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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)
<span title="2020-11-19">2020</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is being migrated to BioStudies.  ...  database (https://www.ebi.ac.uk/biostudies) was established to deal with such multimodal data.  ...  The endpoint changes from https://www.ebi.ac.uk/arrayexpress/xml/v3 to https://www.ebi.ac.uk/biostudies/api/v1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1062">doi:10.1093/nar/gkaa1062</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33211879">pmid:33211879</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p2nyf6ayibhvhif7hcsye7fu2a">fatcat:p2nyf6ayibhvhif7hcsye7fu2a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201122061338/https://watermark.silverchair.com/gkaa1062.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAArcwggKzBgkqhkiG9w0BBwagggKkMIICoAIBADCCApkGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMTs3oMdbEJMxal6E1AgEQgIICaqB4_0t2TaEtRfjjY7Zrrmj32UgNVh1nFxFrIpMcdcuc_TnRnqnZI_HyyIdiQkurK8KFhoS-fa5-nW7AVgUCCHVeVv5xb8ZpPuSsZKIWc6aqgQBIIuNYJiQBAy-O2OK5lslnj9tVQEXTK3OvvgUEZKLzNQQKfXAPn9A7tKLroG6G53Q1bA8awCcwQ0ErXCdYrpt1cnfHsgNfiSC5dTSPs6BjeucitVN8zprgHqPs85YnU_KVTRW-FKLUUA9laFjLjauWl-SmbiCVvQ15BkX12h9Tgf1kHMmsC0Tr-Rh22reyUO2w3mO0KDOP0_Cr3fEFy2W4dvcgrm5HbXu7g9hBS-L0o8Vhq6KcqJxx5s01gVBfl2JTF8YB_ZSyT70JZ54BLqONAnkzNDnAXvuLMn7mBhjm_Wn7Jv98RhlheS1XLMyrVVp_vpi67PjXvsWfJV9hxoNSytKLb1aSeycuADv_uwEECQcEiMe8Bk9n4qLpwwy6hXKmQeFAfOInsWNAEKIC1jXnFs3a_DPUKk9GenoXNp7yqkN_G-lKW_TTFwVyhjc08ZMSUf7Z5fiqdVYURHr0wxaCO8vI996kd1R5LlndkBRocfCahcsv1seSh-R77eQJv6i4rc9oWI928WAScJJE0QgJHGxR28eIunah2hOe8YOUbkX629z6cKV52GCRgC5ymkMWjWPZLir5uK6Be9B32wusUadtZMU_dCcX9X0aorGzELMdCsLoGabVx66ilqhHfRaBeQizrPBq3cox51NgBLlTygpyeDvwiBs93E25q9XpgXgH4DtSpP5xEpAidlm3SxlPT20EGTJzCQ" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7b/20/7b205d222006a9bb043630c4c4dc281eacad9a29.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkaa1062"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a>

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
<span title="2018-10-24">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
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  ...  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  ...  ACKNOWLEDGEMENTS The authors would like to thank Juan Antonio Vicziano. FUNDING  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky964">doi:10.1093/nar/gky964</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30357387">pmid:30357387</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6323929/">pmcid:PMC6323929</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/p2n5pu6dgffvtf3jp5ypftowxu">fatcat:p2n5pu6dgffvtf3jp5ypftowxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228125022/http://pdfs.semanticscholar.org/9240/052791d9457085b13a8ef3331913c3ee5ff9.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/92/40/9240052791d9457085b13a8ef3331913c3ee5ff9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky964"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323929" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Biostudies Database - Filling In The Gaps Between Publications And Structured Datasets

