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 goal of our current proposal is to discover temporal relations from clinical free text through achieving four specific aims:
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.
Specific Aim 2: Extend and evaluate existing methods and/or develop new algorithms for temporal relation discovery in the clinical domain. Component-level evaluation
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.
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.
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.
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.
The project period is October, 2010 - September, 2014.
Who We Are
- University of Colorado
- Martha Palmer (PI)
- Jim Martin
- Wayne Ward
- Steven Bethard (at University of Alabama at Burmingham as of Sept, 2013)
- William Styler
- Arrick Lanfranchi (through August, 2012)
- Tim O'Gorman
- Kevin Crooks
- and several Lingustics and Computer Science graduate students
- Boston Childrens Hospital/Harvard Medical School
- Guergana Savova (PI)
- Dmitriy Dligach
- Timothy Miller
- Sameer Pradhan
- Sean Finan
- Chen Lin
- David Harris
- Jennifer Green (through December, 2013)
- Mayo Clinic
- Piet de Groen
- Brad Erickson
- James Masanz
- Donna Ihrke (through December, 2012)
- Pauline Funk (through January, 2013)
- Brandeis University
- James Pustejovsky
Publications and presentations crediting THYME
- Savova, Guergana; Pradhan, Sameer; Palmer, Martha; Styler, Will; Chapman, Wendy; Elhadad, Noemie. Forthcoming. Annotating the clinical text – MiPACQ, ShARe, SHARPn and THYME corpora. In Handbook of Linguistic Annotations. Ed. James Pustejovsky and Nancy Ide. Springer.
- 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
- 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
- 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.
- 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.
- Savova, Guergana; Chapman, Wendy; Elhadad, Noemie; Palmer, Martha. 2011. Shared annotated resources for the clinical domain. AMIA Annual Symposium, Panel. Washington, DC.
THYME Annotation Guidelines
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 in March, 2014 for a more up-to-date copy of the guidelines.
Annotations and availability
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.
Viewing annotations (Anafora)
(available to the team only)
To view the Temporal-Entity data, use the URL:
TASK_NAME is the filestem, for example, ID074_path_219b
to view Temporal-Relation data:
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"
THYME system is available as part of Apache cTAKES at ctakes.apache.org. Team members can track development progress.
Venues for manuscript submissions
Clinical Temporal Relations Annotation Guidelines - Release notes and latest versions
Annotations - Describes the corpus, the layers of annotations and annotation progress
Annotation Tools - Describes the progress and information pertaining to the Anafora annotation tool
Software - Describes the software modules and their organization
- Use this split for experiments with the THYME data (% 8)!
- (A note about Protege/Knowtator and Anafora annotation tools: annotations)
Colon Cancer Data
- All sets summary: 1-4,6-36,38-41,43-56,58-74,76,90,94,114,120
- 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, 43, 48, 49, 50, 51, 56, 58, 59, 64, 65, 66, 67, 72, 73, 74, 90, 114, 120
- Development sets: (Residue 4,5) 4, 12, 13, 20, 21, 28, 29, 36, 44, 45, 52, 53, 60, 61, 68, 69, 76
- Test sets: (Residue 6,7) 6, 7, 14, 15, 22, 23, 30, 31, 38, 39, 46, 47, 54, 55, 62, 63, 70, 71, 94
Brain Cancer Data
- All sets summary: 2-9
- Train sets: 2, 3, 8, 9
- Development sets: 4, 5
- Test sets: 6, 7
- January 8, 2014 Agenda and notes
- December 20, 2013 Methods meeting agenda and notes
- December 18, 2013 Agenda and notes
- December 13, 2013 Methods meeting agenda and notes
- December 6, 2013 Methods meeting agenda and notes
- December 4, 2013 Agenda and notes
- Nov 22, 2013 Methods meeting agenda and notes
- Nov 15, 2013 Methods meeting agenda and notes
- Nov 8, 2013 Methods meeting agenda and notes
- Nov 6, 2013 Agenda and notes
- Nov 1, 2013 Methods meeting agenda and notes
- Oct 23, 2013 Agenda and notes
- Oct 11, 2013 Methods meeting agenda and notes
- Oct 9, 2013 Agenda and notes
- Oct 4, 2013 Methods meeting agenda and notes
- Sep 27, 2013 Methods meeting agenda and notes
- Sep 25, 2013 Agenda and notes
- Sep 20, 2013 Methods meeting agenda and notes
- Sep 13, 2013 Methods meeting agenda and notes
- Sep 11, 2013 Agenda and notes
- Sep 06, 2013 Methods meeting agenda and notes
- Aug 30, 2013 Methods meeting agenda and notes
- August 28, 2013 Agenda and notes
- Aug 23, 2013 Methods meeting agenda and notes
- August 14, 2013 Agenda and notes
- Aug 16, 2013 Methods meeting agenda and notes
- Aug 2, 2013 Methods meeting agenda and notes
- July 31, 2013 Agenda and notes
- July 25, 2013 Methods meeting agenda and notes
- July 19, 2013 Methods meeting agenda and notes
- July 17, 2013 Agenda and notes
- July 12, 2013 Methods meeting agenda and notes
- No conference call on July 3, 2013. Happy 4th of July!
- June 28, 2013 Methods meeting agenda and notes
- June 19, 2013 Agenda and notes
- June 5, 2013 Agenda and notes
- May 31, 2013 Methods meeting agenda and notes
- May 24, 2013 Methods meeting agenda and notes
- May 22, 2013 Agenda and notes
- May 17, 2013 Methods meeting agenda and notes
- May 9, 2013 Methods meeting agenda and notes
- May 8, 2013 Agenda and notes
- May 3, 2013 Methods meeting agenda and notes
- April 24, 2013 Agenda and notes
- April 10, 2013 Agenda and notes
- March 27, 2013 Agenda and notes
- March 13, 2013 Agenda and notes
- February 27, 2013 Agenda and notes
- February 13, 2013 Agenda and notes
- January 30, 2013 Agenda and notes
- January 28, 2013 (annotations subgroup) Agenda and notes
- January 16, 2013 Agenda and notes
- January 2, 2013 Agenda and notes
- December 19, 2012 Agenda and notes
- December 5, 2012 Agenda and notes
- November 21, 2012 Agenda and notes
- November 6, 2012 Agenda and notes
- October 24, 2012 Agenda and notes
- October 10, 2012 Agenda and notes
- September 12, 2012 Agenda and notes
- August 29, 2012 Agenda and notes
- August 15, 2012 Agenda and notes
- August 1, 2012 Agenda and notes
- July 18, 2012 Agenda and notes
- June 22, 2012 Agenda and notes
- June 20, 2012 Agenda and notes
- June 6, 2012 Agenda and notes
- May 23, 2012 Agenda and notes
- May 9, 2012 Agenda and notes
- April 25, 2012 Agenda and notes
- April 11, 2012 Agenda and notes
- March 28, 2012 Agenda and notes
- March 14, 2012 Agenda and notes
- Feb 29, 2012 Agenda and notes
- Feb 14, 2012 Agenda and notes
- Feb 1, 2012 Agenda and notes
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