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Bioinformatics: Databases

Araport - A Community Platform for Data Sharing, Discovery and Integration
Agnes P Chan, J. Craig Venter Institute; Vivek Krishnakumar, J. Craig Venter Institute; Chia-Yi Cheng, J. Craig Venter Institute; Irina Belyaeva, J. Craig Venter Institute; Sergio Contrino, Cambridge University; Erik Ferlanti, J. Craig Venter Institute; Seth Schobel, J. Craig Venter Institute; Matt Hanlon, Texas Advanced Computing Center; Walter Moreira, Texas Advanced Computing Center; Joe Stubbs, Texas Advanced Computing Center; Rion Dooley, Texas Advanced Computing Center; Steve Mock, Texas Advanced Computing Center; Gos Micklem, Cambridge University; Jason R. Miller, J. Craig Venter Institute; Matthew Vaughn, Texas Advanced Computing Center; Christopher D. Town, J. Craig Venter Institute

Prometheus: Omics Portal for Comparative Genomics
Seongjin Park, Korea Research Institute Bioscience and Biotechnology(KRIBB); Yong-Min Kim, Korea Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology; Insu Jang, Korea Research Institute of Bioscience and Biotechnology; Yong Jin Jeon, Korea Research Institute of Bioscience and Biotechnology

Ensembl Genomes: Genomic Resources for Plants, Pests, Pathogens and Pollinators
Paul J. Kersey, EMBL - The European Bioinformatics Institute

Expert Curation of Plant Proteins in UniProtKB/Swiss-Prot
Damien Lieberherr, SIB Swiss Institute of Bioinformatics; Sylvain Poux, SIB Swiss Institute of Bioinformatics

Database Resources of DNA Data Bank of Japan
Yuichi Kodama, DNA Data Bank of Japan; Jun Mashima, DNA Data Bank of Japan; Eli Kaminuma, Genome Informatics Laboratory, NIG, ROIS; Osamu Ogasawara, DNA Data Bank of Japan; Kousaku Okubo, DNA Data Bank of Japan; Yasukazu Nakamura, DNA Data Bank of Japan; Toshihisa Takagi, DNA Data Bank of Japan

Plant Genome Database Japan (PGDBj) in 2016: A Comprehensive Database Covering Information of Plant Genome-Related Database in Japan
Hisako Ichihara, Kazusa DNA Research Institute; Sachiko Shirasawa, Kazusa DNA Research Institute; Taeko Shibaya, Kazusa DNA Research Institute; Yasukazu Nakamura, Kazusa DNA Research Institute; Akihiro Nakaya, Graduate School of Medicine, Osaka University; Masataka Kikuchi, Osaka University; Erika Asamizu, Ryukoku University; Hideki Hirakawa, Kazusa DNA Research Institute; Satoshi Tabata, Kazusa DNA Research Institute

dbSNP and dbVar: NCBI Databases of Simple and Structural Variations for All Organisms
Lon Phan, NIH/NLM/NCBI; Ming Ward, NIH/NLM/NCBI; Hua Zhang, NIH/NLM/NCBI; Qiang Wang, NIH/NLM/NCBI; Rama Maiti, NIH/NLM/NCBI; David Shao, NIH/NLM/NCBI; Eugene Shekhtman, NIH/NLM/NCBI; Juliana Sampson, NIH/NLM/NCBI; Tim Hefferon, NIH; John Garner, NIH/NLM/NCBI; John Lopez, NIH/NLM/NCBI

Curation of Genome Assemblies by NCBI Tools and Resources
Tayebeh Rezaie, National Center for Biotechnology Information (NCBI/NLM/NIH); Clifford O. Clausen, National Center for Biotechnology Information (NCBI/NLM/NIH); Nathan Bouk, National Center for Biotechnology Information (NCBI/NLM/NIH); Hsiu-Chuan Chen, National Center for Biotechnology Information (NCBI/NLM/NIH); Valerie A. Schneider, National Center for Biotechnology Information (NCBI/NLM/NIH)

Efficient Curation of Gene Banks Using Next-Generation Sequencing
Narinder Singh, Interdepartmental Genetics, Wheat Genetics Resource Center, Kansas State University; Shuangye Wu, Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University; John Raupp, Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University; Bikram S. Gill, Kansas State University; Jesse Poland, Kansas State University

