Biomedical Statistics and Informatics

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  • A conceptual-model-based computational alembic for a web of knowledge

    Embley, D. W., Liddle, S. W., Lonsdale, D., Nagy, G., Tijerino, Y., Clawson, R., Crabtree, J., Ding, Y., Jha, P., Lian, Z., Lynn, S., Padmanabhan, R. K., Peters, J., Tao, C., Watts, R., Woodbury, C. & Zitzelberger, A., 2008, Conceptual Modeling - ER 2008 - 27th International Conference on Conceptual Modeling, Proceedings. Springer Verlag, p. 532-533 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5231 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • An integrative computational approach to identify disease-specific networks from PubMed literature information

    Zhang, Y., Li, D., Tao, C., Shen, F. & Liu, H., 2013, Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013. p. 72-75 4 p. 6732738. (Proceedings - 2013 IEEE International Conference on Bioinformatics and Biomedicine, IEEE BIBM 2013).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    7 Scopus citations
  • An overview of electronic health information management systems quality assessment

    Bouamrane, M. M., Mair, F. S. & Tao, C., Dec 7 2012, MIX-HS'12 - Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems, Co-located with CIKM 2012. p. 37-46 10 p. (International Conference on Information and Knowledge Management, Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    7 Scopus citations
  • A prototype mobile virtual assistant for semantic-based vaccine information retrieval

    Amith, M. & Tao, C., 2014, Smart Health - International Conference, ICSH 2014, Proceedings. Springer Verlag, p. 200-205 6 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8549 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    4 Scopus citations
  • A semantic-web oriented representation of clinical element model for secondary use of electronic healthcare data

    Tao, C., Jiang, G., Oniki, T. A., Freimuth, R. R., Pathak, J., Zhu, Q., Sharma, D., Huff, S. M. & Chute, C. G., Dec 1 2012, Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012. 1 p. 6366225. (Proceedings - 2012 IEEE 2nd Conference on Healthcare Informatics, Imaging and Systems Biology, HISB 2012).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Automatic creation of Web services from extraction ontologies

    Tao, C., Ding, Y. & Lonsdale, D., 2006, Advances in Conceptual Modeling: Theory and Practice - ER 2006 Workshops BP-UML, CoMoGIS, COSS, ECDM, OIS, QoIS, SemWAT, Proceedings. Springer Verlag, p. 415-424 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4231 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • Automatic hidden-web table interpretation by sibling page comparison

    Tao, C. & Embley, D. W., 2007, Conceptual Modeling - ER 2007 - 26th International Conference on Conceptual Modeling, Proceedings. Springer Verlag, p. 566-581 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4801 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    8 Scopus citations
  • Bioinformatics strategies for identifying regions of epigenetic deregulation associated with aberrant transcript splicing and RNA-editing

    Champion, M. D., Hlady, R. A., Yan, H., Evans, J., Nie, J., Lee, J. H., Bogenberger, J., Nandakumar, K., Davila, J., Moore, R., Nair, A., O'Brien, D., Zhu, Y. X., Kortum, K. M., Ordog, T., Zhang, Z., Joseph, R. W., Stewart, A. K., Kocher, J. P., Jonasch, E. & 3 others, Robertson, K. D., Tibes, R. & Ho, T. H., 2015, BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015. Pastor, O., Sinoquet, C., Fred, A., Gamboa, H. & Elias, D. (eds.). SciTePress, p. 163-170 8 p. (BIOINFORMATICS 2015 - 6th International Conference on Bioinformatics Models, Methods and Algorithms, Proceedings; Part of 8th International Joint Conference on Biomedical Engineering Systems and Technologies, BIOSTEC 2015).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
  • Developing customizable cancer information extraction modules for pathology reports using clamp

    Soysal, E., Warner, J. L., Wang, J., Jiang, M., Harvey, K., Jain, S. K., Dong, X., Song, H. Y., Siddhanamatha, H., Wang, L., Dai, Q., Chen, Q., Du, X., Tao, C., Yang, P., Denny, J. C., Liu, H. & Xu, H., Aug 21 2019, MEDINFO 2019: Health and Wellbeing e-Networks for All - Proceedings of the 17th World Congress on Medical and Health Informatics. Seroussi, B., Ohno-Machado, L., Ohno-Machado, L. & Seroussi, B. (eds.). IOS Press, p. 1041-1045 5 p. (Studies in Health Technology and Informatics; vol. 264).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

  • FOCIH: Form-based ontology creation and information harvesting

    Tao, C., Embley, D. W. & Liddle, S. W., 2009, Conceptual Modeling - ER 2009 - 28th International Conference on Conceptual Modeling, Proceedings. p. 346-359 14 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 5829 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    12 Scopus citations
  • Isosemantic rendering of clinical information using formal ontologies and RDF

