@conference {IT405,
	title = {IT405: Building Concordant Ontologies for Drug Discovery},
	booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)},
	series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)},
	year = {2016},
	month = {11/30/16},
	publisher = {CEUR-ws.org Volume 1747},
	organization = {CEUR-ws.org Volume 1747},
	abstract = {<p>n this study we demonstrate how we interconnect three different ontologies, the BioAssay Ontology (BAO), LINCS Information FramEwork ontology (LIFEo), and the Drug Target Ontology (DTO). The three ontologies are built and maintained for three different projects: BAO for the BioAssay Ontology Project, LIFEo for the Library of Integrated Network-Based Cellular Signatures (LINCS) project, and DTO for the Illuminating the Druggable Genome (IDG) project. DTO is a new ontology that aims to formally describe drug target knowledge relevant to drug discovery. LIFEo is an application ontology to describe information in the LIFE software system. BAO is a highly accessed NCBO ontology; it has been extended formally to describe several LINCS assays. The three ontologies use the same principle architecture that allows for re-use and easy integration of ontology modules and instance data. Using the formal definitions in DTO, LIFEo, and BAO and data from various resources one can quickly identify disease-relevant and tissue- specific genes, proteins, and prospective small molecules. We show a simple use case example demonstrating knowledge-based linking of life science data with the potential to empower drug discovery.</p>
},
	url = {http://ceur-ws.org/Vol-1747/IT405_ICBO2016.pdf},
	author = {Hande K{\"u}{\c c}{\"u}k-Mcginty and Saurabh Metha and Yu Lin and Nooshin Nabizadeh and Vasileios Stathias and Dusica Vidovic and Amar Koleti and Christopher Mader and Jianbin Duan and Ubbo Visser and Stephan Schurer}
}
@conference {IP07,
	title = {IP07: The Cell Line Ontology integration and analysis of the knowledge of LINCS cell lines},
	booktitle = {International Conference on Biomedical Ontology and BioCreative (ICBO BioCreative 2016)},
	series = {Proceedings of the Joint International Conference on Biological Ontology and BioCreative (2016)},
	year = {2016},
	month = {11/30/16},
	publisher = {CEUR-ws.org Volume 1747},
	organization = {CEUR-ws.org Volume 1747},
	abstract = {<p>Cell lines are crucial to study molecular signatures and pathways, and are widely used in the NIH Common Fund LINCS project. The Cell Line Ontology (CLO) is a community-based ontology representing and classifying cell lines from different resources. To better serve the LINCS research community, from the LINCS Data Portal and ChEMBL, we identified 1,097 LINCS cell lines, among which 717 cell lines were associated with 121 cancer types, and 352 cell line terms did not exist in CLO. To harmonize LINCS cell line representation and CLO, CLO design patterns were slightly updated to add new information of the LINCS cell lines including different database cross-reference IDs. A new shortcut relation was generated to directly link a cell line to the disease of the patient from whom the cell line was originated. After new LINCS cell lines and related information were added to CLO, a CLO subset/view (LINCS-CLOview) of LINCS cell lines was generated and analyzed to identify scientific insights into these LINCS cell lines. This study provides a first time use case on how CLO can be updated and applied to support cell line research from a specific research community or project initiative.</p>
},
	url = {http://ceur-ws.org/Vol-1747/IP07_ICBO2016.pdf},
	author = {Edison Ong and Jiangan Xie and Zhaohui Ni and Qingping Liu and Yu Lin and Vasileios Stathias and Caty Chung and Stephan Schurer and Yongqun He}
}
