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A UIMA wrapper for the NCBO annotator.

Bioinformatics (Oxford, England)

Roeder C, Jonquet C, Shah NH, Baumgartner WA, Verspoor K, Hunter L.
PMID: 20505005
Bioinformatics. 2010 Jul 15;26(14):1800-1. doi: 10.1093/bioinformatics/btq250. Epub 2010 May 26.

SUMMARY: The Unstructured Information Management Architecture (UIMA) framework and web services are emerging as useful tools for integrating biomedical text mining tools. This note describes our work, which wraps the National Center for Biomedical Ontology (NCBO) Annotator-an ontology-based annotation...

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Roeder C, Jonquet C, Shah NH, et al. A UIMA wrapper for the NCBO annotator. Bioinformatics. 2010;26(14):1800-1doi: 10.1093/bioinformatics/btq250.
Roeder, C., Jonquet, C., Shah, N. H., Baumgartner, W. A., Verspoor, K., & Hunter, L. (2010). A UIMA wrapper for the NCBO annotator. Bioinformatics (Oxford, England), 26(14), 1800-1. https://doi.org/10.1093/bioinformatics/btq250
Roeder, Christophe, et al. "A UIMA wrapper for the NCBO annotator." Bioinformatics (Oxford, England) vol. 26,14 (2010): 1800-1. doi: https://doi.org/10.1093/bioinformatics/btq250
Roeder C, Jonquet C, Shah NH, Baumgartner WA, Verspoor K, Hunter L. A UIMA wrapper for the NCBO annotator. Bioinformatics. 2010 Jul 15;26(14):1800-1. doi: 10.1093/bioinformatics/btq250. Epub 2010 May 26. PMID: 20505005; PMCID: PMC2894505.
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HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA.

Computational intelligence

Cohen KB, Verspoor K, Johnson HL, Roeder C, Ogren PV, Baumgartner WA, White E, Tipney H, Hunter L.
PMID: 25937701
Comput Intell. 2011 Nov;27(4):681-701. doi: 10.1111/j.1467-8640.2011.00405.x.

We approached the problems of event detection, argument identification, and negation and speculation detection in the BioNLP'09 information extraction challenge through concept recognition and analysis. Our methodology involved using the OpenDMAP semantic parser with manually written rules. The original...

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Cohen KB, Verspoor K, Johnson HL, et al. HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. Comput Intell. 2011;27(4):681-701doi: 10.1111/j.1467-8640.2011.00405.x.
Cohen, K. B., Verspoor, K., Johnson, H. L., Roeder, C., Ogren, P. V., Baumgartner, W. A., White, E., Tipney, H., & Hunter, L. (2011). HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. Computational intelligence, 27(4), 681-701. https://doi.org/10.1111/j.1467-8640.2011.00405.x
Cohen, K Bretonnel, et al. "HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA." Computational intelligence vol. 27,4 (2011): 681-701. doi: https://doi.org/10.1111/j.1467-8640.2011.00405.x
Cohen KB, Verspoor K, Johnson HL, Roeder C, Ogren PV, Baumgartner WA, White E, Tipney H, Hunter L. HIGH-PRECISION BIOLOGICAL EVENT EXTRACTION: EFFECTS OF SYSTEM AND OF DATA. Comput Intell. 2011 Nov;27(4):681-701. doi: 10.1111/j.1467-8640.2011.00405.x. PMID: 25937701; PMCID: PMC4414063.
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Consistent visualizations of changing knowledge.

Summit on translational bioinformatics

Tipney HJ, Schuyler RP, Hunter L.
PMID: 21347184
Summit Transl Bioinform. 2009 Mar 01;2009:129-32.

Networks are increasingly used in biology to represent complex data in uncomplicated symbolic form. However, as biological knowledge is continually evolving, so must those networks representing this knowledge. Capturing and presenting this type of knowledge change over time is...

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Tipney HJ, Schuyler RP, Hunter L. Consistent visualizations of changing knowledge. Summit Transl Bioinform. 2009;2009:129-32
Tipney, H. J., Schuyler, R. P., & Hunter, L. (2009). Consistent visualizations of changing knowledge. Summit on translational bioinformatics, 2009129-32.
Tipney, Hannah J, et al. "Consistent visualizations of changing knowledge." Summit on translational bioinformatics vol. 2009 (2009): 129-32.
Tipney HJ, Schuyler RP, Hunter L. Consistent visualizations of changing knowledge. Summit Transl Bioinform. 2009 Mar 01;2009:129-32. PMID: 21347184; PMCID: PMC3041575.
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U-Compare: share and compare text mining tools with UIMA.

Bioinformatics (Oxford, England)

Kano Y, Baumgartner WA, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J.
PMID: 19414535
Bioinformatics. 2009 Aug 01;25(15):1997-8. doi: 10.1093/bioinformatics/btp289. Epub 2009 May 04.

SUMMARY: Due to the increasing number of text mining resources (tools and corpora) available to biologists, interoperability issues between these resources are becoming significant obstacles to using them effectively. UIMA, the Unstructured Information Management Architecture, is an open framework...

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Kano Y, Baumgartner WA, McCrohon L, et al. U-Compare: share and compare text mining tools with UIMA. Bioinformatics. 2009;25(15):1997-8doi: 10.1093/bioinformatics/btp289.
Kano, Y., Baumgartner, W. A., McCrohon, L., Ananiadou, S., Cohen, K. B., Hunter, L., & Tsujii, J. (2009). U-Compare: share and compare text mining tools with UIMA. Bioinformatics (Oxford, England), 25(15), 1997-8. https://doi.org/10.1093/bioinformatics/btp289
Kano, Yoshinobu, et al. "U-Compare: share and compare text mining tools with UIMA." Bioinformatics (Oxford, England) vol. 25,15 (2009): 1997-8. doi: https://doi.org/10.1093/bioinformatics/btp289
Kano Y, Baumgartner WA, McCrohon L, Ananiadou S, Cohen KB, Hunter L, Tsujii J. U-Compare: share and compare text mining tools with UIMA. Bioinformatics. 2009 Aug 01;25(15):1997-8. doi: 10.1093/bioinformatics/btp289. Epub 2009 May 04. PMID: 19414535; PMCID: PMC2712335.
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Showing 1 to 4 of 4 entries