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Ontology-Based Methods for Analyzing Life Science Data
Habilitation a` Diriger des Recherches pr´esent´ee par Olivier Dameron Ontology-based methods for analyzing life science data Soutenue publiquement le 11 janvier 2016 devant le jury compos´ede Anita Burgun Professeur, Universit´eRen´eDescartes Paris Examinatrice Marie-Dominique Devignes Charg´eede recherches CNRS, LORIA Nancy Examinatrice Michel Dumontier Associate professor, Stanford University USA Rapporteur Christine Froidevaux Professeur, Universit´eParis Sud Rapporteure Fabien Gandon Directeur de recherches, Inria Sophia-Antipolis Rapporteur Anne Siegel Directrice de recherches CNRS, IRISA Rennes Examinatrice Alexandre Termier Professeur, Universit´ede Rennes 1 Examinateur 2 Contents 1 Introduction 9 1.1 Context ......................................... 10 1.2 Challenges . 11 1.3 Summary of the contributions . 14 1.4 Organization of the manuscript . 18 2 Reasoning based on hierarchies 21 2.1 Principle......................................... 21 2.1.1 RDF for describing data . 21 2.1.2 RDFS for describing types . 24 2.1.3 RDFS entailments . 26 2.1.4 Typical uses of RDFS entailments in life science . 26 2.1.5 Synthesis . 30 2.2 Case study: integrating diseases and pathways . 31 2.2.1 Context . 31 2.2.2 Objective . 32 2.2.3 Linking pathways and diseases using GO, KO and SNOMED-CT . 32 2.2.4 Querying associated diseases and pathways . 33 2.3 Methodology: Web services composition . 39 2.3.1 Context . 39 2.3.2 Objective . 40 2.3.3 Semantic compatibility of services parameters . 40 2.3.4 Algorithm for pairing services parameters . 40 2.4 Application: ontology-based query expansion with GO2PUB . 43 2.4.1 Context . 43 2.4.2 Objective . -
Ploidetect Enables Pan-Cancer Analysis of the Causes and Impacts of Chromosomal Instability
bioRxiv preprint doi: https://doi.org/10.1101/2021.08.06.455329; this version posted August 8, 2021. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. Ploidetect enables pan-cancer analysis of the causes and impacts of chromosomal instability Luka Culibrk1,2, Jasleen K. Grewal1,2, Erin D. Pleasance1, Laura Williamson1, Karen Mungall1, Janessa Laskin3, Marco A. Marra1,4, and Steven J.M. Jones1,4, 1Canada’s Michael Smith Genome Sciences Center at BC Cancer, Vancouver, British Columbia, Canada 2Bioinformatics training program, University of British Columbia, Vancouver, British Columbia, Canada 3Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada 4Department of Medical Genetics, Faculty of Medicine, Vancouver, British Columbia, Canada Cancers routinely exhibit chromosomal instability, resulting in tumors mutate, these variants are considerably more difficult the accumulation of changes in the abundance of genomic ma- to detect accurately compared to other types of mutations terial, known as copy number variants (CNVs). Unfortunately, and consequently they may represent an under-explored the detection of these variants in cancer genomes is difficult. We facet of tumor biology. 20 developed Ploidetect, a software package that effectively iden- While small mutations can be determined through base tifies CNVs within whole-genome sequenced tumors. Ploidetect changes embedded within aligned sequence reads, CNVs was more sensitive to CNVs in cancer related genes within ad- are variations in DNA quantity and are typically determined vanced, pre-treated metastatic cancers than other tools, while also segmenting the most contiguously. -
AI and Bioinformatics
AI Magazine Volume 25 Number 1 (2004) (© AAAI) Articles Editorial Introduction AI and Bioinformatics Janice Glasgow, Igor Jurisica, and Burkhard Rost ■ This article is an editorial introduction to the re- modern-day biology is far more complex than search discipline of bioinformatics and to the articles suggested by the simplified sketch presented in this special issue. In particular, we address the issue here. In fact, researchers in life sciences live off of how techniques from AI can be applied to many of the introduction of new concepts; the discov- the open and complex problems of modern-day mol- ecular biology. ery of exceptions; and the addition of details that usually complicate, rather than simplify, his special issue of AI Magazine focuses the overall understanding