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The overarching long-term vision of our research is to create novel technologies for processing clinical free text. Such technologies will enable sophisticated and efficient indexing, retrieval and data mining over the ever increasing amounts of electronic clinical data. Processing free text poses a number of challenges to which the fields of Artificial intelligence, natural language processing and computer science in general have made advances. Methods for processing free text are informed by linguistic theory combined with the power of statistical inferencing. A key component to the next step, natural language understanding, is discovering events and their relations on a timeline. Temporal relations are of prime importance in biomedicine as they are intrinsically linked to diseases, signs and symptoms, and treatments. Understanding the timeline of clinically relevant events is key to the next generation of translational research where the importance of generalizing over large amounts of data holds the promise of deciphering biomedical puzzles.  
The overarching long-term vision of our research is to create novel technologies for processing clinical free text. Such technologies will enable sophisticated and efficient indexing, retrieval and data mining over the ever increasing amounts of electronic clinical data. Processing free text poses a number of challenges to which the fields of Artificial intelligence, natural language processing and computer science in general have made advances. Methods for processing free text are informed by linguistic theory combined with the power of statistical inferencing. A key component to the next step, natural language understanding, is discovering events and their relations on a timeline. Temporal relations are of prime importance in biomedicine as they are intrinsically linked to diseases, signs and symptoms, and treatments. Understanding the timeline of clinically relevant events is key to the next generation of translational research where the importance of generalizing over large amounts of data holds the promise of deciphering biomedical puzzles.  
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The goal of our current proposal is to discover temporal relations from clinical free text through achieving four specific aims:
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The best methods have been/will be released as part of the cTAKES (ctakes.apache.org) for the larger community to use and contribute to. We will test the methods against biomedical queries.
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Specific Aim 1: Develop (1) a temporal relation annotation schema and guidelines for clinical free text based on TimeML, which will require extensions to Treebank, PropBank and VerbNet annotation guidelines to the clinical domain, (2) an annotated corpus (500K words of clinical narrative) following the temporal relations schema with additions to Treebank, PropBank and VerbNet, (3) a descriptive study comparing temporal relations in the clinical and general domains.
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== Funding ==
 +
Phase 1 of the project (2010-2014) was supported in part by the i2b2 project (U54LM008748 from the National Library of Medicine) and THYME R01LM010090 from the National Library Of Medicine.  
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Specific Aim 2: Extend and evaluate existing methods and/or develop new algorithms for temporal relation discovery in the clinical domain. Component-level evaluation
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Phase 2 (2015-2018) is supported by THYME R01LM010090 from the National Library Of Medicine. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Library Of Medicine or the National Institutes of Health.
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Specific Aim 3: Integrate best method and/or a variety of methods for temporal relation discovery into Apache cTAKES (ctakes.apache.org) and release as open source annotators in the pipeline. Functional testing. Dissemination activities.
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Specific Aim 4: System-level evaluation. Test the functionality of the enhanced Apache cTAKES (ctakes.apache.org) on translational research use cases, e.g. the progression of colon cancer as documented in clinical notes and pathology reports, the progression of brain tumor as documented in radiology reports.
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The methods we will use for the temporal relation discovery are based on machine learning, e.g., Support Vector Machine technology. Such methods require the annotation of a reference standard from which the computations are derived. The best methods will be released as part of the cTAKES for the larger community to use and contribute to. We will test the methods against biomedical queries.
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ACKNOWLEDGMENT: The project described is supported by Grant Number R01LM010090 from the National Library Of Medicine. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Library Of Medicine or the National Institutes of Health.
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The project period is October, 2010 - September, 2014.
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== Who We Are ==
== Who We Are ==
 +
* Boston Childrens Hospital/Harvard Medical School
 +
** Guergana Savova (MPI)
 +
** Dmitriy Dligach
 +
** Timothy Miller
 +
** Sean Finan
 +
** Chen Lin
 +
** David Harris
 +
* University of Colorado
* University of Colorado
-
** Martha Palmer (PI)
+
** Martha Palmer (MPI)
** Jim Martin
** Jim Martin
** Wayne Ward
** Wayne Ward
-
** Steven Bethard
+
** Jordan Boyd-Graber
-
** William Styler
+
** Will Styler
** Arrick Lanfranchi (through August, 2012)
** Arrick Lanfranchi (through August, 2012)
** Tim O'Gorman
** Tim O'Gorman
-
** Kevin Crooks
+
** Kevin Crooks (through December 2013)
 +
** Mariah Hamang
** and several Lingustics and Computer Science graduate students
** and several Lingustics and Computer Science graduate students
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* Boston Childrens Hospital/Harvard Medical School
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* University of Arizona
-
** Guergana Savova (PI)
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** Steven Bethard
-
** Dmitriy Dligach
+
 
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** Timothy Miller
+
* University of Alabama, Birmingham
-
** Sameer Pradhan
+
** John Osborne
-
** Sean Finan
+
-
** Chen Lin
+
-
** David Harris
+
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** Jennifer Green
+
* Mayo Clinic
* Mayo Clinic
** Piet de Groen
** Piet de Groen
** Brad Erickson
** Brad Erickson
-
** James Masanz
+
** James Masanz (through July, 2015)
** Donna Ihrke (through December, 2012)
** Donna Ihrke (through December, 2012)
-
** Pauline Funk
+
** Pauline Funk (through January, 2013)
* Brandeis University
* Brandeis University
** James Pustejovsky
** James Pustejovsky
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== THYME Annotation Guidelines ==
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== Publications and presentations crediting THYME ==
 +
=== 2019 ===
 +
* Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2019. A BERT-based Universal Model for Both Within-and Cross-sentence Clinical Temporal Relation Extraction. Proceedings of the 2nd Clinical Natural Language Processing Workshop. 2019.
 +
* Savova, G. K., Danciu, I., Alamudun, F., Miller, T., Lin, C., Bitterman, D. S., ... & Warner, J. L. (2019). Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records. Cancer Research, canres-0579.
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These guidelines were provided to the organizers of the 2012 Temporal relations i2b2 challenge for consideration during planning, and reflect an earlier stage of our guidelines.  As such, although representative, '''These guidelines are out of date.'''  Please check back Mid-July for a more up-to-date copy of the guidelines.
 
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* [[Media:i2b2simplifiedthymeguidelines.pdf|i2b2 Simplified THYME Guidelines (PDF)]]
 
