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Recommendations for the FAIRification of genomic track metadata

Sveinung Gundersen, Sanjay Boddu, Salvador Capella-Gutierrez, Finn Drabløs, José M. Fernández, Radmila Kompova, Kieron Taylor, Dmytro Titov, Daniel Zerbino, Eivind Hovig
2021 F1000Research  
Many types of data from genomic analyses can be represented as genomic tracks, i.e. features linked to the genomic coordinates of a reference genome. Examples of such data are epigenetic DNA methylation data, ChIP-seq peaks, germline or somatic DNA variants, as well as RNA-seq expression levels. Researchers often face difficulties in locating, accessing and combining relevant tracks from external sources, as well as locating the raw data, reducing the value of the generated information.
more » ... ion of work: We propose to advance the application of FAIR data principles (Findable, Accessible, Interoperable, and Reusable) to produce searchable metadata for genomic tracks. Findability and Accessibility of metadata can then be ensured by a track search service that integrates globally identifiable metadata from various track hubs in the Track Hub Registry and other relevant repositories. Interoperability and Reusability need to be ensured by the specification and implementation of a basic set of recommendations for metadata. We have tested this concept by developing such a specification in a JSON Schema, called FAIRtracks, and have integrated it into a novel track search service, called TrackFind. We demonstrate practical usage by importing datasets through TrackFind into existing examples of relevant analytical tools for genomic tracks: EPICO and the GSuite HyperBrowser. Conclusion: We here provide a first iteration of a draft standard for genomic track metadata, as well as the accompanying software ecosystem. It can easily be adapted or extended to future needs of the research community regarding data, methods and tools, balancing the requirements of both data submitters and analytical end-users.
doi:10.12688/f1000research.28449.1 pmid:34249331 pmcid:PMC8226415 fatcat:n5xal7ssrjf4jaybqfyoygcmia

Ensembl Genomes 2016: more genomes, more complexity

Paul Julian Kersey, James E. Allen, Irina Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay Humphrey, Arnaud Kerhornou (+26 others)
2015 Nucleic Acids Research  
Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the context of the Ensembl project (http://www.ensembl. org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including reference sequence, gene models, transcriptional data, genetic variation and comparative analysis. This paper
more » ... es an update to the previous publications about the resource, with a focus on recent developments. These include the development of new analyses and views to represent polyploid genomes (of which bread wheat is the primary exemplar); and the continued up-scaling of the resource, which now includes over 23 000 bacterial genomes, 400 fungal genomes and 100 protist genomes, in addition to 55 genomes from invertebrate metazoa and 39 genomes from plants. This dramatic increase in the number of included genomes is one part of a broader effort to automate the integra-
doi:10.1093/nar/gkv1209 pmid:26578574 pmcid:PMC4702859 fatcat:n3oewab7gvei5fbg6wfrx2ydaa

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species

Paul Julian Kersey, James E Allen, Alexis Allot, Matthieu Barba, Sanjay Boddu, Bruce J Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Christoph Grabmueller, Navin Kumar, Zicheng Liu (+34 others)
2017 Nucleic Acids Research  
Ensembl Genomes (http://www.ensemblgenomes. org) is an integrating resource for genome-scale data from non-vertebrate species, complementing the resources for vertebrate genomics developed in the Ensembl project (http://www.ensembl.org). Together, the two resources provide a consistent set of programmatic and interactive interfaces to a rich range of data including genome sequence, gene models, transcript sequence, genetic variation, and comparative analysis. This paper provides an update to
more » ... previous publications about the resource, with a focus on recent developments and expansions. These include the incorporation of almost 20 000 additional genome sequences and over 35 000 tracks of RNA-Seq data, which have been aligned to genomic sequence and made available for visualization. Other advances since 2015 include the release of the database in Resource Description Framework (RDF) format, a large increase in community-derived curation, a new high-performance protein sequence search, additional cross-references, improved annotation of non-protein-coding genes, and the launch of pre-release and archival sites. Collectively, these changes are part of a continuing response to the increasing quantity of publicly-available genome-scale data, and the consequent need to archive, integrate, annotate and disseminate these using automated, scalable methods.
doi:10.1093/nar/gkx1011 pmid:29092050 pmcid:PMC5753204 fatcat:mmgammsp3fcrpdfrwprhsxl4g4

Author index with paper numbers

2013 2013 National Conference on Communications (NCC)  
Chaira, Tamalika Chaitanya A., Krishna Indu, Sreedevi Kalamkar, Sanket Sanjay Kulkarni, Anup Mandpura, Anup Kumar Gadre, Vikram M.  ...  Janardhanan Karthikeyan, Sholampettai Subramanian Kundu, Sumit Mukherjee, Manuj p1.6_6_1569694029 p1.3_1_1569693061 p4.6_6_1569698167 p3.4_7_1569697799 p2.5_2_1569697363 p1.5_3_1569697225 p2.2_4_1569697299 Boddu  ... 
doi:10.1109/ncc.2013.6487897 fatcat:kd2fahympjde5ntlaieivnyqm4

Ensembl 2019

Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M Ridwan Amode, Irina M Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla Cummins, Claire Davidson (+56 others)
2018 Nucleic Acids Research  
The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources. This year we describe our new and expanded gene, variant and comparative annotation capabilities, which led to a 50% increase in the number of vertebrate genomes we support. We have
more » ... doubled the number of available human variants and added regulatory regions for many mouse cell types and developmental stages. Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download.
doi:10.1093/nar/gky1113 pmid:30407521 fatcat:q2roq24hdjaqrlqc6r52kemvzi