U. Sarkans
<span title="2016-09-22">2016</span> <i title="Zenodo"> Zenodo </i> &nbsp;
It is able to accept and make available data from new and emergent technologies where data is produced in formats not (yet) supported by the current EMBL-EBI data resources.  ...  BioStudies is also able to link to data in other databases, as well as accept what is usually treated as supplementary data, creating a data ?package?  ...  the essential metadata locally and link out to external data (e.g., Eurobioimaging) • www.ebi.ac.uk/biostudies • descriptions of biological studies, links to data from these studies in other databases  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.162783">doi:10.5281/zenodo.162783</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/x3ecvxnnwfg2rgbnadq7vzmwdy">fatcat:x3ecvxnnwfg2rgbnadq7vzmwdy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200302103224/https://zenodo.org/record/162783/files/BLSW_2016.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ac/eb/aceb4b4850404ea47e060744b07b8eb1e33ade32.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.162783"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

The BioStudies database

J. McEntyre, U. Sarkans, A. Brazma
<span title="2015-12-23">2015</span> <i title="EMBO"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oayrvwhnr5a2jm4pbva2dvz3ui" style="color: black;">Molecular Systems Biology</a> </i> &nbsp;
A BioStudy aggregating links to Europe PMC, ArrayExpress, Ensembl, and supplementary data files that do not fit into structured repositories.  ...  The primary goal of the BioStudies Database therefore is to collect all the data from a study in a single record.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15252/msb.20156658">doi:10.15252/msb.20156658</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26700850">pmid:26700850</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4704487/">pmcid:PMC4704487</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2vjnytlv3bag5grczy2kdd53he">fatcat:2vjnytlv3bag5grczy2kdd53he</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190224164635/http://pdfs.semanticscholar.org/5832/4b38e2a333b94f3371f4197a09a54d4b32ff.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/58/32/58324b38e2a333b94f3371f4197a09a54d4b32ff.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.15252/msb.20156658"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4704487" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The BioStudies database—one stop shop for all data supporting a life sciences study

Ugis Sarkans, Mikhail Gostev, Awais Athar, Ehsan Behrangi, Olga Melnichuk, Ahmed Ali, Jasmine Minguet, Juan Camillo Rada, Catherine Snow, Andrew Tikhonov, Alvis Brazma, Johanna McEntyre
<span title="2017-10-23">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
BioStudies (www.ebi.ac.uk/biostudies) is a new public database that organizes data from biological studies. Typically, but not exclusively, a study is associated with a publication.  ...  BioStudies offers a simple way to describe the study structure, and provides flexible data deposition tools and data access interfaces.  ...  ACKNOWLEDGEMENTS We would like to thank the early adopters of BioStudies for helping us to define our processes and were patient with the bugs, in particular, Vid Vartak, Xingjun Pi, Florian Graef, Robert  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx965">doi:10.1093/nar/gkx965</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29069414">pmid:29069414</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5753238/">pmcid:PMC5753238</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nfkm3shribfr3ix24l775s7kha">fatcat:nfkm3shribfr3ix24l775s7kha</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225130143/http://pdfs.semanticscholar.org/62eb/1d66a320dcf6476ed283840961937f9f5386.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/eb/62eb1d66a320dcf6476ed283840961937f9f5386.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx965"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753238" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

On The Way To Realising The Full Potential Of Pids In Biosciences: Thor Work At Embl-Ebi

Robert Petryszak
<span title="2017-11-21">2017</span> <i title="Zenodo"> Zenodo </i> &nbsp;
• Part of the European Molecular Biology Laboratory, an intergovernmental research organisation • International: 570 members of staff from 57 nations • Home of the ELIXIR Technical hub Data resources at  ...  & Enzyme Portal IntAct/Complex motifs InterPro Pfam/Rfam UniProt Portal Reactome Molecular structures Protein Data Bank in Europe Electron Microscopy Data Bank Europe PubMed Central Chemical biology BioStudies  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1064003">doi:10.5281/zenodo.1064003</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/liejbob3m5ggvmwrdnzsfmud6i">fatcat:liejbob3m5ggvmwrdnzsfmud6i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200114185551/https://zenodo.org/record/1064003/files/EMBL%20EBI.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/07/ca/07ca8317340af9081b86bb29a83a3998b9d449c2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5281/zenodo.1064003"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> zenodo.org </button> </a>