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== Annotations and availability ==
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=== 2018 ===
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Annotation layers are treebank and propbank annotations as well as temporal annotations for events, temporal expressions and temporal relations. The corpus will be made available to the research community under a data use agreement. Instructions as to how to get the corpus will be posted soon.
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* Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Amiry, Hadi; Bethard, Steven; Savova, Guergana. 2018. Self-training improves Recurrent Neural Networks performance for Temporal Relation Extraction. LOUHI 2018: The Ninth International Workshop on Health Text Mining and Information Analysis. October 31, 2018, Brussels, Belgium
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* Viewing annotations (Anaphora) - available to the team only
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=== 2017 ===
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  to view the Temporal-Entity data, use the URL:
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* Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2017. Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks. BioNLP workshop at the Association for Computational Linguistics conference. Vancouver, Canada, Friday August 4, 2017
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  https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Entity/gold/
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* Dligach, Dmitriy; Miller, Timothy; Lin, Chen; Bethard, Steven; Savova, Guergana. 2017. Neural temporal relation extraction. European Chapter of the Association for Computational Linguistics (EACL 2017). April 3-7, 2017. Valencia, Spain. http://www.aclweb.org/anthology/E17-2118.
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  TASK_NAME is the filestem, for example, ID074_path_219b
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* Clinical TempEval 2017: http://alt.qcri.org/semeval2017/task12/
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  to view Temporal-Relation data:
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=== 2016 ===
 +
* Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2016. Improving Temporal Relation Extraction with Training Instance Augmentation. BioNLP workshop at the Association for Computational Linguistics conference. Berlin, Germany, Aug 2016
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* Miller, Timothy; Dligach, Dmitriy; Chen, Lin; Bethard, Steven; Savova, Guergana. 2016. Cross-domain Coreference Feature Exploration. AMIA Annual Symposium. Chicago, IL. November, 2016
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* Steven Bethard and Jonathan Parker (May 2016). “A Semantically Compositional Annotation Scheme for Time Normalization”. In: Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016).
 +
* Steven Bethard, Guergana Savova, Wei-Te Chen, Leon Derczynski, James Pustejovsky, and Marc Verhagen. 2016. “SemEval-2016 Task 12: Clinical TempEval”. In: Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval 2016). San Diego, CA
 +
* Ethan Hartzell, Chen Lin. 2016. Enhancing Clinical Temporal Relation Discovery with Syntactic Embeddings from GloVe. International Conference on Intelligent Biology and Medicine (ICIBM 2016). December 2016, Houston, Texas, USA
 +
* Clinical TempEval 2016: http://alt.qcri.org/semeval2016/task12/
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  https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Relation/gold/
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=== 2015 ===
 +
* Lin, Chen; Dligach, Dmitriy; Miller, Timothy; Bethard, Steven; Savova, Guergana. 2015. Layered temporal modeling for the clinical domain. Journal of the American Medical Informatics Association. http://jamia.oxfordjournals.org/content/early/2015/10/31/jamia.ocv113
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* Bethard, Steven; Derczynski, Leon; Savova, Guergana; Pustejovsky, James; Verhagen, Marc. 2015. SemEval-2015 Task 6: Clinical TempEval. Proceedings of the 9th International Workshop on Semantic Evaluation (SemEval 2015). http://www.aclweb.org/anthology/S15-2136. http://aclweb.org/anthology/S/S15/S15-2136.pdf
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* Miller, Timothy; Bethard, Steven; Dligach, Dmitriy; Lin, Chen; Savova, Guergana. 2015. Extracting Time Expressions from Clinical Text. Proceedings of BioNLP 15. http://www.aclweb.org/anthology/W15-3809
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* Clinical TempEval 2015: http://alt.qcri.org/semeval2015/task6/
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* Clinical TempEval 2015 papers:
 +
** Sumithra Velupillai; Danielle L Mowery; Samir Abdelrahman; Lee Christensen; Wendy Chapman. BluLab: Temporal Information Extraction for the 2015 Clinical TempEval Challenge. http://aclweb.org/anthology/S/S15/S15-2137.pdf
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** Hegler Tissot; Genevieve Gorrell; Angus Roberts; Leon Derczynski; Marcos Didonet Del Fabro. UFPRSheffield: Contrasting Rule-based and Support Vector Machine Approaches to Time Expression Identification in Clinical TempEval. http://aclweb.org/anthology/S/S15/S15-2141.pdf
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  you could find the available Entity/Relation gold data on verbs by
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=== 2014 ===
-
  using:
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*Lin, Chen; Karlson, Elizabeth; Dligach, Dmitriy; Ramirez, Monica; Miller, Timothy; Mo, Huan; Braggs, Natalie; Cagan, Andrew; Denny, Joshua; Savova, Guergana. 2014. Automatic identification of Methotrexade-induced liver toxicity in Rheumatoid Arthritis patients from the electronic medical records. Journal of the Medical Informatics Association. http://jamia.bmj.com/content/early/2014/10/24/amiajnl-2014-002642.abstract
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* Pascal B. Pfiffner, JiWon Oh, Timothy A. Miller, Kenneth D. Mandl. 2014. ClinicalTrials.gov as a Data Source for Semi-Automated Point-Of-Care Trial Eligibility Screening. PlosOne. DOI: 10.1371/journal.pone.0111055. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0111055#abstract0
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*Pradhan, Sameer; Elhadad, Noemie; South, Brett; Martinez, David; Christensen, Lee; Vogel, Amy; Suominen, Hanna; Chapman, Wendy; Savova, Guergana.2014. Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. Journal of the Medical Informatics Association. http://jamia.bmj.com/content/early/2014/08/21/amiajnl-2013-002544.full.pdf+html
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* Sameer Pradhan, Noemie Elhadad, Wendy Chapman, Suresh Manandhar, Guergana Savova. 2014. SemEval 2014: Task 7. In Proceedings of the International Workshop on Semantic Evaluations, Dublin, Ireland. August. http://alt.qcri.org/semeval2014/cdrom/
 +
* Finan, Sean; De Groen, Piet; Savova, Guergana. 2014. Narrative event and temporal relation visualization tool. American Medical Informatics Association annual symposium. November 2014. Washington, DC.
 +
* Bethard, Steven. 2014. The state of the art of temporal relation extraction. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
 +
* Miller, Timothy. 2014. Methods for temporal relation discovery in the clinical narrative. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
 +
* Pradhan, Sameer. 2014. Extrinsic evaluation of temporal relation discovery system. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
 +
* Finan, Sean. 2014. Visualization tool for temporal relations from the clinical narrative. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
 +
* Chen, Pei. 2014. Modules for temporal relation discovery from the clinical narrative in Apache cTAKES. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
 +
* Sameer Pradhan, Xiaoqiang Luo, Marta Recasens, Eduard Hovy, Vincent Ng and Michael Strube. 2014. Scoring Coreference Partitions of Predicted Mentions: A Reference Implementation. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
 +
* Xiaoqiang Luo, Sameer Pradhan, Marta Recasens and Eduard Hovy. 2014. An Extension of BLANC to System Mentions. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
 +
* Chen Lin, Timothy Miller, Alvin Kho, Steven Bethard, Dmitriy Dligach, Sameer Pradhan and Guergana Savova. 2014. Descending-Path Convolution Kernel for Syntactic Structures. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
 +
* Savova, Guergana. 2014. Temporal relation discovery from the clinical narrative. Invited talk at the National Library of Medicine Informatics Series. June 4, 2014. Bethesda, MD.
 +
* Finan, Sean; de Groen, Piet; Savova, Guergana. 2014. Narrative Event and Temporal Relation Visualization Tool. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 31 Annual Human-Computer Interaction Lab Symposium. May 29 2014. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2014/
 +
* Bethard, Steven; Ogren, Philip; Becker, Lee. 2014. ClearTK 2.0: Design Patterns for Machine Learning in UIMA. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14). http://anthology.aclweb.org//
 +
* Styler, William; Bethard, Steven; Finan, Sean; Palmer, Martha; Pradhan, Sameer; de Groen, Piet; Erickson, Brad; Miller, Timothy; Chen, Lin; Savova, Guergana K.; Pustejovsky, James. 2014. Temporal annotations in the clinical domain. Transactions of the Association for Computational Linguistics. http://www.transacl.org/wp-content/uploads/2014/04/47.pdf
 +
* Savova, Guergana; Pradhan, Sameer; Palmer, Martha; Styler, Will; Chapman, Wendy; Elhadad, Noemie. (in press). Annotating the clinical text – MiPACQ, ShARe, SHARPn and THYME corpora. In Handbook of Linguistic Annotations. Ed. James Pustejovsky and Nancy Ide. Springer.
 +
* Miller, Tim. 2014. Discovering narrative containers in clinical text. i2b2 All Hands meeting, Jan 17, 2014. Boston, MA (presentation)
 +
 
