From ArrayExpress to BioStudies

Uğis Sarkans

doi:10.1093/nar/gkaa1062

2020-11-19

DOI：10.1093/nar/gkaa1062

原文链接

查看原文

摘要

En 中文

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 extended to accept sequencing-based data. Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus the BioStudies database (https:// www.ebi.ac.uk/biostudies) was established to deal with such multimodal data. Its central concept is a study, which typically is associated with a publication. BioStudies stores metadata describing the study, provides links to the relevant databases, such as European Nucleotide Archive (ENA), as well as hosts the types of data for which specialized databases do not exist. With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is beingmigrated toBioStudies. In future, all functional genomics data will be archived at BioStudies. The process will be seamless for the users, who will continue to submit data using the online tool Annotare and will be able to query and download data largely in the same manner as before. Nevertheless, some technical aspects, particularly programmatic access, will change. This update guides the users through these changes.

Keyword:

INFRASTRUCTURE

AI总结

对已上传原文的论文进行重点信息的提取，主要内容包括：简要概述、研究摘要、背景介绍、关键亮点、图文解析、展望与总结。

期刊

Nucleic Acids Research

IF:

13.1

论文数:

3.6W

被引数:

29.0W

机构

european molecular biology laboratory (embl)

学者数:

8.3K

论文数: 5.1K

被引数: 31

引用论文

Europe PMC in 2017

NUCLEIC ACIDS RESEARCH

IF13.1

2017-11-17

OAAI

Levchenko, Maria; Gou, Yuci; Graef, Florian; Hamelers, Audrey; Huang, Zhan; Ide-Smith, Michele; Iyer, Anusha; Kilian, Oliver; Katuri, Jyothi; Kim, Jee-Hyub; Marinos, Nikos; Nambiar, Rakesh; Parkin, Michael; Pi, Xingjun; Rogers, Frances; Talo, Francesco; Vartak, Vid; Venkatesan, Aravind; McEntyre, Johanna

The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences

NUCLEIC ACIDS RESEARCH

IF13.1

2019-11-08

OAAI

Cook, Charles E.; Stroe, Oana; Cochrane, Guy; Birney, Ewan; Apweiler, Roif

RNA-Seq: a revolutionary tool for transcriptomics Rna-seq: 转录组学的革命性工具

NATURE REVIEWS GENETICS

IF52

2009-01-01

1.1W

OAAI

Wang, Zhong; Gerstein, Mark; Snyder, Michael

ArrayExpress update - from bulk to single-cell expression data

NUCLEIC ACIDS RESEARCH

IF13.1

2018-10-24

434

OAAI

Athar, Awais; Fullgrabe, Anja; George, Nancy; Iqbal, Haider; Huerta, Laura; Ali, Ahmed; Snow, Catherine; Fonseca, Nuno A.; Petryszak, Robert; Papatheodorou, Irene; Sarkans, Ugis; Brazma, Alvis

ArrayExpress - a public repository for microarray gene expression data at the EBI

NUCLEIC ACIDS RESEARCH

IF13.1

2003-01-01

712

OAAI

Brazma, A; Parkinson, H; Sarkans, U; Shojatalab, M; Vilo, J; Abeygunawardena, N; Holloway, E; Kapushesky, M; Kemmeren, P; Lara, GG; Oezcimen, A; Rocca-Serra, P; Sansone, SA

Dissipative extension of the Ghirardi-Rimini-Weber model

Physical Review A

IF0

2014-12-31

OAAI

Andrea Smirne; Bassano Vacchini; Angelo Bassi

Forward Neutral-Pion Transverse Single-Spin Asymmetries inp+pCollisions ats=200 GeV