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)
<span title="2014-10-31">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
All data in ArrayExpress are available in the MAGE-TAB format, which allows robust linking to data analysis and visualization tools and standardized analysis.  ...  It contains data from over 7000 public sequencing and 42 000 array-based studies comprising over 1.5 million assays in total.  ...  between ArrayExpress and ENA.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1057">doi:10.1093/nar/gku1057</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25361974">pmid:25361974</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4383899/">pmcid:PMC4383899</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c4fvlffcnfcpde7agoxjir4beu">fatcat:c4fvlffcnfcpde7agoxjir4beu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302095016/http://pdfs.semanticscholar.org/a151/d5e8cbf854f71394aaef6f7e8c1966d8ed8e.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/a1/51/a151d5e8cbf854f71394aaef6f7e8c1966d8ed8e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gku1057"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383899" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Open Data to Support CANCER Science—A Bioinformatics Perspective on Glioma Research

Fleur Jeanquartier, Claire Jean-Quartier, Sarah Stryeck, Andreas Holzinger
<span title="2021-12-13">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tbokeukpifeobbyh7tinoxzvhm" style="color: black;">Onco</a> </i> &nbsp;
In our paper, we illustrate the current state of the art with examples from glioma research, in particular, how open data can be used for cancer research in general, and point out several resources and  ...  Our work aims to support and promote the use of publicly available resources in cancer research and demonstrates artificial intelligence (AI) methods to find answers to detailed questions.  ...  ArrayExpress collects data from highthroughput functional genomics experiments. Expression Atlas makes use of ArrayExpress data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/onco1020016">doi:10.3390/onco1020016</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vn54hu3x3fhebfzxtee3c2z2fy">fatcat:vn54hu3x3fhebfzxtee3c2z2fy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211213145719/https://mdpi-res.com/d_attachment/onco/onco-01-00016/article_deploy/onco-01-00016.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b0/11/b011eb3bd86e2adc22e38ccdb457690c4202cb2e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/onco1020016"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a>

Europe PMC in 2017

Maria Levchenko, Yuci Gou, Florian Graef, Audrey Hamelers, Zhan Huang, Michele Ide-Smith, Anusha Iyer, Oliver Kilian, Jyothi Katuri, Jee-Hyub Kim, Nikos Marinos, Rakesh Nambiar (+7 others)
<span title="2017-11-17">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
All the data behind the paper -whether in structured archives, generic archives or as supplemental files -are now available via links to the BioStudies database.  ...  The SciLite community annotation platform accepts text-mining results from various contributors and overlays them on research articles as licence allows.  ...  ACKNOWLEDGEMENTS We would like to thank the Europe PMC and EMBL-EBI Literature Services Advisory Board(s) for strategic guidance on the development of Europe PMC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1005">doi:10.1093/nar/gkx1005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29161421">pmid:29161421</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5753258/">pmcid:PMC5753258</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ctbzxc7ufjerbifj35c4w6dj7m">fatcat:ctbzxc7ufjerbifj35c4w6dj7m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220150418/http://pdfs.semanticscholar.org/2571/596fc6f47046165a5de5d4796bd435154660.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/71/2571596fc6f47046165a5de5d4796bd435154660.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1005"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753258" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Expression Atlas update: gene and protein expression in multiple species

