Robert Hoehndorf

Robert Hoehndorf

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DeepGOPlus: improved protein function prediction from sequence.

Bioinformatics 2020 Jan;36(2):422-429

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, Thuwal 23955, Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btz595DOI Listing
January 2020

Combining lexical and context features for automatic ontology extension.

J Biomed Semantics 2020 Jan 13;11(1). Epub 2020 Jan 13.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s13326-019-0218-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6958746PMC
January 2020

Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.

Bioinformatics 2019 Dec 10. Epub 2019 Dec 10.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Computer, Electrical & Mathematical Sciences and Engineering (CEMSE) Division, Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btz920DOI Listing
December 2019

The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.

Authors:
Naihui Zhou Yuxiang Jiang Timothy R Bergquist Alexandra J Lee Balint Z Kacsoh Alex W Crocker Kimberley A Lewis George Georghiou Huy N Nguyen Md Nafiz Hamid Larry Davis Tunca Dogan Volkan Atalay Ahmet S Rifaioglu Alperen Dalkıran Rengul Cetin Atalay Chengxin Zhang Rebecca L Hurto Peter L Freddolino Yang Zhang Prajwal Bhat Fran Supek José M Fernández Branislava Gemovic Vladimir R Perovic Radoslav S Davidović Neven Sumonja Nevena Veljkovic Ehsaneddin Asgari Mohammad R K Mofrad Giuseppe Profiti Castrense Savojardo Pier Luigi Martelli Rita Casadio Florian Boecker Heiko Schoof Indika Kahanda Natalie Thurlby Alice C McHardy Alexandre Renaux Rabie Saidi Julian Gough Alex A Freitas Magdalena Antczak Fabio Fabris Mark N Wass Jie Hou Jianlin Cheng Zheng Wang Alfonso E Romero Alberto Paccanaro Haixuan Yang Tatyana Goldberg Chenguang Zhao Liisa Holm Petri Törönen Alan J Medlar Elaine Zosa Itamar Borukhov Ilya Novikov Angela Wilkins Olivier Lichtarge Po-Han Chi Wei-Cheng Tseng Michal Linial Peter W Rose Christophe Dessimoz Vedrana Vidulin Saso Dzeroski Ian Sillitoe Sayoni Das Jonathan Gill Lees David T Jones Cen Wan Domenico Cozzetto Rui Fa Mateo Torres Alex Warwick Vesztrocy Jose Manuel Rodriguez Michael L Tress Marco Frasca Marco Notaro Giuliano Grossi Alessandro Petrini Matteo Re Giorgio Valentini Marco Mesiti Daniel B Roche Jonas Reeb David W Ritchie Sabeur Aridhi Seyed Ziaeddin Alborzi Marie-Dominique Devignes Da Chen Emily Koo Richard Bonneau Vladimir Gligorijević Meet Barot Hai Fang Stefano Toppo Enrico Lavezzo Marco Falda Michele Berselli Silvio C E Tosatto Marco Carraro Damiano Piovesan Hafeez Ur Rehman Qizhong Mao Shanshan Zhang Slobodan Vucetic Gage S Black Dane Jo Erica Suh Jonathan B Dayton Dallas J Larsen Ashton R Omdahl Liam J McGuffin Danielle A Brackenridge Patricia C Babbitt Jeffrey M Yunes Paolo Fontana Feng Zhang Shanfeng Zhu Ronghui You Zihan Zhang Suyang Dai Shuwei Yao Weidong Tian Renzhi Cao Caleb Chandler Miguel Amezola Devon Johnson Jia-Ming Chang Wen-Hung Liao Yi-Wei Liu Stefano Pascarelli Yotam Frank Robert Hoehndorf Maxat Kulmanov Imane Boudellioua Gianfranco Politano Stefano Di Carlo Alfredo Benso Kai Hakala Filip Ginter Farrokh Mehryary Suwisa Kaewphan Jari Björne Hans Moen Martti E E Tolvanen Tapio Salakoski Daisuke Kihara Aashish Jain Tomislav Šmuc Adrian Altenhoff Asa Ben-Hur Burkhard Rost Steven E Brenner Christine A Orengo Constance J Jeffery Giovanni Bosco Deborah A Hogan Maria J Martin Claire O'Donovan Sean D Mooney Casey S Greene Predrag Radivojac Iddo Friedberg

Genome Biol 2019 11 19;20(1):244. Epub 2019 Nov 19.

Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA, USA.

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http://dx.doi.org/10.1186/s13059-019-1835-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6864930PMC
November 2019

Ontology-based prediction of cancer driver genes.

Sci Rep 2019 Nov 22;9(1):17405. Epub 2019 Nov 22.

Computer, Electrical and Mathematical Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.

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http://dx.doi.org/10.1038/s41598-019-53454-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6874647PMC
November 2019

Hyaline Arteriolosclerosis in 30 Strains of Aged Inbred Mice.

Vet Pathol 2019 09 6;56(5):799-806. Epub 2019 May 6.

3 The Jackson Laboratory, Bar Harbor, ME, USA.

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http://dx.doi.org/10.1177/0300985819844822DOI Listing
September 2019

Ontology based mining of pathogen-disease associations from literature.

J Biomed Semantics 2019 09 18;10(1):15. Epub 2019 Sep 18.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s13326-019-0208-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6751637PMC
September 2019

OPA2Vec: combining formal and informal content of biomedical ontologies to improve similarity-based prediction.

Bioinformatics 2019 Jun;35(12):2133-2140

Computer, Electrical & Mathematical Sciences and Engineering (CEMSE) Division, Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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https://academic.oup.com/bioinformatics/advance-article/doi/
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http://dx.doi.org/10.1093/bioinformatics/bty933DOI Listing
June 2019

PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research.

Sci Data 2019 Jun 3;6(1):79. Epub 2019 Jun 3.

Computer, Electrical and Mathematical Sciences & Engineering with Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955, Saudi Arabia.

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http://dx.doi.org/10.1038/s41597-019-0090-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6546783PMC
June 2019

Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies.

Sci Rep 2019 Mar 11;9(1):4025. Epub 2019 Mar 11.

King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, 23955-6900, Saudi Arabia.

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http://www.nature.com/articles/s41598-019-40368-1
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http://dx.doi.org/10.1038/s41598-019-40368-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6411989PMC
March 2019

DeepPVP: phenotype-based prioritization of causative variants using deep learning.

BMC Bioinformatics 2019 Feb 6;20(1):65. Epub 2019 Feb 6.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12859-019-2633-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6364462PMC
February 2019

Ontology based text mining of gene-phenotype associations: application to candidate gene prediction.

Database (Oxford) 2019 01;2019

Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1093/database/baz019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6391585PMC
January 2019

A Review of Current Standards and the Evolution of Histopathology Nomenclature for Laboratory Animals.

ILAR J 2018 12;59(1):29-39

Susan A. Elmore, MS, DVM, DCVP, DABT, FIATP, is NTP Pathologist and Staff Scientist at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Robert D. Cardiff, MD, PhD, is Distinguished Professor of Pathology, Emeritus at the UCD Center for Comparative Medicine, University of California, and the Department of Pathology and Laboratory Medicine, School of Medicine, Davis, in Davis, California. Mark F. Cesta, DVM, PhD, DACVP, is NTP Pathologist and Staff Scientist, leading the effort for establishment of the online NTP Nonneoplastic Lesion Atlas at the National Toxicology Program, National Institute of Environmental Health Sciences in the Research Triangle Park, North Carolina. Georgios V. Gkoutos, PhD, DIC, is Professor of Clinical Bioinformatics at College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences Centre for Computational Biology, University of Birmingham in Birmingham, United Kingdom. Robert Hoehndorf, PhD, is Assistant Professor in Computer Science at the Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology in Thuwal, Kingdom of Saudi Arabia. Charlotte M. Keenan, VMD, DACVP, is a principle consultant at C.M. ToxPath Consulting in Doylestown, Pennsylvania, USA and leads the international STP effort for the publication of the harmonization of nomenclature and diagnostic criteria (INHAND) in toxicologic pathology. Colin McKerlie, DVM, DVSc, MRCVS, is a senior associate scientist in the Translational Medicine Research Program at The Hospital for Sick Children and a Professor in the Department of Pathobiology & Laboratory Medicine in the Faculty of Medicine at the University of Toronto, Toronto, Ontario, Canada. Paul N. Schofield, MA DPhil, is the University Reader in Biomedical Informatics at the Department of Physiology, Development & Neuroscience, University of Cambridge in Cambridge, United Kingdom and is also an adjunct professor at The Jackson Laboratory in Bar Harbor, Maine. John P. Sundberg, DVM, PhD, DACVP, is a professor at The Jackson Laboratory in Bar Harbor, Maine. Jerrold M. Ward, DVM, PhD, DACVP, FIATP, is a special volunteer at the National Cancer Institute, National Institutes of Health in Bethesda, MD and is also Adjunct Faculty at The Jackson Laboratory in Bar Harbor, Maine.

