OHSU

Publications

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Haendel M, Balhoff J, Bastian Frederic, Blackburn D, Blake J, Bradford Y, Comte A, Dahdul W, Dececchi T, Druzinsky R, Hayamizu T, Ibrahim N, Lewis S, Mabee P, Niknejad A, Robinson-Rechavi M, Sereno P, Mungall C. Journal of Biomedical Semantics. 2014 July 5:21.

Thematic series on biomedical ontologies in JBMS: challenges and new directions. Hoehndorf R, Haendel M, Stevens R, Rebholz-Schuhmann D. J Biomed Semantics. 2014 Mar 6;5:15.

The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio. Van Slyke CE, Bradford YM, Westerfield M, Haendel MA. J Biomed Semantics. 2014 Feb 25;5(1):12.

From EHRs to Linked Data: representing and mining encounter data for clinical expertise evaluation. Torniai C, Essaid S, Barnes C, Conlon M, Williams S, Hajagos JG, Bremer E, Corson-Rikert J, Haendel M. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:165. 

An ontology-based method for secondary use of electronic dental record data. Schleyer TK, Ruttenberg A, Duncan W, Haendel M, Torniai C, Acharya A, Song M, Thyvalikakath TP, Liu K, Hernandez P. AMIA Jt Summits Transl Sci Proc. 2013 Mar 18;2013:234-8.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, Bailleul-Forestier I, Black GC, Brown DL, Brudno M, Campbell J, FitzPatrick DR, Eppig JT, Jackson AP, Freson K, Girdea M, Helbig I, Hurst JA, Jähn J, Jackson LG, Kelly AM, Ledbetter DH, Mansour S, Martin CL, Moss C, Mumford A, Ouwehand WH, Park SM, Riggs ER, Scott RH, Sisodiya S, Van Vooren S, Wapner RJ, Wilkie AO, Wright CF, Vulto-van Silfhout AT, de Leeuw N, de Vries BB, Washingthon NL, Smith CL, Westerfield M, Schofield P, Ruef BJ, Gkoutos GV, Haendel M, Smedley D, Lewis SE, Robinson PN. Nucleic Acids Res. 2014 Jan;42(Database issue):D966-74.

Improved exome prioritization of disease genes through cross-species phenotype comparison. Robinson PN, Köhler S, Oellrich A; Sanger Mouse Genetics Project, Wang K, Mungall CJ, Lewis SE, Washington N, Bauer S, Seelow D, Krawitz P, Gilissen C, Haendel M, Smedley D. Genome Res. 2014 Feb;24(2):340-8. 

What is an anatomy ontology? Druzinsky R, Mungall C, Haendel M, Lapp H, Mabee P. Anat Rec (Hoboken). 2013 Dec;296(12):1797-9. PMID: 24127438

Enhanced XAO: the ontology of Xenopus anatomy and development underpins more accurate annotation of gene expression and queries on XenbaseSegerdell E, Ponferrada VG, James-Zorn C, Burns KA, Fortriede JD, Dahdul WM, Vize PD, Zorn AM. J Biomed Semantics. 2013 Oct 18;4(1):31.

A sea of standards for omics data: sink or swim? Tenenbaum JD, Sansone SA, Haendel M. J Am Med Inform Assoc. 2014 Mar-Apr;21(2):200-3. 

Data Curation, Part 1 and 2. An Interview with Nicole Vasilevsky, Melissa Haendel, and Chris Shaffer, AHIP, Oregon Health & Science University- Portland. MLA NEWS 2014. 54(2):12 (Part 1) and 54(3):12 (Part 2).

eagle-i: biomedical research resource datasets. Torniai C, Bourges-Waldegg D and Hoffmann S. (2013) Semantic Web Journal.

The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Köhler S, Doelken SC, Mungall CJ, Bauer S, Firth HV, et al. (2013) Nucleic Acids Res. 2013 Nov 11.