Pablo Moreno, Silvie Fexova, Nancy George, Jonathan R Manning, Zhichiao Miao, Suhaib Mohammed, Alfonso Muñoz-Pomer, Anja Fullgrabe, Yalan Bi, Natassja Bush, Haider Iqbal, Upendra Kumbham (+22 others)
<span title="2021-11-24">2021</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Expression Atlas contains data from differential studies (microarray and bulk RNA-Seq) and baseline studies (bulk RNA-Seq and proteomics), whereas Single Cell Expression Atlas is currently dedicated to  ...  Expression Atlas brings together data from &gt;4500 expression studies from &gt;65 different species, across different conditions and tissues.  ...  Sarkans for their help with the Ar-rayExpress interface and assistance in submissions of new functional genomics studies to ArrayExpress.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkab1030">doi:10.1093/nar/gkab1030</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34850121">pmid:34850121</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8728300/">pmcid:PMC8728300</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w4ochry6hreqhjcqkaezuperpe">fatcat:w4ochry6hreqhjcqkaezuperpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220111011844/https://watermark.silverchair.com/gkab1030.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAsUwggLBBgkqhkiG9w0BBwagggKyMIICrgIBADCCAqcGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMc3QGDr7PbYyRl7rcAgEQgIICeBavHSevBuOxDqUN8_9K7RwO85NrVnNy27PMOFlG9z9QbfBBkVIok7y5aBREJaKZTDjuMi6pIRfH29HfY5Hhhinh62Ms5qZHEi4WrDouN913oqG_jvFn5lM6gIu2yG-G8xFRzDwNErkN4BAFTja74vSePcuug-GJnzkfX74WLJm5Cx_VW7B0CbvteL4wU7gqF9ngRwboxGtzkn6yx6F0yMT6iwMxoR_nlBWQ7jPu_A2rpw1i9KWRQTqWaVW35tDEXqXBzfO8etP-movDyAz5WO4p0FSXPoNeQFIwHMdfF9lG1I0E-09A9R8XAnyp8Bxqf1oRxzQr1V7rX0_gXTcW2EuvzVq1u3ym7GTHbQ38ESkvuNXoodqcLXyEzudP0lmYqy_ZkbI_hk3SiDBeYvBk3kn9KYI48Aac0QfGboyoUPGr8JPm0DAm8UIGEkHvRwYaRCng4fx07uJ6ojE3aLTA7v9KXnWzpXy0D-cvLOGFSai6hdzh0o1jCbZQ4H2mRjpSB50AXRcSNwsalOY7BEZfT7zcIuLqC2p9fhkaSmO7ROZ8e4Xgue89I6IzGiz4rtrPksgJHd8vAxgkN7W17CNPUizs5U6bo6X-V_gPWm8QGJ3AbclHhhCdgP1f3C0qcIKqEbP1yq1UvBuWP6Rl7u3rlj4nMq01Iqece7Zg2h1iI_RDW0BQYZXIhfcvptUGYTEr5iubc3OnbtM-9602ijsCShexuFXf9tEpZHRkyx7sQ7LlVW6pNXw8aEOnzx-vuhKqio15j_qz_UANeF8184rxel0sVd53_-P6wdEjDm-w_oznKSd8uH4Mmv7aZbsmxswiCAAdscyiMShR" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dd/3d/dd3dc029e0b660aa69e90a8fc2b682949b9a8587.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkab1030"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8728300" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The European Bioinformatics Institute in 2017: data coordination and integration

Charles E Cook, Mary T Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney
<span title="2017-11-25">2017</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data.  ...  Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes.  ...  databases to be included in the near future: BioSamples (17) , BioStudies (18) , EVA (19) and Electron Microscopy Data Bank (EMDB) (20) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1154">doi:10.1093/nar/gkx1154</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29186510">pmid:29186510</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5753251/">pmcid:PMC5753251</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ubzlegb2kjcltbtdftwsh6mlja">fatcat:ubzlegb2kjcltbtdftwsh6mlja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222230321/http://pdfs.semanticscholar.org/3dff/93b08e168c74769553ba1246da4f9e9c027e.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3d/ff/3dff93b08e168c74769553ba1246da4f9e9c027e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkx1154"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753251" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A call for public archives for biological image data