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http://dx.doi.org/10.1093/ilar/ily005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927895PMC
December 2018

OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants.

Sci Rep 2018 10 2;8(1):14681. Epub 2018 Oct 2.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

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http://www.nature.com/articles/s41598-018-32876-3
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http://dx.doi.org/10.1038/s41598-018-32876-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6168481PMC
October 2018

The anatomy of phenotype ontologies: principles, properties and applications.

Brief Bioinform 2018 09;19(5):1008-1021

Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, King Abdullah University of Science and Technology, Thuwal.

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http://dx.doi.org/10.1093/bib/bbx035DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6169674PMC
September 2018

Ontology-based validation and identification of regulatory phenotypes.

Bioinformatics 2018 09;34(17):i857-i865

Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Centre, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

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https://academic.oup.com/bioinformatics/article/34/17/i857/5
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http://dx.doi.org/10.1093/bioinformatics/bty605DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129279PMC
September 2018

Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes.

Bioinformatics 2018 09;34(17):i901-i907

Computer, Electrical and Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.

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https://academic.oup.com/bioinformatics/article/34/17/i901/5
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http://dx.doi.org/10.1093/bioinformatics/bty559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6129260PMC
September 2018

Onto2Vec: joint vector-based representation of biological entities and their ontology-based annotations.

Bioinformatics 2018 07;34(13):i52-i60

Computer, Electrical and Mathematical Sciences & Engineering Division (CEMSE), Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/bty259DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6022543PMC
July 2018

In silico exploration of Red Sea Bacillus genomes for natural product biosynthetic gene clusters.

BMC Genomics 2018 May 22;19(1):382. Epub 2018 May 22.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12864-018-4796-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964695PMC
May 2018

DeepGO: predicting protein functions from sequence and interactions using a deep ontology-aware classifier.

Bioinformatics 2018 02;34(4):660-668

Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.

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https://academic.oup.com/bioinformatics/article/34/4/660/426
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http://dx.doi.org/10.1093/bioinformatics/btx624DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860606PMC
February 2018

Inferring ontology graph structures using OWL reasoning.

BMC Bioinformatics 2018 01 5;19(1). Epub 2018 Jan 5.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12859-017-1999-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5756413PMC
January 2018

Datamining with Ontologies.

Methods Mol Biol 2016 ;1415:385-97

Department of Physiology, Development & Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.

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http://dx.doi.org/10.1007/978-1-4939-3572-7_19DOI Listing
December 2017

Integrating phenotype ontologies with PhenomeNET.

J Biomed Semantics 2017 Dec 19;8(1):58. Epub 2017 Dec 19.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s13326-017-0167-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5735523PMC
December 2017

Usage of cell nomenclature in biomedical literature.

BMC Bioinformatics 2017 12 21;18(Suppl 17):561. Epub 2017 Dec 21.

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s12859-017-1978-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5763300PMC
December 2017

Neuro-symbolic representation learning on biological knowledge graphs.

Bioinformatics 2017 Sep;33(17):2723-2730

Computer, Electrical and Mathematical Sciences & Engineering Division, Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1093/bioinformatics/btx275DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860058PMC
September 2017

Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining.

PLoS One 2016 8;11(7):e0158896. Epub 2016 Jul 8.

Softberry Inc., 116 Radio Circle, Suite 400, Mount Kisco, NY 10549, United States of America.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0158896PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4938425PMC
July 2017

DES-TOMATO: A Knowledge Exploration System Focused On Tomato Species.

Sci Rep 2017 07 20;7(1):5968. Epub 2017 Jul 20.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1038/s41598-017-05448-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5519719PMC
July 2017

Semantic prioritization of novel causative genomic variants.

