Semantic Phenotyping of Diseases

The Matchmaker Exchange: A Platform for Rare Disease Gene Discovery. Philippakis AA, Azzariti DR, Beltran S, Brookes AJ, Brownstein CA, et al. Hum Mutat. 2015 Oct;36(10):915-21. doi: 10.1002/humu.22858.

Use of Model Organism and Disease Databases to Support Matchmaking for Human Disease Gene Discovery. Mungall CJ, Washington NL, Nguyen-Xuan J, Condit C, Smedley D, et al. Hum Mutat. 2015 Oct;36(10):979-84. doi: 10.1002/humu.22857.

PhenomeCentral: A Portal for Phenotypic and Genotypic Matchmaking of Patients with Rare Genetic Diseases. Buske OJ, Girdea M, Dumitriu S, Gallinger B, Hartley T, et al. Hum Mutat. 2015 Oct;36(10):931-40. doi: 10.1002/humu.22851.

Disease insights through cross-species phenotype comparisons. Haendel MA, Vasilevsky N, Brush M, Hochheiser HS, Jacobsen J, et al. Mamm Genome. 2015 Oct;26(9-10):548-55. doi: 10.1007/s00335-015-9577-8. 

Finding our way through phenotypes. Deans AR, Lewis SE, Huala E, Anzaldo SS, Ashburner M, et al. PLoS Biol. 2015 Jan 6;13(1):e1002033. doi: 10.1371/journal.pbio.1002033. eCollection 2015 Jan.

The Human Phenotype Ontology: Semantic Unification of Common and Rare Disease. Groza T, Köhler S, Moldenhauer D, Vasilevsky N, Baynam G, Zemojtel T, et al. Am J Hum Genet. 2015 Jul 2;97(1):111-24. doi: 10.1016/j.ajhg.2015.05.020. Epub 2015 Jun 25.PMID: 26119816 

Clinical interpretation of CNVs with cross-species phenotype data. Köhler S, et al. (2014) J Med Genet. 2014 Nov;51(11):766-72.Effective diagnosis of genetic disease by computational phenotype analysis of the disease-associated genome. Tomasz Zemojtel et al. (2014) Sci Transl Med 3 September 2014: Vol. 6, Issue 252, p. 252ra123.

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. Nucleic Acids Res. 2014 Jan;42(Database issue):D966-74. 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. 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.  

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.

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.


Improving Research Resource Identification

Achieving human and machine accessibility of cited data in scholarly publications. Starr J, Castro E, Crosas M, Dumontier M, Downs RR, et al. PeerJ Comput Sci. 2015;1. pii: e1.

The Resource Identification Initiative: A cultural shift in publishing. Anita Bandrowski, Matthew Brush, Jeffery S. Grethe, Melissa A. Haendel, David N. Kennedy,  et al.  [version 1; referees: 2 approved] F1000Research 2015, 4:134 (doi: 10.12688/f1000research.6555.1)

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


Data Management, Curation, Data Standards and Altmetrics

PlumX. Champieux R. (2015) J Med Libr Assoc. 2015 Jan; 103(1): 63–64.

Lions, Tigers, and Gummi Bears: Springing Towards Effective Engagement with Research Data Management. Vasilevsky N Wirz J, Champieux R, Hannon T, Laraway B, Banerjee K, Shaffer C and Haendel M. (2014).Scholar Archive. Paper 3571.

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).

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


Biomedical Ontologies and Bioinformatics

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology. Thacker RW, Díaz MC, Kerner A, Vignes-Lebbe R, Segerdell E, Haendel MA, Mungall CJ. J Biomed Semantics. 2014 Sep 8;5(1):39.

Nose to tail, roots to shoots: spatial descriptors for phenotypic diversity in the Biological Spatial Ontology. Dahdul WM, Cui H, Mabee PM, Mungall CJ, Osumi-Sutherland D, Walls RL, Haendel MA. J Biomed Semantics. 2014 Aug 11;5:34.

Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon. Haendel M, Balhoff J, Bastian F, 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.

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. 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 Xenbase. Segerdell 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.

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.

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.

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.

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

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)


Representing Researcher Expertise

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. 

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. 

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

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.

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.

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.

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.


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.

Unique ID datasets. Vasilevsky, Nicole; Brush, Matthew; Paddock, Holly; Ponting, Laura; Tripathy, Shreejoy; LaRocca, Gregory; Haendel, Melissa (2013): figshare.