The 10 Annual Bio-Ontologies Meeting

There is a strong need to map the OBO format to OWL and provide tools that enable end users to easily perform this translation. To fulfill this need, the National Center for Biomedical Ontology created the NCBO OBO to OWL mapping and a set of tools to perform the translations for the Protégé and OBO-Edit editors and for command line use. A group of OBO developers and OWL experts worked cooperatively to develop this mapping. This paper summarizes our experiences and main design decisions, so users can better understand the mapping. Contact: dilvan@gmail.com

[1]  References , 1971 .

[2]  D. Wetlaufer.  Nucleation, rapid folding, and globular intrachain regions in proteins. , 1973, Proceedings of the National Academy of Sciences of the United States of America.

[3]  Kyo Kageura,et al.  METHODS OF AUTOMATIC TERM RECOGNITION : A REVIEW , 1996 .

[4]  David W. Conrath,et al.  Semantic Similarity Based on Corpus Statistics and Lexical Taxonomy , 1997, ROCLING/IJCLCLP.

[5]  《中华放射肿瘤学杂志》编辑部.  Medline , 2001, Current Biology.

[6]  Dekang Lin,et al.  An Information-Theoretic Definition of Similarity , 1998, ICML.

[7]  Ben Shneiderman,et al.  Interface and data architecture for query preview in networked information systems , 1999, TOIS.

[8]  Philip Resnik,et al.  Semantic Similarity in a Taxonomy: An Information-Based Measure and its Application to Problems of Ambiguity in Natural Language , 1999, J. Artif. Intell. Res..

[9]  Sophia Ananiadou,et al.  The C-value/NC-value domain-independent method for multi-word term extraction , 1999 .

[10]  Jean Carletta,et al.  An annotation scheme for discourse-level argumentation in research articles , 1999, EACL.

[11]  D. Eisenberg,et al.  Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[12]  Ben Shneiderman,et al.  Readings in information visualization - using vision to think , 1999 .

[13]  N Linial,et al.  ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space , 1999, Proteins.

[14]  A. Valencia,et al.  Practical limits of function prediction , 2000, Proteins.

[15]  Alan L. Rector,et al.  GALEN's model of parts and wholes: experience and comparisons , 2000, AMIA.

[16]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[17]  Carole A. Goble,et al.  Ontology-based Knowledge Representation for Bioinformatics , 2000, Briefings Bioinform..

[18]  Steffen Staab,et al.  Engineering Ontologies using Semantic Patterns , 2001, OIS@IJCAI.

[19]  S. Trent Rosenbloom,et al.  Derivation and evaluation of a document-naming nomenclature. , 2001, Journal of the American Medical Informatics Association : JAMIA.

[20]  Steffen Schulze-Kremer,et al.  Ontologies for Molecular Biology , 2001, Electron. Trans. Artif. Intell..

[21]  Martin Romacker,et al.  Creating Knowledge Repositories from Biomedical Reports: The MEDSYNDIKATE Text Mining System , 2001, Pacific Symposium on Biocomputing.

[22]  Michael Hehenberger,et al.  Text-based knowledge discovery: search and mining of life-sciences documents. , 2002, Drug discovery today.

[23]  Simone Teufel,et al.  Meta-discourse markers and problem-structuring in scientific articles , 2002 .

[24]  Andrew Walenstein,et al.  COGNITIVE SUPPORT IN SOFTWARE ENGINEERING TOOLS: A DISTRIBUTED COGNITION FRAMEWORK , 2002 .

[25]  M. Petró‐Turza,et al.  The International Organization for Standardization. , 2003 .

[26]  Stuart K. Card,et al.  The effects of information scent on visual search in the hyperbolic tree browser , 2003, TCHI.

[27]  Alfonso Valencia,et al.  Automatic annotation of protein function based on family identification , 2003, Proteins.

[28]  Carole A. Goble,et al.  Semantic Similarity Measures as Tools for Exploring the Gene Ontology , 2002, Pacific Symposium on Biocomputing.

[29]  Ori Sasson,et al.  ProtoNet: hierarchical classification of the protein space , 2003, Nucleic Acids Res..

[30]  Carole A. Goble,et al.  Investigating Semantic Similarity Measures Across the Gene Ontology: The Relationship Between Sequence and Annotation , 2003, Bioinform..

[31]  Olivier Bodenreider,et al.  The Unified Medical Language System (UMLS): integrating biomedical terminology , 2004, Nucleic Acids Res..

[32]  M. Ashburner,et al.  An ontology for cell types , 2005, Genome Biology.

[33]  J. Blake.  Bio-ontologies—fast and furious , 2004, Nature Biotechnology.

[34]  V. Svátek.  Design Patterns for Semantic Web Ontologies : Motivation and Discussion , 2004 .

[35]  Hongfang Liu,et al.  Pacific Symposium on Biocomputing 9:238-249(2004) BIOLOGICAL NOMENCLATURES: A SOURCE OF LEXICAL KNOWLEDGE AND AMBIGUITY , 2022 .

[36]  B Marshall,et al.  Gene Ontology Consortium: The Gene Ontology (GO) database and informatics resource , 2004, Nucleic Acids Res..

[37]  Pierre Brézellec,et al.  Cluster-C, an algorithm for the large-scale clustering of protein sequences based on the extraction of maximal cliques , 2004, Comput. Biol. Chem..

[38]  José L. V. Mejino,et al.  Problems and Solutions with Integrating Terminologies into Evolving Knowledge Bases , 2004, MedInfo.

[39]  Emily Dimmer,et al.  The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology , 2004, Nucleic Acids Res..

[40]  A. Rector,et al.  Relations in biomedical ontologies , 2005, Genome Biology.