PLoS Comput Biol 2017 04 17;13(4):e1005500. Epub 2017 Apr 17.

King Abdullah University of Science and Technology, Computer, Electrical & Mathematical Sciences and Engineering Division, Computational Bioscience Research Center, Thuwal, Saudi Arabia.

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http://dx.doi.org/10.1371/journal.pcbi.1005500DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5411092PMC
April 2017

Evaluating the effect of annotation size on measures of semantic similarity.

J Biomed Semantics 2017 Feb 13;8(1). Epub 2017 Feb 13.

Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s13326-017-0119-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5307803PMC
February 2017

In silico screening for candidate chassis strains of free fatty acid-producing cyanobacteria.

BMC Genomics 2017 01 5;18(1):33. Epub 2017 Jan 5.

Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Kingdom of Saudi Arabia.

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http://dx.doi.org/10.1186/s12864-016-3389-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5217662PMC
January 2017

Using AberOWL for fast and scalable reasoning over BioPortal ontologies.

J Biomed Semantics 2016 08 8;7(1):49. Epub 2016 Aug 8.

Computational Bioscience Research Center, Computer, Electrical and Mathematical Sciences & Engineering Division, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia.

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http://dx.doi.org/10.1186/s13326-016-0090-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4976511PMC
August 2016

DermO; an ontology for the description of dermatologic disease.

J Biomed Semantics 2016 Jun 13;7:38. Epub 2016 Jun 13.

Dept. of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge, CB2 3EG, UK.

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http://dx.doi.org/10.1186/s13326-016-0085-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4907256PMC
June 2016

DESM: portal for microbial knowledge exploration systems.

Nucleic Acids Res 2016 Jan 5;44(D1):D624-33. Epub 2015 Nov 5.

King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal 23955-6900, Kingdom of Saudi Arabia King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal 23955-6900, Kingdom of Saudi Arabia

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http://dx.doi.org/10.1093/nar/gkv1147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702830PMC
January 2016

Best behaviour? Ontologies and the formal description of animal behaviour.

Mamm Genome 2015 Oct 28;26(9-10):540-7. Epub 2015 Jul 28.

Department of Physiology Development and Neuroscience, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1007/s00335-015-9590-yDOI Listing
October 2015

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

Authors:
Martin Hrabě de Angelis George Nicholson Mohammed Selloum Jacqui White Hugh Morgan Ramiro Ramirez-Solis Tania Sorg Sara Wells Helmut Fuchs Martin Fray David J Adams Niels C Adams Thure Adler Antonio Aguilar-Pimentel Dalila Ali-Hadji Gregory Amann Philippe André Sarah Atkins Aurelie Auburtin Abdel Ayadi Julien Becker Lore Becker Elodie Bedu Raffi Bekeredjian Marie-Christine Birling Andrew Blake Joanna Bottomley Mike Bowl Véronique Brault Dirk H Busch James N Bussell Julia Calzada-Wack Heather Cater Marie-France Champy Philippe Charles Claire Chevalier Francesco Chiani Gemma F Codner Roy Combe Roger Cox Emilie Dalloneau André Dierich Armida Di Fenza Brendan Doe Arnaud Duchon Oliver Eickelberg Chris T Esapa Lahcen El Fertak Tanja Feigel Irina Emelyanova Jeanne Estabel Jack Favor Ann Flenniken Alessia Gambadoro Lilian Garrett Hilary Gates Anna-Karin Gerdin George Gkoutos Simon Greenaway Lisa Glasl Patrice Goetz Isabelle Goncalves Da Cruz Alexander Götz Jochen Graw Alain Guimond Wolfgang Hans Geoff Hicks Sabine M Hölter Heinz Höfler John M Hancock Robert Hoehndorf Tertius Hough Richard Houghton Anja Hurt Boris Ivandic Hughes Jacobs Sylvie Jacquot Nora Jones Natasha A Karp Hugo A Katus Sharon Kitchen Tanja Klein-Rodewald Martin Klingenspor Thomas Klopstock Valerie Lalanne Sophie Leblanc Christoph Lengger Elise le Marchand Tonia Ludwig Aline Lux Colin McKerlie Holger Maier Jean-Louis Mandel Susan Marschall Manuel Mark David G Melvin Hamid Meziane Kateryna Micklich Christophe Mittelhauser Laurent Monassier David Moulaert Stéphanie Muller Beatrix Naton Frauke Neff Patrick M Nolan Lauryl Mj Nutter Markus Ollert Guillaume Pavlovic Natalia S Pellegata Emilie Peter Benoit Petit-Demoulière Amanda Pickard Christine Podrini Paul Potter Laurent Pouilly Oliver Puk David Richardson Stephane Rousseau Leticia Quintanilla-Fend Mohamed M Quwailid Ildiko Racz Birgit Rathkolb Fabrice Riet Janet Rossant Michel Roux Jan Rozman Ed Ryder Jennifer Salisbury Luis Santos Karl-Heinz Schäble Evelyn Schiller Anja Schrewe Holger Schulz Ralf Steinkamp Michelle Simon Michelle Stewart Claudia Stöger Tobias Stöger Minxuan Sun David Sunter Lydia Teboul Isabelle Tilly Glauco P Tocchini-Valentini Monica Tost Irina Treise Laurent Vasseur Emilie Velot Daniela Vogt-Weisenhorn Christelle Wagner Alison Walling Bruno Weber Olivia Wendling Henrik Westerberg Monja Willershäuser Eckhard Wolf Anne Wolter Joe Wood Wolfgang Wurst Ali Önder Yildirim Ramona Zeh Andreas Zimmer Annemarie Zimprich Chris Holmes Karen P Steel Yann Herault Valérie Gailus-Durner Ann-Marie Mallon Steve Dm Brown