    Martínez-Costa, C., Bosca, D., Legaz-García, M. C., Tao, C., Fernández Breis, J. T., Schulz, S. & Chute, C. G., Jan 1 2013, MEDINFO 2013 - Proceedings of the 14th World Congress on Medical and Health Informatics. 1-2 ed. IOS Press, 1 p. (Studies in Health Technology and Informatics; vol. 192, no. 1-2).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    4 Scopus citations
  • KBB: A knowledge-bundle builder for research studies

    Embley, D. W., Liddle, S. W., Lonsdale, D. W., Stewart, A. & Tao, C., Dec 15 2010, Advances in Conceptual Modeling - Applications and Challenges, ER 2010 Workshops ACM-L, CMLSA, CMS, DE@ER, FP-UML, SeCoGIS, WISM, Proceedings. p. 148-157 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6413 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Learning on weighted hypergraphs to integrate protein interactions and gene expressions for cancer outcome prediction

    Hwang, T., Tian, Z., Kuang, R. & Kocher, J. P., Dec 1 2008, Proceedings - 8th IEEE International Conference on Data Mining, ICDM 2008. p. 293-302 10 p. 4781124. (Proceedings - IEEE International Conference on Data Mining, ICDM).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    32 Scopus citations
  • Linked vaccine adverse event data representation from VAERS for biomedical informatics research

    Tao, C., Wu, P. & Zhang, Y., 2014, Trends and Applications in Knowledge Discovery and Data Mining - PAKDD 2014 International Workshops: DANTH, BDM, MobiSocial, BigEC, CloudSD, MSMV-MBI, SDA, DMDA-Health, ALSIP, SocNet, DMBIH, BigPMA, Revised Selected Papers. Peng, W-C., Wang, H., Zhou, Z-H., Ho, T. B., Tseng, V. S., Chen, A. L. P. & Bailey, J. (eds.). Springer Verlag, p. 652-661 10 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8643).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Managing complexity in pre-operative information management systems

    Bouamrane, M. M., Mair, F. & Tao, C., 2011, CIKM 2011 Glasgow: MIXHS'11 - Proceedings of the 1st International Workshop on Managing Interoperability and Complexity in Health Systems. p. 3-10 8 p. (International Conference on Information and Knowledge Management, Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    5 Scopus citations
  • Managing interoperability and complexity inhealth systems: MIXHS'11 workshop summary

    Bouamrane, M. M. & Tao, C., Dec 13 2011, CIKM'11 - Proceedings of the 2011 ACM International Conference on Information and Knowledge Management. p. 2635-2636 2 p. (International Conference on Information and Knowledge Management, Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Managing interoperability and compleXity in health systems - MIXHS'12

    Tao, C. & Bouamrane, M. M., Dec 19 2012, CIKM 2012 - Proceedings of the 21st ACM International Conference on Information and Knowledge Management. p. 2758-2759 2 p. (ACM International Conference Proceeding Series).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Modeling UIMA type system using web ontology language - Towards interoperability among UIMA-based NLP tools

    Liu, H., Wu, S., Tao, C. & Chute, C., Dec 7 2012, MIX-HS'12 - Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems, Co-located with CIKM 2012. p. 31-36 6 p. (International Conference on Information and Knowledge Management, Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    3 Scopus citations
  • Ontology-based temporal relation modeling with map-reduce latent dirichlet allocations for big EHR data

    Li, D., Tao, C., Liu, H. & Chute, C., Dec 1 2012, Proceedings - 2nd International Conference on Cloud and Green Computing and 2nd International Conference on Social Computing and Its Applications, CGC/SCA 2012. p. 708-715 8 p. 6382894. (Proceedings - 2nd International Conference on Cloud and Green Computing and 2nd International Conference on Social Computing and Its Applications, CGC/SCA 2012).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Optimizing semantic MEDLINE for translational science studies using semantic web technologies

    Tao, C., Zhang, Y., Jiang, G., Bouamrane, M. M. & Chute, C. G., 2012, MIX-HS'12 - Proceedings of the 2nd International Workshop on Managing Interoperability and Complexity in Health Systems, Co-located with CIKM 2012. p. 53-57 5 p. (International Conference on Information and Knowledge Management, Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    11 Scopus citations
  • Pharmacological class data representation in the Web Ontology Language (OWL)

    Zhu, Q. & Tao, C., Jan 7 2015, Proceedings - 2014 IEEE International Conference on Big Data, IEEE Big Data 2014. Chang, W., Huan, J., Cercone, N., Pyne, S., Honavar, V., Lin, J., Hu, X. T., Aggarwal, C., Mobasher, B., Pei, J. & Nambiar, R. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 77-84 8 p. 7004397. (Proceedings - 2014 IEEE International Conference on Big Data, IEEE Big Data 2014).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Phenotyping on EHR data using OWL and semantic web technologies

