Planning for Globally Sustainable Life Sciences Data Resources
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A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles
ModeScore: A Method to Infer Changed Activity of Metabolic Function from Transcript Profiles Andreas Hoppe and Hermann-Georg Holzhütter Charité University Medicine Berlin, Institute for Biochemistry, Computational Systems Biochemistry Group [email protected] Abstract Genome-wide transcript profiles are often the only available quantitative data for a particular perturbation of a cellular system and their interpretation with respect to the metabolism is a major challenge in systems biology, especially beyond on/off distinction of genes. We present a method that predicts activity changes of metabolic functions by scoring reference flux distributions based on relative transcript profiles, providing a ranked list of most regulated functions. Then, for each metabolic function, the involved genes are ranked upon how much they represent a specific regulation pattern. Compared with the naïve pathway-based approach, the reference modes can be chosen freely, and they represent full metabolic functions, thus, directly provide testable hypotheses for the metabolic study. In conclusion, the novel method provides promising functions for subsequent experimental elucidation together with outstanding associated genes, solely based on transcript profiles. 1998 ACM Subject Classification J.3 Life and Medical Sciences Keywords and phrases Metabolic network, expression profile, metabolic function Digital Object Identifier 10.4230/OASIcs.GCB.2012.1 1 Background The comprehensive study of the cell’s metabolism would include measuring metabolite concentrations, reaction fluxes, and enzyme activities on a large scale. Measuring fluxes is the most difficult part in this, for a recent assessment of techniques, see [31]. Although mass spectrometry allows to assess metabolite concentrations in a more comprehensive way, the larger the set of potential metabolites, the more difficult [8]. -
The Kyoto Encyclopedia of Genes and Genomes (KEGG)
Kyoto Encyclopedia of Genes and Genome Minoru Kanehisa Institute for Chemical Research, Kyoto University HFSPO Workshop, Strasbourg, November 18, 2016 The KEGG Databases Category Database Content PATHWAY KEGG pathway maps Systems information BRITE BRITE functional hierarchies MODULE KEGG modules KO (KEGG ORTHOLOGY) KO groups for functional orthologs Genomic information GENOME KEGG organisms, viruses and addendum GENES / SSDB Genes and proteins / sequence similarity COMPOUND Chemical compounds GLYCAN Glycans Chemical information REACTION / RCLASS Reactions / reaction classes ENZYME Enzyme nomenclature DISEASE Human diseases DRUG / DGROUP Drugs / drug groups Health information ENVIRON Health-related substances (KEGG MEDICUS) JAPIC Japanese drug labels DailyMed FDA drug labels 12 manually curated original DBs 3 DBs taken from outside sources and given original annotations (GENOME, GENES, ENZYME) 1 computationally generated DB (SSDB) 2 outside DBs (JAPIC, DailyMed) KEGG is widely used for functional interpretation and practical application of genome sequences and other high-throughput data KO PATHWAY GENOME BRITE DISEASE GENES MODULE DRUG Genome Molecular High-level Practical Metagenome functions functions applications Transcriptome etc. Metabolome Glycome etc. COMPOUND GLYCAN REACTION Funding Annual budget Period Funding source (USD) 1995-2010 Supported by 10+ grants from Ministry of Education, >2 M Japan Society for Promotion of Science (JSPS) and Japan Science and Technology Agency (JST) 2011-2013 Supported by National Bioscience Database Center 0.8 M (NBDC) of JST 2014-2016 Supported by NBDC 0.5 M 2017- ? 1995 KEGG website made freely available 1997 KEGG FTP site made freely available 2011 Plea to support KEGG KEGG FTP academic subscription introduced 1998 First commercial licensing Contingency Plan 1999 Pathway Solutions Inc. -