Nat Genet 2015 Sep 27;47(9):969-978. Epub 2015 Jul 27.

MRC Harwell, Medical Research Council, Harwell, UK.

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http://dx.doi.org/10.1038/ng.3360DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4564951PMC
September 2015

Analysis of the human diseasome using phenotype similarity between common, genetic, and infectious diseases.

Sci Rep 2015 Jun 8;5:10888. Epub 2015 Jun 8.

Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB, UK.

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http://dx.doi.org/10.1038/srep10888DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4458913PMC
June 2015

GFVO: the Genomic Feature and Variation Ontology.

PeerJ 2015 5;3:e933. Epub 2015 May 5.

Stanford Center for Biomedical Informatics Research, School of Medicine, Stanford University , Stanford, CA , USA.

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http://dx.doi.org/10.7717/peerj.933DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435477PMC
May 2015

Similarity-based search of model organism, disease and drug effect phenotypes.

J Biomed Semantics 2015 19;6. Epub 2015 Feb 19.

Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB UK.

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http://dx.doi.org/10.1186/s13326-015-0001-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4355138PMC
March 2015

Ranking adverse drug reactions with crowdsourcing.

J Med Internet Res 2015 Mar 23;17(3):e80. Epub 2015 Mar 23.

Department of Genetics, Stanford University, Stanford, CA, United States.

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http://dx.doi.org/10.2196/jmir.3962DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4387295PMC
March 2015

Aber-OWL: a framework for ontology-based data access in biology.

BMC Bioinformatics 2015 Jan 28;16:26. Epub 2015 Jan 28.

Department of Computer Science, Aberystwyth University, Llandinam Building, Aberystwyth, SY23 3DB, UK.

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http://dx.doi.org/10.1186/s12859-015-0456-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384359PMC
January 2015

Evaluation and cross-comparison of lexical entities of biological interest (LexEBI).

PLoS One 2013 4;8(10):e75185. Epub 2013 Oct 4.

Department of Computational Linguistics, University of Zürich, Zürich, Switzerland ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0075185PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3790750PMC
July 2014

Thematic series on biomedical ontologies in JBMS: challenges and new directions.

J Biomed Semantics 2014 6;5:15. Epub 2014 Mar 6.

Department of Computational Linguistics, University of Zürich, Binzmühlestrasse 14, 8050 Zürich, Switzerland ; European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/2041-1480-5-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4006457PMC
June 2014

Mouse model phenotypes provide information about human drug targets.

Bioinformatics 2014 Mar 24;30(5):719-25. Epub 2013 Oct 24.