 +
=== 2013 ===
 +
* Albright, Daniel; Lanfranchi, Arrick; Fredriksen, Anwen; Styler, William; Warner, Collin; Hwang, Jena; Choi, Jinho; Dligach, Dmitriy; Nielsen, Rodney; Martin, James; Ward, Wayne; Palmer, Martha; Savova, Guergana. 2013. Towards syntactic and semantic annotations of the clinical narrative. Journal of the American Medical Informatics Association. 2013;0:1–9. doi:10.1136/amiajnl-2012-001317; http://jamia.bmj.com/cgi/rapidpdf/amiajnl-2012-001317?ijkey=z3pXhpyBzC7S1wC&keytype=ref. PMID: 23355458
 +
* Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Pradhan, Sameer; Lin, Chen; Savova, Guergana. 2013. Discovering time expressions in clinical text. Late breaking abstract. American Medical Informatics Association Conference. November, 2014. Washington, DC.
 +
* Chen, Wei-Te  and  Styler, Will. 2013. Anafora: A Web-based General Purpose Annotation Tool. Proceeding of the North American Association for Computational Linguistics Conference. Atlanta, GA, June 9-13. http://www.aclweb.org/anthology/N13-3004. Anafora is available open source from https://github.com/weitechen/anafora
 +
* Miller, Timothy; Bethard, Steven; Dligach, Dmitriy; Pradhan, Sameer; Lin, Chen; and Savova, Guergana. 2013. Discovering narrative containers in clinical text. BioNLP workshop at the Association for Computational Linguistics. http://aclweb.org/anthology/W/W13/W13-1903.pdf
 +
* Bethard, Steven. 2013. A Synchronous Context Free Grammar for Time Normalization. In: Proceedings of the 2013 Conference on Empirical Methods in Natural Language Processing. http://www.aclweb.org/anthology/D13-1078
 +
* Bethard, Steven. 2013. ClearTK-TimeML: A minimalist approach to TempEval 2013. In: Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013). Atlanta, Georgia, USA: Association for Computational Linguistics, pp. 10-14. http://www.aclweb.org/anthology/S13-2002
 +
* Sameer Pradhan, Alessandro Moschitti, Nianwen Xue, Hwee Tou Ng, Anders Bjorkelund, Olga Uryupina, Yuchen Zhang and Zhi Zhong. 2013. Towards Robust Linguistic Analysis Using OntoNotes. Proceedings of the Conference on Natural Language Learning. Sofia, Bulgaria. August, 2013.
 +
* Dligach, Dmitriy; Bethard, Steven; Becker, Lee; Miller, Timothy; Savova, Guergana. 2013. Discovering body site and severity modifiers in clinical texts. Journal of the American Medical Informatics Association. http://jamia.bmj.com/content/early/2013/10/03/amiajnl-2013-001766.full
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* Dmitriy Dligach, Timothy A. Miller, Guergana K. Savova. 2013. Active Learning for Phenotyping Tasks. In Proceedings of the 2013 NLP for Medicine and Biology workshop held in conjunction with RANLP-2013. September 2013. Hissar, Bulgaria. http://aclweb.org/anthology//W/W13/W13-5101.pdf
 +
* Finan, Sean. 2013. Challenges of visually representing rich temporal information of the clinical narrative. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 30th Annual Human-Computer Interaction Lab Symposium. May 22-23 2013. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2013/
 +
* American Medical Informatics Association (AMIA) national webinar. “Towards semantic annotations of the clinical narrative”.  National webinar. April 2013 (invited presentation)
 +
* Natural Language Processing Working Group Pre-Symposium – doctoral consortium and a data workshop. “Shared Annotated Resources for the Clinical Domain”. American Medical Informatics Association. Washington, DC, USA. November 2013.
 +
* Savova, Guergana; Chapman, Wendy; Elhadad, Noemie; Palmer, Martha. 2013. Shared resources, shared code and shared activities in clinical natural language processing. AMIA Annual Symposium, Panel. Washington, DC.
 +
* AMIA Fall symposium workshop on Natural Language Processing and data. Dr. Savova presented THYME work as part of the data workshop.
 +
 
 +
=== 2012 ===
 +
* Savova, Guergana. 2012. Shared Annotated Resources for the Clinical Domain. Natural Language Processing (NLP) Annotation workshop collocated with the 2nd annual IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology. San Diego, CA, USA. September 2012.
 +
* Drs. Pustejovsky, Palmer and Savova are members of the Program Committee of the 2012 i2b2 shared task whose topic is temporal relations in the clinical domain. The THYME annotation guidelines are the basis of the annotation guidelines for that shared task.
 +
* Participation in the State of the Art of Clinical NLP workshop organized by the NLM in April, 2012. Dr. Savova chaired a session, Prof. Pustejovsky was an invited speaker presenting on Temporal relations/TimeML.
 +
* Participation and presentation in the AMIA Fall symposium workshop on Natural Language Processing and data. Dr. Savova presented THYME work as part of the data workshop.
 +
 
 +
=== 2011 ===
 +
* Savova, Guergana; Chapman, Wendy; Elhadad, Noemie; Palmer, Martha. 2011. Shared annotated resources for the clinical domain. AMIA Annual Symposium, Panel. Washington, DC.
 +
 
 +
== Shared NLP Tasks with THYME participation ==
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* CLEF/ShARe 2014 (in collaboration with the ShARe project): http://clefehealth2014.dcu.ie/task-2
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* SemEval 2014 Analysis of Clinical Text Task 7 (in collaboration with the ShARe project): http://alt.qcri.org/semeval2014/task7/
 +
* SemEval 2015 Analysis of Clinical Text Task 14 (in collaboration with the ShARe project): http://alt.qcri.org/semeval2015/task14/
 +
* SemEval 2015 Clinical TempEval Task 6: http://alt.qcri.org/semeval2015/task6/
 +
* SemEval 2016 Clinical TempEval Task 12: http://alt.qcri.org/semeval2016/task12/
 +
* SemEval 2017 Clinical TempEval Task 12: http://alt.qcri.org/semeval2017/task12/
 +
 
 +
== Getting access to the THYME corpus and gold standard annotations ==
 +
 
 +
The THYME corpus with the gold standard annotations is available to others involved in NLP research under a data use agreement (DUA) with Mayo Clinic. The steps for obtaining a DUA are outlined below. After the DUA has been completed, the THYME corpus is available via a secure download mechanism. Distribution of the corpus is supported by grant LM010090 from the NIH; include the funding acknowledgment in your publications.
 +
 
 +
The corpus is released to an established or junior NLP investigator, formally associated with an institution; thus it is not released to a student. However, all students working with the investigator can have full access to the corpus under the DUA of the investigator. The investigator is urged to have the students work on the corpus on workstations that stay within the laboratory space of the investigator.
 +
 
 +
The steps for obtaining a DUA are:
 +
 
 +
#  Submit the [https://docs.google.com/forms/d/1EwixkePCA-pefHSOTfq-M1lMny9DjPtsOf1H37uMU3w/viewform THYME corpus request form], informing us about your institution, your principal investigator, and your intended use of the data.
 +
# A THYME investigator will send your principal investigator a DUA for you to add information to, and for you to have signed by your site's official signatory. The THYME investigator will provide instructions for returning the signed and completed DUA.
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# When you return the DUA, a THYME investigator will arrange to talk with your principal investigator. Of note, the discussion must be with the lab's principal investigator, not a student/postdoc/administrator. Topics that will be addressed include allowable uses of the data and proper security measures.
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# Once the DUA is complete and a THYME investigator has confirmed your understanding of the DUA, you will be sent instructions for obtaining the corpus via a secure downloading mechanism.
 +
 
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When using the THYME corpus, please
 +
 
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# Include the Mayo Clinic in your acknowledgements
 +
# Cite the article: William F. Styler IV, Steven Bethard, Sean Finan, Martha Palmer, Sameer Pradhan, Piet C. de Groen, Brad Erickson, Timothy Miller, Chen Lin, Guergana Savova, James Pustejovsky. Temporal Annotation in the Clinical Domain. Transactions of the Association for Computational Linguistics. Vol 2 (2014). https://tacl2013.cs.columbia.edu/ojs/index.php/tacl/article/view/305
 +
 
 +
== THYME Gold Standard Annotations ==
 +
Annotation layers are treebank and propbank annotations as well as temporal annotations for events, temporal expressions and temporal relations.
 +
 
 +
 
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=== Annotation guidelines ===
 +
 
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* [http://clear.colorado.edu/compsem/documents/THYME_guidelines.pdf The THYME Temporal Relations Guidelines (PDF)] - The current version of the THYME Temporal Relations Guidelines and release notes.  Updated February 28th, 2014.
 +
 
