• SIPHS (2015 - 2020) # Semantic Interpretation of Personal Health messageS [Web site, GitHub repo, Zenodo repo]

Canonical reference: Limsopatham, N. and Collier, N. (2016), “Normalising medical concepts in social media texts by learning semantic representation”, in Proceedings of the Association of Computational Linguistics Annual Meeting (ACL 2016), Berlin, Germany, August 1^st to 7^th [pdf].

Funded by EPSRC (EP/M005089/1)

• Panda Alert (2015 - 2018) # Panda Alert: understanding the significance of adverse health event reports using distributed semantic models

Canonical reference: Gritta, M., Pilehvar, M. T., Limsopatham, N., & Collier, N. (2017), "What’s missing in geographical parsing?", Language Resources and Evaluation, 1-21.[pdf].

Funded by NERC DREAM CDT (1649558)

• PheneBank (2015 - 2018) # PheneBank: automatic extraction and validation of a database of human phenotype-disease associations from the scientific literature [Web site]

Funded by MRC (MR/M025160/1)

• PhenoMiner (2012 - 2014) # Semantic mining of phenotypes and their assocations from the biomedical literature [Database, Web site, GitHub repo, Zenodo repo]

Canonical reference: Collier, N., Groza, T., Smedley, D., Robinson, P., Oellrich, A. and Rebholz-Schuhmann, D. (2015). "PhenoMiner: from text to 4,000 phenotypes associated with OMIM diseases", Database, Oxford University Press, vol. 2015, bav104. DOI: 10.1093/bav104. [pdf]

Funded by EC Marie Curie (301806)

• BioCaster (2006 - 2012) # Infectious disease detection and tracking from newswire [web site]

Canonical reference: Collier, N. Doan, S., Kawazoe, A., Matsuda Goodwin, R., Conway, M., Tateno, Y., Ngo, Q., Dien, D., Kawtrakul, A., Takeuchi, K., Shigematsu, M. and Taniguchi, K. (2008), “BioCaster: detecting public health rumors with a Web-based text mining system”, Bioinformatics, 24(24):2940-2941, Oxford University Press, DOI: 10.1093/bioinformatics/btn534. [html] [pubmed]

Funded under multiple grants including the JST PRESTO programme and the JSPS Young Researcher programme.

• ZAISA (2003 - 2006) # Zone Analysis in Scientific Articles [web site]

Reference: Mizuta, Y., Korhonen, A., Mullen, T. and Collier, N. (2006), “Zone analysis in biology articles as a basis for information extraction”, International Journal of Medical Informatics, Elsevier, 75(6): 468-487. [pubmed]

• PASBio (2002 - 2005) # Predicate Argument Structures for Biology [web site]

Reference: Wattarujeekrit, T., Shah, P. and Collier, N. (2004), “PASBio: predicate-argument structures for event extraction in molecular biology”, BMC Bioinformatics, 5:155, DOI: 10.1186/1471-2105-5-155. [pdf][pubmed][PASBio data]

• PIA (2000 - 2004) # Portable Information Access project [web site]

Reference: Collier, N. (2001), “Machine learning for information extraction from XML markup-up text on the Semantic Web”, Proc. Semantic Web Workshop at the Tenth International Conference on the World Wide Web (WWW’10), Hong Kong, May 1-5, pp. 29-36. [pdf]