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Article Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines BABIC, Zeljana, et al. Abstract The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. Research Resource Identifiers (RRIDs) should reduce the prevalence of misidentified and contaminated cell lines in the literature by alerting researchers to cell lines that are on the list of problematic cell lines, which is maintained by the International Cell Line Authentication Committee (ICLAC) and the Cellosaurus database. To test this assertion, we text-mined the methods sections of about two million papers in PubMed Central, identifying 305,161 unique cell-line names in 150,459 articles. We estimate that 8.6% of these cell lines were on the list of problematic cell lines, whereas only 3.3% of the cell lines in the 634 papers that included RRIDs were on the problematic list. This suggests that the use of RRIDs is associated with a lower reported use of problematic cell lines. Reference BABIC, Zeljana, et al. Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines. eLife, 2019, vol. 8, p. e41676 DOI : 10.7554/eLife.41676 PMID : 30693867 Available at: http://archive-ouverte.unige.ch/unige:119832 Disclaimer: layout of this document may differ from the published version. 1 / 1 FEATURE ARTICLE META-RESEARCH Incidences of problematic cell lines are lower in papers that use RRIDs to identify cell lines Abstract The use of misidentified and contaminated cell lines continues to be a problem in biomedical research. -
Annual Scientific Report 2013 on the Cover Structure 3Fof in the Protein Data Bank, Determined by Laponogov, I
EMBL-European Bioinformatics Institute Annual Scientific Report 2013 On the cover Structure 3fof in the Protein Data Bank, determined by Laponogov, I. et al. (2009) Structural insight into the quinolone-DNA cleavage complex of type IIA topoisomerases. Nature Structural & Molecular Biology 16, 667-669. © 2014 European Molecular Biology Laboratory This publication was produced by the External Relations team at the European Bioinformatics Institute (EMBL-EBI) A digital version of the brochure can be found at www.ebi.ac.uk/about/brochures For more information about EMBL-EBI please contact: [email protected] Contents Introduction & overview 3 Services 8 Genes, genomes and variation 8 Molecular atlas 12 Proteins and protein families 14 Molecular and cellular structures 18 Chemical biology 20 Molecular systems 22 Cross-domain tools and resources 24 Research 26 Support 32 ELIXIR 36 Facts and figures 38 Funding & resource allocation 38 Growth of core resources 40 Collaborations 42 Our staff in 2013 44 Scientific advisory committees 46 Major database collaborations 50 Publications 52 Organisation of EMBL-EBI leadership 61 2013 EMBL-EBI Annual Scientific Report 1 Foreword Welcome to EMBL-EBI’s 2013 Annual Scientific Report. Here we look back on our major achievements during the year, reflecting on the delivery of our world-class services, research, training, industry collaboration and European coordination of life-science data. The past year has been one full of exciting changes, both scientifically and organisationally. We unveiled a new website that helps users explore our resources more seamlessly, saw the publication of ground-breaking work in data storage and synthetic biology, joined the global alliance for global health, built important new relationships with our partners in industry and celebrated the launch of ELIXIR. -
The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data Hinxton, Cambridge, UK, 19–20 October 2002
Comparative and Functional Genomics Comp Funct Genom 2003; 4: 16–19. Published online in Wiley InterScience (www.interscience.wiley.com). DOI: 10.1002/cfg.232 Feature Meeting Review: The HUPO Proteomics Standards Initiative meeting: towards common standards for exchanging proteomics data Hinxton, Cambridge, UK, 19–20 October 2002 Sandra Orchard, Paul Kersey, Henning Hermjakob* and Rolf Apweiler EMBL Outstation–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK *Correspondence to: Abstract Henning Hermjakob, EMBL Outstation–European The Proteomics Standards Initiative (PSI) aims to define community standards Bioinformatics Institute, for data representation in proteomics and to facilitate data comparison, exchange Wellcome Trust Genome and verification. Initially the fields of protein–protein interactions (PPI) and mass Campus, Hinxton, Cambridge, spectroscopy have been targeted and the inaugural meeting of the PSI addressed the UK. questions of data storage and exchange in both of these areas. The PPI group rapidly E-mail: reached consensus as to the minimum requirements for a data exchange model; an [email protected] XML draft is now being produced. The mass spectroscopy group have achieved major advances in the definition of a required data model and working groups are currently taking these discussions further. A further meeting is planned in January 2003 to Received: 14 November 2002 advance both these projects. Copyright 2003 John Wiley & Sons, Ltd. Accepted: 14 November 2002 Keywords: proteomics; spectroscopy; protein–protein interactions Introduction process, before splitting into two working parties to address the issues facing their respective fields. The Proteomics Standards Initiative was estab- lished following a meeting in April 2002, jointly organized by HUPO and NAS, at which the urgent Protein–protein interactions (PPI) group need for standardization of proteomics data was recognized. -