Physical Review Letters

IF0

2008-11-25

OAAI

B. I. Abelev; M. M. Aggarwal; Z. Ahammed; B. D. Anderson; D. Arkhipkin; G. S. Averichev; Y. Bai; J. Balewski; O. Barannikova; L. S. Barnby; J. Baudot; S. Baumgart; D. R. Beavis; R. Bellwied; F. Benedosso; R. R. Betts; S. Bhardwaj; A. Bhasin; A. K. Bhati; H. Bichsel; J. Bielcik; J. Bielcikova; L. C. Bland; S-L. Blyth; M. Bombara; B. E. Bonner; M. Botje; J. Bouchet; E. Braidot; A. V. Brandin; S. Bueltmann; T. P. Burton; M. Bystersky; X. Z. Cai; H. Caines; M. Calderón de la Barca Sánchez; J. Callner; O. Catu; D. Cebra; M. C. Cervantes; Z. Chajecki; P. Chaloupka; S. Chattopadhyay; H. F. Chen; J. H. Chen; J. Y. Chen; J. Cheng; M. Cherney; A. Chikanian; K. E. Choi; W. Christie; S. U. Chung; R. F. Clarke; M. J. M. Codrington; J. P. Coffin; T. M. Cormier; M. R. Cosentino; J. G. Cramer; H. J. Crawford; D. Das; S. Dash; M. Daugherity; M. M. de Moura; T. G. Dedovich; M. DePhillips; A. A. Derevschikov; R. Derradi de Souza; L. Didenko; T. Dietel; P. Djawotho; S. M. Dogra; X. Dong; J. L. Drachenberg; J. E. Draper; F. Du; J. C. Dunlop; M. R. Dutta Mazumdar; W. R. Edwards; L. G. Efimov; E. Elhalhuli; V. Emelianov; J. Engelage; G. Eppley; B. Erazmus; M. Estienne; L. Eun; P. Fachini; R. Fatemi; J. Fedorisin; A. Feng; P. Filip; E. Finch; V. Fine; Y. Fisyak; J. Fu; C. A. Gagliardi; L. Gaillard; M. S. Ganti; E. Garcia-Solis; V. Ghazikhanian; P. Ghosh; Y. N. Gorbunov; A. Gordon; H. Gos; O. Grebenyuk; D. Grosnick; B. Grube; S. M. Guertin; K. S. F. F. Guimaraes; A. Gupta; N. Gupta; W. Guryn; B. Haag; T. J. Hallman; A. Hamed; J. W. Harris; W. He; M. Heinz; T. W. Henry; S. Heppelmann; B. Hippolyte; A. Hirsch; E. Hjort; A. M. Hoffman; G. W. Hoffmann; D. J. Hofman; R. S. Hollis; M. J. Horner; H. Z. Huang; E. W. Hughes; T. J. Humanic; G. Igo; A. Iordanova; P. Jacobs; W. W. Jacobs; P. Jakl; F. Jin; P. G. Jones; E. G. Judd; S. Kabana; K. Kajimoto; K. Kang; J. Kapitan; M. Kaplan; D. Keane; A. Kechechyan; D. Kettler; V. Yu. Khodyrev; J. Kiryluk; A. Kisiel; S. R. Klein; A. G. Knospe; A. Kocoloski; D. D. Koetke; T. Kollegger; M. Kopytine; L. Kotchenda; V. Kouchpil; K. L. Kowalik; P. Kravtsov; V. I. Kravtsov; K. Krueger; C. Kuhn; A. Kumar; P. Kurnadi; M. A. C. Lamont; J. M. Landgraf; J. Langdon; S. Lange; S. LaPointe; F. Laue; J. Lauret; A. Lebedev; R. Lednicky; C-H. Lee; M. J. LeVine; C. Li; Q. Li; Y. Li; G. Lin; X. Lin; S. J. Lindenbaum; M. A. Lisa; F. Liu; H. Liu; J. Liu; L. Liu; T. Ljubicic; W. J. Llope; R. S. Longacre; W. A. Love; Y. Lu; T. Ludlam; D. Lynn; G. L. Ma; J. G. Ma; Y. G. Ma; D. P. Mahapatra; R. Majka; L. K. Mangotra; R. Manweiler; S. Margetis; C. Markert; H. S. Matis; Yu. A. Matulenko; T. S. McShane; A. Meschanin; J. Millane; C. Miller; M. L. Miller; N. G. Minaev; S. Mioduszewski; A. Mischke; J. Mitchell; B. Mohanty; D. A. Morozov; M. G. Munhoz; B. K. Nandi; C. Nattrass; T. K. Nayak; J. M. Nelson; C. Nepali; P. K. Netrakanti; M. J. Ng; L. V. Nogach; S. B. Nurushev; G. Odyniec; A. Ogawa; H. Okada; V. Okorokov; D. Olson; M. Pachr; S. K. Pal; Y. Panebratsev; A. I. Pavlinov; T. Pawlak; T. Peitzmann; V. Perevoztchikov; C. Perkins; W. Peryt; S. C. Phatak; M. Planinic; J. Pluta; N. Poljak; N. Porile; A. M. Poskanzer; M. Potekhin; B. V. K. S. Potukuchi; D. Prindle; C. Pruneau; N. K. Pruthi; J. Putschke; I. A. Qattan; G. Rakness; R. Raniwala; S. Raniwala; R. L. Ray; D. Relyea; A. Ridiger; H. G. Ritter; J. B. Roberts; O. V. Rogachevskiy; J. L. Romero; A. Rose; C. Roy; L. Ruan; M. J. Russcher; V. Rykov; R. Sahoo; I. Sakrejda; T. Sakuma; S. Salur; J. Sandweiss; M. Sarsour; J. Schambach; R. P. Scharenberg; N. Schmitz; J. Seger; I. Selyuzhenkov; P. Seyboth; A. Shabetai; E. Shahaliev; M. Shao; M. Sharma; X-H. Shi; E. P. Sichtermann; F. Simon; R. N. Singaraju; M. J. Skoby; N. Smirnov; R. Snellings; P. Sorensen; J. Sowinski; J. Speltz; H. M. Spinka; B. Srivastava; A. Stadnik; T. D. S. Stanislaus; D. Staszak; R. Stock; M. Strikhanov; B. Stringfellow; A. A. P. Suaide; M. C. Suarez; N. L. Subba; M. Sumbera; X. M. Sun; Z. Sun; B. Surrow; T. J. M. Symons; A. Szanto de Toledo; J. Takahashi; A. H. Tang; Z. Tang; T. Tarnowsky; J. Tatarowicz; D. Thein; J. H. Thomas; J. Tian; A. R. Timmins; S. Timoshenko; M. Tokarev; T. A. Trainor; V. N. Tram; A. L. Trattner; S. Trentalange; R. E. Tribble; O. D. Tsai; J. Ulery; T. Ullrich; D. G. Underwood; G. Van Buren; N. van der Kolk; M. van Leeuwen; A. M. Vander Molen; R. Varma; G. M. S. Vasconcelos; I. M. Vasilevski; A. N. Vasiliev; R. Vernet; F. Videbaek; S. E. Vigdor; Y. P. Viyogi; S. Vokal; S. A. Voloshin; M. Wada; W. T. Waggoner; F. Wang; G. Wang; J. S. Wang; Q. Wang; X. Wang; X. L. Wang; Y. Wang; J. C. Webb; G. D. Westfall; C. Whitten; H. Wieman; S. W. Wissink; R. Witt; J. Wu; Y. Wu; N. Xu; Q. H. Xu; Z. Xu; P. Yepes; I-K. Yoo; Q. Yue; N. Zachariou; M. Zawisza; W. Zhan; H. Zhang; S. Zhang; W. M. Zhang; Y. Zhang; Z. P. Zhang; Y. Zhao; C. Zhong; J. Zhou; R. Zoulkarneev; Y. Zoulkarneeva; J. X. Zuo

