Maria Kim, Benjamin D. Rosen, Chia-Yi Cheng, Walter Moreira, Stephen A. Mock, Joseph Stubbs, Julie M. Sullivan (+5 others)
2014 Nucleic Acids Research  
The Arabidopsis Information Portal (https://www. araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation.  ...  Designed for sustainability, the Arabidopsis Information Portal strategy exploits existing scientific computing infrastructure, adopts a practical mixture of data integration technologies and encourages  ...  ACKNOWLEDGEMENTS We would like to thank Eva Huala and Bob Muller (Phoenix Bioinformatics, formerly TAIR) for their assistance with the migration of Arabidopsis data to AIP; summer interns Eleanor Pence  ... 
doi:10.1093/nar/gku1200 pmid:25414324 pmcid:PMC4383980 fatcat:2saksp5dzvgdtnzjnyrj7dt7dm

Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future

2019 Plant Direct  
TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more  ...  Workshop participants proposed a "one-stop shop" website, an Arabidopsis "Super-Portal" to link tools, data resources, programmatic standards, and best practice descriptions for each data type.  ...  TAIR (The Arabidopsis Information Resource) and Araport (originally named the Arabidopsis Information Portal) are community informatics resources that provide tools, data, and applications to the more  ... 
doi:10.1002/pld3.109 pmid:31245752 pmcid:PMC6508773 fatcat:7vrvjbolnzaaxjs6kghbkvtgje

ThaleMine: A Warehouse for Arabidopsis Data Integration and Discovery

Vivek Krishnakumar, Sergio Contrino, Chia-Yi Cheng, Irina Belyaeva, Erik S. Ferlanti, Jason R. Miller, Matthew W. Vaughn, Gos Micklem, Christopher D. Town, Agnes P. Chan
2016 Plant and Cell Physiology  
Developed by the Arabidopsis Information Portal (Araport, https://www.araport.org/) project, ThaleMine uses the InterMine software framework, which builds wellstructured data, and provides powerful data  ...  ThaleMine (https://apps.araport.org/thalemine/) is a comprehensive data warehouse that integrates a wide array of genomic information of the model plant Arabidopsis thaliana.  ...  Acknowledgements We would like to thank the InterMine team at the University of Cambridge for their valuable input and continuous support over the course of development of ThaleMine, the TACC Technology  ... 
doi:10.1093/pcp/pcw200 pmid:28013278 fatcat:peu7pyxi5bcevkhk2xzue6uq44

ePlant: Visualizing and Exploring Multiple Levels of Data for Hypothesis Generation in Plant Biology

Jamie Waese, Jim Fan, Asher Pasha, Hans Yu, Geoffrey Fucile, Ruian Shi, Matthew Cumming, Lawrence A. Kelley, Michael J. Sternberg, Vivek Krishnakumar, Erik Ferlanti, Jason Miller (+3 others)
2017 The Plant Cell  
We also describe the process of deploying ePlant as an "app" on Araport. Building on readily available web services, the code for ePlant is freely available for any other biological species research.  ...  Data are displayed with a set of visualization tools that are presented using a conceptual hierarchy from big to small, and many of the tools combine information from more than one data type.  ...  We have successfully deployed ePlant on the new international portal for Arabidopsis information, Araport.org (Krishnakumar et al., 2015) .  ... 
doi:10.1105/tpc.17.00073 pmid:28808136 pmcid:PMC5590499 fatcat:4pvtzaax5bdghbr7ib674rloiy

The arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome

Tanya Z. Berardini, Leonore Reiser, Donghui Li, Yarik Mezheritsky, Robert Muller, Emily Strait, Eva Huala
2015 Genesis  
The Arabidopsis Information Resource (TAIR) is a continuously updated, online database of genetic and molecular biology data for the model plant Arabidopsis thaliana that provides a global research community  ...  making that information computationally accessible.  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
doi:10.1002/dvg.22877 pmid:26201819 pmcid:PMC4545719 fatcat:o4jldjd7lzfilomkzp7bvk4tay

