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BioProject and BioSample databases at NCBI: facilitating capture and organization of metadata

T. Barrett, K. Clark, R. Gevorgyan, V. Gorelenkov, E. Gribov, I. Karsch-Mizrachi, M. Kimelman, K. D. Pruitt, S. Resenchuk, T. Tatusova, E. Yaschenko, J. Ostell
2011 Nucleic Acids Research  
The BioProject database was recently established to facilitate organization and classification of project data submitted to NCBI, EBI and DDBJ databases.  ...  As the volume and complexity of data sets archived at NCBI grow rapidly, so does the need to gather and organize the associated metadata.  ...  We also wish to thank the many NCBI staff members who have contributed to discussions and provided data or feedback on these resources, in particu- Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkr1163 pmid:22139929 pmcid:PMC3245069 fatcat:xjhql7u355bqtfmkq3ba2vtzjq

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

T.B.K. Reddy, Alex D. Thomas, Dimitri Stamatis, Jon Bertsch, Michelle Isbandi, Jakob Jansson, Jyothi Mallajosyula, Ioanna Pagani, Elizabeth A. Lobos, Nikos C. Kyrpides
2014 Nucleic Acids Research  
GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database.  ...  The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects.  ...  We thank the members of the microbial genomics and metagenomics programs at the JGI for support, useful discussions and exchange of ideas.  ... 
doi:10.1093/nar/gku950 pmid:25348402 pmcid:PMC4384021 fatcat:hgal77wrpjb4rp5ivjquzs7dsm

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Olena Verezemska, Michelle Isbandi, Alex D. Thomas, Rida Ali, Kaushal Sharma, Nikos C. Kyrpides, T. B. K. Reddy
2016 Nucleic Acids Research  
In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing  ...  The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, singlecell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome  ...  ACKNOWLEDGEMENTS The authors are thankful to researchers who take time to accurately document and provide metadata directly to GOLD or via other public resources.  ... 
doi:10.1093/nar/gkw992 pmid:27794040 pmcid:PMC5210664 fatcat:t7onakl2t5g67e42szgto4n35m

The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories

Syed Ahmad Chan Bukhari, Martin J. O'Connor, Marcos Martínez-Romero, Attila L. Egyedi, Debra Willrett, John Graybeal, Mark A. Musen, Florian Rubelt, Kei-Hoi Cheung, Steven H. Kleinstein
2018 Frontiers in Immunology  
the ontology-linked metadata and sequence files (FASTQ) to the NCBI BioProject, BioSample, and Sequence Read Archive databases.  ...  This pipeline is available at http://cairr.miairr.org, and will facilitate the NCBI submission process and improve the metadata quality of AIRR-seq studies.  ...  and sequence files (FASTQ) (16) to the NCBI BioProject, BioSample, and SRA databases.  ... 
doi:10.3389/fimmu.2018.01877 pmid:30166985 fatcat:62ao6hzerrefndzzqeqjpkpw4u

Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens

Ruth E. Timme, William J. Wolfgang, Maria Balkey, Sai Laxmi Gubbala Venkata, Robyn Randolph, Marc Allard, Errol Strain
2020 One Health Outlook  
We then provide an overview of NCBI data submission along with step by step details. And finally, we provide curation guidance and an SOP for keeping your public data current within the database.  ...  Ongoing work by NCBI and the GenomeTrakr project illustrates how open data platforms can help meet the needs of federal and state regulators, public health laboratories, departments of agriculture, and  ...  We also thank our Genometrakr collaborators (including CDC, FSIS, NCBI, and David Lipman) for reviewing the manuscript and providing feedback prior to publication.  ... 
doi:10.1186/s42522-020-00026-3 pmid:33103064 pmcid:PMC7568946 fatcat:yfexo6xtobcm3ffw3gexlxlg2u

