Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research [v2; ref status: indexed, http://f1000r.es/2td]

Köhler, Sebastian; Doelken, Sandra C.; Ruef, Barbara J.; Bauer, Sebastian; Washington, Nicole; Westerfield, Monte; Gkoutos, George; Schofield, Paul; Smedley, Damian; Lewis, Suzanna E.; Robinson, Peter N.; Mungall, Christopher J.

doi:10.12688/f1000research.2-30.v2

Title: Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research [v2; ref status: indexed, http://f1000r.es/2td]

Journal Article · Fri Feb 01 00:00:00 EST 2013 · F1000Research

DOI:https://doi.org/10.12688/f1000research.2-30.v2· OSTI ID:1629554

Köhler, Sebastian ^[1]; Doelken, Sandra C. ^[2]; Ruef, Barbara J. ^[3]; Bauer, Sebastian ^[2]; Washington, Nicole ^[4]; Westerfield, Monte ^[3]; Gkoutos, George ^[5]; Schofield, Paul ^[6]; Smedley, Damian ^[7]; Lewis, Suzanna E. ^[4]; Robinson, Peter N. ^[8]; Mungall, Christopher J. ^[4]

Charité-Universitatsmedizin Berlin (Germany). Inst. for Medical and Human Genetics; Charité-Universitatsmedizin Berlin (Germany). Berlin-Brandenberg Center for Regenerative Therapies (BCRT)
Charité-Universitatsmedizin Berlin (Germany). Inst. for Medical and Human Genetics
Univ. of Oregon, Eugene, OR (United States). Inst. of Neuroscience, Zebrafish Facility (ZFIN)
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Univ. of Aberystwyth (United Kingdom). Dept. of Computer Science
Univ. of Cambridge (United Kingdom). Dept. of Genetics
Wellcome Trust Sanger Inst., Cambridge (United Kingdom)
Charité-Universitatsmedizin Berlin (Germany). Inst. for Medical and Human Genetics; Charité-Universitatsmedizin Berlin (Germany). Berlin-Brandenberg Center for Regenerative Therapies (BCRT); Max Planck Inst. for Molecular Genetics, Berlin (Germany)

Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained fromhttp://purl.obolibrary.org/obo/hp/uberpheno/.

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division; USDOE Office of Science (SC), Basic Energy Sciences (BES); German Research Foundation (DFG); Bundesministerium für Bildung und Forschung (BMBF); National Institutes of Health (NIH)

Grant/Contract Number:: AC02-05CH11231; DFG RO 2005/4-1; HG000330; U41-HG002659; R01-HG004838; R24-OD011883

OSTI ID:: 1629554

Journal Information:: F1000Research, Vol. 2; ISSN 2046-1402

Publisher:: F1000ResearchCopyright Statement

Country of Publication:: United States

Language:: English

References (45)