 +
* [[Media:i2b2simplifiedthymeguidelines.pdf|i2b2 Simplified THYME Guidelines (PDF)]] The guidelines provided to the organizers of the 2012 Temporal relations i2b2 challenge for consideration during planning. They reflect an earlier stage of our guidelines.
 +
 
 +
* Syntactic Tree (Treebank): http://clear.colorado.edu/compsem/documents/treebank_guidelines.pdf
 +
 
 +
* Semantic Role (Propbank): http://clear.colorado.edu/compsem/documents/propbank_guidelines.pdf
 +
 
 +
* UMLS entity and relations annotations/templates: http://clear.colorado.edu/compsem/documents/umls_guidelines.pdf
 +
 +
* Clinical coreference guidelines (based on ODIE, OntoNotes, MUC-7): http://clear.colorado.edu/compsem/documents/Coreference%20Guidelines.pdf
 +
 
 +
=== Tool for viewing the gold standard annotations - Anafora ===
 +
We developed a web-based annotation tool. It is open source and available at https://github.com/weitechen/anafora. Use it to view the THYME annotations. Citation for the tool is:
 +
 
 +
Chen, Wei-Te  and  Styler, Will. 2013. Anafora: A Web-based General Purpose Annotation Tool. Proceeding of the North American Association for Computational Linguistics Conference. Atlanta, GA, June 9-13. http://www.aclweb.org/anthology/N13-3004.
 +
 
 +
=== Viewing the gold standard annotations (Anafora) ===
 +
 
 +
(available to the team only)
 +
 
 +
To view the Temporal-Entity data, use the URL:
 +
 
 +
https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Entity/gold/
 +
 
 +
TASK_NAME is the filestem, for example, ID074_path_219b
 +
 
 +
to view Temporal-Relation data:
 +
 
 +
https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Relation/gold/
 +
 
 +
you could find the available Entity/Relation gold data on verbs by using:
   find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Entity.gold.completed.xml"
   find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Entity.gold.completed.xml"
   find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Relation.gold.completed.xml"
   find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Relation.gold.completed.xml"
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== THYME system ==
 
-
THYME system is available as part of Apache cTAKES at ctakes.apache.org. Team members can track [[development progress]].
 
-
== Relevant Papers ==
+
== Train/Development/Test splits ==
 +
* Use this split for experiments with the THYME data (% 8)!
 +
* (A note about [[Protege/Knowtator and Anafora annotation tools: annotations]])
 +
 
 +
===Colon Cancer Data ===
 +
 
 +
* Train sets (Residue 0,1,2,3): [1, 2, 3, 8, 9, 10, 11, 16, 17, 18, 19, 24, 25, 26, 27, 32, 33, 34, 35, 40, 41, 42, 43, 48, 49, 50, 51, 56, 57, 58, 59, 64, 65, 66, 67, 72, 73, 74, 75, 80, 81, 82, 83, 88, 89, 90, 91, 96, 97, 98, 99, 104, 105, 106, 107, 112, 113, 114, 115, 120, 121, 122, 123, 128, 129, 130, 131, 136, 137, 138, 139, 144, 145, 146, 147, 152, 153, 154, 155, 160, 161, 162, 163, 168, 169, 170, 171, 176, 177, 178, 179, 184, 185, 186, 187, 192, 193, 194, 195, 200, 201, 202, 203, 208, 209, 210, 211, 216, 217]
 +
 
 +
* Development sets (Residue 4,5): [4, 5, 12, 13, 20, 21, 28, 29, 36, 37, 44, 45, 52, 53, 60, 61, 68, 69, 76, 77, 84, 85, 92, 93, 100, 101, 108, 109, 116, 117, 124, 125, 132, 133, 140, 141, 148, 149, 156, 157, 164, 165, 172, 173, 180, 181, 188, 189, 196, 197, 204, 205, 212, 213]
 +
 
 +
* Test sets (Residue 6,7): [6, 7, 14, 15, 22, 23, 30, 31, 38, 39, 46, 47, 54, 55, 62, 63, 70, 71, 78, 79, 86, 87, 94, 95, 102, 103, 110, 111, 118, 119, 126, 127, 134, 135, 142, 143, 150, 151, 158, 159, 166, 167, 174, 175, 182, 183, 190, 191, 198, 199, 206, 207, 214, 215]
 +
 
 +
=== Brain Cancer Data ===
 +
* Train sets: [1, 2, 3, 8, 9, 10, 11, 16, 17, 18, 19, 24, 25, 26, 27, 32, 33, 34, 35, 40, 41, 42, 43, 48, 49, 50, 51, 56, 57, 58, 59, 64, 65, 66, 67, 72, 73, 74, 75, 80, 81, 82, 83, 88, 89, 90, 91, 96, 97, 98, 99, 104, 105, 106, 107, 112, 113, 114, 115, 120, 121, 122, 123, 128, 129, 130, 131, 136, 137, 138, 139, 144, 145, 146, 147, 152, 153, 154, 155, 160, 161, 162, 163, 168, 169, 170, 171, 176, 177, 178, 179, 184, 185, 186, 187, 192, 193, 194, 195, 200, 201]
 +
 
 +
* Development sets: [4, 5, 12, 13, 20, 21, 28, 29, 36, 37, 44, 45, 52, 53, 60, 61, 68, 69, 76, 77, 84, 85, 92, 93, 100, 101, 108, 109, 116, 117, 124, 125, 132, 133, 140, 141, 148, 149, 156, 157, 164, 165, 172, 173, 180, 181, 188, 189, 196, 197]
 +
 
 +
* Test sets: [6, 7, 14, 15, 22, 23, 30, 31, 38, 39, 46, 47, 54, 55, 62, 63, 70, 71, 78, 79, 86, 87, 94, 95, 102, 103, 110, 111, 118, 119, 126, 127, 134, 135, 142, 143, 150, 151, 158, 159, 166, 167, 174, 175, 182, 183, 190, 191, 198, 199]
 +
 
 +
== THYME Software ==
 +
The THYME system is available as part of Apache cTAKES at http://ctakes.apache.org/
 +
 
 +
Demo of the system: ctakes.apache.org -> get started -> demos -> ctakes-temporal (http://alt.qcri.org/semeval2016/task12/)
 +
 
 +
* [[Software|System diagram]]
 +
* [[development progress]]
 +
 
 +
We are also developing a visualization tool (THYME viz tool) which will be made available in cTAKES. A prototype and details of the THYME vizualization tool was presented by Sean Finan at several annual workshops.
 +
 
 +
Finan, Sean. 2013. Challenges of visually representing rich temporal information of the clinical narrative. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 30th Annual Human-Computer Interaction Lab Symposium. May 22-23 2013. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2013/
 +
 
 +
Finan, Sean. De Groen, Piet. Savova, Guergana. 2014.  Narrative Event and Temporal Relation Visualization Tool. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 31st Annual Human-Computer Interaction Lab Symposium. May 29 2014. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2014/
 +
 
 +
Finan, Sean. De Groen, Piet. Savova, Guergana. 2014.  Narrative Event and Temporal Relation Visualization Tool. Natural Language Processing Workshop.  Informatics for Integrating Biology & the Bedside (I2B2).  4th Annual Academic User Group Meeting. July 9 2014.  Harvard Medical School.
 +
https://www.i2b2.org/events/slides/NarrativeVisualizer.pdf
 +
 
 +
* [http://youtu.be/Kp9YE0o3urU Visualization Tool Demonstration Video]
 +
 
 +
== Relevant Background Papers ==
[[Relevant Papers]]
[[Relevant Papers]]
 +
 +
== Reading Group ==
 +
[[Paper Queue]]
 +
 +
== Internal Presentations ==
 +
[[Presentations]]
 +
== Venues for manuscript submissions ==  
== Venues for manuscript submissions ==  
[[Venues for manuscript submissions/publications]]
[[Venues for manuscript submissions/publications]]
 +
== Project materials ==
== Project materials ==
Line 93: Line 255:
[[Progress_reports|Progress reports]]
[[Progress_reports|Progress reports]]
-
 
-
[[Annotation_Guidelines|Clinical Temporal Relations Annotation Guidelines]] - Release notes and latest versions
 
[[Annotations|Annotations]] - Describes the corpus, the layers of annotations and annotation progress
[[Annotations|Annotations]] - Describes the corpus, the layers of annotations and annotation progress
Line 100: Line 260:
[[Annotation Tools|Annotation Tools]] - Describes the progress and information pertaining to the Anafora annotation tool
[[Annotation Tools|Annotation Tools]] - Describes the progress and information pertaining to the Anafora annotation tool
-
[[Software|Software]] - Describes the software modules and their organization
 
-
 
-
== Train/Development/Test splits ==
 
-
* Use this split for experiments with the THYME data (% 8)!
 
