Alan Ruttenberg

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Barry SmithProfessor of Philosophy, Biomedical Informatics, and Computer Science, University at BuffaloVerified email at buffalo.edu
Christopher J MungallLawrence Berkeley National LaboratoryVerified email at lbl.gov
Mélanie CourtotOntario Institute for Cancer Research (OICR)Verified email at oicr.on.ca
Ryan BrinkmanBritish Columbia Cancer AgencyVerified email at bccrc.ca
Karen EilbeckProfessor, Biomedical Informatics, University of UtahVerified email at genetics.utah.edu
Darren A. NataleProtein Information Resource, Georgetown University Medical CenterVerified email at georgetown.edu
Yongqun HeProfessor, University of Michigan Medical SchoolVerified email at med.umich.edu
Philippe Rocca-SerraUniversity of OxfordVerified email at oerc.ox.ac.uk
Alexander D. DiehlAssociate Professor of Biomedical Informatics, University at BuffaloVerified email at buffalo.edu
Susanna-Assunta SansoneUniversity of Oxford, Academic Lead for Research Practice; Professor of Data ReadinessVerified email at oerc.ox.ac.uk
Werner CeustersUniversity at BuffaloVerified email at buffalo.edu
Judith BlakeProfessor of Mammalian GeneticsVerified email at jax.org
Jie ZhengUniversity of MichiganVerified email at med.umich.edu
Bijan ParsiaProfessor of Computer Science, University of ManchesterVerified email at manchester.ac.uk
Richard H. ScheuermannJ. Craig Venter InstituteVerified email at jcvi.org
James MaloneCTO, BenevolentAIVerified email at benevolent.ai
Suzanna LewisLawrence Berkeley National LaboratoryVerified email at lbl.gov
Ian HorrocksProfessor of Computer Science, University of OxfordVerified email at cs.ox.ac.uk
Jonathan A ReesRonin InstituteVerified email at mumble.net
Bjoern PetersProfessor at La Jolla Institute for ImmunologyVerified email at lji.org

Alan Ruttenberg

Senior Research Associate, Department of Philosophy, University at Buffalo

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applied ontology biomedical knowledge sharing open access computational biology


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The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration B Smith, M Ashburner, C Rosse, J Bard, W Bug, W Ceusters, LJ Goldberg, ... Nature biotechnology 25 (11), 1251-1255, 2007	3075	2007
OWL 2 web ontology language: Structural specification and functional-style syntax B Motik, PF Patel-Schneider, B Parsia, C Bock, A Fokoue, P Haase, ... W3C Recommendation 27, 2009	1063	2009
The ontology for biomedical investigations A Bandrowski, R Brinkman, M Brochhausen, MH Brush, B Bug, ... PloS one 11 (4), e0154556, 2016	397	2016
Advancing translational research with the Semantic Web A Ruttenberg, T Clark, W Bug, M Samwald, O Bodenreider, H Chen, ... BMC bioinformatics 8, 1-16, 2007	349	2007
Modeling biomedical experimental processes with OBI RR Brinkman, M Courtot, D Derom, JM Fostel, Y He, P Lord, J Malone, ... Journal of biomedical semantics 1, 1-11, 2010	327	2010
The Cell Ontology 2016: enhanced content, modularization, and ontology interoperability AD Diehl, TF Meehan, YM Bradford, MH Brush, WM Dahdul, DS Dougall, ... Journal of biomedical semantics 7, 1-10, 2016	265	2016
Finding our way through phenotypes AR Deans, SE Lewis, E Huala, SS Anzaldo, M Ashburner, JP Balhoff, ... PLoS biology 13 (1), e1002033, 2015	237	2015
OntoFox: web-based support for ontology reuse Z Xiang, M Courtot, RR Brinkman, A Ruttenberg, Y He BMC research notes 3, 1-12, 2010	233	2010
The SWAN biomedical discourse ontology P Ciccarese, E Wu, G Wong, M Ocana, J Kinoshita, A Ruttenberg, T Clark Journal of biomedical informatics 41 (5), 739-751, 2008	181	2008
Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration E Ong, Z Xiang, B Zhao, Y Liu, Y Lin, J Zheng, C Mungall, M Courtot, ... Nucleic acids research 45 (D1), D347-D352, 2017	167	2017
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies R Jackson, N Matentzoglu, JA Overton, R Vita, JP Balhoff, PL Buttigieg, ... Database 2021, baab069, 2021	160	2021
Ontobee: A Linked Data Server and Browser for Ontology Terms Z Xiang, C Mungall, A Ruttenberg, Y He International Conference on Biomedical Ontology, 2011	158	2011
MIREOT: the minimum information to reference an external ontology term M Courtot, F Gibson, AL Lister, J Malone, D Schober, RR Brinkman, ... Applied Ontology 6 (1), 23-33, 2011	156	2011
Life sciences on the Semantic Web: the Neurocommons and beyond A Ruttenberg, JA Rees, M Samwald, MS Marshall Briefings in bioinformatics 10 (2), 193-204, 2009	144	2009
Protein Ontology (PRO): enhancing and scaling up the representation of protein entities DA Natale, CN Arighi, JA Blake, J Bona, C Chen, SC Chen, KR Christie, ... Nucleic acids research 45 (D1), D339-D346, 2017	101	2017
Protein Ontology: a controlled structured network of protein entities DA Natale, CN Arighi, JA Blake, CJ Bult, KR Christie, J Cowart, ... Nucleic acids research 42 (D1), D415-D421, 2014	90	2014
BFO: Basic formal ontology JN Otte, J Beverley, A Ruttenberg Applied ontology 17 (1), 17-43, 2022	83	2022
MIREOT: the minimum information to reference an external ontology term M Courtot, F Gibson, A Lister, J Malone, D Schober, RR Brinkman, ... Aug-2009, 2009	78	2009
Basic Formal Ontology 2.0: Specification and user’s guide B Smith, M Almeida, J Bona, M Brochhausen, W Ceusters, M Courtot, ... National Center for Ontological Research: Buffalo, NY, USA, 2015	77	2015
The neurological disease ontology M Jensen, AP Cox, N Chaudhry, M Ng, D Sule, W Duncan, P Ray, ... Journal of biomedical semantics 4, 1-10, 2013	57	2013

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