Genomes OnLine Database (GOLD) v.8: overview and updates

Supratim Mukherjee, Dimitri Stamatis, Jon Bertsch, Galina Ovchinnikova, Jagadish Chandrabose Sundaramurthi, Janey Lee, Mahathi Kandimalla, I-Min A Chen, Nikos C Kyrpides, T B K Reddy
2020 Nucleic Acids Research  
The current version of the database includes over 1.17 million entries organized broadly into Studies (45 770), Organisms (387 382) or Biosamples (101 207), Sequencing Projects (355 364) and Analysis Projects  ...  The Genomes OnLine Database (GOLD) (https://gold.jgi.doe.gov/) is a manually curated, daily updated collection of genome projects and their metadata accumulated from around the world.  ...  ACKNOWLEDGEMENTS The authors would like to thank our broad user base and members of the research community for submitting projects and metadata to GOLD.  ... 
doi:10.1093/nar/gkaa983 pmid:33152092 fatcat:gdmujnzdqzcwxd2moq43badro4

Standardized Metadata for Human Pathogen/Vector Genomic Sequences

Vivien G. Dugan, Scott J. Emrich, Gloria I. Giraldo-Calderón, Omar S. Harb, Ruchi M. Newman, Brett E. Pickett, Lynn M. Schriml, Timothy B. Stockwell, Christian J. Stoeckert, Dan E. Sullivan, Indresh Singh, Doyle V. Ward (+47 others)
2014 PLoS ONE  
It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology  ...  To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and  ...  Acknowledgments We are grateful to the various data providers for their participation in the definition of important metadata to capture for sequencing projects.  ... 
doi:10.1371/journal.pone.0099979 pmid:24936976 pmcid:PMC4061050 fatcat:xr3rkfcxtndi7owhcl6k6mmiyi

Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases

2019 Database: The Journal of Biological Databases and Curation  
for Biotechnology Information BioSample and European Bioinformatics Institute BioSamples.  ...  Secondary problems include the lack of validation and sparse use of standardized terms or ontologies when authoring metadata.  ...  All software described in this paper is open source and available on GitHub (https://github.com/ metadatacenter).  ... 
doi:10.1093/database/baz059 pmid:31210270 pmcid:PMC6866600 fatcat:7u2ul2osevf23nvqhvi3ii3ri4

Adaptive Immune Receptor Repertoire Community recommendations for sharing immune-repertoire sequencing data

Florian Rubelt, Christian E Busse, Syed Ahmad Chan Bukhari, Jean-Philippe Bürckert, Encarnita Mariotti-Ferrandiz, Lindsay G Cowell, Corey T Watson, Nishanth Marthandan, William J Faison, Uri Hershberg, Uri Laserson, Brian D Corrie (+7 others)
2017 Nature Immunology  
Luxembourg 5 Sorbonne Universités, UPMC Univ Paris 06, INSERM, UMR_S 959, Immunology-Immunopathology-Immunotherapy (i3), Abstract High-throughput sequencing of B and T cell receptors is routinely being  ...  applied in studies of adaptive immunity.  ...  We hope that readers of this Comment will use the MiAIRR standard, and encourage their publishers to require authors to use it, for AIRR-seq data submission and sharing.  ... 
doi:10.1038/ni.3873 pmid:29144493 pmcid:PMC5790180 fatcat:vfzzmxmi45c2fig636nzzmrnt4

Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases [article]

Marcos Martínez-Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, Josef Hardi, John Graybeal, Mark A. Musen
2019 arXiv   pre-print
for Biotechnology Information (NCBI) BioSample and European Bioinformatics Institute (EBI) BioSamples.  ...  Secondary problems include the lack of validation and sparse use of standardized terms or ontologies when authoring metadata.  ...  Acknowledgements Availability of software and data We have created a Jupyter notebook describing in detail the steps to reproduce our evaluation using Python and R scripts.  ... 
arXiv:1903.09270v1 fatcat:3xgbrlyyinfppklbpczk7ffkk4

