Publications - Semantics of Biological Processes

Publications

2021

Welsh C, Nickerson DP , Rampadarath A , Neal ML , Sauro HM, Gennari JH. libOmexMeta: Enabling semantic annotation of models to support FAIR principles. Bioinformatics. (accepted)

2020

Neal ML, Gennari JH, Waltemath D, Nickerson DP, König M. Open modeling and exchange metadata specification version 1.0. Journal of Integrative Bioinformatics. 2020. 17(2-3):20200020.

2019

Wang LL, Hayman T, Smith JR, Tutaj M, Shimoyama ME, Gennari JH. Predicting instances of pathway ontology classes for pathway integration. Journal of Biomedical Semantics. 2019. 10, 11.

Sarwar DM, Kalbasi R, Gennari JH, Carlson BE, Neal ML, de Bono B, Atalag K, Hunter PJ, Nickerson DP. Model annotation and discovery with the Physiome Model Repository. BMC Bioinformatics. 2019. 20(1):457.

Neal ML, König M, Nickerson D, Misirli G, Kalbasi R, Dräger A, et al. Harmonizing semantic annotations for computational models in biology. Briefings in Bioinformatics. 2019. 20(2):540–550.

Neal ML, Thompson CT, Kim KG, James RC, Cook DL, Carlson BE, Gennari JH. SemGen: a tool for semantics-based annotation and composition of biosimulation models. Bioinformatics. 2019. 35(9):1600–1602.

Cook DL, Gennari JH, Neal ML. The Ontology of Physics for Biology – A companion to Basic Formal Ontology. Proceedings of the 2019 International Conference on Biomedical Ontology.

2017

Wang L, Gennari JH. Similarity Metrics for Determining Overlap Among Biological Pathways. Proceedings of the 2017 International Conference on Biomedical Ontology.

Cook DL, Gennari JH, Neal ML. Extending the Ontology of Physics for Biology with Thermodynamics. Proceedings of the 2017 International Conference on Biomedical Ontology.

2016

Neal ML, Gennari JH, Cook DL. Qualitative causal analyses of biosimulation models. Proceedings of the 2016 International Conference on Biomedical Ontology.

2015

Neal ML, Carlson BE, Thompson CT, James RC, Kim KG, Tran K, Crampin EJ, Cook DL, Gennari JH. Semantics-based composition of integrated cardiomyocyte models motivated by real-world use cases. PLoS One. 2015. 10(12): e0145621.

2014

Neal ML, Cooling MT, Smith LP, Thompson CT, Sauro HM, Carlson BE, Cook DL, Gennari JH. A reappraisal of how to build modular, reusable models of biological systems. PLoS Computational Biology. 2014. 10(10): e1003849.

Neal ML, Galdzicki M, Gallimore JT, Sauro HM. A C library for retrieving specific reactions from the BioModels database. Bioinformatics. 2014. 30(1):129-130.

2013

Cook DL, Neal ML, Bookstein FL, Gennari JH. Ontology of Physics for Biology: representing physical dependencies as a basis for biological processes. Journal of Biomedical Semantics. 2013. 4:41.

Neal ML, Cook DL, Gennari JH. An OWL knowledge base for classifying and querying collections of physiological models: A prototype human physiome. Proceedings of the 2013 International Conference on Biomedical Ontology.
Cook DL, Neal ML, Hoehndorf R, Gkoutos G, Gennari JH. Representing physiological processes and their participants with PhysioMaps. Journal of Biomedical Semantics. 2013. 4(Suppl 1):S2.

2012

Galdzicki M. The Synthetic Biology Open Language: A data exchange standard for biological engineering. Ph.D. Dissertation. University of Washington. 2012.

Beard D, Neal ML, Tabesh-Saleki N, Thompson CT, Bassingthwaighte JB, Shimoyama M, Carlson B. Multiscale modeling and data integration in the Virtual Physiological Rat Project. Annals of Biomedical Engineering. 2012. 40(11):2365-2378.

Gennari JH, Neal ML, Hoehndorf R, Gkoutos GV, Cook DL. Discovering model-model connections in biological model repositories. Proceedings of the VPH2012: International Conference on Computational Biomedicine - The Virtual Physiological Human Initiative Scientific Sessions 2012.

2011

Cook DL, Bookstein FL, Gennari JH. Physical Properties of Biological Entities: An Introduction to the Ontology of Physics for Biology. PLoS One. 2011. 6(12): e28708

Hoehndorf R, Dumontier M, Gennari JH, Wimalaratne S, de Bono B, Cook DL, Gkoutos GV. Integrating systems biology models and biomedical ontologies. BMC Systems Biology. 2011. 5:124.

Cook DL, Galdzicki M, Neal ML, Mejino JLV, Gennari JH. HeartCyc, a cardiac cycle process ontology based in the Ontology of Physics for Biology. Proceedings of the International Conference on Biomedical Ontology. 2011. 41:46.

Galdzicki M, Rodriguez C, Chandran D, Sauro HM, Gennari JH. Standard Biological Parts Knowledgebase. PLoS One. 2011. 6(2): e17005.

Peccoud J, Anderson JC, Chandran D, Densmore D, Galdzicki M, Lux MW, Rodriguez CA, Guy-Bart S, Sauro HM. Essential information for synthetic DNA sequences. Nature Biotechnology. 2011. 29:22.

Gennari JH, Neal ML, Galdzicki M, Cook DL. Multiple ontologies in action: composite annotations for biosimulation models. Journal of Biomedical Informatics. 2011. 44(1):146-154.

2010

Neal ML. Modular, semantics-based composition of biosimulation models. Ph.D. Dissertation. University of Washington. 2010.

Neal ML, Kerckhoffs RC. Current progress in patient-specific modeling. Briefings in Bioinformatics. 2010. 11(1):111-126.

2009

Neal ML, Gennari JH, Arts T, Cook DL. Advances in semantic representation for multiscale biosimulation: A case study in merging models. Proceedings of the Pacific Symposium on Biocomputing, 2009:304-315.

Gennari JH, Neal ML, Mejino Jr JLV, Cook DL. Using Multiple Reference Ontologies: Managing Composite Annotations. Proceedings of the International Conference on Biomedical Ontology. Buffalo, NY., 2009:83-86.

Cook DL, Mejino JLV, Neal ML, Gennari JH. Composite annotations: requirements for mapping multiscale data and models to biomedical ontologies. Proceedings of the 31st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC'09), Minneapolis, MN. 2009. 1:2791-2794.

2008

Cook DL, Mejino Jr JLV, Neal ML, Gennari JH. Bridging Biological Ontologies and Biosimulation: The Ontology of Physics for Biology. Proceedings of the American Medical Informatics Association Annual Symposium. 2008:136-140.

Gennari JH, Neal ML, Carlson BE, Cook DL. Integration of multi-scale biosimulation models via light-weight semantics. Proceedings of the Pacific Symposium on Biocomputing. 2008. 13:414-25.

2007

Cook DL, Wiley JC, Gennari JH. Chalkboard: ontology-based pathway modeling and qualitative inference of disease mechanisms. Proceedings of the Pacific Symposium on Biocomputing, 2007:16-29.

2006

Rubin DL, Grossman D, Neal ML, Cook DL, Bassingthwaighte J, Musen M. Ontology-based representation of simulation models of physiology. Proceedings of the American Medical Informatics Association Conference. 2006:664-8.