3 13437143.Pdf
Title Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones Imanishi, Tadashi; Itoh, Takeshi; Suzuki, Yutaka; O'Donovan, Claire; Fukuchi, Satoshi; Koyanagi, Kanako O.; Barrero, Roberto A.; Tamura, Takuro; Yamaguchi-Kabata, Yumi; Tanino, Motohiko; Yura, Kei; Miyazaki, Satoru; Ikeo, Kazuho; Homma, Keiichi; Kasprzyk, Arek; Nishikawa, Tetsuo; Hirakawa, Mika; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Ashurst, Jennifer; Jia, Libin; Nakao, Mitsuteru; Thomas, Michael A.; Mulder, Nicola; Karavidopoulou, Youla; Jin, Lihua; Kim, Sangsoo; Yasuda, Tomohiro; Lenhard, Boris; Eveno, Eric; Suzuki, Yoshiyuki; Yamasaki, Chisato; Takeda, Jun-ichi; Gough, Craig; Hilton, Phillip; Fujii, Yasuyuki; Sakai, Hiroaki; Tanaka, Susumu; Amid, Clara; Bellgard, Matthew; Bonaldo, Maria de Fatima; Bono, Hidemasa; Bromberg, Susan K.; Brookes, Anthony J.; Bruford, Elspeth; Carninci, Piero; Chelala, Claude; Couillault, Christine; Souza, Sandro J. de; Debily, Marie-Anne; Devignes, Marie-Dominique; Dubchak, Inna; Endo, Toshinori; Estreicher, Anne; Eyras, Eduardo; Fukami-Kobayashi, Kaoru; R. Gopinath, Gopal; Graudens, Esther; Hahn, Yoonsoo; Han, Michael; Han, Ze-Guang; Hanada, Kousuke; Hanaoka, Hideki; Harada, Erimi; Hashimoto, Katsuyuki; Hinz, Ursula; Hirai, Momoki; Hishiki, Teruyoshi; Hopkinson, Ian; Imbeaud, Sandrine; Inoko, Hidetoshi; Kanapin, Alexander; Kaneko, Yayoi; Kasukawa, Takeya; Kelso, Janet; Kersey, Author(s) Paul; Kikuno, Reiko; Kimura, Kouichi; Korn, Bernhard; Kuryshev, Vladimir; Makalowska, Izabela; Makino, Takashi; Mano, Shuhei; -
Genbank by Walter B
GenBank by Walter B. Goad o understand the significance of the information stored in memory—DNA—to the stuff of activity—proteins. The idea that GenBank, you need to know a little about molecular somehow the bases in DNA determine the amino acids in proteins genetics. What that field deals with is self-replication—the had been around for some time. In fact, George Gamow suggested in T process unique to life—and mutation and 1954, after learning about the structure proposed for DNA, that a recombination—the processes responsible for evolution-at the triplet of bases corresponded to an amino acid. That suggestion was fundamental level of the genes in DNA. This approach of working shown to be true, and by 1965 most of the genetic code had been from the blueprint, so to speak, of a living system is very powerful, deciphered. Also worked out in the ’60s were many details of what and studies of many other aspects of life—the process of learning, for Crick called the central dogma of molecular genetics—the now example—are now utilizing molecular genetics. firmly established fact that DNA is not translated directly to proteins Molecular genetics began in the early ’40s and was at first but is first transcribed to messenger RNA. This molecule, a nucleic controversial because many of the people involved had been trained acid like DNA, then serves as the template for protein synthesis. in the physical sciences rather than the biological sciences, and yet These great advances prompted a very distinguished molecular they were answering questions that biologists had been asking for geneticist to predict, in 1969, that biology was just about to end since years. -