Using GFF for Genome Annotation Submissions to GenBank
Terence D. Murphy, National Center for Biotechnology Information, NLM, NIH; Karen Clark, National Center for Biotechnology Information, NLM, NIH; Frank Ludwig, National Center for Biotechnology Information, NLM, NIH; Vincent Calhoun, National Center for Biotechnology Information, NLM, NIH; Sergiy Gotvyanskyy, National Center for Biotechnology Information, NLM, NIH; Colleen Bollin, National Center for Biotechnology Information, NLM, NIH

From Plants to Human Health: Bridging the Gap with Knowledge Based Discovery
Richard Linchangco, University of NC Charlotte; Jeremy Jay, University of North Carolina at Charlotte; Cory Brouwer, University of North Carolina at Charlotte

DNA Polymorphism Annotation Database (DNApod): Toward an Integration of SRA-Driven Genotypic Data and Public Phenotypic Data
Takako Mochizuki, Genome Informatics Laboratory, NIG, ROIS; Yasuhiro Tanizawa, Genome Informatics Laboratory, NIG, ROIS; Takatomo Fujisawa, Genome Informatics Laboratory, NIG, ROIS; Naruo Nikoh, Liberal Arts, OUJ; Tokurou Shimizu, NARO Institute of Fruit Tree Science; Atsushi Toyoda, Comparative Genomics laboratory, NIG, ROIS; Asao Fujiyama, Comparative Genomics laboratory, NIG, ROIS; Nori Kurata, Plant Genetics Laboratory, NIG, ROIS; Hideki Nagasaki, Genome Informatics Laboratory, NIG, ROIS; Eli Kaminuma, Genome Informatics Laboratory, NIG, ROIS; Yasukazu Nakamura, Genome Informatics Laboratory, NIG, ROIS

Increasing Discoverability and Connectivity of Scientific Media Through Annotation with iCLiKVAL
Todd D. Taylor, RIKEN Center for Integrative Medical Sciences; Naveen Kumar, RIKEN Center for Integrative Medical Sciences

Deliver Searchable Genomic, Genetic and Related Data Online Using Tripal
Stephen P. Ficklin, Washington State University; Lacey-Anne Sanderson, University of Saskatchewan; Chun-Huai Cheng, Washington State University; Brian Soto, Washington State University; Connor Wytko, Washington State University; Sook Jung, Washington State University; Alex Feltus, Genetics & Biochemistry, Clemson University; Kirstin Bett, University of Saskatchewan; Dorrie Main, Washington State University

An Integrated Database Connecting Expression Data, Meta-Data and Variants
Modupeore Adetunji, University of Delaware; Carl J. Schmidt, University of Delaware

iPTMnet: An Integrated Resource for Protein Post-Translational Modification Network Discovery
Jung-Youn Lee, Plant and Soil Sciences – University of Delaware; Hongzhan Huang, Center Bioinformatics & Comp Bio – University of Delaware; Jia Ren, University of Delaware; Cecilia Arighi, CBCB – University of Delaware; Karen Ross, Georgetown University Medical Ctr.; Gang Li, Center Bioinformatics & Comp Bio – University of Delaware; Catalina Oana Tudor Tudor, Center Bioinformatics & Comp Bio – University of Delaware; Mengxi LV, University of Delaware; Vijay Shanker, University of Delaware; Cathy H. Wu, CBCB, University of Delaware

GSP: A Web-Based Platform for Designing Genome-Specific Primers in Polyploids
Yong Q. Gu, USDA ARS, Western Regional Research Center; Yi Wang, USDA ARS, Western Regional Research Center; Vijay K. Tiwari, Kansas State University; Nidhi Rawat, Kansas State University; Bikram S. Gill, Kansas State University; Naxin Huo, USDA ARS, Western Regional Research Center; Frank M. You, Agriculture and Agri-Food Canada; Devin Coleman-Derr, Plant Gene Expression Center, USDA-ARS

Repbase: A Comprehensive Database of Eukaryotic Repeat Sequences and Transposons
Kenji K. Kojima, Genetic Information Research Institute; Weidong Bao, Genetic Information Research Institute; Oleksiy Kohany, Genetic Information Research Institute

