@conference {IT503, title = {IT503: Malaria study data integration and information retrieval based on OBO Foundry ontologies}, 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 = {

The International Centers of Excellence in Malaria Research (ICEMR) projects involve studies to understand the epidemiology and transmission patterns of malaria in different geographic regions. Two major challenges of integrating data across these projects are: (1) standardization of highly heterogeneous epidemiologic data collected by various ICEMR projects; (2) provision of user-friendly search strategies to identify and retrieve information of interest from the very complex ICEMR data. We pursued an ontology-based strategy to address these challenges. We utilized and contributed to the Open Biological and Biomedical Ontologies to generate a consistent semantic representation of three different ICEMR data dictionaries that included ontology term mappings to data fields and allowed values. This semantic representation of ICEMR data served to guide data loading into a relational database and presentation of the data on web pages in the form of search filters that reveal relationships specified in the ontology and the structure of the underlying data. This effort resulted in the ability to use a common logic for storing and display of data on study participants, their clinical visits, and epidemiological information on their living conditions (dwelling) and geographic location. Users of the Plasmodium Genomics Resource, PlasmoDB, accessing the ICEMR data will be able to search for participants based on environmental factors such as type of dwelling, location or mosquito biting rate, characteristics such as age at enrollment, relevant genotypes or gender and visit data such as laboratory findings, diagnoses, malaria medications, symptoms, and other factors.

}, url = {http://ceur-ws.org/Vol-1747/IT503_ICBO2016.pdf}, author = {Jie Zheng and Jashon Cade and Brian Brunk and David Roos and Chris Stoeckert and San James and Emmanuel Arinaitwe and Bryan Greenhouse and Grant Dorsey and Steven Sullivan and Jane Carlton and Gabriel Carrasco-Escobar and Dionicia Gamboa and Paula Maguina-Mercedes and Joseph Vinetz} } @conference {IP04, title = {IP04: EGO: a biomedical ontology for integrative epigenome representation and analysis}, 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 = {

Epigenomics is crucial to understand biological mechanisms beyond genome DNA. To better represent epigenomic knowledge and support data integration, we developed a prototype Epigenome Ontology (EGO). EGO top level hierarchy and design pattern are provided with a use case illustration. EGO is proposed to be used for statistically analyzing enriched epigenomic features based on given sequence data input using statistical methods.

}, url = {http://ceur-ws.org/Vol-1747/IP04_ICBO2016.pdf}, author = {Yongqun He and Zhaohui Qin and Jie Zheng} } @conference {D202, title = {D201: Ontobull and BFOConvert: Web-based programs to support automatic ontology conversion}, 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 = {

When a widely reused ontology appears in a new version which is not compatible with older versions, the ontologies reusing it need to be updated accordingly. Ontobull (http://ontobull.hegroup.org) has been developed to automatically update ontologies with new term IRI(s) and associated metadata to take account of such version changes. To use the Ontobull web interface a user is required to (i) upload one or more ontology OWL source files; (ii) input an ontology term IRI mapping; and (where needed) (iii) provide update settings for ontology headers and XML namespace IDs. Using this information, the backend Ontobull Java program automatically updates the OWL ontology files with desired term IRIs and ontology metadata. The Ontobull subprogram BFOConvert supports the conversion of an ontology that imports a previous version of BFO. A use case is pro- vided to demonstrate the features of Ontobull and BFOConvert.

}, url = {http://ceur-ws.org/Vol-1747/D201_ICBO2016.pdf}, author = {Edison Ong and Zuoshuang Xiang and Jie Zheng and Barry Smith and Yongqun He} }