[41]  R. Durbin,et al.  The Sequence Ontology: a tool for the unification of genome annotations , 2005, Genome Biology.

[42]  Anand Kumar,et al.  Text mining and ontologies in biomedicine: Making sense of raw text , 2005, Briefings Bioinform..

[43]  Qicheng Ma,et al.  Clustering protein sequences with a novel metric transformed from sequence similarity scores and sequence alignments with neural networks , 2005, BMC Bioinformatics.

[44]  Emily Dimmer,et al.  An evaluation of GO annotation retrieval for BioCreAtIvE and GOA , 2005, BMC Bioinformatics.

[45]  John Moult,et al.  Protein family clustering for structural genomics. , 2005, Journal of molecular biology.

[46]  David I. Ellis,et al.  Metabolomics: Current analytical platforms and methodologies , 2005 .

[47]  Victoria Petri,et al.  Using Multiple Ontologies to Integrate Complex Biological Data , 2005, Comparative and functional genomics.

[48]  Dan Tidhar,et al.  Retrieving Hierarchical Text Structure from Typeset Scientific Articles – a Prerequisite for E-Science Text Mining , 2005 .

[49]  Mário J. Silva,et al.  Semantic similarity over the gene ontology: family correlation and selecting disjunctive ancestors , 2005, CIKM '05.

[50]  Angel Rubio,et al.  Correlation between Gene Expression and GO Semantic Similarity , 2005, TCBB.

[51]  Robert Petryszak,et al.  The predictive power of the CluSTr database , 2005, Bioinform..

[52]  Kuo-Chen Chou,et al.  Using supervised fuzzy clustering to predict protein structural classes. , 2005, Biochemical and biophysical research communications.

[53]  Aldo Gangemi,et al.  Ontology Design Patterns for Semantic Web Content , 2005, SEMWEB.

[54]  Rolf Apweiler,et al.  The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries , 2006, BMC Bioinformatics.

[55]  Henning Hermjakob,et al.  The HUPO Proteomics Standards Initiative – Overcoming the Fragmentation of Proteomics Data , 2006, Proteomics.

[56]  Olivier Bodenreider,et al.  Law and order: Assessing and enforcing compliance with ontological modeling principles in the Foundational Model of Anatomy , 2006, Comput. Biol. Medicine.

[57]  Mathew W. Wright,et al.  Human and orthologous gene nomenclature. , 2006, Gene.

[58]  Barry Smith,et al.  From concepts to clinical reality: An essay on the benchmarking of biomedical terminologies , 2006, J. Biomed. Informatics.

[59]  Cathy H. Wu,et al.  The Universal Protein Resource (UniProt): an expanding universe of protein information , 2005, Nucleic Acids Res..

[60]  Olivier Bodenreider,et al.  Bio-ontologies: current trends and future directions , 2006, Briefings Bioinform..

[61]  Robert Stevens,et al.  The Manchester OWL Syntax , 2006, OWLED.

[62]  Simone Teufel,et al.  Flexible Interfaces in the Application of Language Technology to an eScience Corpus , 2006 .

[63]  J J Cimino,et al.  The Practical Impact of Ontologies on Biomedical Informatics , 2006, Yearbook of Medical Informatics.

[64]  Werner Ceusters,et al.  Towards a Reference Terminology for Ontology Research and Development in the Biomedical Domain , 2006, KR-MED.

[65]  Kevin D. Reilly,et al.  SEQOPTICS: a protein sequence clustering system , 2006, BMC Bioinformatics.

[66]  John C. Lindon,et al.  Metabolomics Standards Workshop and the development of international standards for reporting metabolomics experimental results , 2006, Briefings Bioinform..

[67]  Kei-Hoi Cheung,et al.  Semantic Web: Revolutionizing Knowledge Discovery in the Life Sciences , 2006 .

[68]  Alexander C. Yu,et al.  Methods in biomedical ontology , 2006, J. Biomed. Informatics.

[69]  Christopher G Chute,et al.  National Center for Biomedical Ontology: advancing biomedicine through structured organization of scientific knowledge. , 2006, Omics : a journal of integrative biology.

[70]  Lothar Reichel,et al.  The relationship between protein sequences and their gene ontology functions , 2006, First International Multi-Symposiums on Computer and Computational Sciences (IMSCCS'06).

[71]  Susanna-Assunta Sansone,et al.  A Special Issue on Data Standards , 2006 .

[72]  Chris F. Taylor,et al.  The work of the Human Proteome Organisation's Proteomics Standards Initiative (HUPO PSI). , 2006, Omics : a journal of integrative biology.

[73]  Stefan Wetzel,et al.  Protein structure similarity clustering: dynamic treatment of PDB structures facilitates clustering. , 2006, Angewandte Chemie.

[74]  Ross D King,et al.  An ontology of scientific experiments , 2006, Journal of The Royal Society Interface.

[75]  Vladimir Shulaev,et al.  Metabolomics technology and bioinformatics , 2006, Briefings Bioinform..

[76]  Thomas Lengauer,et al.  A new measure for functional similarity of gene products based on Gene Ontology , 2006, BMC Bioinformatics.

[77]  P. Hiberty,et al.  The physical origin of large covalent-ionic resonance energies in some two-electron bonds. , 2007, Faraday discussions.

[78]  L. Soldatova,et al.  Ontology Engineering for Biological Applications , 2007 .

[79]  Carole A. Goble,et al.  Taverna/myGrid: Aligning a Workflow System with the Life Sciences Community , 2007, Workflows for e-Science, Scientific Workflows for Grids.

[80]  Peter Pirolli,et al.  Information Foraging , 2009, Encyclopedia of Database Systems.

[81]  David James Sherman,et al.  Family relationships: should consensus reign? - consensus clustering for protein families , 2007, Bioinform..