General Assembly and Consortium Meeting 2020
EJP RD GA and Consortium meeting Final program EJP RD General Assembly and Consortium meeting 2020 Online September 14th – 18th Page 1 of 46 EJP RD GA and Consortium meeting Final program Program at a glance: Page 2 of 46 EJP RD GA and Consortium meeting Final program Table of contents Program per day ....................................................................................................................... 4 Plenary GA Session .................................................................................................................. 8 Parallel Session Pillar 1 .......................................................................................................... 10 Parallel Session Pillar 2 .......................................................................................................... 11 Parallel Session Pillar 3 .......................................................................................................... 14 Parallel Session Pillar 4 .......................................................................................................... 16 Experimental data resources available in the EJP RD ............................................................. 18 Introduction to translational research for clinical or pre-clinical researchers .......................... 21 Funding opportunities in EJP RD & How to build a successful proposal ............................... 22 RD-Connect Genome-Phenome Analysis Platform ................................................................. 26 Improvement -
The European Bioinformatics Institute in 2020: Building a Global Infrastructure of Interconnected Data Resources for the Life Sciences Charles E
Published online 8 November 2019 Nucleic Acids Research, 2020, Vol. 48, Database issue D17–D23 doi: 10.1093/nar/gkz1033 The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences Charles E. Cook *, Oana Stroe, Guy Cochrane ,EwanBirney and Rolf Apweiler European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK Received September 21, 2019; Revised October 18, 2019; Editorial Decision October 21, 2019; Accepted November 06, 2019 ABSTRACT ature. EMBL-EBI’s data resources collate, integrate, curate and make freely available to the public the world’s scientific Data resources at the European Bioinformatics In- data. stitute (EMBL-EBI, https://www.ebi.ac.uk/)archive, Our resources (www.ebi.ac.uk/services) include archival organize and provide added-value analysis of re- or deposition databases that store primary experimental search data produced around the world. This year’s data submitted by researchers, as well as knowledgebases update for EMBL-EBI focuses on data exchanges that integrate and add value to experimental data, with among resources, both within the institute and with many having both functions (1,2). All EMBL-EBI data re- a wider global infrastructure. Within EMBL-EBI, data sources, are open access and freely available to any user resources exchange data through a rich network of worldwide at any time, and EMBL-EBI strongly supports data flows mediated by automated systems. This net- the concept of FAIR data (findable, accessible, interopera- work ensures that users are served with as much ble, and resuable) (3). -
MPGM: Scalable and Accurate Multiple Network Alignment
MPGM: Scalable and Accurate Multiple Network Alignment Ehsan Kazemi1 and Matthias Grossglauser2 1Yale Institute for Network Science, Yale University 2School of Computer and Communication Sciences, EPFL Abstract Protein-protein interaction (PPI) network alignment is a canonical operation to transfer biological knowledge among species. The alignment of PPI-networks has many applica- tions, such as the prediction of protein function, detection of conserved network motifs, and the reconstruction of species’ phylogenetic relationships. A good multiple-network align- ment (MNA), by considering the data related to several species, provides a deep understand- ing of biological networks and system-level cellular processes. With the massive amounts of available PPI data and the increasing number of known PPI networks, the problem of MNA is gaining more attention in the systems-biology studies. In this paper, we introduce a new scalable and accurate algorithm, called MPGM, for aligning multiple networks. The MPGM algorithm has two main steps: (i) SEEDGENERA- TION and (ii) MULTIPLEPERCOLATION. In the first step, to generate an initial set of seed tuples, the SEEDGENERATION algorithm uses only protein sequence similarities. In the second step, to align remaining unmatched nodes, the MULTIPLEPERCOLATION algorithm uses network structures and the seed tuples generated from the first step. We show that, with respect to different evaluation criteria, MPGM outperforms the other state-of-the-art algo- rithms. In addition, we guarantee the performance of MPGM under certain classes of net- work models. We introduce a sampling-based stochastic model for generating k correlated networks. We prove that for this model if a sufficient number of seed tuples are available, the MULTIPLEPERCOLATION algorithm correctly aligns almost all the nodes. -