-
* Train sets: 1, 2, 3, 8, 9, 10, 11, 16, 17, 18, 19, 24, 25, 26, 27
 
-
* Development sets: 4, 12, 13, 20, 21
 
-
* Test sets: 6, 7, 14, 15, 22, 23
 
-
* [[Protege/Knowtator and Anafora annotation tools: annotations]]
 
== Communication ==
== Communication ==
-
* Bi-weekly meetings, Wed 11-noon ET
+
* Bi-weekly team meetings, Tue 1:30-2:30 pm ET
** [[Call_in_detals| Call in details]]
** [[Call_in_detals| Call in details]]
 +
* Weekly methods meetings, Fri 3:30-5 pm ET
* [[Distribution_lists|Distribution Lists]]
* [[Distribution_lists|Distribution Lists]]
 +
 +
== IDEAS notebook ==
 +
[[IDEAS_notebook|Ideas notebook]]
 +
== Meeting Notes ==
== Meeting Notes ==
-
*[[THYME_Meeting_10112013 | Oct 11, 2013]] Methods meeting agenda and notes
+
*[[Methods_11112019|November 11, 2019]] Methods meeting
-
*[[THYME_Meeting_10092013 | Oct 9, 2013]] Agenda and notes
+
*[[THYME_All_team_11072019|November 7, 2019]] THYME all team meeting
-
*[[THYME_Meeting_10042013 | Oct 4, 2013]] Methods meeting agenda and notes
+
*[[Methods_11042019|November 4, 2019]] Methods meeting
-
*[[THYME_Meeting_09272013 | Sep 27, 2013]] Methods meeting agenda and notes
+
*[[Methods_10282019|October 28, 2019]] Methods meeting
-
*[[THYME_Meeting_09252013 | Sep 25, 2013]] Agenda and notes
+
*[[THYME_All_team_10242019|October 24, 2019]] THYME all team meeting
-
*[[THYME_Meeting_09202013 | Sep 20, 2013]] Methods meeting agenda and notes
+
*[[Methods_10142019|October 14, 2019]] Methods meeting
-
*[[THYME_Meeting_09132013 | Sep 13, 2013]] Methods meeting agenda and notes
+
*[[THYME_All_team_10102019|October 10, 2019]] THYME all team meeting
-
*[[THYME_Meeting_09112013 | Sep 11, 2013]] Agenda and notes
+
*[[hNLP_Methods_10072019|October 7, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_09062013 | Sep 06, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_09302019|September 30, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_08302013 | Aug 30, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_09232019|September 23, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_08282013 | August 28, 2013]] Agenda and notes
+
*[[hNLP_Methods_09092019|September 9, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_08232013 | Aug 23, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_08262019|August 26, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_08142013 | August 14, 2013]] Agenda and notes
+
*[[hNLP_Methods_08192019|August 19, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_08162013 | Aug 16, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_08122019|August 12, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_08022013 | Aug 2, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_08052019|August 5, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_07312013 | July 31, 2013]] Agenda and notes
+
*[[hNLP_Methods_07292019|July 29, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_07252013 | July 25, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_07222019|July 22, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_07192013 | July 19, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_07152019|July 15, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_07172013 | July 17, 2013]] Agenda and notes
+
*[[hNLP_Methods_07012019|July 1, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_07122013 | July 12, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_06242019|June 24, 2019]] hNLP Methods meeting
-
* No conference call on July 3, 2013. Happy 4th of July!
+
*[[hNLP_Methods_05202019|May 20, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_06282013 | June 28, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_05132019|May 13, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_06192013 | June 19, 2013]] Agenda and notes
+
*[[hNLP_Methods_05062019|May 6, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_06052013 | June 5, 2013]] Agenda and notes
+
*[[hNLP_Methods_04292019|April 29, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_05312013 | May 31, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_04222019|April 22, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_05242013 | May 24, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_04082019|April 8, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_05222013 | May 22, 2013]] Agenda and notes
+
*[[hNLP_Methods_04012019|April 1, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_05172013 | May 17, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_03252019|March 25, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_05092013 | May 9, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_03182019|March 18, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_05082013 | May 8, 2013]] Agenda and notes
+
*[[hNLP_Methods_03112019|March 11, 2019]] hNLP Methods meeting
-
*[[THYME_Methods_05032013 | May 3, 2013]] Methods meeting agenda and notes
+
*[[hNLP_Methods_03042019|March 4, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_04242013 | April 24, 2013]] Agenda and notes
+
*[[hNLP_Methods_02252019|Feb 25, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_04102013 | April 10, 2013]] Agenda and notes
+
*[[hNLP_Methods_02112019|Feb 11, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_03272013 | March 27, 2013]] Agenda and notes
+
*[[hNLP_Methods_02042019|Feb 4, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_03132013 | March 13, 2013]] Agenda and notes
+
*[[hNLP_Methods_01282019|Jan 28, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_02272013 | February 27, 2013]] Agenda and notes
+
* January 21, 2019: No meeting
-
*[[THYME_Meeting_02132013 | February 13, 2013]] Agenda and notes
+
*[[hNLP_Methods_01142019|Jan 14, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_01302030 | January 30, 2013]] Agenda and notes
+
*[[hNLP_Methods_01072019|Jan 07, 2019]] hNLP Methods meeting
-
*[[THYME_Meeting_01282030 | January 28, 2013 (annotations subgroup)]] Agenda and notes
+
*[[Meeting_notes_2018 | 2018 Meeting notes]]
-
*[[THYME_Meeting_01162013 | January 16, 2013]] Agenda and notes
+
*[[Meeting_notes_2017 | 2017 Meeting notes]]
-
*[[THYME_Meeting_01022013 | January 2, 2013]] Agenda and notes
+
*[[Meeting_notes_2016 | 2016 Meeting notes]]
-
*[[THYME_Meeting_12192012 | December 19, 2012]] Agenda and notes
+
*[[Meeting_notes_2015 | 2015 Meeting notes]]
-
*[[THYME_Meeting_12052012 | December 5, 2012]] Agenda and notes
+
*[[Meeting_notes_2014 | 2014 Meeting notes]]
-
*[[THYME_Meeting_11212012 | November 21, 2012]] Agenda and notes
+
*[[Meeting_notes_2013 | 2013 Meeting notes]]
-
*[[THYME_Meeting_11062012 | November 6, 2012]] Agenda and notes
+
*[[Meeting_notes_2012 | 2012 Meeting notes]]
-
*[[THYME_Meeting_10242012 | October 24, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_10102012 | October 10, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_09122012 | September 12, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_08292012 | August 29, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_08152012 | August 15, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_08012012 | August 1, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_07182012 | July 18, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_06272012 | June 22, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_06202012 | June 20, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_06062012 | June 6, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_05232012 | May 23, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_05092012 | May 9, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_04252012 | April 25, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_04112012 | April 11, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_03282012 | March 28, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_03142012 | March 14, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_02292012 | Feb 29, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_02142012 | Feb 14, 2012]] Agenda and notes
+
-
*[[THYME_Meeting_02012012 | Feb 1, 2012]] Agenda and notes
+
== Getting started ==
== Getting started ==
Line 184: Line 322:
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [http://www.mediawiki.org/wiki/Manual:FAQ MediaWiki FAQ]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
 +
 +
== Contact ==
== Contact ==
-
If you need assistance and/or if you have questions about the project, feel free to send e-mail to steven.bethard at colorado dot edu OR Guergana.Savova at childrens dot harvard dot edu
+
If you need assistance and/or if you have questions about the project, feel free to send e-mail to guergana dot savova at childrens dot harvard dot edu, martha dot palmer at colorado dot edu, or bethard at email dot arizona dot edu.