Functional Organization of Public Gene Expression Data
Hidemasa Bono, Database Center for Life Science; Hiromasa Ono, Database Center for Life Science

ORCAE: Online Resource for Community Annotation of Eukaryotes
Lieven Sterck, VIB Ghent University, Department of Plant Biotechnology and Bioinformatics; Stephane Rombauts, VIB Ghent University, Department of Plant Biotechnology and Bioinformatics; Pierre Rouzé, VIB Ghent University, Department of Plant Biotechnology and Bioinformatics; Yves Van de Peer, VIB Ghent University, Department of Plant Biotechnology and Bioinformatics

Recent updates in the Eukaryotic Genome Annotation Pipeline
Francoise Thibaud-Nissen, National Center for Biotechnology Information (NCBI/NLM/NIH); the Eukaryotic Genome Annotation Team, NCBI/NLM/NIH

Search Functionality Intended for Medical Research in a Bioresource Database
Mika Nagahora, National Institute of Genetics; Haruka Kouyama, National Institute of Genetics; Tohru Watanabe, National Institute of Genetics; Hiroki Watanabe, National Institute of Genetics; Gaku Kimura, National Institute of Genetics; Yukiko Yamazaki, National Institute of Genetics

Planteome: A Resource for Common Reference Ontologies and Applications for Plant Biology
Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University; Laurel Cooper, Department of Botany & Plant Pathology, Oregon State University; Justin L. Elser, Department of Botany & Plant Pathology, Oregon State University; Austin Meier, Oregon State University; Marie-Angélique Laporte, Bioversity International; Christopher Mungall, Berkeley Bioinformatics Open-Source Projects; Barry Smith, University at Buffalo; Ethan KS. Johnson, Oregon State University; Megan Seymour, Oregon State University; Justin Preece, Department of Botany & Plant Pathology, Oregon State University; Xu Xu, Oregon State University; Ryan S. Kitchen, Oregon State University; Botong Qu, Oregon State University; Eugene Zhang, Oregon State University; Elizabeth Arnaud, Bioversity International; Seth Carbon, Lawrence Berkeley National Laboratory; Sinisa Todorovic, Oregon State University; Dennis Wm. Stevenson, New York Botanical Garden

Plant Omics Data Center: An Integrated Web Repository for Interspecies Gene Expression Networks with NLP-based Curation
Shin Terashima, School of Agri., Meiji University; Toru Kudo, School of Agri., Meiji University; Tomoyuki Takano, School of Agri., Meiji University; Maasa Kanno, School of Agri., Meiji University; Misa Saito, School of Agriculture, Meiji University; Noriko Matsuda, School of Agri., Meiji University; Satomi Asano, School of Agri., Meiji University; Yohei Sasaki, School of Agri., Meiji University; Koji Yokoyama, School of Agri., Meiji University; Hajime Ohyanagi, King Abdullah University of Science and Technology; Kentaro Yano, School of Agri., Meiji University

Gene Family Construction and Analysis in Phytozome
Jeremy L. Phillips, DOE Joint Genome Institute; Joseph W. Carlson, DOE Joint Genome Institute; Sajeev Batra, DOE Joint Genome Institute; David M. Goodstein, DOE Joint Genome Institute; Daniel S. Rokhsar, DOE Joint Genome Institute

Developing Bioinformatics Core Competencies for Agricultural Biotechnology
Todd M Smith, Bio-Link.org; Sandra Porter, Digital World Biology; Linnea Fletcher, Austin Community College

PIGD: A Database for Intronless Genes in the Poaceae
Jun Fan, School of Life Science, Anhui Agricultural University

Exploring Gramene’s Comparative Genomics Datasets Using New Search Tools
Joseph Mulvaney, Cold Spring Harbor Laboratory; Andrew Olson, Cold Spring Harbor Laboratory; Jim Thomason, Cold Spring Harbor Laboratory; Doreen Ware, Cold Spring Harbor Laboratory/USDA-ARS