AtPID: a genome-scale resource for genotype–phenotype associations in Arabidopsis

Qi Lv, Yiheng Lan, Yan Shi, Huan Wang, Xia Pan, Peng Li, Tieliu Shi
2016 Nucleic Acids Research  
Arabidopsis in AtPID 5.0.  ...  In our updated website, all the new genotype-phenotype associations from mutants, protein network, and the protein annotation information can be vividly displayed in a comprehensive network view, which  ...  Information Portal) and TAIR (4-10).  ... 
doi:10.1093/nar/gkw1029 pmid:27899679 pmcid:PMC5210528 fatcat:gm2fslshavgrrl37uptxgw5mtq

An "eFP‐Seq Browser" for Visualizing and Exploring RNA‐Seq Data

Alexander Sullivan, Priyank Purohit, Nowlan H. Freese, Asher Pasha, Eddi Esteban, Jamie Waese, Alison Wu, Michelle Chen, Chih Ying Chin, Richard Song, Sneha Ramesh Watharkar, Agnes P. Chan (+5 others)
2019 The Plant Journal  
Tool is at https://bar.utoronto.ca/eFP-Seq_Browser/; RNA-seq data at https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam/ and https://s3.amazonaws.com/iplant-cdn/iplant/home/araport/rnaseq_bam  ...  The URL for the browser is https://bar.utoronto.ca/eFP-Seq_Browser/.  ...  This work was funded by Genome Canada/Ontario Genomics grant 5452, 'Large Data Sets and Novel Tools for Plant Biology for use in International Consolidation-Tier Data Repositories and Portals'.  ... 
doi:10.1111/tpj.14468 pmid:31350781 pmcid:PMC6899666 fatcat:ihlbiyc27ffujmmuix2tfco3am

Preliminary Study on the Impact of Literature Curation in a Model Organism Database on Article Citation Rates

Tanya Berardini, Ron Daniel, Amanda Clare, Michael Lauruhn, Leonore Reiser
2016 D-Lib Magazine  
Araport: the Arabidopsis information portal. Nucleic Acids Research . 2015. Volume 43 (Database issue), Issue D1, pp. D1003-9.  ...  Berardini is a Scientific Curator at The Arabidopsis Information Resource and Phoenix Bioinformatics.  ... 
doi:10.1045/september2016-berardini fatcat:udzvw2d3pneoddv2vkhtveiv2q

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

Annemarie H. Eckes, Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham King, Sarah C. Dyer, Wiktor Jurkowski
2017 F1000Research  
Krishnakumar V, Hanlon MR, Contrino S, et al.: Araport: the Arabidopsis information portal. Nucleic Acids Res. 2015; 43(Database issue): D1003-9.  ...  The Brassica Information Portal (BIP) is a centralised repository for Brassica phenotypic data.  ...  Resources, such as TAIR (arabidopsis.org) 9 , or Araport (araport. org) 10 and the 1001genomes project 11 , provide data storage and analysis tools for the Arabidopsis Scientific community.  ... 
doi:10.12688/f1000research.11301.1 pmid:28529710 pmcid:PMC5428495 fatcat:zppbrzq3kvejrlzx6oob6ila3e

Current status of the multinational Arabidopsis community

Geraint Parry, Nicholas J. Provart, Siobhan M. Brady, Baris Uzilday, Keith Adams, Wagner Araújo, Sébastien Aubourg, Sacha Baginsky, Erica Bakker, Katja Bärenfaller, Jacqui Batley, Mike Beale (+125 others)
2020 Plant Direct  
The multinational Arabidopsis research community is highly collaborative and over the past thirty years these activities have been documented by the Multinational Arabidopsis Steering Committee (MASC).  ...  with MASC and from MASC country representatives; and (c) initiate a call for ideas and foci for the "fourth decadal roadmap," which will advise and coordinate the global activities of the Arabidopsis  ...  | Bioinformatics Over the past year the Arabidopsis bioinformatics community had to overcome the unfortunate loss of funding for the Araport resource.  ... 
doi:10.1002/pld3.248 pmid:32775952 pmcid:PMC7396448 fatcat:nzs5zlnwejftpfrf2drvvgikfa

