International Society for Biocuration
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Original Article Text Mining in the Biocuration Workflow: Applications for Literature Curation at Wormbase, Dictybase and TAIR
Database, Vol. 2012, Article ID bas040, doi:10.1093/database/bas040 ............................................................................................................................................................................................................................................................................................. Original article Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR Kimberly Van Auken1,*, Petra Fey2, Tanya Z. Berardini3, Robert Dodson2, Laurel Cooper4, Donghui Li3, Juancarlos Chan1, Yuling Li1, Siddhartha Basu2, Hans-Michael Muller1, Downloaded from Rex Chisholm2, Eva Huala3, Paul W. Sternberg1,5 and the WormBase Consortium 1Division of Biology, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, 2Northwestern University Biomedical Informatics Center and Center for Genetic Medicine, 420 E. Superior Street, Chicago, IL 60611, 3Department of Plant Biology, Carnegie Institution, 260 Panama Street, Stanford, CA 94305, 4Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331 and 5Howard Hughes Medical Institute, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA 91125, USA http://database.oxfordjournals.org/ *Corresponding author: Tel: +1 609 937 1635; Fax: +1 626 568 8012; Email: [email protected] Submitted 18 June 2012; Revised 30 September 2012; Accepted 2 October 2012 ............................................................................................................................................................................................................................................................................................ -
Enhanced Representation of Natural Product Metabolism in Uniprotkb
H OH metabolites OH Article Diverse Taxonomies for Diverse Chemistries: Enhanced Representation of Natural Product Metabolism in UniProtKB Marc Feuermann 1,* , Emmanuel Boutet 1,* , Anne Morgat 1 , Kristian B. Axelsen 1, Parit Bansal 1, Jerven Bolleman 1 , Edouard de Castro 1, Elisabeth Coudert 1, Elisabeth Gasteiger 1,Sébastien Géhant 1, Damien Lieberherr 1, Thierry Lombardot 1,†, Teresa B. Neto 1, Ivo Pedruzzi 1, Sylvain Poux 1, Monica Pozzato 1, Nicole Redaschi 1 , Alan Bridge 1 and on behalf of the UniProt Consortium 1,2,3,4,‡ 1 Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 Michel-Servet, CH-1211 Geneva 4, Switzerland; [email protected] (A.M.); [email protected] (K.B.A.); [email protected] (P.B.); [email protected] (J.B.); [email protected] (E.d.C.); [email protected] (E.C.); [email protected] (E.G.); [email protected] (S.G.); [email protected] (D.L.); [email protected] (T.L.); [email protected] (T.B.N.); [email protected] (I.P.); [email protected] (S.P.); [email protected] (M.P.); [email protected] (N.R.); [email protected] (A.B.); [email protected] (U.C.) 2 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 3 Protein Information Resource, University of Delaware, 15 Innovation Way, Suite 205, Newark, DE 19711, USA 4 Protein Information Resource, Georgetown University Medical Center, 3300 Whitehaven Street NorthWest, Suite 1200, Washington, DC 20007, USA * Correspondence: [email protected] (M.F.); [email protected] (E.B.); Tel.: +41-22-379-58-75 (M.F.); +41-22-379-49-10 (E.B.) † Current address: Centre Informatique, Division Calcul et Soutien à la Recherche, University of Lausanne, CH-1015 Lausanne, Switzerland. -
The EMBL-European Bioinformatics Institute the Hub for Bioinformatics in Europe
The EMBL-European Bioinformatics Institute The hub for bioinformatics in Europe Blaise T.F. Alako, PhD [email protected] www.ebi.ac.uk What is EMBL-EBI? • Part of the European Molecular Biology Laboratory • International, non-profit research institute • Europe’s hub for biological data, services and research The European Molecular Biology Laboratory Heidelberg Hamburg Hinxton, Cambridge Basic research Structural biology Bioinformatics Administration Grenoble Monterotondo, Rome EMBO EMBL staff: 1500 people Structural biology Mouse biology >60 nationalities EMBL member states Austria, Belgium, Croatia, Denmark, Finland, France, Germany, Greece, Iceland, Ireland, Israel, Italy, Luxembourg, the