Clinical Diagnostics in Human Genetics with Semantic Similarity Searches in Ontologies Köhler, Sebastian; Schulz, Marcel H.; Krawitz, Peter The American Journal of Human Genetics, Vol. 85, Issue 4 https://doi.org/10.1016/j.ajhg.2009.09.003	journal	October 2009
Characterization of the proteome, diseases and evolution of the human postsynaptic density Bayés, Àlex; van de Lagemaat, Louie N.; Collins, Mark O. Nature Neuroscience, Vol. 14, Issue 1 https://doi.org/10.1038/nn.2719	journal	December 2010
Uberon, an integrative multi-species anatomy ontology Mungall, Christopher J.; Torniai, Carlo; Gkoutos, Georgios V. Genome Biology, Vol. 13, Issue 1 https://doi.org/10.1186/gb-2012-13-1-r5	journal	January 2012
Bayesian ontology querying for accurate and noise-tolerant semantic searches Bauer, S.; Kohler, S.; Schulz, M. H. Bioinformatics, Vol. 28, Issue 19 https://doi.org/10.1093/bioinformatics/bts471	journal	July 2012
The Gene Ontology (GO) database and informatics resource Nucleic Acids Research, Vol. 32, Issue 90001 https://doi.org/10.1093/nar/gkh036	journal	January 2004
The Protein Ontology: a structured representation of protein forms and complexes Natale, D. A.; Arighi, C. N.; Barker, W. C. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq907	journal	October 2010
Pathbase and the MPATH Ontology: Community Resources for Mouse Histopathology Schofield, P. N.; Gruenberger, M.; Sundberg, J. P. Veterinary Pathology, Vol. 47, Issue 6 https://doi.org/10.1177/0300985810374845	journal	June 2010
PhenomeNET: a whole-phenome approach to disease gene discovery Hoehndorf, R.; Schofield, P. N.; Gkoutos, G. V. Nucleic Acids Research, Vol. 39, Issue 18 https://doi.org/10.1093/nar/gkr538	journal	July 2011
A reference ontology for biomedical informatics: the Foundational Model of Anatomy Rosse, Cornelius; Mejino, José L. V. Journal of Biomedical Informatics, Vol. 36, Issue 6 https://doi.org/10.1016/j.jbi.2003.11.007	journal	December 2003
The mouse ascending: perspectives for human-disease models Rosenthal, Nadia; Brown, Steve Nature Cell Biology, Vol. 9, Issue 9 https://doi.org/10.1038/ncb437	journal	September 2007
Cross-product extensions of the Gene Ontology Mungall, Christopher J.; Bada, Michael; Berardini, Tanya Z. Journal of Biomedical Informatics, Vol. 44, Issue 1 https://doi.org/10.1016/j.jbi.2010.02.002	journal	February 2011
Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation Washington, Nicole L.; Haendel, Melissa A.; Mungall, Christopher J. PLoS Biology, Vol. 7, Issue 11 https://doi.org/10.1371/journal.pbio.1000247	journal	November 2009
OBO-Edit an ontology editor for biologists Day-Richter, J.; Harris, M. A.; Haendel, M. Bioinformatics, Vol. 23, Issue 16 https://doi.org/10.1093/bioinformatics/btm112	journal	June 2007
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish Doelken, S. C.; Kohler, S.; Mungall, C. J. Disease Models & Mechanisms, Vol. 6, Issue 2 https://doi.org/10.1242/dmm.010322	journal	October 2012
Improving ontologies by automatic reasoning and evaluation of logical definitions Köhler, Sebastian; Bauer, Sebastian; Mungall, Chris J. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-418	journal	October 2011