On the reproducibility of science: unique identification of research resources in the biomedical literature Vasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, LaRocca GM, Haendel MA. (2013) PeerJ 1:e148

Ontology based molecular signatures for immune cell types via gene expression analysis Meehan TF, Vasilevsky NA, Mungall CJ, Dougall DS, Haendel MA, Blake JA, Diehl AD. BMC Bioinformatics. 2013 Aug 30;14(1):263.

eagle-i: ontology-driven federated search and data entry tools for discovering biomedical research resources. Haendel M, Torniai C, Vasilevsky N, Hoffmann S, Bourges-Waldegg D. (2013) International Conference on Biomedical Ontology; July 7-13, 2013; Montreal, Canada.

Finding common ground: integrating the eagle-i and VIVO ontologies. Torniai C, Essaid S, Lowe B, Corson-Rikert J, Haendel M. (2013) International Conference on Biomedical Ontology; July 7-13, 2013; Montreal, Canada.

Enabling semantic search in a bio-specimen repository. Essaid S, Torniai C, Haendel MA. (2013) International Conference on Biomedical Ontology; July 7-13, 2013; Montreal, Canada.

What's in a Genotype?: An Ontological Characterization for Integration of Genetic Variation Data. Brush MH, Mungall C, Washington N, Haendel MA. (2013) International Conference on Biomedical Ontology; July 7-13, 2013; Montreal, Canada.

Alignment of Cultured Cell Modeling Across OBO Foundry Ontologies: Key Outcomes, Insights. Brush MH, Zheng J, He Y, Sarntivijai S, Peters B, Diehl AD, Stoeckert CJ, Haendel MA. (2013) International Conference on Biomedical Ontology; July 7-13, 2013; Montreal, Canada.

Lost and found in behavioral informatics Haendel MA, Chesler EJ. Int Rev Neurobiol. 2012;103:1-18. doi: 10.1016/B978-0-12-388408-4.00001-0.

Dealing with data: a case study on information and data management literacy Haendel MA, Vasilevsky N, Wirz J. PLoS Biol 10(5): e1001339.

Research resources: curating the new eagle-i discovery system Vasilevsky N, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, Wilson M, Shaffer C, Robinson D, Haendel M. Database (Oxford). 2012 Mar 20;2012:bar067. doi: 10.1093/database/bar067.

A unified anatomy ontology of the vertebrate skeletal system. Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. PLoS One. 2012;7(12):e51070.

Uberon, an integrative multi-species anatomy ontology Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Genome Biol. 2012 Jan 31;13(1):R5.

Ontology Extraction Tools: An Empirical Study with Educators. M Hatala, D Gasevic, M Siadaty, J Jovanovic, C Torniai. IEEE, TLE 2012

Developing an application ontology for biomedical resource annotation and retrieval: Challenges and lessons learned. Torniai, C, Brush, M, Vasilevsky, N, Segerdell, E, Wison, M, Johnson, T, Corday, K, Shaffer, C, and Haendel, M. (2011) International Conference on Biomedical Ontology 2011; July 26–30, 2011; Buffalo, NY.

An Approach to Folksonomy-based Ontology Maintenance for Learning Environments. D Gasevic, A Zouaq, C Torniai, J Jovanovic, M Hatala. Learning Technologies, IEEE Transactions on, 1-18 (2011)

Integrating phenotype ontologies across multiple species Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Genome Biol. 2010 Jan 8;11(1):R2.

Eagle-i: Making Invisible Resources, Visible M Haendel, M Wilson, C Torniai, E Segerdell, C Shaffer, R Frost, D Bourges, J Brownstein, K McInnerney. (2010) Journal of Biomolecular Techniques: JBT 21 (3 Suppl), S64.

Linking human diseases to animal models using ontology-based phenotype annotation. Washington NL, Haendel MA, Mungall CJ, Ashburner M, Westerfield M, Lewis SE. PLoS Biol. 2009 Nov;7(11):e1000247.

Datasets

Unique identification of research resources in studies in Reproducibility Project: Cancer Biology. Vasilevsky, Nicole; Kavanagh, David J; Deusen, Amy Van; Haendel, Melissa; Iorns, Elizabeth (2014): figshare. http://dx.doi.org/10.6084/m9.figshare.1015757

Unique ID datasets. Vasilevsky, Nicole; Brush, Matthew; Paddock, Holly; Ponting, Laura; Tripathy, Shreejoy; LaRocca, Gregory; Haendel, Melissa (2013): figshare. http://dx.doi.org/10.6084/m9.figshare.773119