Jan Ellenberg, Jason R. Swedlow, Mary Barlow, Charles E. Cook, Ugis Sarkans, Ardan Patwardhan, Alvis Brazma, Ewan Birney
<span title="2018-10-30">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l6cw2tyvgrhytbvantrj2os37y" style="color: black;">Nature Methods</a> </i> &nbsp;
In the last few years, the technical barriers to building such resources have been solved and the first examples of scientific outputs from public image data resources, often through linkage to existing  ...  We are currently working to connect BioStudies and the IDR so that reference-image data in BioStudies can be easily imported into IDR for inclusion in the added-value resource.  ...  This is an established guiding concept in biomolecular data archiving; for instance, the Gene Expression Omnibus and the Functional Genomics Data Archive ArrayExpress 19,20 accept data from different experimental  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41592-018-0195-8">doi:10.1038/s41592-018-0195-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30377375">pmid:30377375</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6884425/">pmcid:PMC6884425</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nfco5xexabaptbbykawe3mcl3y">fatcat:nfco5xexabaptbbykawe3mcl3y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426115101/https://discovery.dundee.ac.uk/ws/files/28912081/s41592_018_0195_8.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2a/5f/2a5fe0b83df074e72f093505fa561506badacc55.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41592-018-0195-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884425" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Best practice data life cycle approaches for the life sciences

Philippa C. Griffin, Jyoti Khadake, Kate S. LeMay, Suzanna E. Lewis, Sandra Orchard, Andrew Pask, Bernard Pope, Ute Roessner, Keith Russell, Torsten Seemann, Andrew Treloar, Sonika Tyagi (+15 others)
<span title="2017-08-31">2017</span> <i title="F1000 Research, Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
One key approach in best-practice metadata collection is to use controlled vocabularies built from ontology terms.  ...  Repository for genomic expression data RNA-seq, microarray, CHIP-seq, Bisulfite-seq and more (see https://www.ebi.ac.uk/arrayexpress/ help/experiment_types.html for full list) https://www.ebi.ac.uk/arrayexpress  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.12344.1">doi:10.12688/f1000research.12344.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30109017">pmid:30109017</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6069748/">pmcid:PMC6069748</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qoh22nmk4vcjdovnblpkyk3vxq">fatcat:qoh22nmk4vcjdovnblpkyk3vxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226082522/http://pdfs.semanticscholar.org/6ebc/988cd5d966e94f42bc4450a2db4c638e2cba.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6e/bc/6ebc988cd5d966e94f42bc4450a2db4c638e2cba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.12344.1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069748" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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

<span title="2020-01-08">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
This network ensures that users are served with as much information as possible from any search and any starting point within EMBL-EBI's websites.  ...  We also describe the BioImage Archive, a deposition database for raw images derived from primary research that will supply data for future knowledgebases that will add value through curation of primary  ...  ACKNOWLEDGEMENTS We were able to continue to scale our infrastructure and meet demand thanks in part to support from the UK's Large Facilities Capital Fund (LFCF).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz1033">doi:10.1093/nar/gkz1033</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31701143">pmid:31701143</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6943058/">pmcid:PMC6943058</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i2gcxbfkprb37etd37stq4t74a">fatcat:i2gcxbfkprb37etd37stq4t74a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200510034354/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6943058&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e5/ae/e5ae5f0af31142c684ebd103d1c54faf300295bc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkz1033"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6943058" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The European Bioinformatics Institute in 2018: tools, infrastructure and training

Charles E Cook, Rodrigo Lopez, Oana Stroe, Guy Cochrane, Cath Brooksbank, Ewan Birney, Rolf Apweiler
<span title="2018-11-16">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Additionally, Europe PMC (http://europepmc.org/) has added preprint abstracts to its search results, supplementing results from peer-reviewed publications.  ...  Our training team, with support from all of our staff, continued to provide on-site, off-site and web-based training opportunities for thousands of researchers worldwide this year.  ...  We were able to continue to scale our infrastructure and meet demand thanks in part to support from the UK's Large Facilities Capital Fund (LFCF).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1124">doi:10.1093/nar/gky1124</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30445657">pmid:30445657</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6323906/">pmcid:PMC6323906</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ww5xqc5aorgone5pt43p43o6tu">fatcat:ww5xqc5aorgone5pt43p43o6tu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210523124334/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6323906&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/1c/c6/1cc6f93e40e80157c0adb59d780b024028c2333d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky1124"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6323906" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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