MaizeGDB: New Tools and Resources
John Portwood, USDA-ARS; Ethalinda Cannon, Iowa State University; Bremen M Braun, MaizeGDB; Lisa Harper, USDA ARS; Mary Schaeffer, USDA ARS and University of Missouri; Jack Gardiner, Department of Genetics, Cellular, and Developmental Biology; Michael Brumfield, Iowa State University; Kyoung Tak Cho, Iowa State University; Brittney Dunfee, Iowa State University; David Schott, Iowa State University; Taner Z. Sen, USDA -ARS /Iowa State University; Carson M Andorf, USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University

Data Management and Analysis Solutions for Maize Predictive Phenomics: A Partnership with the GxE Subgroup of the Genomes to Fields (G2F) Initiative
GXE Data Management Team, Iowa State University; Genome2Fields Initiative, University of Wisconsin; Jack Gardiner, Department of Genetics, Cellular, and Developmental Biology; Ramona Walls, University of Arizona; Jeremy de Barry, IPlant Collaborative; Matthew Berrigan, Leafnode; Carolyn J. Dill, Bioinformatics and Computational Biology Program, Iowa State University

TENOR: Database for Comprehensive mRNA-Seq Experiments in Rice
Yoshihiro Kawahara, National Institute of Agrobiological Sciences; Youko Oono, National Institute of Agrobiological Sciences; Hironobu Wakimoto, National Institute of Agrobiological Sciences; Jun Ogata, National Institute of Agrobiological Sciences; Hiroyuki Kanamori, National Institute of Agrobiological Sciences; Harumi Sasaki, National Institute of Agrobiological Sciences; Satomi Mori, National Institute of Agrobiological Sciences; Takashi Matsumoto, National Institute of Agrobiological Sciences; Takeshi Itoh, National Institute of Agrobiological Sciences

Exploration of Genomic Selection Options for a Commercial Perennial Ryegrass Breeding Program
Zibei Lin, Biosciences Research, DEDJTR; Junping Wang, Hamilton Centre, Biosciences Research, DEDJTR; Noel O. I. Cogan, Biosciences Research, DEDJTR; John Forster, Biosciences Research, DEDJTR; German Spangenberg, Biosciences Research, DEDJTR; Ben Hayes, Biosciences Research, DEDJTR; Hans D. Daetwyler, Biosciences Research, DEDJTR

TreeGenes: Enabling Visualization and Analysis in Forest Tree Genomics
Emily Grau, University of Connecticut; Steven A Demurjian Jr, University of Connecticut; Hans Vasquez-Gross, University of California Davis; Damian Gessler, Semantic Options; David Neale, Dept. Plant Sciences University of California Davis; Jill Wegrzyn, Department of Ecology and Evolutionary Biology, University of Connecticut

Hardwood Genomics Database (HGD): A Genomic and Genetic Web-Database for Hardwood Trees Research
Ming Chen, University of Tennessee; Nate Henry, University of Tennessee; Thomas Lane, University of Tennessee, Knoxville; Nathaniel Cannon, Penn State University; Mark Coggeshall, University of Missouri; Oliver Gailing, Michigan Technological University; Haiying Liang, Clemson University; Jeanne Romero-Severson, University of Notre Dame; Scott Schlarbaum, University of Tennessee, Knoxville; Ketia Shumaker, The University of West Alabama; John E. Carlson, Penn State University; Margaret Staton, University of Tennessee

FragariaCyc: A Metabolic Pathway Network for Diploid Strawberry F. vesca
Sushma Naithani, Department of Botany & Plant Pathology, Oregon State University; Christina Partipilo, Department of Botany & Plant Pathology, Oregon State University; Rajani Raja, Department of Botany & Plant Pathology, Oregon State University; Justin L. Elser, Department of Botany & Plant Pathology, Oregon State University; Pankaj Jaiswal, Department of Botany & Plant Pathology, Oregon State University