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. -
Integrative Annotation of 21,037 Human Genes Validated by Full-Length Cdna Clones
Title Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones Imanishi, Tadashi; Itoh, Takeshi; Suzuki, Yutaka; O'Donovan, Claire; Fukuchi, Satoshi; Koyanagi, Kanako O.; Barrero, Roberto A.; Tamura, Takuro; Yamaguchi-Kabata, Yumi; Tanino, Motohiko; Yura, Kei; Miyazaki, Satoru; Ikeo, Kazuho; Homma, Keiichi; Kasprzyk, Arek; Nishikawa, Tetsuo; Hirakawa, Mika; Thierry-Mieg, Jean; Thierry-Mieg, Danielle; Ashurst, Jennifer; Jia, Libin; Nakao, Mitsuteru; Thomas, Michael A.; Mulder, Nicola; Karavidopoulou, Youla; Jin, Lihua; Kim, Sangsoo; Yasuda, Tomohiro; Lenhard, Boris; Eveno, Eric; Suzuki, Yoshiyuki; Yamasaki, Chisato; Takeda, Jun-ichi; Gough, Craig; Hilton, Phillip; Fujii, Yasuyuki; Sakai, Hiroaki; Tanaka, Susumu; Amid, Clara; Bellgard, Matthew; Bonaldo, Maria de Fatima; Bono, Hidemasa; Bromberg, Susan K.; Brookes, Anthony J.; Bruford, Elspeth; Carninci, Piero; Chelala, Claude; Couillault, Christine; Souza, Sandro J. de; Debily, Marie-Anne; Devignes, Marie-Dominique; Dubchak, Inna; Endo, Toshinori; Estreicher, Anne; Eyras, Eduardo; Fukami-Kobayashi, Kaoru; R. Gopinath, Gopal; Graudens, Esther; Hahn, Yoonsoo; Han, Michael; Han, Ze-Guang; Hanada, Kousuke; Hanaoka, Hideki; Harada, Erimi; Hashimoto, Katsuyuki; Hinz, Ursula; Hirai, Momoki; Hishiki, Teruyoshi; Hopkinson, Ian; Imbeaud, Sandrine; Inoko, Hidetoshi; Kanapin, Alexander; Kaneko, Yayoi; Kasukawa, Takeya; Kelso, Janet; Kersey, Author(s) Paul; Kikuno, Reiko; Kimura, Kouichi; Korn, Bernhard; Kuryshev, Vladimir; Makalowska, Izabela; Makino, Takashi; Mano, Shuhei; -
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. -
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). -
2003 Mulder Nucl Acids Res {22
The InterPro Database, 2003 brings increased coverage and new features Nicola J Mulder, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Daniel Barrell, Alex Bateman, David Binns, Margaret Biswas, Paul Bradley, Peer Bork, et al. To cite this version: Nicola J Mulder, Rolf Apweiler, Teresa K Attwood, Amos Bairoch, Daniel Barrell, et al.. The InterPro Database, 2003 brings increased coverage and new features. Nucleic Acids Research, Oxford University Press, 2003, 31 (1), pp.315-318. 10.1093/nar/gkg046. hal-01214149 HAL Id: hal-01214149 https://hal.archives-ouvertes.fr/hal-01214149 Submitted on 9 Oct 2015 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. # 2003 Oxford University Press Nucleic Acids Research, 2003, Vol. 31, No. 1 315–318 DOI: 10.1093/nar/gkg046 The InterPro Database, 2003 brings increased coverage and new features Nicola J. Mulder1,*, Rolf Apweiler1, Teresa K. Attwood3, Amos Bairoch4, Daniel Barrell1, Alex Bateman2, David Binns1, Margaret Biswas5, Paul Bradley1,3, Peer Bork6, Phillip Bucher7, Richard R. Copley8, Emmanuel Courcelle9, Ujjwal Das1, Richard Durbin2, Laurent Falquet7, Wolfgang Fleischmann1, Sam Griffiths-Jones2, Downloaded from Daniel Haft10, Nicola Harte1, Nicolas Hulo4, Daniel Kahn9, Alexander Kanapin1, Maria Krestyaninova1, Rodrigo Lopez1, Ivica Letunic6, David Lonsdale1, Ville Silventoinen1, Sandra E. -
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. -
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: