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ArrayExpress update—simplifying data submissions

Nikolay Kolesnikov, Emma Hastings, Maria Keays, Olga Melnichuk, Y. Amy Tang, Eleanor Williams, Miroslaw Dylag, Natalja Kurbatova, Marco Brandizi, Tony Burdett, Karyn Megy, Ekaterina Pilicheva (+6 others)
2014 Nucleic Acids Research  
In the near future, Annotare will become the only submission route into ArrayExpress, alongside MAGE-TAB format-based pipelines. ArrayExpress is a stable and highly accessed resource.  ...  The main development over the last two years has been the release of a new data submission tool Annotare, which has reduced the average submission time almost 3-fold.  ...  between ArrayExpress and ENA.  ... 
doi:10.1093/nar/gku1057 pmid:25361974 pmcid:PMC4383899 fatcat:c4fvlffcnfcpde7agoxjir4beu

ArrayExpress update – from bulk to single-cell expression data

Awais Athar, Anja Füllgrabe, Nancy George, Haider Iqbal, Laura Huerta, Ahmed Ali, Catherine Snow, Nuno A Fonseca, Robert Petryszak, Irene Papatheodorou, Ugis Sarkans, Alvis Brazma
2018 Nucleic Acids Research  
Data submissions will continue unchanged; all existing ArrayExpress data will be incorporated into BioStudies and the existing accession numbers and application programming interfaces will be maintained  ...  ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data from a variety of technologies assaying functional modalities of a genome, such as gene expression or promoter  ...  GROWTH OF SEQUENCING BASED DATA ArrayExpress receives ∼1000 experiment submissions per year via the submission tool Annotare.  ... 
doi:10.1093/nar/gky964 pmid:30357387 pmcid:PMC6323929 fatcat:p2n5pu6dgffvtf3jp5ypftowxu

ArrayExpress update—trends in database growth and links to data analysis tools

Gabriella Rustici, Nikolay Kolesnikov, Marco Brandizi, Tony Burdett, Miroslaw Dylag, Ibrahim Emam, Anna Farne, Emma Hastings, Jon Ison, Maria Keays, Natalja Kurbatova, James Malone (+14 others)
2012 Nucleic Acids Research  
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression Omnibus  ...  The proportion of sequencing-based submissions has grown significantly over the last 2 years and has reached, in 2012, 15% of all new data.  ...  The ArrayExpress user documentation has recently been updated and several online courses, covering how to search, interpret and submit data to ArrayExpress, can be found on the EBI e-Learning portal, Train  ... 
doi:10.1093/nar/gks1174 pmid:23193272 pmcid:PMC3531147 fatcat:un6k6u4xqfdjpjt6yhdg5lf6de

ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments

H. Parkinson, U. Sarkans, N. Kolesnikov, N. Abeygunawardena, T. Burdett, M. Dylag, I. Emam, A. Farne, E. Hastings, E. Holloway, N. Kurbatova, M. Lukk (+10 others)
2010 Nucleic Acids Research  
The ArrayExpress Archive (http://www.ebi.ac.uk/ arrayexpress) is one of the three international public repositories of functional genomics data supporting publications.  ...  It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus.  ...  This effort will significantly simplify all internal data management tasks and will benefit the users in improved data load times, faster issuing of accession numbers, faster data exchange with GEO and  ... 
doi:10.1093/nar/gkq1040 pmid:21071405 pmcid:PMC3013660 fatcat:4rn24k5lvzhajj4huiufljvsgy

From ArrayExpress to BioStudies

Ugis Sarkans, Anja Füllgrabe, Ahmed Ali, Awais Athar, Ehsan Behrangi, Nestor Diaz, Silvie Fexova, Nancy George, Haider Iqbal, Sandeep Kurri, Jhoan Munoz, Juan Rada (+2 others)
2020 Nucleic Acids Research  
ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later  ...  This update guides the users through these changes.  ...  The roadmap toward simplifying this process will be described in the next BioStudies update.  ... 
doi:10.1093/nar/gkaa1062 pmid:33211879 fatcat:p2nyf6ayibhvhif7hcsye7fu2a

Plant-Based Microarray Data at the European Bioinformatics Institute. Introducing AtMIAMExpress, a Submission Tool for Arabidopsis Gene Expression Data to ArrayExpress

G. Mukherjee
2005 Plant Physiology  
AtMIAMExpress is an open-source Web-based software application for the submission of Arabidopsis-based microarray data to ArrayExpress.  ...  Plant-based data sets represent approximately onequarter of the experiments in ArrayExpress.  ...  There are three types of data submission in ArrayExpress: experiments, protocols, and array designs.  ... 
doi:10.1104/pp.105.063156 pmid:16219923 pmcid:PMC1255982 fatcat:ylj2obzlzjho7pratwpr2btcba

The European Bioinformatics Institute's data resources: towards systems biology

C. Brooksbank
2004 Nucleic Acids Research  
The EBI's data resources are all available on our website at http://www.ebi.ac.uk.  ...  different data types, thereby helping them to put the parts together to understand biology at the systems level.  ...  www.ebi.ac.uk/arrayexpress/ www.ebi.ac.uk/arrayexpress/ ftp.ebi.ac.uk/pub/databases/ www.ebi.ac.uk/arrayexpress/Help Submissions arrayexpress/ arrayexpress@ebi.ac.uk arraysubs@ebi.ac.uk  ... 
doi:10.1093/nar/gki026 pmid:15608238 pmcid:PMC539980 fatcat:ccwgkwuws5fsjaz7zp7i5jfjzy