LIS (Legume Information System): A Clade Based Web Resource for Legumes
Sudhansu Dash, National Center for Genome Resources (NCGR); Wei Huang, Iowa State University; Jacqueline D. Campbell, Iowa State University; Jugpreet Singh, ORISE Fellow, USDA-ARS-CICGRU; Alex G. Rice, National Center for Genome Resources (NCGR); Pooja E. Umale, National Center for Genome Resources (NCGR); Alan Cleary, Montana State University; Scott R. Kalberer, USDA-ARS-CICGRU; Nathan T. Weeks, USDA-ARS-CICGRU; Vijay Karingula, Iowa State University; Prateek Gupta, Iowa State University; Shivan Gunda, Iowa State University; Ethalinda Cannon, Iowa State University; Andrew D. Farmer, National Center for Genome Resources (NCGR); Steven B. Cannon, USDA-ARS-CICGRU

The LegumeIP (2016 Release) - a Web-Based Comparative Genomics and Gene Expression Atlas Platform for the Study of Gene Function and Genome Evolution in Legumes
Jun Li, University of Texas MD Anderson Cancer Center; Xinbin Dai, The Samuel Roberts Noble Foundation; Zhaohong Zhuang, The Samuel Roberts Noble Foundation; Patrick Xuechun Zhao, The Samuel Roberts Noble Foundation

Cool Season Food Legume Genome Database: An up-to-Date Resource Enabling Genetics, Genomics and Breeding Research in Pea, Lentil, Faba Bean and Chickpea
Jodi L. Humann, Washington State University; Sook Jung, Washington State University; Ping Zheng, Washington State University; Chun-Huai Cheng, Washington State University; Taein Lee, Washington State University; Morgan Frank, Washington State University; Deah McGaughey, Washington State University; Kristin Scott, Washington State University; Jing Yu, Washington State University; Stephen P. Ficklin, Washington State University; Marwa N.M.E. Sanad, National Research Center- Egypt; Heidi Hough, Washington State University; Clare Coyne, USDA ARS; Rebecca McGee, Washington State University; Dorrie Main, Washington State University

The Vigna Genome Server, 'VigGS': A Genomic Knowledge Base of the Genus Vigna
Hiroaki Sakai, National Institute of Agrobiological Sciences; Ken Naito, National Institute of Agrobiological Sciences; Yu Takahashi, National Institute of Agrobiological Sciences; Takeshi Itoh, National Institute of Agrobiological Sciences; Norihiko Tomooka, National Institute of Agrobiological Sciences

PeanutBase: A Resource for Peanut Researchers and Breeders
Ethalinda Cannon, Iowa State University; Wei Huang, Iowa State University; Sudhansu Dash, National Center for Genome Resources (NCGR); Jugpreet Singh, ORISE Fellow, USDA-ARS-CICGRU; Scott R. Kalberer, USDA-ARS-CICGRU; Longhui Ren, Iowa State University; Pooja E. Umale, National Center for Genome Resources (NCGR); Nathan Weeks, USDA-ARS-CICGRU; Julie Dickerson, National Science Foundation; Andrew D. Farmer, National Center for Genome Resources (NCGR); Steven B. Cannon, USDA-ARS-CICGRU

The Federated Plant Database Initiative for the Legumes
Steven B. Cannon, USDA-ARS-CICGRU; Ethalinda Cannon, Iowa State University; Jacqueline D. Campbell, Iowa State University; Sudhansu Dash, National Center for Genome Resources; Wei Huang, Iowa State University; Akshay Yadav, Iowa State University; Nathan T. Weeks, USDA-ARS-CICGRU; Andrew Wilkey, Iowa State University; Sam Hokin, National Center for Genome Resources; David Grant, USDA-ARS-CICGR; Rex Nelson, USDA-ARS-CICGRU; Kevin H. Feeley, USDA-ARS-CICGRU; Vivek Krishnakumar, J. Craig Venter Institute; Jeremy D. DeBarry, University of Arizona; Andrew D. Farmer, National Center for Genome Resources (NCGR); David Fernandez-Baca, Iowa State University; Christopher D. Town, J. Craig Venter Institute

Protocols for Representation of Protein Domain Annotations in Clade-Oriented Databases: a Case Study at the Legume Information System using Chado/Tripal
Pooja E. Umale, National Center for Genome Resources (NCGR); Andrew D. Farmer, National Center for Genome Resources (NCGR)

HRGRN: Model and Decipher Arabidopsis Signaling Transduction, Metabolism and Gene Regulation Networks using Graph Theory
Xinbin Dai, The Samuel Roberts Noble Foundation; Patrick Xuechun Zhao, The Samuel Roberts Noble Foundation