Netherlands, Norway, Portugal, Spain, Sweden, Switzerland and the United Kingdom Associate member state: Australia Who we are ~500 members of staff ~400 work in services & support >53 nationalities ~120 focus on basic research EMBL-EBI’s mission • Provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress • Contribute to the advancement of biology through basic investigator-driven research in bioinformatics • Provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators • Help disseminate cutting-edge technologies to industry • Coordinate biological data provision throughout Europe Services Data and tools for molecular life science www.ebi.ac.uk/services Browse our services 9 What services do we provide? Labs around the -
Tunca Doğan , Alex Bateman , Maria J. Martin Your Choice
(—THIS SIDEBAR DOES NOT PRINT—) UniProt Domain Architecture Alignment: A New Approach for Protein Similarity QUICK START (cont.) DESIGN GUIDE Search using InterPro Domain Annotation How to change the template color theme This PowerPoint 2007 template produces a 44”x44” You can easily change the color theme of your poster by going to presentation poster. You can use it to create your research 1 1 1 the DESIGN menu, click on COLORS, and choose the color theme of poster and save valuable time placing titles, subtitles, text, Tunca Doğan , Alex Bateman , Maria J. Martin your choice. You can also create your own color theme. and graphics. European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), We provide a series of online tutorials that will guide you Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK through the poster design process and answer your poster Correspondence: [email protected] production questions. To view our template tutorials, go online to PosterPresentations.com and click on HELP DESK. ABSTRACT METHODOLOGY RESULTS & DISCUSSION When you are ready to print your poster, go online to InterPro Domains, DAs and DA Alignment PosterPresentations.com Motivation: Similarity based methods have been widely used in order to Generation of the Domain Architectures: You can also manually change the color of your background by going to VIEW > SLIDE MASTER. After you finish working on the master be infer the properties of genes and gene products containing little or no 1) Collect the hits for each protein from InterPro. Domain annotation coverage Overlap domain hits problem in Need assistance? Call us at 1.510.649.3001 difference b/w domain databases: the InterPro database: sure to go to VIEW > NORMAL to continue working on your poster. -
Evolution and Function of Drososphila Melanogaster Cis-Regulatory Sequences
Evolution and Function of Drososphila melanogaster cis-regulatory Sequences By Aaron Hardin A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Molecular and Cell Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Professor Michael Eisen, Chair Professor Doris Bachtrog Professor Gary Karpen Professor Lior Pachter Fall 2013 Evolution and Function of Drososphila melanogaster cis-regulatory Sequences This work is licensed under a Creative Commons Attribution-ShareAlike 4.0 International License 2013 by Aaron Hardin 1 Abstract Evolution and Function of Drososphila melanogaster cis-regulatory Sequences by Aaron Hardin Doctor of Philosophy in Molecular and Cell Biology University of California, Berkeley Professor Michael Eisen, Chair In this work, I describe my doctoral work studying the regulation of transcription with both computational and experimental methods on the natural genetic variation in a population. This works integrates an investigation of the consequences of polymorphisms at three stages of gene regulation in the developing fly embryo: the diversity at cis-regulatory modules, the integration of transcription factor binding into changes in chromatin state and the effects of these inputs on the final phenotype of embryonic gene expression. i I dedicate this dissertation to Mela Hardin who has been here for me at all times, even when we were apart. ii Contents List of Figures iv List of Tables vi Acknowledgments vii 1 Introduction1 2 Within Species Diversity in cis-Regulatory Modules6 2.1 Introduction....................................6 2.2 Results.......................................8 2.2.1 Genome wide diversity in transcription factor binding sites......8 2.2.2 Genome wide purifying selection on cis-regulatory modules......9 2.3 Discussion.....................................9 2.4 Methods for finding polymorphisms...................... -