Simultaneous epitope and transcriptome measurement in single cells 在单细胞中同时测量表位和转录组

NATURE METHODS

IF32.1

2017-07-31

2.1K

OAAI

Stoeckius, Marlon; Hafemeister, Christoph; Stephenson, William; Houck-Loomis, Brian; Chattopadhyay, Pratip K.; Swerdlow, Harold; Satija, Rahul; Smibert, Peter

ArrayExpress update-simplifying data submissions ArrayExpress更新-简化数据提交

NUCLEIC ACIDS RESEARCH

IF13.1

2014-10-31

570

OAAI

Kolesnikov, Nikolay; Hastings, Emma; Keays, Maria; Melnichuk, Olga; Tang, Y. Amy; Williams, Eleanor; Dylag, Miroslaw; Kurbatova, Natalja; Brandizi, Marco; Burdett, Tony; Megy, Karyn; Pilicheva, Ekaterina; Rustici, Gabriella; Tikhonov, Andrew; Parkinson, Helen; Petryszak, Robert; Sarkans, Ugis; Brazma, Alvis

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

NUCLEIC ACIDS RESEARCH

IF13.1

2010-11-10

269

OAAI

Parkinson, Helen; Sarkans, Ugis; Kolesnikov, Nikolay; Abeygunawardena, Niran; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Farne, Anna; Hastings, Emma; Holloway, Ele; Kurbatova, Natalja; Lukk, Margus; Malone, James; Mani, Roby; Pilicheva, Ekaterina; Rustici, Gabriella; Sharma, Anjan; Williams, Eleanor; Adamusiak, Tomasz; Brandizi, Marco; Sklyar, Nataliya; Brazma, Alvis

查看更多内容