Revision as of 19:47, 11 November 2019

Contents

Welcome to the THYME project

Welcome to the Temporal Histories of Your Medical Event (THYME) project (THYME is pronounced [taim]).

The overarching long-term vision of our research is to create novel technologies for processing clinical free text. Such technologies will enable sophisticated and efficient indexing, retrieval and data mining over the ever increasing amounts of electronic clinical data. Processing free text poses a number of challenges to which the fields of Artificial intelligence, natural language processing and computer science in general have made advances. Methods for processing free text are informed by linguistic theory combined with the power of statistical inferencing. A key component to the next step, natural language understanding, is discovering events and their relations on a timeline. Temporal relations are of prime importance in biomedicine as they are intrinsically linked to diseases, signs and symptoms, and treatments. Understanding the timeline of clinically relevant events is key to the next generation of translational research where the importance of generalizing over large amounts of data holds the promise of deciphering biomedical puzzles.

The best methods have been/will be released as part of the cTAKES (ctakes.apache.org) for the larger community to use and contribute to. We will test the methods against biomedical queries.

Funding

Phase 1 of the project (2010-2014) was supported in part by the i2b2 project (U54LM008748 from the National Library of Medicine) and THYME R01LM010090 from the National Library Of Medicine.

Phase 2 (2015-2018) is supported by THYME R01LM010090 from the National Library Of Medicine. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Library Of Medicine or the National Institutes of Health.

Who We Are

  • Boston Childrens Hospital/Harvard Medical School
    • Guergana Savova (MPI)
    • Dmitriy Dligach
    • Timothy Miller
    • Sean Finan
    • Chen Lin
    • David Harris
  • University of Colorado
    • Martha Palmer (MPI)
    • Jim Martin
    • Wayne Ward
    • Jordan Boyd-Graber
    • Will Styler
    • Arrick Lanfranchi (through August, 2012)
    • Tim O'Gorman
    • Kevin Crooks (through December 2013)
    • Mariah Hamang
    • and several Lingustics and Computer Science graduate students
  • University of Arizona
    • Steven Bethard
  • University of Alabama, Birmingham
    • John Osborne
  • Mayo Clinic
    • Piet de Groen
    • Brad Erickson
    • James Masanz (through July, 2015)
    • Donna Ihrke (through December, 2012)
    • Pauline Funk (through January, 2013)
  • Brandeis University
    • James Pustejovsky

Publications and presentations crediting THYME

2019

  • Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2019. A BERT-based Universal Model for Both Within-and Cross-sentence Clinical Temporal Relation Extraction. Proceedings of the 2nd Clinical Natural Language Processing Workshop. 2019.
  • Savova, G. K., Danciu, I., Alamudun, F., Miller, T., Lin, C., Bitterman, D. S., ... & Warner, J. L. (2019). Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records. Cancer Research, canres-0579.


2018

  • Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Amiry, Hadi; Bethard, Steven; Savova, Guergana. 2018. Self-training improves Recurrent Neural Networks performance for Temporal Relation Extraction. LOUHI 2018: The Ninth International Workshop on Health Text Mining and Information Analysis. October 31, 2018, Brussels, Belgium

2017

  • Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2017. Representations of Time Expressions for Temporal Relation Extraction with Convolutional Neural Networks. BioNLP workshop at the Association for Computational Linguistics conference. Vancouver, Canada, Friday August 4, 2017
  • Dligach, Dmitriy; Miller, Timothy; Lin, Chen; Bethard, Steven; Savova, Guergana. 2017. Neural temporal relation extraction. European Chapter of the Association for Computational Linguistics (EACL 2017). April 3-7, 2017. Valencia, Spain. http://www.aclweb.org/anthology/E17-2118.

2016

  • Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Savova, Guergana. 2016. Improving Temporal Relation Extraction with Training Instance Augmentation. BioNLP workshop at the Association for Computational Linguistics conference. Berlin, Germany, Aug 2016
  • Miller, Timothy; Dligach, Dmitriy; Chen, Lin; Bethard, Steven; Savova, Guergana. 2016. Cross-domain Coreference Feature Exploration. AMIA Annual Symposium. Chicago, IL. November, 2016
  • Steven Bethard and Jonathan Parker (May 2016). “A Semantically Compositional Annotation Scheme for Time Normalization”. In: Proceedings of the Tenth International Conference on Language Resources and Evaluation (LREC 2016).
  • Steven Bethard, Guergana Savova, Wei-Te Chen, Leon Derczynski, James Pustejovsky, and Marc Verhagen. 2016. “SemEval-2016 Task 12: Clinical TempEval”. In: Proceedings of the 10th International Workshop on Semantic Evaluation (SemEval 2016). San Diego, CA
  • Ethan Hartzell, Chen Lin. 2016. Enhancing Clinical Temporal Relation Discovery with Syntactic Embeddings from GloVe. International Conference on Intelligent Biology and Medicine (ICIBM 2016). December 2016, Houston, Texas, USA
  • Clinical TempEval 2016: http://alt.qcri.org/semeval2016/task12/

2015

2014

  • Lin, Chen; Karlson, Elizabeth; Dligach, Dmitriy; Ramirez, Monica; Miller, Timothy; Mo, Huan; Braggs, Natalie; Cagan, Andrew; Denny, Joshua; Savova, Guergana. 2014. Automatic identification of Methotrexade-induced liver toxicity in Rheumatoid Arthritis patients from the electronic medical records. Journal of the Medical Informatics Association. http://jamia.bmj.com/content/early/2014/10/24/amiajnl-2014-002642.abstract
  • Pascal B. Pfiffner, JiWon Oh, Timothy A. Miller, Kenneth D. Mandl. 2014. ClinicalTrials.gov as a Data Source for Semi-Automated Point-Of-Care Trial Eligibility Screening. PlosOne. DOI: 10.1371/journal.pone.0111055. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0111055#abstract0
  • Pradhan, Sameer; Elhadad, Noemie; South, Brett; Martinez, David; Christensen, Lee; Vogel, Amy; Suominen, Hanna; Chapman, Wendy; Savova, Guergana.2014. Evaluating the state of the art in disorder recognition and normalization of the clinical narrative. Journal of the Medical Informatics Association. http://jamia.bmj.com/content/early/2014/08/21/amiajnl-2013-002544.full.pdf+html
  • Sameer Pradhan, Noemie Elhadad, Wendy Chapman, Suresh Manandhar, Guergana Savova. 2014. SemEval 2014: Task 7. In Proceedings of the International Workshop on Semantic Evaluations, Dublin, Ireland. August. http://alt.qcri.org/semeval2014/cdrom/
  • Finan, Sean; De Groen, Piet; Savova, Guergana. 2014. Narrative event and temporal relation visualization tool. American Medical Informatics Association annual symposium. November 2014. Washington, DC.
  • Bethard, Steven. 2014. The state of the art of temporal relation extraction. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
  • Miller, Timothy. 2014. Methods for temporal relation discovery in the clinical narrative. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
  • Pradhan, Sameer. 2014. Extrinsic evaluation of temporal relation discovery system. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
  • Finan, Sean. 2014. Visualization tool for temporal relations from the clinical narrative. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
  • Chen, Pei. 2014. Modules for temporal relation discovery from the clinical narrative in Apache cTAKES. Presentation at the NLP workshop at the 4th i2b2 Academic User Group conference. July 9, 2014. Boston, MA.
  • Sameer Pradhan, Xiaoqiang Luo, Marta Recasens, Eduard Hovy, Vincent Ng and Michael Strube. 2014. Scoring Coreference Partitions of Predicted Mentions: A Reference Implementation. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
  • Xiaoqiang Luo, Sameer Pradhan, Marta Recasens and Eduard Hovy. 2014. An Extension of BLANC to System Mentions. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
  • Chen Lin, Timothy Miller, Alvin Kho, Steven Bethard, Dmitriy Dligach, Sameer Pradhan and Guergana Savova. 2014. Descending-Path Convolution Kernel for Syntactic Structures. Short paper. Association for Computational Linguistics Conference. Baltimore, Maryland. http://anthology.aclweb.org//
  • Savova, Guergana. 2014. Temporal relation discovery from the clinical narrative. Invited talk at the National Library of Medicine Informatics Series. June 4, 2014. Bethesda, MD.
  • Finan, Sean; de Groen, Piet; Savova, Guergana. 2014. Narrative Event and Temporal Relation Visualization Tool. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 31 Annual Human-Computer Interaction Lab Symposium. May 29 2014. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2014/
  • Bethard, Steven; Ogren, Philip; Becker, Lee. 2014. ClearTK 2.0: Design Patterns for Machine Learning in UIMA. In: Proceedings of the Ninth International Conference on Language Resources and Evaluation (LREC'14). http://anthology.aclweb.org//
  • Styler, William; Bethard, Steven; Finan, Sean; Palmer, Martha; Pradhan, Sameer; de Groen, Piet; Erickson, Brad; Miller, Timothy; Chen, Lin; Savova, Guergana K.; Pustejovsky, James. 2014. Temporal annotations in the clinical domain. Transactions of the Association for Computational Linguistics. http://www.transacl.org/wp-content/uploads/2014/04/47.pdf
  • Savova, Guergana; Pradhan, Sameer; Palmer, Martha; Styler, Will; Chapman, Wendy; Elhadad, Noemie. (in press). Annotating the clinical text – MiPACQ, ShARe, SHARPn and THYME corpora. In Handbook of Linguistic Annotations. Ed. James Pustejovsky and Nancy Ide. Springer.
  • Miller, Tim. 2014. Discovering narrative containers in clinical text. i2b2 All Hands meeting, Jan 17, 2014. Boston, MA (presentation)