    Tao, C., Li, D., Shen, F., Lian, Z., Pathak, J., Liu, H. & Chute, C. G., Aug 12 2013, Smart Health - International Conference, ICSH 2013, Proceedings. p. 31-32 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 8040 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Proposed SKOS extensions for bioportal terminology services

    Tao, C., Noy, N. F., Solbrig, H. R., Shah, N. H., Musen, M. A. & Chute, C. G., Jun 18 2012, The Semantic Web - Joint International Semantic Technology Conference, JIST 2011, Proceedings. p. 342-349 8 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 7185 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    1 Scopus citations
  • Seed-based generation of personalized bio-ontologies for information extraction

    Tao, C. & Embley, D. W., 2007, Advances in Conceptual Modeling - Foundations and Applications - ER 2007 Workshops CMLSA, FP-UML, ONISW, QoIS, RIGiM, SeCoGIS, Proceedings. Springer Verlag, p. 74-84 11 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4802 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    9 Scopus citations
  • Time-oriented question answering from clinical narratives using semantic-web techniques

    Tao, C., Solbrig, H. R., Sharma, D. K., Wei, W. Q., Savova, G. K. & Chute, C. G., 2010, The Semantic Web, ISWC 2010 - 9th International Semantic Web Conference, ISWC 2010, Revised Selected Papers. PART 2 ed. Springer Verlag, p. 241-256 16 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 6497 LNCS, no. PART 2).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    25 Scopus citations
  • Toward making online biological data machine understandable

    Tao, C., 2006, The Semantic Web - ISWC 2006 - 5th International Semantic Web Conference, ISWC 2006, Proceedings. Springer Verlag, p. 992-993 2 p. (Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics); vol. 4273 LNCS).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    Open Access
    1 Scopus citations
  • Towards an Ontology-driven Framework to Enable Development of Personalized mHealth Solutions for Cancer Survivors' Engagement in Healthy Living

    Myneni, S., Amith, M., Geng, Y. & Tao, C., 2015, MEDINFO 2015: eHealth-Enabled Health - Proceedings of the 15th World Congress on Health and Biomedical Informatics. Georgiou, A., Sarkar, I. N. & de Azevedo Marques, P. M. (eds.). IOS Press, p. 113-117 5 p. (Studies in Health Technology and Informatics; vol. 216).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    5 Scopus citations
  • Toward semantic web based knowledge representation and extraction from electronic health records

    Tao, C., Pathak, J., Welch, S. R., Bouamrane, M. M., Huff, S. M. & Chute, C. G., Dec 15 2011, CIKM 2011 Glasgow: MIXHS'11 - Proceedings of the 1st International Workshop on Managing Interoperability and Complexity in Health Systems. p. 75-78 4 p. (International Conference on Information and Knowledge Management, Proceedings).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    8 Scopus citations
  • Towards event sequence representation, reasoning and visualization for EHR data

    Tao, C., Wongsuphasawat, K., Clark, K., Plaisant, C., Shneiderman, B. & Chute, C. G., 2012, IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium. p. 801-805 5 p. (IHI'12 - Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    12 Scopus citations
  • Trivalent Influenza Vaccine Adverse Event Analysis Based on MedDRA System Organ Classes Using VAERS Data

    Tao, C., Du, J., Cai, Y. & Chen, Y., 2015, MEDINFO 2015: eHealth-Enabled Health - Proceedings of the 15th World Congress on Health and Biomedical Informatics. Georgiou, A., Sarkar, I. N. & de Azevedo Marques, P. M. (eds.). IOS Press, p. 1076 1 p. (Studies in Health Technology and Informatics; vol. 216).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    2 Scopus citations
  • Unraveling complex local genomic rearrangements from long-read data

    Stephens, Z. D., Iyer, R. K., Wang, C. & Kocher, J. P. A., Dec 15 2017, Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017. Yoo, I., Zheng, J. H., Gong, Y., Hu, X. T., Shyu, C-R., Bromberg, Y., Gao, J. & Korkin, D. (eds.). Institute of Electrical and Electronics Engineers Inc., p. 181-187 7 p. (Proceedings - 2017 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2017; vol. 2017-January).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution

    2 Scopus citations
  • Using semantic web technologies for quality measure phenotyping algorithm representation and automatic execution on EHR data

    Shen, F., Li, D., Liu, H., Lee, Y., Pathak, J., Chute, C. G. & Tao, C., Jan 1 2014, 2014 IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2014. IEEE Computer Society, p. 531-534 4 p. 6864419. (2014 IEEE-EMBS International Conference on Biomedical and Health Informatics, BHI 2014).

    Research output: Chapter in Book/Report/Conference proceedingConference contribution