of the field. on some areas of research in bioinfor- Possibly the most rapidly growing area of re- Tmatics that have benefited from applying cent activity in bioinformatics is the analysis AI techniques. Undoubtedly, bioinformatics is of microarray data. The article by Michael Mol- a truly interdisciplinary field: Although some la, Michael Waddell, David Page, and Jude researchers continuously affect wet labs in life Shavlik (“Using Machine Learning to Design science through collaborations or provision of and Interpret Gene-Expression Microarrays”) tools, others are rooted in the theory depart- introduces some background information and ments of exact sciences (physics, chemistry, or provides a comprehensive description of how engineering) or computer sciences. This wide techniques from machine learning can be used variety creates many different perspectives and to help understand this high-dimensional and terminologies. One result of this Babel of lan- prolific gene-expression data. -
Floral Preformation in the Warming Boreal Forest: the Effects of Temperature on the Development of Vaccinium Vitis-Idaea Eileen Schaub [email protected]
University of Connecticut OpenCommons@UConn Master's Theses University of Connecticut Graduate School 8-30-2019 Floral Preformation in the Warming Boreal Forest: the Effects of Temperature on the Development of Vaccinium vitis-idaea Eileen Schaub [email protected] Recommended Citation Schaub, Eileen, "Floral Preformation in the Warming Boreal Forest: the Effects of Temperature on the Development of Vaccinium vitis-idaea" (2019). Master's Theses. 1434. https://opencommons.uconn.edu/gs_theses/1434 This work is brought to you for free and open access by the University of Connecticut Graduate School at OpenCommons@UConn. It has been accepted for inclusion in Master's Theses by an authorized administrator of OpenCommons@UConn. For more information, please contact [email protected]. Floral Preformation in the Warming Boreal forest: the Effects of Temperature on the Development of Vaccinium vitis-idaea Eileen Patricia Schaub B.A., Western Connecticut State University, 2013 A Thesis Submitted in Partial Fulfillment of the Requirements of the Degree of Master of Science At the University of Connecticut 2019 Copyright by Eileen Patricia Schaub 2019 ii Approval Page Master of Science Thesis Floral Preformation in the Warming Boreal Forest: the Effects of Temperature on the Development of Vaccinium vitis-idaea Presented by Eileen P. Schaub, B.A. Major Advisor _________________________________________________________________ Pamela K. Diggle Associate Advisor ______________________________________________________________ Cynthia S. Jones Associate Advisor ______________________________________________________________ Donald Les University of Connecticut 2019 iii Introduction The boreal zone, located between 50 and 70º north latitude, is the largest terrestrial biome, comprising 11% of Earth’s landmass across North America, Europe, and Asia (Brandt, 2009). It consists primarily of coniferous forest, with some deciduous tree species and numerous shrub and grass species. -
BIOINFORMATICS APPLICATIONS NOTE Pages 380-381
Vol. 14 no. 4 1998 BIOINFORMATICS APPLICATIONS NOTE Pages 380-381 MView: a web-compatible database search or multiple alignment viewer NigelP. Brown, ChristopheLeroy and Chris Sander European Bioinformatics Institute (EMBLĆEBI), Wellcome Genome Campus, CambridgeCB10 1SD, UK Received on December 10, 1997; revised and accepted on January 15, 1998 Abstract may be hyperlinked to the SRS system (Etzold et al., 1996), a text field, a field of scoring information from searches, and Summary: MView is a tool for converting the results of a a field reporting the per cent identity of each sequence with sequence database search into the form of a coloured multiple respect to a preferred sequence in the alignment, usually the alignment of hits stacked against the query. Alternatively, an query in the case of a search. existing multiple alignment can be processed. In either case, Multiple alignments require minimal parsing and are the output is simply HTML, so the result is platform independent and does not require a separate application or subjected only to formatting stages. Search hits are first applet to be loaded. stacked