2013

  • Albright, Daniel; Lanfranchi, Arrick; Fredriksen, Anwen; Styler, William; Warner, Collin; Hwang, Jena; Choi, Jinho; Dligach, Dmitriy; Nielsen, Rodney; Martin, James; Ward, Wayne; Palmer, Martha; Savova, Guergana. 2013. Towards syntactic and semantic annotations of the clinical narrative. Journal of the American Medical Informatics Association. 2013;0:1–9. doi:10.1136/amiajnl-2012-001317; http://jamia.bmj.com/cgi/rapidpdf/amiajnl-2012-001317?ijkey=z3pXhpyBzC7S1wC&keytype=ref. PMID: 23355458
  • Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Pradhan, Sameer; Lin, Chen; Savova, Guergana. 2013. Discovering time expressions in clinical text. Late breaking abstract. American Medical Informatics Association Conference. November, 2014. Washington, DC.
  • Chen, Wei-Te and Styler, Will. 2013. Anafora: A Web-based General Purpose Annotation Tool. Proceeding of the North American Association for Computational Linguistics Conference. Atlanta, GA, June 9-13. http://www.aclweb.org/anthology/N13-3004. Anafora is available open source from https://github.com/weitechen/anafora
  • Miller, Timothy; Bethard, Steven; Dligach, Dmitriy; Pradhan, Sameer; Lin, Chen; and Savova, Guergana. 2013. Discovering narrative containers in clinical text. BioNLP workshop at the Association for Computational Linguistics. http://aclweb.org/anthology/W/W13/W13-1903.pdf
  • Bethard, Steven. 2013. A Synchronous Context Free Grammar for Time Normalization. In: Proceedings of the 2013 Conference on Empirical Methods in Natural Language Processing. http://www.aclweb.org/anthology/D13-1078
  • Bethard, Steven. 2013. ClearTK-TimeML: A minimalist approach to TempEval 2013. In: Second Joint Conference on Lexical and Computational Semantics (*SEM), Volume 2: Proceedings of the Seventh International Workshop on Semantic Evaluation (SemEval 2013). Atlanta, Georgia, USA: Association for Computational Linguistics, pp. 10-14. http://www.aclweb.org/anthology/S13-2002
  • Sameer Pradhan, Alessandro Moschitti, Nianwen Xue, Hwee Tou Ng, Anders Bjorkelund, Olga Uryupina, Yuchen Zhang and Zhi Zhong. 2013. Towards Robust Linguistic Analysis Using OntoNotes. Proceedings of the Conference on Natural Language Learning. Sofia, Bulgaria. August, 2013.
  • Dligach, Dmitriy; Bethard, Steven; Becker, Lee; Miller, Timothy; Savova, Guergana. 2013. Discovering body site and severity modifiers in clinical texts. Journal of the American Medical Informatics Association. http://jamia.bmj.com/content/early/2013/10/03/amiajnl-2013-001766.full
  • Dmitriy Dligach, Timothy A. Miller, Guergana K. Savova. 2013. Active Learning for Phenotyping Tasks. In Proceedings of the 2013 NLP for Medicine and Biology workshop held in conjunction with RANLP-2013. September 2013. Hissar, Bulgaria. http://aclweb.org/anthology//W/W13/W13-5101.pdf
  • Finan, Sean. 2013. Challenges of visually representing rich temporal information of the clinical narrative. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 30th Annual Human-Computer Interaction Lab Symposium. May 22-23 2013. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2013/
  • American Medical Informatics Association (AMIA) national webinar. “Towards semantic annotations of the clinical narrative”. National webinar. April 2013 (invited presentation)
  • Natural Language Processing Working Group Pre-Symposium – doctoral consortium and a data workshop. “Shared Annotated Resources for the Clinical Domain”. American Medical Informatics Association. Washington, DC, USA. November 2013.
  • Savova, Guergana; Chapman, Wendy; Elhadad, Noemie; Palmer, Martha. 2013. Shared resources, shared code and shared activities in clinical natural language processing. AMIA Annual Symposium, Panel. Washington, DC.
  • AMIA Fall symposium workshop on Natural Language Processing and data. Dr. Savova presented THYME work as part of the data workshop.

2012

  • Savova, Guergana. 2012. Shared Annotated Resources for the Clinical Domain. Natural Language Processing (NLP) Annotation workshop collocated with the 2nd annual IEEE International Conference on Healthcare Informatics, Imaging and Systems Biology. San Diego, CA, USA. September 2012.
  • Drs. Pustejovsky, Palmer and Savova are members of the Program Committee of the 2012 i2b2 shared task whose topic is temporal relations in the clinical domain. The THYME annotation guidelines are the basis of the annotation guidelines for that shared task.
  • Participation in the State of the Art of Clinical NLP workshop organized by the NLM in April, 2012. Dr. Savova chaired a session, Prof. Pustejovsky was an invited speaker presenting on Temporal relations/TimeML.
  • Participation and presentation in the AMIA Fall symposium workshop on Natural Language Processing and data. Dr. Savova presented THYME work as part of the data workshop.

2011

  • Savova, Guergana; Chapman, Wendy; Elhadad, Noemie; Palmer, Martha. 2011. Shared annotated resources for the clinical domain. AMIA Annual Symposium, Panel. Washington, DC.

Shared NLP Tasks with THYME participation

Getting access to the THYME corpus and gold standard annotations

The THYME corpus with the gold standard annotations is available to others involved in NLP research under a data use agreement (DUA) with Mayo Clinic. The steps for obtaining a DUA are outlined below. After the DUA has been completed, the THYME corpus is available via a secure download mechanism. Distribution of the corpus is supported by grant LM010090 from the NIH; include the funding acknowledgment in your publications.

The corpus is released to an established or junior NLP investigator, formally associated with an institution; thus it is not released to a student. However, all students working with the investigator can have full access to the corpus under the DUA of the investigator. The investigator is urged to have the students work on the corpus on workstations that stay within the laboratory space of the investigator.