Introducing the Brassica Information Portal: Towards integrating genotypic and phenotypic Brassica crop data

Annemarie H. Eckes, Tomasz Gubała, Piotr Nowakowski, Tomasz Szymczyszyn, Rachel Wells, Judith A. Irwin, Carlos Horro, John M. Hancock, Graham King, Sarah C. Dyer, Wiktor Jurkowski
2017 F1000Research  
Krishnakumar V, Hanlon MR, Contrino S, et al.: Araport: the Arabidopsis information portal. Nucleic Acids Res. 2015; 43(Database issue): D1003-9.  ...  The Brassica Information Portal (BIP) is a centralised repository for brassica phenotypic data.  ...  like to show our gratitude to Paweł Krajewski and Hanna Ćwiek-Kupczyńska (Institute of Plant Genetics, Polish Academy of Sciences, Poland) for discussions on phenotyping data standards including Minimum Information  ... 
doi:10.12688/f1000research.11301.2 pmid:28529710 pmcid:PMC5428495 fatcat:zgrhawfj65de5gqngd755tcawi

The 2015 Nucleic Acids Research Database Issue and Molecular Biology Database Collection

Michael Y. Galperin, Daniel J. Rigden, Xosé M. Fernández-Suárez
2015 Nucleic Acids Research  
Complex Portal.  ...  This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB,  ...  ACKNOWLEDGEMENTS We thank Dr Martine Bernardes-Silva and the Oxford University Press team led by Jennifer Boyd and Caoimhe Ní Dhónaill for their help in compiling this issue.  ... 
doi:10.1093/nar/gku1241 pmid:25593347 pmcid:PMC4383995 fatcat:rpqeohyapre5rijy7vfn7r2p7a

Finding the Subcellular Location of Barley, Wheat, Rice and Maize Proteins: The Compendium of Crop Proteins with Annotated Locations (cropPAL)

Cornelia M. Hooper, Ian R. Castleden, Nader Aryamanesh, Richard P. Jacoby, A. Harvey Millar
2015 Plant and Cell Physiology  
The data collection including meta data for proteins and published studies can be accessed through a search portal http://crop-PAL.org.  ...  The genomes of these crops each contain more than 40,000 genes encoding proteins, however, the major genome databases for these species lack annotation information of protein subcellular location for >  ...  Acknowledgments The authors would like to acknowledge Katina Toufexis and Catherine Clark from the UWA Library for their advice and help with the data repository and generation of DOIs.  ... 
doi:10.1093/pcp/pcv170 pmid:26556651 fatcat:eoclpuskmvadriho6gew3wcm64

Araport11: a complete reannotation of theArabidopsis thalianareference genome [article]

CHIA-YI Cheng, Vivek Krishnakumar, Agnes Chan, Seth Schobel, Christopher D. Town
2016 bioRxiv   pre-print
Maintaining the accuracy of the annotation continues to be a prerequisite for future progress.  ...  A comprehensive annotation of its genome paves the way for understanding the functions and activities of all types of transcripts, including mRNA, noncoding RNA, and small RNA.  ...  Araport11 will be accessible from the Araport portal (www.araport.org) and NCBI GenBank.  ... 
doi:10.1101/047308 fatcat:so77kv467jbbxfxz4we5v5zitm

Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model

Leonore Reiser, Tanya Z. Berardini, Donghui Li, Robert Muller, Emily M. Strait, Qian Li, Yarik Mezheritsky, Andrey Vetushko, Eva Huala
2016 Database: The Journal of Biological Databases and Curation  
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model.  ...  Fueled by a desire to find long term, sustainable solutions to database funding, staff from the Arabidopsis Information Resource (TAIR), founded the nonprofit organization, Phoenix Bioinformatics, using  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the Sloan Foundation or the National Institutes of Health.  ... 
doi:10.1093/database/baw018 pmid:26989150 pmcid:PMC4795935 fatcat:oze7eglyj5a3viggk44kydcqse
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