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius, Philipp Senger
2015 Database: The Journal of Biological Databases and Curation  
Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially  ...  We additionally thank the researchers, who deposit experimental data for public use. The authors are grateful for the comments and valuable recommendations from two anonymous reviewers.  ...  GEO allows data submission in Excel, SOFT or MINiML format and ArrayExpress as MAGE-TAB through Annotare webform tool (http://www.ncbi.nlm.nih.gov/geo/info/submission. html and http://www.ebi.ac.uk/arrayexpress  ... 
doi:10.1093/database/bav099 pmid:26475471 pmcid:PMC4608514 fatcat:r5sachf3wjhqzcgb6lycqo6gre

The sequence read archive: explosive growth of sequencing data

Y. Kodama, M. Shumway, R. Leinonen
2011 Nucleic Acids Research  
New generation sequencing platforms are producing data with significantly higher throughput and lower cost.  ...  The SRA has updated the metadata model to better represent new sequencing technologies and applications.  ...  ChIP-seq and RNA-seq) can be submitted via the Gene Expression Omnibus at NCBI (http://www.ncbi.nlm.nih.gov/geo) (5), ArrayExpress at EBI (http://www.ebi.ac.uk/arrayexpress) (6) and DDBJ Omics Archive  ... 
doi:10.1093/nar/gkr854 pmid:22009675 pmcid:PMC3245110 fatcat:rntew4uuynashk2y2ugo67ph7q

Cell-level metadata are indispensable for documenting single-cell sequencing datasets

Sidhant Puntambekar, Jay R Hesselberth, Kent A Riemondy, Rui Fu
2021 PLoS Biology  
We encourage investigators, reviewers, journals, and data repositories to improve their standards and ensure proper documentation of these valuable datasets.  ...  Metadata omission hinders reproduction, exploration, validation, and knowledge transfer and is a common problem across journals, data repositories, and publication dates.  ...  Updating submission guidelines and examples to require metadata with cell-level annotations for single-cell dataset submissions.  ... 
doi:10.1371/journal.pbio.3001077 pmid:33945522 pmcid:PMC8121533 fatcat:y4ndrqnb7zf2xjlls5ix2v2xvi

MUGEN mouse database; Animal models of human immunological diseases

V. Aidinis, C. Chandras, M. Manoloukos, A. Thanassopoulou, K. Kranidioti, M. Armaka, E. Douni, D. L. Kontoyiannis, M. Zouberakis, G. Kollias
2007 Nucleic Acids Research  
Each gene/transgene index also includes IDs and direct links to Ensembl, ArrayExpress, EURExpress and NCBI's Entrez Gene database.  ...  Database access is free of charge and there are no registration requirements for data querying.  ...  Although, MMdb is freely accessible to all individuals, data submission is restricted to registered users for the moment.  ... 
doi:10.1093/nar/gkm838 pmid:17932065 pmcid:PMC2238830 fatcat:dtorv5jrcza3jkfcwtugpmdfgu

DATABASE DEVELOPMENT IN TOXICOGENOMICS: ISSUES AND EFFORTS

William B. Mattes, Syril D. Pettit, Susanna-Assunta Sansone, Pierre R. Bushel, Michael D. Waters
2004 Environmental Health Perspectives  
A successful publicly accessible toxicogenomics database will serve as a repository for data sharing and as a resource for analysis, data mining, and discussion.  ...  and record data quality, and the development of standardized analytical approaches.  ...  data (ArrayExpress; http://www.ebi.ac.uk/arrayexpress) (Brazma et al. 2003) has been accepting submissions since February 2002 and sees a rapidly growing volume of data deposited.  ... 
doi:10.1289/txg.6697 fatcat:ppyxs2lpljel3hhtnrztipe7em

Database development in toxicogenomics: issues and efforts

William B Mattes, Syril D Pettit, Susanna-Assunta Sansone, Pierre R Bushel, Michael D Waters
2004 Environmental Health Perspectives  
A successful publicly accessible toxicogenomics database will serve as a repository for data sharing and as a resource for analysis, data mining, and discussion.  ...  and record data quality, and the development of standardized analytical approaches.  ...  data (ArrayExpress; http://www.ebi.ac.uk/arrayexpress) (Brazma et al. 2003) has been accepting submissions since February 2002 and sees a rapidly growing volume of data deposited.  ... 
doi:10.1289/ehp.6697 pmid:15033600 pmcid:PMC1241904 fatcat:pyf67afwgbeynnwrg472tv2vxm

Sharing and Reusing Gene Expression Profiling Data in Neuroscience

Xiang Wan, Paul Pavlidis
2007 Neuroinformatics  
As public availability of gene expression profiling data increases, it is natural to ask how these data can be used by neuroscientists.  ...  There is increasing interest in making expression data re-use a routine part of the neuroscience tool-kit, but there are a number of challenges.  ...  We are indebted to the many groups who generously provide expression data. Supported by NIH GM076990 and a Michael Smith Foundation for Health Research Career Award to P.P.  ... 
doi:10.1007/s12021-007-0012-5 pmid:17917127 pmcid:PMC2980754 fatcat:kh3doe5dyjck3bqrzeo73aggau

MiMiR: an integrated platform for microarray data sharing, mining and analysis

Chris Tomlinson, Manjula Thimma, Stelios Alexandrakis, Tito Castillo, Jayne L Dennis, Anthony Brooks, Thomas Bradley, Carly Turnbull, Ekaterini Blaveri, Geraint Barton, Norie Chiba, Klio Maratou (+3 others)
2008 BMC Bioinformatics  
Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package.  ...  Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online.  ...  MiMiR is compliant with MAGE and uses MAGE-ML for data exchange with other MAGE databases (e.g. ArrayExpress and Resolver) rather than the simplified MAGE-TAB format [26] .  ... 
doi:10.1186/1471-2105-9-379 pmid:18801157 pmcid:PMC2572073 fatcat:sibwzmjesvgy5ppk44r7cifawm
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