Department of Computer Science, University of Aberystwyth, Old College, King Street, Aberystwyth SY23 2AX, Department of Biology, Institute of Biochemistry and School of Computer Science, Carleton University, 1125 Colonel By Drive, Ottawa, Ontario K1S 5B6, Canada and Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.

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http://dx.doi.org/10.1093/bioinformatics/btt613DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933875PMC
March 2014

Analyzing gene expression data in mice with the Neuro Behavior Ontology.

Mamm Genome 2014 Feb 1;25(1-2):32-40. Epub 2013 Nov 1.

Department of Computer Science, University of Aberystwyth, Old College, King Street, Aberystwyth, SY23 2AX, UK,

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http://dx.doi.org/10.1007/s00335-013-9481-zDOI Listing
February 2014

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.

J Biomed Semantics 2014 Feb 5;5(1). Epub 2014 Feb 5.

Database Center for Life Science, Research Organization of Information and Systems, 2-11-16, Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3978116PMC
February 2014

Linking PharmGKB to phenotype studies and animal models of disease for drug repurposing.

Pac Symp Biocomput 2012 :388-99

Department of Genetics, University of Cambridge, Cambridge, UK.

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December 2013

Evaluation of research in biomedical ontologies.

Brief Bioinform 2013 Nov 8;14(6):696-712. Epub 2012 Sep 8.

Department of Computer Science, Aberystwyth University, Aberystwyth, Ceredigion, SY23 3DB, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3888109PMC
November 2013

Systematic analysis of experimental phenotype data reveals gene functions.

PLoS One 2013 16;8(4):e60847. Epub 2013 Apr 16.

Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3628905PMC
November 2013

Evaluating gold standard corpora against gene/protein tagging solutions and lexical resources.

J Biomed Semantics 2013 Oct 11;4(1):28. Epub 2013 Oct 11.

Institute of Computational Linguistics, University of Zürich, CH-8050 Zürich, Switzerland.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4021975PMC
October 2013

The neurobehavior ontology: an ontology for annotation and integration of behavior and behavioral phenotypes.

Int Rev Neurobiol 2012 ;103:69-87

Department of Genetics, University of Cambridge, Cambridge, UK.

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http://dx.doi.org/10.1016/B978-0-12-388408-4.00004-6DOI Listing
May 2013

The Units Ontology: a tool for integrating units of measurement in science.

Database (Oxford) 2012 10;2012:bas033. Epub 2012 Oct 10.

Department of Computer Science, University of Aberystwyth, Old College, King Street, SY23 2AX.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3468815PMC
April 2013

Representing physiological processes and their participants with PhysioMaps.

J Biomed Semantics 2013 Apr 15;4 Suppl 1:S2. Epub 2013 Apr 15.

Biomedical & Health Informatics, Univ, of Washington, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3632997PMC
April 2013

An integrative, translational approach to understanding rare and orphan genetically based diseases.

Interface Focus 2013 Apr;3(2):20120055

Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK ; Department of Computer Science, University of Aberystwyth, Old College, King Street, Aberystwyth SY23 2AX, UK.

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http://dx.doi.org/10.1098/rsfs.2012.0055DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3638468PMC
April 2013

Text-mining solutions for biomedical research: enabling integrative biology.

Nat Rev Genet 2012 Dec 14;13(12):829-39. Epub 2012 Nov 14.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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December 2012

Computational tools for comparative phenomics: the role and promise of ontologies.

Mamm Genome 2012 Oct 20;23(9-10):669-79. Epub 2012 Jul 20.

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488439PMC
October 2012

Quantitative comparison of mapping methods between Human and Mammalian Phenotype Ontology.

J Biomed Semantics 2012 Sep 21;3 Suppl 2:S1. Epub 2012 Sep 21.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, CB10 1SD, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448526PMC
September 2012

Towards improving phenotype representation in OWL.

J Biomed Semantics 2012 Sep 21;3 Suppl 2:S5. Epub 2012 Sep 21.

Department of Computer Science, University of Leipzig, 04103 Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448528PMC
September 2012

Ontology-based cross-species integration and analysis of Saccharomyces cerevisiae phenotypes.

J Biomed Semantics 2012 Sep 21;3 Suppl 2:S6. Epub 2012 Sep 21.

Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3448529PMC
September 2012

Identifying aberrant pathways through integrated analysis of knowledge in pharmacogenomics.