Biocuration 2016 - Posters
Biocuration 2016 - Posters Source: http://www.sib.swiss/events/biocuration2016/posters 1 RAM: A standards-based database for extracting and analyzing disease-specified concepts from the multitude of biomedical resources Jinmeng Jia and Tieliu Shi Each year, millions of people around world suffer from the consequence of the misdiagnosis and ineffective treatment of various disease, especially those intractable diseases and rare diseases. Integration of various data related to human diseases help us not only for identifying drug targets, connecting genetic variations of phenotypes and understanding molecular pathways relevant to novel treatment, but also for coupling clinical care and biomedical researches. To this end, we built the Rare disease Annotation & Medicine (RAM) standards-based database which can provide reference to map and extract disease-specified information from multitude of biomedical resources such as free text articles in MEDLINE and Electronic Medical Records (EMRs). RAM integrates disease-specified concepts from ICD-9, ICD-10, SNOMED-CT and MeSH (http://www.nlm.nih.gov/mesh/MBrowser.html) extracted from the Unified Medical Language System (UMLS) based on the UMLS Concept Unique Identifiers for each Disease Term. We also integrated phenotypes from OMIM for each disease term, which link underlying mechanisms and clinical observation. Moreover, we used disease-manifestation (D-M) pairs from existing biomedical ontologies as prior knowledge to automatically recognize D-M-specific syntactic patterns from full text articles in MEDLINE. Considering that most of the record-based disease information in public databases are textual format, we extracted disease terms and their related biomedical descriptive phrases from Online Mendelian Inheritance in Man (OMIM), National Organization for Rare Disorders (NORD) and Orphanet using UMLS Thesaurus. -
![Biocuration - Mapping Resources and Needs [Version 2; Peer Review: 2 Approved]](https://docslib.b-cdn.net/cover/5552/biocuration-mapping-resources-and-needs-version-2-peer-review-2-approved-1045552.webp)
Biocuration - Mapping Resources and Needs [Version 2; Peer Review: 2 Approved]
F1000Research 2020, 9(ELIXIR):1094 Last updated: 22 JUL 2021 RESEARCH ARTICLE Biocuration - mapping resources and needs [version 2; peer review: 2 approved] Alexandra Holinski 1, Melissa L. Burke 1, Sarah L. Morgan 1, Peter McQuilton 2, Patricia M. Palagi 3 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, CB10 1SD, UK 2Oxford e-Research Centre, Department of Engineering Science, University of Oxford, Oxford, Oxfordshire, OX1 3QG, UK 3SIB Swiss Institute of Bioinformatics, Lausanne, 1015, Switzerland v2 First published: 04 Sep 2020, 9(ELIXIR):1094 Open Peer Review https://doi.org/10.12688/f1000research.25413.1 Latest published: 02 Dec 2020, 9(ELIXIR):1094 https://doi.org/10.12688/f1000research.25413.2 Reviewer Status Invited Reviewers Abstract Background: Biocuration involves a variety of teams and individuals 1 2 across the globe. However, they may not self-identify as biocurators, as they may be unaware of biocuration as a career path or because version 2 biocuration is only part of their role. The lack of a clear, up-to-date (revision) report profile of biocuration creates challenges for organisations like ELIXIR, 02 Dec 2020 the ISB and GOBLET to systematically support biocurators and for biocurators themselves to develop their own careers. Therefore, the version 1 ELIXIR Training Platform launched an Implementation Study in order 04 Sep 2020 report report to i) identify communities of biocurators, ii) map the type of curation work being done, iii) assess biocuration training, and iv) draw a picture of biocuration career development. 1. Tanya Berardini , Phoenix Bioinformatics, Methods: To achieve the goals of the study, we carried out a global Fremont, USA survey on the nature of biocuration work, the tools and resources that are used, training that has been received and additional training 2. -
Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’S Disease Data
G C A T T A C G G C A T genes Article Improving the Gene Ontology Resource to Facilitate More Informative Analysis and Interpretation of Alzheimer’s Disease Data Barbara Kramarz 1 , Paola Roncaglia 2 , Birgit H. M. Meldal 2 , Rachael P. Huntley 1 , Maria J. Martin 2, Sandra Orchard 2, Helen Parkinson 2, David Brough 3, Rina Bandopadhyay 4, Nigel M. Hooper 3 and Ruth C. Lovering 1,* 1 UCL Institute of Cardiovascular Science, University College London, Rayne Building, 5 University Street, London WC1E 6JF, UK; [email protected] (B.K.); [email protected] (R.P.H.) 2 European Bioinformatics Institute (EMBL-EBI), European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; [email protected] (P.R.); [email protected] (B.H.M.M.); [email protected] (M.J.M.); [email protected] (S.O.); [email protected] (H.P.) 3 Division of Neuroscience and Experimental Psychology, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, AV Hill Building, Oxford Road, Manchester M13 9PT, UK; [email protected] (D.B.); [email protected] (N.M.H.) 4 UCL Queen Square Institute of Neurology and Reta Lila Weston Institute of Neurological Studies, 1 Wakefield Street, London WC1N 1PJ, UK; [email protected] * Correspondence: [email protected] or [email protected]; Tel.: +44-207-679-6965 Received: 31 October 2018; Accepted: 23 November 2018; Published: 29 November 2018 Abstract: The analysis and interpretation of high-throughput datasets relies on access to high-quality bioinformatics resources, as well as processing pipelines and analysis tools. -
EYAL AKIVA, Phd
Eyal Akiva CV, Nov. 2017 EYAL AKIVA, PhD Department of Bioengineering and Therapeutic Sciences Phone +1-650-504-9008 University of California at San Francisco Email [email protected] 1700 4th street, San Francisco, Web www.babbittlab.ucsf.edu/eakiva CA, USA EDUCATION 2012-2017 Post-doctoral fellowship at UCSF, Dept. Of Bioengineering and Therapeutic Sciences. Host: Prof. Patricia Babbitt. 2010-2012 Post-doctoral fellowship at UCSF, Dept. Of Bioengineering and Therapeutic Sciences. Host: Prof. Tanja Kortemme. 2004-2010 PhD at The Hebrew University of Jerusalem (Israel), bioinformatics. Host: Prof. Hanah Margalit. “Various Aspects of Modularity in Protein-Protein Interaction". 2001-2004 MSc at The Hebrew University of Jerusalem (Israel), bioinformatics and human genetics. Host: Prof. Muli Ben-Sasson. “Exploiting the Exploiters: Identification of Virus-Host Pep- tide Mimicry as a Source for Modules of Functional Significance”. MAGNA CUM LAUDE. 1997-2000 BSc at Bar-Ilan University (Israel), biology (major) and computer science (minor). Final project advisor: Prof. Ramit Mehr “Modeling the Evolution of the Immune System: a Sim- ulation of the Evolution of Genes that Encode the Variable Regions of Immunoglobulins”. MAGNA CUM LAUDE. 1996-1997 First year of "Industrial Engineering and Management" studies, Tel-Aviv University, Israel. OTHER WORK EXPERIENCE 2000-01 ‘Do-coop technologies’: Team leader and chemistry/microbiology researcher; development of biological applications and manufacture of proprietary nanoparticles (Or Yehuda, Israel and Tel-Aviv University (Prof. Eshel Ben-Jacob’s lab at the school of physics)). FUNDING, HONORS AND AWARDS 2017 Grant: Co-PI, “Utilizing metagenomic sequences for enzyme function prediction”, Joint Genome Institute (US Department of Energy) (http://jgi.doe.gov/doe-user-facilities-ficus- join-forces-to-tackle-biology-big-data/). -
Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases
Genomics Proteomics Bioinformatics 18 (2020) 91–103 Genomics Proteomics Bioinformatics www.elsevier.com/locate/gpb www.sciencedirect.com PERSPECTIVE Quality Matters: Biocuration Experts on the Impact of Duplication and Other Data Quality Issues in Biological Databases Qingyu Chen 1,*, Ramona Britto 2, Ivan Erill 3, Constance J. Jeffery 4, Arthur Liberzon 5, Michele Magrane 2, Jun-ichi Onami 6,7, Marc Robinson-Rechavi 8,9, Jana Sponarova 10, Justin Zobel 1,*, Karin Verspoor 1,* 1 School of Computing and Information Systems, University of Melbourne, Melbourne, VIC 3010, Australia 2 European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK 3 Department of Biological Sciences, University of Maryland, Baltimore, MD 21250, USA 4 Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA 5 Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA 6 Japan Science and Technology Agency, National Bioscience Database Center, Tokyo 102-8666, Japan 7 National Institute of Health Sciences, Tokyo 158-8501, Japan 8 Swiss Institute of Bioinformatics, CH-1015 Lausanne, Switzerland 9 Department of Ecology and Evolution, University of Lausanne, CH-1015 Lausanne, Switzerland 10 Nebion AG, 8048 Zurich, Switzerland Received 8 December 2017; revised 24 October 2018; accepted 14 December 2018 Available online 9 July 2020 Handled by Zhang Zhang Introduction assembled, annotated, and ultimately submitted to primary nucleotide databases such as GenBank [2], European Nucleo- tide Archive (ENA) [3], and DNA Data Bank of Japan Biological databases represent an extraordinary collective vol- (DDBJ) [4] (collectively known as the International Nucleotide ume of work. -
Molecular Genetics & Genomics
page 46 Lab Times 5-2010 Ranking Illustration: Christina Ullman Publication Analysis 1997-2008 Molecular Genetics & Genomics Under the premise of a “narrow” definition of the field, Germany and England co-dominated European molecular genetics/genomics. The most frequently citated sub-fields were bioinformatical genomics, epigenetics, RNA biology and DNA repair. irst of all, a little science history (you’ll soon see why). As and expression. That’s where so-called computational biology is well known, in the 1950s genetics went molecular – and and systems biology enter research into basic genetic problems. Fdid not just become molecular genetics but rather molec- Given that development, it is not easy to answer the question ular bio logy. In 1963, however, Sydney Brenner wrote in his fa- what “molecular genetics & genomics” today actually is – and, mous letter to Max Perutz: “[...] I have long felt that the future of in particular, what is it in the context of our publication analy- molecular biology lies in the extension of research to other fields sis of the field? It is obvious that, as for example science historian of biology, notably development and the nervous system.” He Robert Olby put it, a “wide” definition can be distinguished from appeared not to be alone with this view and, as a consequence, a “narrow” definition of the field. The wide definition includes along with Brenner many of the leading molecular biologists all fields, into which molecular biology has entered as an exper- from the classical period redirected their research agendas, utilis- imental and theoretical paradigm. The “narrow” definition, on ing the newly developed molecular techniques to investigate un- the other hand, still tries to maintain the status as an explicit bio- solved problems in other fields. -
Daniel Aalberts Scott Aa
PLOS Computational Biology would like to thank all those who reviewed on behalf of the journal in 2015: Daniel Aalberts Jeff Alstott Benjamin Audit Scott Aaronson Christian Althaus Charles Auffray Henry Abarbanel Benjamin Althouse Jean-Christophe Augustin James Abbas Russ Altman Robert Austin Craig Abbey Eduardo Altmann Bruno Averbeck Hermann Aberle Philipp Altrock Ferhat Ay Robert Abramovitch Vikram Alva Nihat Ay Josep Abril Francisco Alvarez-Leefmans Francisco Azuaje Luigi Acerbi Rommie Amaro Marc Baaden Orlando Acevedo Ettore Ambrosini M. Madan Babu Christoph Adami Bagrat Amirikian Mohan Babu Frederick Adler Uri Amit Marco Bacci Boris Adryan Alexander Anderson Stephen Baccus Tinri Aegerter-Wilmsen Noemi Andor Omar Bagasra Vera Afreixo Isabelle Andre Marc Baguelin Ashutosh Agarwal R. David Andrew Timothy Bailey Ira Agrawal Steven Andrews Wyeth Bair Jacobo Aguirre Ioan Andricioaei Chris Bakal Alaa Ahmed Ioannis Androulakis Joseph Bak-Coleman Hasan Ahmed Iris Antes Adam Baker Natalie Ahn Maciek Antoniewicz Douglas Bakkum Thomas Akam Haroon Anwar Gabor Balazsi Ilya Akberdin Stefano Anzellotti Nilesh Banavali Eyal Akiva Miguel Aon Rahul Banerjee Sahar Akram Lucy Aplin Edward Banigan Tomas Alarcon Kevin Aquino Martin Banks Larissa Albantakis Leonardo Arbiza Mukul Bansal Reka Albert Murat Arcak Shweta Bansal Martí Aldea Gil Ariel Wolfgang Banzhaf Bree Aldridge Nimalan Arinaminpathy Lei Bao Helen Alexander Jeffrey Arle Gyorgy Barabas Alexander Alexeev Alain Arneodo Omri Barak Leonidas Alexopoulos Markus Arnoldini Matteo Barberis Emil Alexov