Improving Disease Gene Prioritization by Comparing the Semantic Similarity of Phenotypes in Mice with Those of Human Diseases Oellrich, Anika; Hoehndorf, Robert; Gkoutos, Georgios V. PLoS ONE, Vol. 7, Issue 6 https://doi.org/10.1371/journal.pone.0038937	journal	June 2012
Gene Ontology: tool for the unification of biology Ashburner, Michael; Ball, Catherine A.; Blake, Judith A. Nature Genetics, Vol. 25, Issue 1 https://doi.org/10.1038/75556	journal	May 2000
The Human Phenotype Ontology: A Tool for Annotating and Analyzing Human Hereditary Disease Robinson, Peter N.; Köhler, Sebastian; Bauer, Sebastian The American Journal of Human Genetics, Vol. 83, Issue 5 https://doi.org/10.1016/j.ajhg.2008.09.017	journal	November 2008
Semantic Similarity in Biomedical Ontologies Pesquita, Catia; Faria, Daniel; Falcão, André O. PLoS Computational Biology, Vol. 5, Issue 7 https://doi.org/10.1371/journal.pcbi.1000443	journal	July 2009
The Zebrafish Information Network: the zebrafish model organism database provides expanded support for genotypes and phenotypes Sprague, J.; Bayraktaroglu, L.; Bradford, Y. Nucleic Acids Research, Vol. 36, Issue Database https://doi.org/10.1093/nar/gkm956	journal	December 2007
The Neurobehavior Ontology: An Ontology for Annotation and Integration of Behavior and Behavioral Phenotypes Gkoutos, Georgios V.; Schofield, Paul N.; Hoehndorf, Robert International Review of Neurobiology https://doi.org/10.1016/B978-0-12-388408-4.00004-6	book	January 2012
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration Smith, Barry; Ashburner, Michael; Rosse, Cornelius Nature Biotechnology, Vol. 25, Issue 11 https://doi.org/10.1038/nbt1346	journal	November 2007
Chemical Entities of Biological Interest: an update de Matos, Paula; Alcántara, Rafael; Dekker, Adriano Nucleic Acids Research, Vol. 38, Issue suppl_1 https://doi.org/10.1093/nar/gkp886	journal	October 2009
Mouse, man, and meaning: bridging the semantics of mouse phenotype and human disease Hancock, John M.; Mallon, Ann-Marie; Beck, Tim Mammalian Genome, Vol. 20, Issue 8 https://doi.org/10.1007/s00335-009-9208-3	journal	August 2009
The mammalian gene function resource: the international knockout mouse consortium Bradley, Allan; Anastassiadis, Konstantinos; Ayadi, Abdelkader Mammalian Genome, Vol. 23, Issue 9-10 https://doi.org/10.1007/s00335-012-9422-2	journal	September 2012
The Mammalian Phenotype Ontology as a unifying standard for experimental and high-throughput phenotyping data Smith, Cynthia L.; Eppig, Janan T. Mammalian Genome, Vol. 23, Issue 9-10 https://doi.org/10.1007/s00335-012-9421-3	journal	September 2012
Towards an encyclopaedia of mammalian gene function: the International Mouse Phenotyping Consortium Brown, Steve D. M.; Moore, Mark W. Disease Models & Mechanisms, Vol. 5, Issue 3 https://doi.org/10.1242/dmm.009878	journal	May 2012
Ontological phenotype standards for neurogenetics Köhler, Sebastian; Doelken, Sandra C.; Rath, Ana Human Mutation, Vol. 33, Issue 9 https://doi.org/10.1002/humu.22112	journal	July 2012
Representation of rare diseases in health information systems: The orphanet approach to serve a wide range of end users Rath, Ana; Olry, Annie; Dhombres, Ferdinand Human Mutation, Vol. 33, Issue 5 https://doi.org/10.1002/humu.22078	journal	April 2012