CorkOakDB—The Cork Oak Genome Database Portal

Cirenia Arias-Baldrich, Marta Contreiras Silva, Filippo Bergeretti, Inês Chaves, Célia Miguel, Nelson J M Saibo, Daniel Sobral, Daniel Faria, Pedro M Barros
2020 Database: The Journal of Biological Databases and Curation  
Database URL: http://corkoakdb.org/  ...  In an effort to integrate this information in a comprehensive, accessible and intuitive format, we have developed The Cork Oak Genome Database Portal (CorkOakDB).  ...  Conflict of Interest There is no conflict of interest. Funding  ... 
doi:10.1093/database/baaa114 pmid:33382885 fatcat:hmic5lcpnjcqzfvtt3srehseyy

Cyberbiosecurity Challenges of Pathogen Genome Databases

Boris A. Vinatzer, Lenwood S. Heath, Hussain M. J. Almohri, Michael J. Stulberg, Christopher Lowe, Song Li
2019 Frontiers in Bioengineering and Biotechnology  
of the next generation of pathogen genome databases.  ...  Here, we define a number of potential cybersecurity weaknesses in today's pathogen genome databases to raise awareness, and we provide potential solutions to strengthen cyberbiosecurity during the development  ...  Department of Agriculture and should not be construed to represent any agency determination or policy.  ... 
doi:10.3389/fbioe.2019.00106 pmid:31157218 pmcid:PMC6529814 fatcat:d2npjjees5cfbn2cdavc6zkuzi

SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes

Jennifer Wyffels, Benjamin L. King, James Vincent, Chuming Chen, Cathy H. Wu, Shawn W. Polson
2014 F1000Research  
Last (maps and taxonomy), Shannon Corrigan and Lei Yang (gene capture data), and Callie Crawford and Thomas Fussell (CT scanning and anatomy) for providing a description of the project scope.  ...  We thank Gavin Naylor and the Chondrichthyan Tree of Life project team including Lindsay Marshall (illustrations), Jason Davies (database, computational work, and visualizations), Will White and Peter  ...  Because the BioProject and BioSample databases were estab- lished in 2012, not all existing datasets have metadata or details of the biological source to populate a BioSample and BioProject entry.  ... 
doi:10.12688/f1000research.4996.1 pmid:25309735 pmcid:PMC4184313 fatcat:twejm6v2tfcbng7mopnsoeqqvu

Database resources of the National Center for Biotechnology Information

2012 Nucleic Acids Research  
In addition to maintaining the GenBank Õ nucleic acid sequence database, the National Center for Biotechnology Information (NCBI, http://www.ncbi. nlm.nih.gov) provides analysis and retrieval resources  ...  for the data in GenBank and other biological data made available through the NCBI web site.  ...  GENOMES BioProject The BioProject database (www.ncbi.nlm.nih.gov/ bioproject/) is a central access point for metadata about research projects whose data are deposited in databases maintained by members  ... 
doi:10.1093/nar/gks1189 pmid:23193264 pmcid:PMC3531099 fatcat:hp2biq76anavbavtbbz4jcvwqm

IBM Functional Genomics Platform, A Cloud-Based Platform for Studying Microbial Life at Scale [article]

Edward E. Seabolt, Gowri Nayar, Harsha Krishnareddy, Akshay Agarwal, Kristen L. Beck, Ignacio Terrizzano, Eser Kandogan, Mary Roth, Vandana Mukherjee, James H. Kaufman
2020 arXiv   pre-print
To address these challenges, we pre-computed important relationships between biological entities spanning the Central Dogma of Molecular Biology and captured this information in a relational database.  ...  life at scale.  ...  Haiminen and Dr. L. Parida of IBM Research for helpful discussion and insights into new applications of IBM Functional Genomics Platform.  ... 
arXiv:1911.02095v3 fatcat:bn6kssh2ezbqnashkxqzga3faq
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