The steps for obtaining a DUA are:

  1. Submit the THYME corpus request form, informing us about your institution, your principal investigator, and your intended use of the data.
  2. A THYME investigator will send your principal investigator a DUA for you to add information to, and for you to have signed by your site's official signatory. The THYME investigator will provide instructions for returning the signed and completed DUA.
  3. When you return the DUA, a THYME investigator will arrange to talk with your principal investigator. Of note, the discussion must be with the lab's principal investigator, not a student/postdoc/administrator. Topics that will be addressed include allowable uses of the data and proper security measures.
  4. Once the DUA is complete and a THYME investigator has confirmed your understanding of the DUA, you will be sent instructions for obtaining the corpus via a secure downloading mechanism.

When using the THYME corpus, please

  1. Include the Mayo Clinic in your acknowledgements
  2. Cite the article: William F. Styler IV, Steven Bethard, Sean Finan, Martha Palmer, Sameer Pradhan, Piet C. de Groen, Brad Erickson, Timothy Miller, Chen Lin, Guergana Savova, James Pustejovsky. Temporal Annotation in the Clinical Domain. Transactions of the Association for Computational Linguistics. Vol 2 (2014). https://tacl2013.cs.columbia.edu/ojs/index.php/tacl/article/view/305

THYME Gold Standard Annotations

Annotation layers are treebank and propbank annotations as well as temporal annotations for events, temporal expressions and temporal relations.


Annotation guidelines

  • i2b2 Simplified THYME Guidelines (PDF) The guidelines provided to the organizers of the 2012 Temporal relations i2b2 challenge for consideration during planning. They reflect an earlier stage of our guidelines.

Tool for viewing the gold standard annotations - Anafora

We developed a web-based annotation tool. It is open source and available at https://github.com/weitechen/anafora. Use it to view the THYME annotations. Citation for the tool is:

Chen, Wei-Te and Styler, Will. 2013. Anafora: A Web-based General Purpose Annotation Tool. Proceeding of the North American Association for Computational Linguistics Conference. Atlanta, GA, June 9-13. http://www.aclweb.org/anthology/N13-3004.

Viewing the gold standard annotations (Anafora)

(available to the team only)

To view the Temporal-Entity data, use the URL:

https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Entity/gold/

TASK_NAME is the filestem, for example, ID074_path_219b

to view Temporal-Relation data:

https://verbs.colorado.edu/anafora/annotate/Temporal/ColonCancer/TASK_NAME/Temporal.Relation/gold/

you could find the available Entity/Relation gold data on verbs by using:

  find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Entity.gold.completed.xml"
  find /data/anafora/anaforaProjectFile/Temporal/ -name "*Temporal-Relation.gold.completed.xml"


Train/Development/Test splits

Colon Cancer Data

  • Train sets (Residue 0,1,2,3): [1, 2, 3, 8, 9, 10, 11, 16, 17, 18, 19, 24, 25, 26, 27, 32, 33, 34, 35, 40, 41, 42, 43, 48, 49, 50, 51, 56, 57, 58, 59, 64, 65, 66, 67, 72, 73, 74, 75, 80, 81, 82, 83, 88, 89, 90, 91, 96, 97, 98, 99, 104, 105, 106, 107, 112, 113, 114, 115, 120, 121, 122, 123, 128, 129, 130, 131, 136, 137, 138, 139, 144, 145, 146, 147, 152, 153, 154, 155, 160, 161, 162, 163, 168, 169, 170, 171, 176, 177, 178, 179, 184, 185, 186, 187, 192, 193, 194, 195, 200, 201, 202, 203, 208, 209, 210, 211, 216, 217]
  • Development sets (Residue 4,5): [4, 5, 12, 13, 20, 21, 28, 29, 36, 37, 44, 45, 52, 53, 60, 61, 68, 69, 76, 77, 84, 85, 92, 93, 100, 101, 108, 109, 116, 117, 124, 125, 132, 133, 140, 141, 148, 149, 156, 157, 164, 165, 172, 173, 180, 181, 188, 189, 196, 197, 204, 205, 212, 213]
  • Test sets (Residue 6,7): [6, 7, 14, 15, 22, 23, 30, 31, 38, 39, 46, 47, 54, 55, 62, 63, 70, 71, 78, 79, 86, 87, 94, 95, 102, 103, 110, 111, 118, 119, 126, 127, 134, 135, 142, 143, 150, 151, 158, 159, 166, 167, 174, 175, 182, 183, 190, 191, 198, 199, 206, 207, 214, 215]

Brain Cancer Data

  • Train sets: [1, 2, 3, 8, 9, 10, 11, 16, 17, 18, 19, 24, 25, 26, 27, 32, 33, 34, 35, 40, 41, 42, 43, 48, 49, 50, 51, 56, 57, 58, 59, 64, 65, 66, 67, 72, 73, 74, 75, 80, 81, 82, 83, 88, 89, 90, 91, 96, 97, 98, 99, 104, 105, 106, 107, 112, 113, 114, 115, 120, 121, 122, 123, 128, 129, 130, 131, 136, 137, 138, 139, 144, 145, 146, 147, 152, 153, 154, 155, 160, 161, 162, 163, 168, 169, 170, 171, 176, 177, 178, 179, 184, 185, 186, 187, 192, 193, 194, 195, 200, 201]
  • Development sets: [4, 5, 12, 13, 20, 21, 28, 29, 36, 37, 44, 45, 52, 53, 60, 61, 68, 69, 76, 77, 84, 85, 92, 93, 100, 101, 108, 109, 116, 117, 124, 125, 132, 133, 140, 141, 148, 149, 156, 157, 164, 165, 172, 173, 180, 181, 188, 189, 196, 197]
  • Test sets: [6, 7, 14, 15, 22, 23, 30, 31, 38, 39, 46, 47, 54, 55, 62, 63, 70, 71, 78, 79, 86, 87, 94, 95, 102, 103, 110, 111, 118, 119, 126, 127, 134, 135, 142, 143, 150, 151, 158, 159, 166, 167, 174, 175, 182, 183, 190, 191, 198, 199]

THYME Software

The THYME system is available as part of Apache cTAKES at http://ctakes.apache.org/

Demo of the system: ctakes.apache.org -> get started -> demos -> ctakes-temporal (http://alt.qcri.org/semeval2016/task12/)

We are also developing a visualization tool (THYME viz tool) which will be made available in cTAKES. A prototype and details of the THYME vizualization tool was presented by Sean Finan at several annual workshops.

Finan, Sean. 2013. Challenges of visually representing rich temporal information of the clinical narrative. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 30th Annual Human-Computer Interaction Lab Symposium. May 22-23 2013. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2013/

Finan, Sean. De Groen, Piet. Savova, Guergana. 2014. Narrative Event and Temporal Relation Visualization Tool. Workshop: Exploring Temporal Patterns in Electronic Health Record Data. 31st Annual Human-Computer Interaction Lab Symposium. May 29 2014. University of Maryland. http://www.cs.umd.edu/hcil/eventflow/workshop2014/

Finan, Sean. De Groen, Piet. Savova, Guergana. 2014. Narrative Event and Temporal Relation Visualization Tool. Natural Language Processing Workshop. Informatics for Integrating Biology & the Bedside (I2B2). 4th Annual Academic User Group Meeting. July 9 2014. Harvard Medical School. https://www.i2b2.org/events/slides/NarrativeVisualizer.pdf

Relevant Background Papers

Relevant Papers

Reading Group

Paper Queue

Internal Presentations

Presentations


Venues for manuscript submissions

Venues for manuscript submissions/publications


Project materials

Project Charter

Tasks, leads, teams and deadlines

Progress reports

Annotations - Describes the corpus, the layers of annotations and annotation progress

Annotation Tools - Describes the progress and information pertaining to the Anafora annotation tool


Communication

IDEAS notebook

Ideas notebook


Meeting Notes

Getting started


Contact

If you need assistance and/or if you have questions about the project, feel free to send e-mail to guergana dot savova at childrens dot harvard dot edu, martha dot palmer at colorado dot edu, or bethard at email dot arizona dot edu.

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