Evolving BioAssay Ontology (BAO): Modularization, integration and applications

Journal of Biomedical Semantics

Volumn 5, Issue , 2014, Pages

  Abeyruwan, Saminda ^a   Vempati, Uma D ^b   Küçük McGinty, Hande ^a   Visser, Ubbo ^a   Koleti, Amar ^b   Mir, Ahsan ^b   Sakurai, Kunie ^c   Chung, Caty ^b   Bittker, Joshua A ^e   Clemons, Paul A ^e   Brudz, Steve ^e   Siripala, Anosha ^f   Morales, Arturo J ^f   Romacker, Martin ^f   Twomey, David ^f   Bureeva, Svetlana ^g   Lemmon, Vance ^b,c   Schürer, Stephan C ^b,d  

^a Department of Computer Science and Center for Computational Science   (United States)

^b UNIVERSITY OF MIAMI   (United States)

^c UNIVERSITY OF MIAMI   (United States)

^d UNIVERSITY OF MIAMI MILLER SCHOOL OF MEDICINE   (United States)

^e MERSI   (United States)

^f NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH   (United States)

^g Thomson Reuters   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84938093882     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-5-S1-S5     Document Type: Article

References (35)

1. Hertzberg RP, Pope AJ: High-throughput screening: new technology for the 21st century. Current Opinion in Chemical Biology 2000, 4(4):445-451.
2. Swinney DC, Anthony J: How were new medicines discovered? Nature reviews. Drug discovery 2011, 10(7):507-519.
3. Austin CP, BradyL S, Insel TR, Collins FS: NIH molecular libraries initiative. Science 2004, 306(5699):1138-1139.
4. Library of Integrated Network-Based Cellular Signatures (NIH LINCS) program. [http://www.lincsproject.org], Last visited on 11/01/2013.
5. Li Q, Cheng T, Wang Y, Bryant SH: Pubchem as a public resource for drug discovery. Drug Discovery Today 2010, 15(23-24):1052-1057.
6. BioAssay Research Database (BARD). [http://bard.nih.gov], Last visited on 11/01/2013.
7. Library of Integrated Network-based Cellular Signatures (LINCS) Information FramEwork. [http://life.ccs.miami.edu/ life], Last visited on 11/01/2013.
8. Gaulton A, Bellis LJ, Bento AP, Chambers J, Davies M, Hersey A, Light Y, McGlinchey S, Michalovich D, Al-Lazikani B, Overington JP: ChEMBL:a large-scale bioactivity database for drug discovery. Nucleic Acids Research 2012, 40(D1):1100-1107.
9. Jensen NH, Roth BL: Massively parallel screening of the receptorome. Combinatorial Chemistry & High Throughput Screening 2008, 11:420-426.
10. Hohman M, Gregory K, Chibale K, Smith PJ, Ekins S, Bunin B: Novel web-based tools combining chemistry informatics, biology and social networks for drug discovery. Drug Discovery Today 2009, 14(5-6):261-270.
11. James Inglese RKG, Caroline EShamu: Reporting data from high-throughput screening of small-molecule libraries. Nature Chemical Biology 2007, 8: 438-441.
12. Vempati UD, Przydzial MJ, Chung C, Abeyruwan S, Mir A, Sakurai K, Visser U, Lemmon VP, Schürer SC: Formalization, Annotation and Analysis of Diverse Drug and Probe Screening Assay Datasets Using the BioAssay Ontology (BAO). PLoS ONE 2012, 7(11).
13. BAOSearch. [http://baosearch.ccs.miami.edu], Last visited on 11/01/2013.
14. Callahan A, Cruz-Toledo J, Dumontier M: Ontology-based querying with bio2rdf's linked open data. Journal of Biomedical Semantics 2013, 4(Suppl 1):1.
15. Azzaoui K, Jacoby E, Senger S, Rodríguez EC, Loza M, Zdrazil B, Pinto M, Williams AJ, de la Torre V, Mestres J, Pastor M, Taboureau O, Rarey M, Chichester C, Pettifer S, Blomberg N, Harland L, Williams-Jones B, Ecker GF: Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discovery Today 2013, 18(17-18):843-852.
16. Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Kruger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP: The ChEMBL bioactivity database: an update. Nucleic Acids Research Advance Access 2013, 1-8.
17. Baader F, Calvanese D, McGuinness DL, Nardi D, Patel-Schneider PF: The Description Logic Handbook: Theory, Implementation and Applications 2nd edn. Cambridge University Press, New York, NY, USA; 2010.
18. Tsarkov D, Horrocks I: FaCT++ Description Logic Reasoner System Description. In Proceedings of the Third International Joint Conference on Automated Reasoning (IJCAR 2006) Lecture Notes in Artificial Intelligence 2006, 4130:292-297, Springer.
19. Sirin E, Parsia B, Grau BC, Kalyanpur A, Katz Y: Pellet: A Practical OWL-DL Reasoner. Web Semantics: Science,Services and Agents on the World Wide Web 2007, 5(2):51-53.
20. Shearer R, Motik B, Horrocks I: HermiT: A Highly-Efficient OWL Reasoner. Proceedings of the 5th International Workshop on OWL: Experiences and Directions, Karlsruhe, Germany;Ruttenberg, A, Sattler U, Dolbear C 2008:.
21. The Even More Irresistible SROIQ. Proceedings of the 10th International Conference on Principles of Knowledge Representation and Reasoning (KR2006) AAAI Press; 2006, 57-67.
22. Hitzler P, Krötzsch M, Rudolph S: Foundations of Semantic Web Technologies. Chapman and Hall (CRC) 2009.
23. Basic Formal Ontology (BFO) Project. [http://www.ifomis.org/bfo], Last visited on 11/01/2013.
24. Stenzhorn H, Beisswanger E, Schulz S: Towards a Top-Domain Ontology for Linking Biomedical Ontologies. In MedInfo Studies in Health Technology and Informatics. Volume 129. IOS Press;Kuhn, Klaus A. and Warren, James R. and Leong Tze-Yun 2007:1225-1229.
25. Ceusters W, Smith B: A realism-based approach to the evolution of biomedical ontologies. Annual Symposium proceedings/AMIA Symposium. AMIA Symposium 2006, 121-125.
26. Dumontier M, Hoehndorf R: Realism for scientific ontologies. Proceedings of the 2010 Conference on Formal Ontology in Information Systems: Proceedings of the Sixth International Conference (FOIS 2010) IOS Press, Amsterdam, The Netherlands, The Netherlands; 2010, 387-399[http://dl.acm.org/citation.cfm?id=1804715.1804755].
27. Brinkman RR, Courtot M, Derom D, Fostel JM, He Y, Lord P, Malone J, Parkinson H, Peters B, Rocca-Serra P, Ruttenberg A, Sansone SA, Soldatova LN, Stoeckert CJ Jr, Turner JA, Zheng J: Modeling biomedical experimental processes with OBI. J Biomed Semantics 2010, 1(Suppl 1):7.
28. Visser U, Abeyruwan S, Vempati U, Smith R, Lemmon V, Schurer S: BioAssay Ontology (BAO): a semantic description of bioassays and high-throughput screening results. BMC Bioinformatics 2011, 12(1):257.
29. Schurer SC, Vempati U, Smith R, Southern M, Lemmon V: BioAssay Ontology Annotations Facilitate Cross-Analysis of Diverse High-Throughput Screening Data Sets. Journal of Biomolecular Screening 2011, 16(4):415-426.
30. Regeneration Base (RegenBase). [http://regenbase.org], Last visited on 11/01/2013.
31. Przydzial MJ, Bhhatarai B, Koleti A, Vempati U, Schürer SC: GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework. Bioinformatics 2013, 29.
32. OntoFox. [http://ontofox.hegroup.org], Last visited on 11/01/2013.
33. The OWL 2 Web Ontology Language Document Overview. [http://www.w3.org/TR/owl2-overview/], Last visited on 11/01/2013.
34. Koller D, Friedman N: Probabilistic Graphical Models: Principles and Techniques. MIT Press; 2009.
35. Shvachko K, Kuang H, Radia S, Chansler R: The Hadoop Distributed File System. Proceedings of the 2010 IEEE 26th Symposium on Mass Storage Systems and Technologies (MSST) IEEE Computer Society, Washington, DC, USA; 2010, 1-10.