Presentation Sams Patrick Ruch
Genealogy… How can I relevantly answer the invitation from the SAMS’ medical librarians ? Special greetings to Tamara Morcillo and Isabelle de Kaenel ! 2 Today’s agenda 3 Count of bi-gram and tri-grams 4 … to support my presentation ! 5 Objective of text and data mining To support you like TDM helped me today ! 6 How text & data mining can support… ● … medical librarians ? ● … research data and open science ? [well covered by other speakers] ● … clinical knowledge ? 7 History ● Empirical medicine Observation & Cooking ● Evidence-based medicine Statistical power ● Personalized health Deciphering omics 8 Blind spot ● Empirical medicine Observation & Cooking [Mountains are made of stones] ● Evidence-based medicine Statistical power ● Personalized health Deciphering omics ● Access to EHR evidences (80% narratives) • Overcome publication paywalls • Fight silos [researchers, clinicians, institutions…] • Empower patients • Establish circle of trust and clarify legal basis 9 Basis of clinical practice… ● Empirical medicine Observation & Cooking ● Evidence-based medicine Statistical power ● Personalized health Deciphering omics ● Access to EHR evidences (80% narratives) ! Evidence-based “holistic” (including phenotypes) personalized health ! 10 Basis of clinical practice… ● Empirical medicine Observation & Cooking ● Evidence-based medicine Statistical power Open Access, Open Science required ! ● Personalized health Deciphering omics ● Access to EHR evidences (80% narratives) ! 11 How text & data mining can support… ● … medical librarians -
EMBL-EBI-Overview.Pdf
EMBL-EBI Overview EMBL-EBI Overview Welcome Welcome to the European Bioinformatics Institute (EMBL-EBI), a global hub for big data in biology. We promote scientific progress by providing freely available data to the life-science research community, and by conducting exceptional research in computational biology. At EMBL-EBI, we manage public life-science data on a very large scale, offering a rich resource of carefully curated information. We make our data, tools and infrastructure openly available to an increasingly data-driven scientific community, adjusting to the changing needs of our users, researchers, trainees and industry partners. This proactive approach allows us to deliver relevant, up-to-date data and tools to the millions of scientists who depend on our services. We are a founding member of ELIXIR, the European infrastructure for biological information, and are central to global efforts to exchange information, set standards, develop new methods and curate complex information. Our core databases are produced in collaboration with other world leaders including the National Center for Biotechnology Information in the US, the National Institute of Genetics in Japan, SIB Swiss Institute of Bioinformatics and the Wellcome Trust Sanger Institute in the UK. We are also a world leader in computational biology research, and are well integrated with experimental and computational groups on all EMBL sites. Our research programme is highly collaborative and interdisciplinary, regularly producing high-impact works on sequence and structural alignment, genome analysis, basic biological breakthroughs, algorithms and methods of widespread importance. EMBL-EBI is an international treaty organisation, and we serve the global scientific community. -
Annual Scientific Report 2011 Annual Scientific Report 2011 Designed and Produced by Pickeringhutchins Ltd
European Bioinformatics Institute EMBL-EBI Annual Scientific Report 2011 Annual Scientific Report 2011 Designed and Produced by PickeringHutchins Ltd www.pickeringhutchins.com EMBL member states: Austria, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland, United Kingdom. Associate member state: Australia EMBL-EBI is a part of the European Molecular Biology Laboratory (EMBL) EMBL-EBI EMBL-EBI EMBL-EBI EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton Cambridge CB10 1SD United Kingdom Tel. +44 (0)1223 494 444, Fax +44 (0)1223 494 468 www.ebi.ac.uk EMBL Heidelberg Meyerhofstraße 1 69117 Heidelberg Germany Tel. +49 (0)6221 3870, Fax +49 (0)6221 387 8306 www.embl.org [email protected] EMBL Grenoble 6, rue Jules Horowitz, BP181 38042 Grenoble, Cedex 9 France Tel. +33 (0)476 20 7269, Fax +33 (0)476 20 2199 EMBL Hamburg c/o DESY Notkestraße 85 22603 Hamburg Germany Tel. +49 (0)4089 902 110, Fax +49 (0)4089 902 149 EMBL Monterotondo Adriano Buzzati-Traverso Campus Via Ramarini, 32 00015 Monterotondo (Rome) Italy Tel. +39 (0)6900 91402, Fax +39 (0)6900 91406 © 2012 EMBL-European Bioinformatics Institute All texts written by EBI-EMBL Group and Team Leaders. This publication was produced by the EBI’s Outreach and Training Programme. Contents Introduction Foreword 2 Major Achievements 2011 4 Services Rolf Apweiler and Ewan Birney: Protein and nucleotide data 10 Guy Cochrane: The European Nucleotide Archive 14 Paul Flicek: -
Biological Databases an Introduction