Bioinformatics 2012 Aug 17;28(16):2169-75. Epub 2012 Jun 17.

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3493115PMC
August 2012

Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.

Bioinformatics 2012 Jul 26;28(13):1783-9. Epub 2012 Apr 26.

Department of Genetics, University of Cambridge, Downing Street, Cambridge, Cambridge CB2 3EH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3381966PMC
July 2012

Mouse genetic and phenotypic resources for human genetics.

Hum Mutat 2012 May;33(5):826-36

Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, United Kingdom.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3473354PMC
May 2012

Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.

J Biomed Semantics 2012 Apr 24;3 Suppl 1:S3. Epub 2012 Apr 24.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SD, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3337258PMC
April 2012

An infrastructure for ontology-based information systems in biomedicine: RICORDO case study.

Bioinformatics 2012 Feb 29;28(3):448-50. Epub 2011 Nov 29.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

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February 2012

PIDO: the primary immunodeficiency disease ontology.

Bioinformatics 2011 Nov 22;27(22):3193-9. Epub 2011 Sep 22.

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK.

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http://dx.doi.org/10.1093/bioinformatics/btr531DOI Listing
November 2011

PhenomeNET: a whole-phenome approach to disease gene discovery.

Nucleic Acids Res 2011 Oct 6;39(18):e119. Epub 2011 Jul 6.

Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EG, UK.

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http://dx.doi.org/10.1093/nar/gkr538DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3185433PMC
October 2011

Integrating systems biology models and biomedical ontologies.

BMC Syst Biol 2011 Aug 11;5:124. Epub 2011 Aug 11.

Department of Genetics, University of Cambridge, Downing Street, Cambridge, CB2 3EH, UK.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3170340PMC
August 2011

The RICORDO approach to semantic interoperability for biomedical data and models: strategy, standards and solutions.

BMC Res Notes 2011 Aug 30;4:313. Epub 2011 Aug 30.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1756-0500-4-313DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192696PMC
August 2011

OBML - Ontologies in Biomedicine and Life Sciences.

J Biomed Semantics 2011 Aug 9;2 Suppl 4:I1. Epub 2011 Aug 9.

Institute for Medical Informatics, Statistics and Epidemiology (IMISE), University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3194167PMC
August 2011

Interoperability between phenotype and anatomy ontologies.

Bioinformatics 2010 Dec 22;26(24):3112-8. Epub 2010 Oct 22.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.

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http://dx.doi.org/10.1093/bioinformatics/btq578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2995119PMC
December 2010

Relations as patterns: bridging the gap between OBO and OWL.

BMC Bioinformatics 2010 Aug 31;11:441. Epub 2010 Aug 31.

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1186/1471-2105-11-441DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2942855PMC
August 2010

Statistical tests for associations between two directed acyclic graphs.

PLoS One 2010 Jun 16;5(6):e10996. Epub 2010 Jun 16.

Research Group Ontologies in Medicine, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886832PMC
June 2010

Applying the functional abnormality ontology pattern to anatomical functions.

J Biomed Semantics 2010 Mar 31;1(1). Epub 2010 Mar 31.

Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1186/2041-1480-1-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2895731PMC
March 2010

The ontology of biological sequences.

BMC Bioinformatics 2009 Nov 18;10:377. Epub 2009 Nov 18.

Research Group Ontologies in Medicine, Institute for Medical Informatics, Statistics and Epidemiology, University of Leipzig, Haertelstrasse 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2105-10-377DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2785798PMC
November 2009

BOWiki: an ontology-based wiki for annotation of data and integration of knowledge in biology.

BMC Bioinformatics 2009 May 6;10 Suppl 5:S5. Epub 2009 May 6.

Department of Computer Science, Faculty of Mathematics and Computer Science, University of Leipzig, Johannisgasse 26, 04103 Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2679405PMC
May 2009

Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies.

BMC Bioinformatics 2007 Oct 9;8:377. Epub 2007 Oct 9.

Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2180186PMC
October 2007

A top-level ontology of functions and its application in the Open Biomedical Ontologies.

Bioinformatics 2006 Jul;22(14):e66-73

Department of Computer Science, Faculty of Mathematics and Computer Science, University of Leipzig, Augustusplatz 10-11, 04109 Leipzig.

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July 2006