Mouse genetic and phenotypic resources for human genetics Schofield, Paul N.; Hoehndorf, Robert; Gkoutos, Georgios V. Human Mutation, Vol. 33, Issue 5 https://doi.org/10.1002/humu.22077	journal	April 2012
Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community Schindelman, Gary; Fernandes, Jolene S.; Bastiani, Carol A. BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-32	journal	January 2011
A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®) Amberger, Joanna; Bocchini, Carol; Hamosh, Ada Human Mutation, Vol. 32, Issue 5 https://doi.org/10.1002/humu.21466	journal	April 2011
Integrating phenotype ontologies across multiple species Mungall, Christopher J.; Gkoutos, Georgios V.; Smith, Cynthia L. Genome Biology, Vol. 11, Issue 1 https://doi.org/10.1186/gb-2010-11-1-r2	journal	January 2010
Ontologizer 2.0--a multifunctional tool for GO term enrichment analysis and data exploration Bauer, S.; Grossmann, S.; Vingron, M. Bioinformatics, Vol. 24, Issue 14 https://doi.org/10.1093/bioinformatics/btn250	journal	May 2008
Animal models of human disease: zebrafish swim into view Lieschke, Graham J.; Currie, Peter D. Nature Reviews Genetics, Vol. 8, Issue 5 https://doi.org/10.1038/nrg2091	journal	May 2007
ZFIN: enhancements and updates to the zebrafish model organism database Bradford, Y.; Conlin, T.; Dunn, N. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1077	journal	October 2010
The mouse Gene Expression Database (GXD): 2011 update Finger, J. H.; Smith, C. M.; Hayamizu, T. F. Nucleic Acids Research, Vol. 39, Issue Database https://doi.org/10.1093/nar/gkq1132	journal	November 2010
Logical Development of the Cell Ontology Meehan, Terrence F.; Masci, Anna Maria; Abdulla, Amina BMC Bioinformatics, Vol. 12, Issue 1 https://doi.org/10.1186/1471-2105-12-6	journal	January 2011
MouseFinder: Candidate disease genes from mouse phenotype data Chen, Chao-Kung; Mungall, Christopher J.; Gkoutos, Georgios V. Human Mutation, Vol. 33, Issue 5 https://doi.org/10.1002/humu.22051	journal	March 2012
Improving ontologies by automatic reasoning and evaluation of logical definitions Kohler, Sebastian; Bauer, Sebastian; Mungall, Chris J. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.11412	text	January 2011
The mammalian gene function resource: the International Knockout Mouse Consortium. Bradley, Allan; Anastassiadis, Konstantinos; Ayadi, Abdelkader Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.58617	text	January 2012
Cross-Product Extensions of the Gene Ontology Mungall, Christopher; Bada, Michael; Berardini, Tanya Nature Precedings https://doi.org/10.1038/npre.2009.3496.1	journal	July 2009
PhenomeNET: a whole-phenome approach to disease gene discovery. Hoehndorf, Robert; Schofield, Paul; Gkoutos, Georgios Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.11414	text	January 2011
Dietary palmitic acid promotes a prometastatic memory via Schwann cells Pascual, Gloria; Domínguez, Diana; Elosúa-Bayes, Marc Nature, Vol. 599, Issue 7885 https://doi.org/10.1038/s41586-021-04075-0	journal	November 2021
Entity/quality-based logical definitions for the human skeletal phenome using PATO Gkoutos, G. V.; Mungall, C.; Dolken, S. 2009 Annual International Conference of the IEEE Engineering in Medicine and Biology Society https://doi.org/10.1109/iembs.2009.5333362	conference	September 2009