against the ungapped query sequence and require Availability: Free from http://www.sander.ebi.ac.uk/mview/ special processing. Ungapped search (e.g. BLAST) hit subject to copyright restrictions. fragments are assembled into a single string by overlaying Contact: [email protected] them preferentially by score onto a template string, while gapped search (e.g. FASTA) hits have columns corresponding Often when running FASTA (Pearson, 1990) or BLAST to query gaps excised. Consequently, the stacked alignment is (Altschul et al., 1990), it is desired to visualize the database a patchwork of reconstituted sequences that nevertheless is hits stacked against the query sequence. -
Are You an Invited Speaker? a Bibliometric Analysis of Elite Groups for Scholarly Events in Bioinformatics
Are You an Invited Speaker? A Bibliometric Analysis of Elite Groups for Scholarly Events in Bioinformatics Senator Jeong, Sungin Lee, and Hong-Gee Kim Biomedical Knowledge Engineering Laboratory, Seoul National University, 28–22 YeonGeon Dong, Jongno Gu, Seoul 110–749, Korea. E-mail: {senator, sunginlee, hgkim}@snu.ac.kr Participating in scholarly events (e.g., conferences, work- evaluation, but it would be hard to claim that they have pro- shops, etc.) as an elite-group member such as an orga- vided comprehensive lists of evaluation measurements. This nizing committee chair or member, program committee article aims not to provide such lists but to add to the current chair or member, session chair, invited speaker, or award winner is beneficial to a researcher’s career develop- practices an alternative metric that complements existing per- ment.The objective of this study is to investigate whether formance measures to give a more comprehensive picture of elite-group membership for scholarly events is represen- scholars’ performance. tative of scholars’ prominence, and which elite group is By one definition (Jeong, 2008), a scholarly event is the most prestigious. We collected data about 15 global “a sequentially and spatially organized collection of schol- (excluding regional) bioinformatics scholarly events held in 2007. We sampled (via stratified random sampling) ars’ interactions with the intention of delivering and shar- participants from elite groups in each event. Then, bib- ing knowledge, exchanging research ideas, and performing liometric indicators (total citations and h index) of seven related activities.” As such, scholarly events are communica- elite groups and a non-elite group, consisting of authors tion channels from which our new evaluation tool can draw who submitted at least one paper to an event but were its supporting evidence. -
Classification of Botany and Use of Plants
SECTION 1: CLASSIFICATION OF BOTANY AND USE OF PLANTS 1. Introduction Botany refers to the scientific study of the plant kingdom. As a branch of biology, it mainly accounts for the science of plants or ‘phytobiology’. The main objective of the this section is for participants, having completed their training, to be able to: 1. Identify and classify various types of herbs 2. Choose the appropriate categories and types of herbs for breeding and planting 1 2. Botany 2.1 Branches – Objectives – Usability Botany covers a wide range of scientific sub-disciplines that study the growth, reproduction, metabolism, morphogenesis, diseases, and evolution of plants. Subsequently, many subordinate fields are to appear, such as: Systematic Botany: its main purpose the classification of plants Plant morphology or phytomorphology, which can be further divided into the distinctive branches of Plant cytology, Plant histology, and Plant and Crop organography Botanical physiology, which examines the functions of the various organs of plants A more modern but equally significant field is Phytogeography, which associates with many complex objects of research and study. Similarly, other branches of applied botany have made their appearance, some of which are Phytopathology, Phytopharmacognosy, Forest Botany, and Agronomy Botany, among others. 2 Like all other life forms in biology, plant life can be studied at different levels, from the molecular, to the genetic and biochemical, through to the study of cellular organelles, cells, tissues, organs, individual plants, populations and communities of plants. At each of these levels a botanist can deal with the classification (taxonomy), structure (anatomy), or function (physiology) of plant life. -