CAMbase: Developing A Resource for CAM Plant Genomics
Robert Clifford Moseley, University of Tennessee-Knoxville; Xiaohan Yang, Oak Ridge National Laboratory; Gerald A. Tuskan, Oak Ridge National Laboratory

Animal QTLdb: Towards a Comprehensive Database and Tool Set for Livestock Genome Research
Zhiliang Hu, Iowa State University; Carissa Park, Iowa State University; James M. Reecy, Iowa State University

The Vertebrate Gene Nomenclature Committee (VGNC): Standardising Gene Names and Symbols Across Vertebrate Genomes
Susan Tweedie, European Bioinformatics Institute (EMBL-EBI); Bethan Yates, European Bioinformatics Institute (EMBL-EBI); Ruth Seal, EMBL-EBI; Kristian Gray, European Bioinformatics Institute (EMBL-EBI); Elspeth Bruford, EMBL-EBI

BovineMine: A Data Mining Warehouse for the Bos taurus Genome
Christine G. Elsik, Division of Animal Sciences, University of Missouri; Colin M. Diesh, Division of Animal Sciences, University of Missouri; Deepak R. Unni, Division of Animal Sciences, University of Missouri; Aditi Tayal, Division of Animal Sciences, University of Missouri; Hung N. Nguyen, MU Informatics Institute, University of Missouri; Darren E. Hagen, Division of Animal Sciences, University of Missouri

EpiDB: An Omics Data Resource for Cattle
James E. Koltes, Department of Animal Science, University of Arkansas; Eric Fritz-Waters, Department of Animal Science, Iowa State University; James M. Reecy, Iowa State University

The i5k Workspace@NAL - Updates and New Developments of an Arthropod Genome Portal
Monica Poelchau, USDA/Agricultural Resarch Service/National Agricultural Library; Christopher Childers, USDA/Agricultural Resarch Service/National Agricultural Library; Vijaya Tsavatapalli, USDA/Agricultural Resarch Service/National Agricultural Library; Gary Moore, USDA/Agricultural Resarch Service/National Agricultural Library; Ursula Pieper, USDA/Agricultural Resarch Service/National Agricultural Library; Mei-Ju May Chen, Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica; Yu-Yu Lin, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University

Development of an Integrated System to Support Genomics-Based Crop Improvement
Yeisoo Yu, Phyzen Genomics Institute; Beom-Soon Choi, Phyzen Genomics Institute

Crop Ontology: Integration of Standard Variables
Léo Valette, Bioversity International; Julian Pietragalla, Integrated Breeding Platform; Marie-Angélique Laporte, Bioversity International; Agbona Afolabi, International Institute of Tropical Agriculture (IITA); Ousmane Boukar, International Institute of Tropical Agriculture; Steven B. Cannon, USDA-ARS-CICGRU; Brian W. Diers, University of Illinois; Kate A. Dreher, Carnegie Institution for Science; Pooran M Gaur, ICRISAT; Alberto Fabio Guerrero, CIAT; C Tom Hash, ICRISAT; Vilma Hualla, International Potato Center (CIP); Drabo Inoussa, INERA; Scott R. Kalberer, USDA-ARS-CICGRU; Clarisse Kondombo-Barro, INERA; Shiv Kumar, ICARDA; Antonio Lopez-Montes, International Institute of Tropical Agricultutre; Naama Menda, Boyce Thompson Institute for Plant Research; Randall Nelson, USDA-ARS; Sam Ofodile, IITA; Suyash Patil, ICRISAT; Peteti Prasad, ICRISAT; Karthika Rajendran, ICARDA; Jean-Francois Rami, CIRAD; Abhishek Rathore, ICRISAT; N. Ruaraidh Sackville Hamilton, International Rice Research Institute; Reinhard Simon, International Potato Center (CIP); Niaba Teme, IER; Eva Weltzien-Rattunde, ICRISAT; Elizabeth Arnaud, Bioversity International; Rosemary Shrestha, Genetic Resources Prog.,CIMMYT

PlabiPD - Providing Crop Data for Plant Research
Marie E Bolger, IBG2, Forschungszentrum jülich

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