Ensembl 2021

Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu (+67 others)
2020 Nucleic Acids Research  
The Ensembl project (https://www.ensembl.org) annotates genomes and disseminates genomic data for vertebrate species. We create detailed and comprehensive annotation of gene structures, regulatory elements and variants, and enable comparative genomics by inferring the evolutionary history of genes and genomes. Our integrated genomic data are made available in a variety of ways, including genome browsers, search interfaces, specialist tools such as the Ensembl Variant Effect Predictor, download
more » ... iles and programmatic interfaces. Here, we present recent Ensembl developments including two new website portals. Ensembl Rapid Release (http://rapid.ensembl.org) is designed to provide core tools and services for genomes as soon as possible and has been deployed to support large biodiversity sequencing projects. Our SARS-CoV-2 genome browser (https://covid-19.ensembl.org) integrates our own annotation with publicly available genomic data from numerous sources to facilitate the use of genomics in the international scientific response to the COVID-19 pandemic. We also report on other updates to our annotation resources, tools and services. All Ensembl data and software are freely available without restriction.
doi:10.1093/nar/gkaa942 pmid:33137190 pmcid:PMC7778975 fatcat:z5nwlejfpja5zfdbriagabtuga

What Every Intensivist Should Know about Impairment of Cardiac Function and Arrhythmias in Liver Disease Patients: A Review

Prashant Kumar, Sanjay Saxena, Haider Abbas, Sanjeev Arya, Bhuwan Tiwari, Shantanu Belwal
2020 Indian Journal of Critical Care Medicine  
refers to the length of ventricular electric inactivity during cardiac repolarization, its prolongation increases chances of impairment of the cardiac function and ventricular arrhythmias. 17 Reddy and Boddu  ... 
doi:10.5005/jp-journals-10071-23695 pmid:33446981 pmcid:PMC7775933 fatcat:xxbcttsapncszcgsmdjfhy3icm

Table of Contents

2022 2022 International Conference on Applied Artificial Intelligence and Computing (ICAAIC)  
Processing Model for Deformity in Diabetic Polygenic Disease Depiction License Plate Image Super Resolution using Generative Adversarial Carbon Neutrality 138 174 211 Commodities in Gujarat Aditi M Joshi, Sanjay  ...  Prabhakar Reddy, Pramit Brata Chanda A Comprehensive Analysis on Outlier Prediction using Learning Approaches Boddu L V Siva Rama Krishna, V Mahalakshmi, Gopala Krishna Murthy Nookala A Study of Efficient  ... 
doi:10.1109/icaaic53929.2022.9792848 fatcat:x46pxmnqdnbqnoancfrwuxe7v4

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates

Andrew D Yates, James Allen, Ridwan M Amode, Andrey G Azov, Matthieu Barba, Andrés Becerra, Jyothish Bhai, Lahcen I Campbell, Manuel Carbajo Martinez, Marc Chakiachvili, Kapeel Chougule, Mikkel Christensen (+53 others)
2021 Nucleic Acids Research  
Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins, Kamalkumar Dodiya, Bilal El Houdaigui, Carlos Garcia Giron, Thiago Genez, Arthur Gymer, Thibaut Hourlier,  ...  ACKNOWLEDGEMENTS We thank the following Ensembl project members for their work, which underpins our own: Jamie Allen, Jorge Alvarez-Jarreta, Irina Armean, Olanrewaju Austine-Orimoloye, Konstantinos Billis, Sanjay  ... 
doi:10.1093/nar/gkab1007 pmid:34791415 pmcid:PMC8728113 fatcat:dgez6bpcfjdz5ibbp6dmryyirq

scSVAS: CNV clonal visualization online platform for large scale single-cell genomics [article]

Lingxi Chen, Yuhao Qing, Ruikang Li, Chaohui Li, Hechen Li, Xikang Feng, Shuai Cheng Li
2021 bioRxiv   pre-print
Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M Ridwan Amode, Irina M Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, et al.  ... 
doi:10.1101/2021.06.10.437122 fatcat:j3e45xnuz5a3tdrud6rpaogzge

Acknowledgement to Reviewers of International Journal of Molecular Science in 2019

IJMS Editorial Office
2020 International Journal of Molecular Sciences  
Bocianowski, Jan Bock, Karl Walter Böckmann, Rainer A Boda, Sunil Kumar Boddapati, Loukya Boddu, Sai H. S.  ...  Van Veldhoven, Paul Van Waardenburg, Robert Van Zandwijk, Nico Van Haute, Lindsey Vance, David Varga, Balazs Varghese, Mathews Varikuti, Sanjay Varma, Vijaykumar B.  ... 
doi:10.3390/ijms21020668 fatcat:7tvwrglcyneitpglbfx4yhm4nu

A QUARTER CENTURY OF "MANMOHAN SINGH'S REFORM": SOCIO-POLITICAL ASPECT
ЧЕТВЕРТЬ ВЕКА "РЕФОРМЫ М. СИНГХА": СОЦИАЛЬНО-ПОЛИТИЧЕСКОЕ ИЗМЕРЕНИЕ

Ya.O. SADOVNIKOVA
2017 Mirovaya Ekonomika i Mezhdunarodnye Otnosheniya  
SANJAY KUMAR SINGH M IND 409 0.09% 22 . MD. ABRARUL HODA M IND 376 0.08% 23 . BRIJ KISHORE TIWARY M IND 361 0.08% 24 . MD. NAYEEM M DDP 353 0.08% 25 .  ...  HARINADHA RAO BODDU M IND 3428 0.48% 8 . NAGISETTI RAM RAO M IND 2682 0.37% 9 . ARVAPALLI VIDYA SAGAR M JP 2596 0.36% 10 . GANDURI LALAIAH M IND 2563 0.36% 11 .  ... 
doi:10.20542/0131-2227-2017-61-3-100-106 fatcat:3tbpgg3gv5axxeyr4sfwy5f5f4