Hidrobiológica 2020, 30 (1): 29-36
Hidrobiológica 2020, 30 (1): 29-36 OPEN ACCESS HIDROBIOLÓGICA Research Article http:/hidrobiologica.izt.uam.mx April, 2020 ISSN: 2448-7333 Gonadal histology of Erichsonella attenuata (Isopoda: Valvifera: Idoteidae) Histología gonadal de Erichsonella attenuata (Isopoda: Valvifera: Idoteidae) Hugo Enrique Reyes-Aldana1,2 , Adriana Muñoz-Hernández3 y José Luis Bortolini-Rosales4 Recibido: 28 de noviembre de 2018. Aceptado: 31 de marzo de 2020. Publicado: abril de 2020. ABSTRACT Background: Isopods are highly diverse organisms, however, despite of their abundance and importance in ecological dynamics have been neglected in many of the aspects of their biology. Objectives: This paper analyses E. attenuata male and female histological characteristics, especially the reproductive structures, to increase the information of the reproductive biology and help to understand the sexual characteristics 1 Faculty of Biology, Ludwig-Maximi- of other free-living isopods to favour comparative studies with other groups and environmental conditions. lians-Universität München. Großhader- ner Str. 2,Planegg-Martinsreid, 82152. Methods: Organisms sampled between July 2010 and August 2011 were fixed and processed for histological Germany. preparations; Haematoxylin-Eosin and Lendrum staining techniques were applied to differentiate structures. 2 Rachel Carson Center, Ludwig-Maximi- Microphotographies were taken and analysed. Results: The internal organography was found to be similar lians-Universität München. Leopolds- on both sexes. The ovaries are modified during the maturation of the oocytes, after spawning, embryos are traße 11A, Munich, 80802. Germany. born in the marsupium. In some cases, a cohort in initial stages of maturation is observed in the dorsal region 3 Cellular Biology Department, Faculty of of the body in addition of the ones seen in the marsupium. -
Asignaturas Inglés Por Grados Ciencias 19-20.Xlsx
LIST OF SUBJECTS TAUGHT IN ENGLISH ‐ SCHOOL OF SCIENCES DEGREE IN BIOLOGY Subject Semester Year ECTS 1 Animal and vegetal organography Spring 1º 6 2 Basic computer sciences and bibliographic techniques Spring 1º 3 3 Bioinformatics Spring 2º 3 4 Biostatistics Spring 1º 6 5 Environmental Chemistry Spring 3º 6 6 General Chemistry Autumn 1º 6 7 General Microbiology Autumn 3º 6 8 Histology and cell biology Autumn 1º 6 9 Human Molecular Genetics Autumn 3º 6 10 Mathematics Autumn 1º 6 11 Microbial Biotechnology Spring 4º 3 12 Molecular Development Biology Spring 4º 3 13 Physics Autumn 1º 6 14 Radioactivity Spring 4º 3 15 Scientific Academic Skills Autumn 3º 3 16 Structural and functional biochemistry Annual 1º 6 DEGREE IN BIOCHEMISTRY Subject Semester Year ECTS 1 Basic computer studies and bibliographic techniques Spring 1º 3 2 Biology fundamentals Spring 1º 3 3 Biostatistics Spring 1º 6 4 Computational Biology Autumn 4º 6 5 General Chemistry Autumn 1º 6 6 General Microbiology Autumn 3º 6 7 Genetics Engineering Spring 2º 6 8 Genomics Spring 4º 3 9 Histology and cell biology Autumn 1º 6 10 Human Molecular Genetics Autumn 3º 6 11 Mathematics Autumn 1º 6 12 Microbial Biotechnology Spring 4º 3 13 Molecular Development Biology Spring 4º 3 14 Molecular Physiology Spring 3º 6 15 Organography Spring 1º 6 16 Physical Chemistry Spring 1º 6 17 Physics Autumn 1º 6 18 Scientific Academic Skills Autumn 3º 3 19 Structural and functional biochemistry Annual 1º 6 DEGREE IN CHEMISTRY Subject Semester Year ECTS 1 Basic Statistics Spring 1º 3 2 Data Analysis Autumn -
Full List of PCAWG Consortium Working Groups and Writing