Biological databases an introduction By Dr. Erik Bongcam-Rudloff SLU 2017 Biological Databases ▪ Sequence Databases ▪ Genome Databases ▪ Structure Databases Sequence Databases ▪ The sequence databases are the oldest type of biological databases, and also the most widely used Sequence Databases ▪ Nucleotide: ATGC ▪ Protein: MERITSAPLG The nucleotide sequence repositories ▪ There are three main repositories for nucleotide sequences: EMBL, GenBank, and DDBJ. ▪ All of these should in theory contain "all" known public DNA or RNA sequences ▪ These repositories have a collaboration so that any data submitted to one of databases will be redistributed to the others. ▪ The three databases are the only databases that can issue sequence accession numbers. ▪ Accession numbers are unique identifiers which permanently identify sequences in the databases. ▪ These accession numbers are required by many biological journals before manuscripts are accepted. ▪ It should be noted that during the last decade several commercial companies have engaged in sequencing ESTs and genomes that they have not made public. Ideal minimal content of a « sequence » db Sequences !! Accession number (AC) References Taxonomic data ANNOTATION/CURATION Keywords Cross-references Documentation Example: Swiss-Prot entry Entry name Accession number sequence Protein name Gene name Taxonomy References Comments Cross-references Keywords Feature table (sequence description) Sequence database: example …a SWISS-PROT entry, in fasta format: >sp|P01588|EPO_HUMAN ERYTHROPOIETIN PRECURSOR - -
Expert Review of Proteomics
Expert Review of Proteomics Editorial Advisory Panel Overseeing the editorial content and development of Expert Review of Proteomics is an Editorial Advisory Board, composed of many of the world's leading experts in the field, drawn from both research and academia. Albala JS, UC Davis School of Medicine, CA, USA Apweiler R, European Bioinformatics Institute, Cambridge, UK Dr Rolf Apweiler studied Biology with an emphasis on Molecular Biology and Biochemistry at the University of Heidelberg, Germany and the University of Bath, UK. He worked between 1991-1994 in drug discovery at Boehringer Mannheim and has been involved in the Swiss-Prot project since 1987. He co- ordinates the Swiss-Prot knowledgebase group at the EBI since 1994, and started the TrEMBL, InterPro, Proteome analysis and CluSTr projects at the EBI. Since autumn 2001 he is also in charge of the EMBL nucleotide sequence database and started in 2002 the merge of the Swiss-Prot and TrEMBL projects with the PIR to UniProt. Dr Apweiler is heading a team of currently 100 biologists and programmers responsible for the UniProt, InterPro, Proteome analysis, CluSTr and EMBL nucleotide sequence database projects at the EBI. Rolf Apweiler's main research interests are focused on integrating heterogenous functional genomic and proteomic data resources with the main protein and nucleotide sequence databases, and automation of classification and annotation of protein sequences. Blackburn J, Cambridge University, Cambridge, UK Professor Blackburn received a doctorate and an honours degree in chemistry from the University of Oxford. Following his Doctorate, Professor Blackburn carried out post-doctoral research with Professor Fersht at the Centre for Protein Engineering in Cambridge. -
Glycoprotein Hormone Receptors in Sea Lamprey
University of New Hampshire University of New Hampshire Scholars' Repository Doctoral Dissertations Student Scholarship Fall 2007 Glycoprotein hormone receptors in sea lamprey (Petromyzon marinus): Identification, characterization and implications for the evolution of the vertebrate hypothalamic-pituitary-gonadal/thyroid axes Mihael Freamat University of New Hampshire, Durham Follow this and additional works at: https://scholars.unh.edu/dissertation Recommended Citation Freamat, Mihael, "Glycoprotein hormone receptors in sea lamprey (Petromyzon marinus): Identification, characterization and implications for the evolution of the vertebrate hypothalamic-pituitary-gonadal/ thyroid axes" (2007). Doctoral Dissertations. 395. https://scholars.unh.edu/dissertation/395 This Dissertation is brought to you for free and open access by the Student Scholarship at University of New Hampshire Scholars' Repository. It has been accepted for inclusion in Doctoral Dissertations by an authorized administrator of University of New Hampshire Scholars' Repository. For more information, please contact [email protected]. GLYCOPROTEIN HORMONE RECEPTORS IN SEA LAMPREY (PETROMYZON MARI Nil S): IDENTIFICATION, CHARACTERIZATION AND IMPLICATIONS FOR THE EVOLUTION OF THE VERTEBRATE HYPOTHALAMIC-PITUITARY-GONADAL/THYROID AXES BY MIHAEL FREAMAT B.S. University of Bucharest, 1995 DISSERTATION Submitted to the University of New Hampshire in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy In Biochemistry September, 2007 Reproduced with permission of the copyright owner. Further reproduction prohibited without permission. UMI Number: 3277139 INFORMATION TO USERS The quality of this reproduction is dependent upon the quality of the copy submitted. Broken or indistinct print, colored or poor quality illustrations and photographs, print bleed-through, substandard margins, and improper alignment can adversely affect reproduction. In the unlikely event that the author did not send a complete manuscript and there are missing pages, these will be noted.