Cited By (42)

Exome sequencing for gene discovery in lethal fetal disorders - harnessing the value of extreme phenotypes: Gene discovery in lethal fetal phenotypes Filges, Isabel; Friedman, Jan M. Prenatal Diagnosis, Vol. 35, Issue 10 https://doi.org/10.1002/pd.4464	journal	August 2014
The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants Hoehndorf, Robert; Alshahrani, Mona; Gkoutos, Georgios V. Journal of Biomedical Semantics, Vol. 7, Issue 1 https://doi.org/10.1186/s13326-016-0107-8	journal	November 2016
Neuroinformatic analyses of common and distinct genetic components associated with major neuropsychiatric disorders Lotan, Amit; Fenckova, Michaela; Bralten, Janita Frontiers in Neuroscience, Vol. 8 https://doi.org/10.3389/fnins.2014.00331	journal	November 2014
Cross-organism analysis using InterMine: cross-organism analysis using InterMine Lyne, Rachel; Sullivan, Julie; Butano, Daniela genesis, Vol. 53, Issue 8 https://doi.org/10.1002/dvg.22869	journal	July 2015
Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery Mungall, Christopher J.; Washington, Nicole L.; Nguyen-Xuan, Jeremy Human Mutation, Vol. 36, Issue 10 https://doi.org/10.1002/humu.22857	journal	September 2015
Disease insights through cross-species phenotype comparisons Haendel, Melissa A.; Vasilevsky, Nicole; Brush, Matthew Mammalian Genome, Vol. 26, Issue 9-10 https://doi.org/10.1007/s00335-015-9577-8	journal	June 2015
Identification of sequence variants influencing immunoglobulin levels Jonsson, Stefan; Sveinbjornsson, Gardar; de Lapuente Portilla, Aitzkoa Lopez Nature Genetics, Vol. 49, Issue 8 https://doi.org/10.1038/ng.3897	journal	June 2017
Next-generation diagnostics and disease-gene discovery with the Exomiser Smedley, Damian; Jacobsen, Julius O. B.; Jäger, Marten Nature Protocols, Vol. 10, Issue 12 https://doi.org/10.1038/nprot.2015.124	journal	November 2015
Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis Li, Qigang; Zhao, Keyan; Bustamante, Carlos D. Genetics in Medicine, Vol. 21, Issue 9 https://doi.org/10.1038/s41436-019-0439-8	journal	January 2019
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research Kafkas, Şenay; Abdelhakim, Marwa; Hashish, Yasmeen Scientific Data, Vol. 6, Issue 1 https://doi.org/10.1038/s41597-019-0090-x	journal	June 2019
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies Alghamdi, Sarah M.; Sundberg, Beth A.; Sundberg, John P. Scientific Reports, Vol. 9, Issue 1 https://doi.org/10.1038/s41598-019-40368-1	journal	March 2019
Drug-induced adverse events prediction with the LINCS L1000 data Wang, Zichen; Clark, Neil R.; Ma’ayan, Avi Bioinformatics, Vol. 32, Issue 15 https://doi.org/10.1093/bioinformatics/btw168	journal	April 2016
PhenomeScape: a cytoscape app to identify differentially regulated sub-networks using known disease associations Soul, Jamie; Dunn, Sara L.; Hardingham, Tim E. Bioinformatics, Vol. 32, Issue 24 https://doi.org/10.1093/bioinformatics/btw545	journal	August 2016
Formal axioms in biomedical ontologies improve analysis and interpretation of associated data Smaili, Fatima Zohra; Gao, Xin; Hoehndorf, Robert Bioinformatics, Vol. 36, Issue 7 https://doi.org/10.1093/bioinformatics/btz920	journal	December 2019
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction Kafkas, Şenay; Hoehndorf, Robert Database, Vol. 2019 https://doi.org/10.1093/database/baz019	journal	January 2019
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data Köhler, Sebastian; Doelken, Sandra C.; Mungall, Christopher J. Nucleic Acids Research, Vol. 42, Issue D1 https://doi.org/10.1093/nar/gkt1026	journal	November 2013
The Human Phenotype Ontology in 2017 Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1039	journal	November 2016
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species Shefchek, Kent A.; Harris, Nomi L.; Gargano, Michael Nucleic Acids Research, Vol. 48, Issue D1 https://doi.org/10.1093/nar/gkz997	journal	November 2019
A dominant gain-of-function mutation in universal tyrosine kinase SRC causes thrombocytopenia, myelofibrosis, bleeding, and bone pathologies Turro, Ernest; Greene, Daniel; Wijgaerts, Anouck Science Translational Medicine, Vol. 8, Issue 328 https://doi.org/10.1126/scitranslmed.aad7666	journal	March 2016
Aber-OWL: a framework for ontology-based data access in biology Hoehndorf, Robert; Slater, Luke; Schofield, Paul N. BMC Bioinformatics, Vol. 16, Issue 1 https://doi.org/10.1186/s12859-015-0456-9	journal	January 2015
Deletions of chromosomal regulatory boundaries are associated with congenital disease Ibn-Salem, Jonas; Köhler, Sebastian; Love, Michael I. Genome Biology, Vol. 15, Issue 9 https://doi.org/10.1186/s13059-014-0423-1	journal	September 2014
Finding Our Way through Phenotypes Deans, Andrew R.; Lewis, Suzanna E.; Huala, Eva PLoS Biology, Vol. 13, Issue 1 https://doi.org/10.1371/journal.pbio.1002033	journal	January 2015
Phenotype Ontologies and Cross-Species Analysis for Translational Research Robinson, Peter N.; Webber, Caleb PLoS Genetics, Vol. 10, Issue 4 https://doi.org/10.1371/journal.pgen.1004268	journal	April 2014