Supplementary information to: Genomics: data sharing needs an international code of conduct To accompany a Comment published in Nature 578, 31–33 (2020) https://www.nature.com/articles/d41586-020-00082-9 By Mark Phillips, Fruzsina Molnár-Gábor, Jan O. Korbel, Adrian Thorogood, Yann Joly, Don Chalmers, David Townend & Bartha M. Knoppers for the PCAWG Consortium. SUPPLEMENTARY INFORMATION | NATURE | 1 The ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium Working Groups PCAWG Steering committee 1,2 3,4,5,6 7,8 9,10 Peter J Campbell# , Gad Getz# , Jan O Korbel# , Lincoln D Stein# and Joshua M Stuart#11,12 PCAWG Head of project management Jennifer L Jennings13 PCAWG Executive committee 14 15 16 17 18 Sultan T Al-Sedairy , Axel Aretz , Cindy Bell , Miguel Betancourt , Christiane Buchholz , 19 20 21 22 23 Fabien Calvo , Christine Chomienne , Michael Dunn , Stuart Edmonds , Eric Green , Shailja 24 23 25 13 26 Gupta , Carolyn M Hutter , Karine Jegalian , Jennifer L Jennings , Nic Jones , Hyung-Lae 27 28,29,30 31 32 32 26 Kim , Youyong Lu , Hitoshi Nakagama , Gerd Nettekoven , Laura Planko , David Scott , 3 3,34 35 9,10 1 35 Tatsuhiro Shibata , Kiyo Shimizu , Lincoln D Stein# , Michael R Stratton , Takashi Yugawa , 36,37 24 38 39 Giampaolo Tortora , K VijayRaghavan , Huanming Yang and Jean C Zenklusen PCAWG Ethics and Legal Working Group 40 41 41 42 41 Don Chalmers# , Yann Joly , Bartha M Knoppers# , Fruzsina -
Biological Pathways Exchange Language Level 3, Release Version 1 Documentation
BioPAX – Biological Pathways Exchange Language Level 3, Release Version 1 Documentation BioPAX Release, July 2010. The BioPAX data exchange format is the joint work of the BioPAX workgroup and Level 3 builds on the work of Level 2 and Level 1. BioPAX Level 3 input from: Mirit Aladjem, Ozgun Babur, Gary D. Bader, Michael Blinov, Burk Braun, Michelle Carrillo, Michael P. Cary, Kei-Hoi Cheung, Julio Collado-Vides, Dan Corwin, Emek Demir, Peter D'Eustachio, Ken Fukuda, Marc Gillespie, Li Gong, Gopal Gopinathrao, Nan Guo, Peter Hornbeck, Michael Hucka, Olivier Hubaut, Geeta Joshi- Tope, Peter Karp, Shiva Krupa, Christian Lemer, Joanne Luciano, Irma Martinez-Flores, Zheng Li, David Merberg, Huaiyu Mi, Ion Moraru, Nicolas Le Novere, Elgar Pichler, Suzanne Paley, Monica Penaloza- Spinola, Victoria Petri, Elgar Pichler, Alex Pico, Harsha Rajasimha, Ranjani Ramakrishnan, Dean Ravenscroft, Jonathan Rees, Liya Ren, Oliver Ruebenacker, Alan Ruttenberg, Matthias Samwald, Chris Sander, Frank Schacherer, Carl Schaefer, James Schaff, Nigam Shah, Andrea Splendiani, Paul Thomas, Imre Vastrik, Ryan Whaley, Edgar Wingender, Guanming Wu, Jeremy Zucker BioPAX Level 2 input from: Mirit Aladjem, Gary D. Bader, Ewan Birney, Michael P. Cary, Dan Corwin, Kam Dahlquist, Emek Demir, Peter D'Eustachio, Ken Fukuda, Frank Gibbons, Marc Gillespie, Michael Hucka, Geeta Joshi-Tope, David Kane, Peter Karp, Christian Lemer, Joanne Luciano, Elgar Pichler, Eric Neumann, Suzanne Paley, Harsha Rajasimha, Jonathan Rees, Alan Ruttenberg, Andrey Rzhetsky, Chris Sander, Frank Schacherer, -
Systems Biology Graphical Notation: Process Description Language Level 1
Erschienen in: Journal of integrative bioinformatics ; 16 (2019), 2. - 20190022 https://dx.doi.org/10.1515/jib-2019-0022 DE GRUYTER Journal of Integrative Bioinformatics. 2019; 20190022 Adrien Rougny1,2 / Vasundra Touré3 / Stuart Moodie4 / Irina Balaur5 / Tobias Czauderna 6 / Hanna Borlinghaus7 / Ugur Dogrusoz8,9 / Alexander Mazein5,10,11 / Andreas Dräger12,13,14 / Michael L. Blinov15 / Alice Villéger16 / Robin Haw17 / Emek Demir18,19 / Huaiyu Mi20 / Anatoly Sorokin11 / Falk Schreiber6,7 / Augustin Luna21,22 Systems Biology Graphical Notation: Process Description language Level 1 Version 2.0 1 Biotechnology Research Institute for Drug Discovery, AIST, Tokyo135-0064, Japan, E-mail: [email protected]. https://orcid.org/0000-0002-2118-035X. 2 Computational Bio Big-Data Open Innovation Laboratory (CBBD-OIL), AIST, Tokyo 169-8555, Japan, E-mail: [email protected]. https://orcid.org/0000-0002-2118-035X. 3 Department of Biology, Norwegian University of Science and Technology (NTNU), Trondheim, Norway. https://orcid.org/0000-0003-4639-4431. 4 Eight Pillars Ltd, 19 Redford Walk, Edinburgh EH13 0AG, UK 5 European Institute for Systems Biology and Medicine, CIRI UMR5308, CNRS-ENS-UCBL-INSERM, Université de Lyon, 50 Av- enue Tony Garnier, 69007 Lyon, France. https://orcid.org/0000-0002-3671-895X, https://orcid.org/0000-0001-7137-4171. 6 Faculty of Information Technology, Monash University, Melbourne, Australia. https://orcid.org/0000-0002-1788-9593. 7 Department of Computer and Information Science, University of Konstanz, Konstanz, Germany. https://orcid.org/0000-0002-5410-6877. 8 Computer Engineering Department, Bilkent University, Ankara 06800, Turkey. https://orcid.org/0000-0002-7153-0784. 9 i-Vis Research Lab, Bilkent University, Ankara 06800, Turkey.