The digital revolution in phenotyping Ivo, Georgiev,; Gabriella, Rustici,; Ann-Marie, Mallon, The University of North Carolina at Chapel Hill University Libraries https://doi.org/10.17615/x6be-m741	text	January 2016
Integrating phenotype ontologies with PhenomeNET Rodríguez-García, Miguel Á; Gkoutos, Georgios V.; Schofield, Paul N. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.17119	collection	January 2017
DeepPVP: phenotype-based prioritization of causative variants using deep learning. Boudellioua, Imane; Kulmanov, Maxat; Schofield, Paul Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.36763	text	January 2019
The anatomy of phenotype ontologies: principles, properties and applications Gkoutos, Gv; Schofield, Paul; Hoehndorf, R. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.9914	text	January 2017
The anatomy of phenotype ontologies: principles, properties and applications Gkoutos, Georgios V.; Schofield, Paul N.; Hoehndorf, Robert Briefings in Bioinformatics, Vol. 19, Issue 5 https://doi.org/10.1093/bib/bbx035	journal	April 2017
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species Mungall, Christopher J.; McMurry, Julie A.; Köhler, Sebastian Nucleic Acids Research, Vol. 45, Issue D1 https://doi.org/10.1093/nar/gkw1128	journal	November 2016
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies Alghamdi, Sarah M.; Sundberg, Beth A.; Sundberg, John P. https://doi.org/10.1101/378927	posted_content	July 2018
The digital revolution in phenotyping Oellrich, Anika; Collier, Nigel; Groza, Tudor Briefings in Bioinformatics, Vol. 17, Issue 5 https://doi.org/10.1093/bib/bbv083	journal	September 2015
DeepPVP: phenotype-based prioritization of causative variants using deep learning Boudellioua, Imane; Kulmanov, Maxat; Schofield, Paul N. bioRxiv https://doi.org/10.1101/311621	posted_content	May 2018
Integrating phenotype ontologies with PhenomeNET. Rodríguez-García, Miguel Ángel; Gkoutos, Georgios V.; Schofield, Paul Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.20504	text	January 2017
The Human Phenotype Ontology in 2017. Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.23701	text	January 2017
Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies. Alghamdi, Sarah M.; Sundberg, Beth A.; Sundberg, John P. Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.36997	text	January 2019
PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research. Kafkas, Şenay; Abdelhakim, Marwa; Hashish, Yasmeen Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.43596	text	January 2019
The role of ontologies in biological and biomedical research: a functional perspective Hoehndorf, R.; Schofield, P. N.; Gkoutos, G. V. Briefings in Bioinformatics, Vol. 16, Issue 6 https://doi.org/10.1093/bib/bbv011	journal	April 2015
GeneTIER: prioritization of candidate disease genes using tissue-specific gene expression profiles Antanaviciute, Agne; Daly, Catherine; Crinnion, Laura A. Bioinformatics, Vol. 31, Issue 16 https://doi.org/10.1093/bioinformatics/btv196	journal	April 2015
OVA: integrating molecular and physical phenotype data from multiple biomedical domain ontologies with variant filtering for enhanced variant prioritization Antanaviciute, Agne; Watson, Christopher M.; Harrison, Sally M. Bioinformatics, Vol. 31, Issue 23 https://doi.org/10.1093/bioinformatics/btv473	journal	August 2015
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora Groza, T.; Kohler, S.; Doelken, S. Database, Vol. 2015, Issue 0 https://doi.org/10.1093/database/bav005	journal	January 2015
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery Gourdine, Jean-Philippe F.; Brush, Matthew H.; Vasilevsky, Nicole A. Database, Vol. 2019 https://doi.org/10.1093/database/baz114	journal	January 2019
The cellular microscopy phenotype ontology Jupp, Simon; Malone, James; Burdett, Tony Journal of Biomedical Semantics, Vol. 7, Issue 1 https://doi.org/10.1186/s13326-016-0074-0	journal	May 2016

Similar Records

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Journal Article · Wed Jan 01 00:00:00 EST 2014 · Journal of Biomedical Semantics · OSTI ID:1629554

Haendel, Melissa A.; Balhoff, James P.; Bastian, Frederic B.; +15 more

The Ontology of Biological Attributes (OBA)—computational traits for the life sciences

Journal Article · Wed Apr 19 00:00:00 EDT 2023 · Mammalian Genome · OSTI ID:1629554

Stefancsik, Ray; Balhoff, James P.; Balk, Meghan A.; +23 more

Linking Human Diseases to Animal Models Using Ontology-Based Phenotype Annotation

Journal Article · Tue Nov 24 00:00:00 EST 2009 · PLoS Biology (Online) · OSTI ID:1629554

Washington, Nicole L.; Haendel, Melissa A.; Mungall, Christopher J.; +3 more

Related Subjects

59 BASIC BIOLOGICAL SCIENCES

Title: Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research [v2; ref status: indexed, http://f1000r.es/2td]

Citation Formats

References (45)

Cited By (42)

Similar Records

Related Subjects