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== Welcome to the Cancer Deep Phenotype Extraction (DeepPhe) project ==
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== Welcome to the Cancer Deep Phenotype Extraction project ==
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Our goal is to develop novel methods for information extraction to facilitate automatic/unsupervised/minimally supervised extraction of specific discrete cancer-related data from various types of unstructured electronic medical records.  
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Our goal is to develop novel methods for information extraction to facilitate automatic/unsupervised/minimally supervised extraction of specific discrete cancer-related data from various types of unstructured electronic medical records. Our two main use cases are cancer deep phenotyping for translational science (DeepPhe) and a platform for cancer surveillance by the cancer registries (DeepPhe*CR)
  
 
<!-- Welcome to the Cancer Deep Phenotype Extraction (DeepPhe) project.
 
<!-- Welcome to the Cancer Deep Phenotype Extraction (DeepPhe) project.
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== Who We Are ==
 
== Who We Are ==
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* Boston Childrens Hospital/Harvard Medical School
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===Boston Children's Hospital/Harvard Medical School===
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** Guergana Savova (MPI)
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* [https://www.childrenshospital.org/research/researchers/guergana-savova Guergana Savova] (MPI for DeepPhe and DeepPhe*CR)
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** Timothy Miller
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* Timothy Miller
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** Sean Finan
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* Sean Finan
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** David Harris
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* David Harris
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** Chen Lin
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* Chen Lin
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** past members -- Dmitriy Dligach (currently faculty at Loyola University, Chicago), Pei Chen, James Masanz
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* past members -- Dmitriy Dligach (currently faculty at Loyola University, Chicago), James Masanz
  
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* University of Pittburgh
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===University of Pittburgh===
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** Harry Hochheiser (MPI)
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* [https://www.phdl.pitt.edu/people/harry-hochheiser-phd Harry Hochheiser] (MPI for DeepPhe and DeepPhe*CR)
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** Zhou Yuan
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* Zhou Yuan
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** past members - through June 2017: Rebecca Crowley Jacobson (MPI), Roger Day, Adrian Lee, Robert Edwards, John Kirkwood, Kevin Mitchell, Eugene Tseytlin, Girish Chavan, Melissa Castine; Liz Legowski (through Jan 2015), Olga Medvedeva, Mike Davis
+
* John Levander
 +
* past members - through June 2017: Rebecca Crowley Jacobson (MPI), Roger Day, Adrian Lee, Robert Edwards, John Kirkwood, Kevin Mitchell, Eugene Tseytlin, Girish Chavan, Melissa Castine; Liz Legowski (through Jan 2015), Olga Medvedeva, Mike Davis
  
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* Vanderbilt University
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===Rhode Island Hospital (Brown University)===
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** Jeremy Warner (MPI)
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* [https://vivo.brown.edu/display/jwarne11 Jeremy Warner] (MPI for DeepPhe and DeepPhe*CR)
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** Alicia Beeghly-Fadiel
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* [https://vivo.brown.edu/display/dgamsiz Ece Uzun]
 +
* [https://vivo.brown.edu/display/dsdizon Don Dizon]
 +
* Sandeep Jain
 +
* Alex VanHelene
  
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* Dana-Farber Cancer Institute
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===University of Kentucky/Kentucky Cancer Registry===
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** Elizabeth Buchbinder
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* Eric Durbin (MPI for DeepPhe*CR)
 +
* Isaac Hands
 +
* Jong Jeong
 +
* Ramakanth (Rama) Kavuluru
 +
* David Rust
 +
* Lisa Witt
  
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* Kentucky Cancer Registry
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===Dana-Farber Cancer Institute===
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** Eric Durbin (MPI)
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* [https://www.dana-farber.org/find-a-doctor/elizabeth-i-buchbinder Elizabeth Buchbinder]
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** Isaac Hands
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* [https://www.dana-farber.org/find-a-doctor/danielle-s-bitterman Danielle Bitterman]
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** Jong Jeong
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−
** Venkata Kavuluru
+
  
 +
===University of Minnesota===
 +
* Piet de Groen
 +
 +
===Vanderbilt University===
 +
* [https://www.vumc.org/viiii/person/douglas-b-johnson-md-msci Douglas B. Johnson]
 +
* past members - Alicia Beeghly-Fadiel
  
 
== Funding ==
 
== Funding ==
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The project described is supported by the National Cancer Institute at the US National Institutes of Health. It is part of the NCI's Informatics Technology for Cancer Research (ITCR) Initiative (http://itcr.nci.nih.gov/) The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
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The project described is supported by the National Cancer Institute at the US National Institutes of Health. It is part of the National Cancer Institute's Informatics Technology for Cancer Research (ITCR) Initiative (http://itcr.nci.nih.gov/) and the Surveillance, Epidemiology, and End Results Program (SEER; https://seer.cancer.gov/) at the US National Cancer Institute (NCI). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.
 +
 
 +
 
 +
== Cancer Deep Phenotyping for Cancer Surveillance (DeepPhe*CR) ==
 +
=== Scrum Sprints ===
 +
*[[Year1_goals_DeepPheCR | Goals DeepPhe-CR July 2019 - June 2020]]
 +
**[[ScrumSprint_DeepPheCR | Sprint 1 DeepPhe-CR, August 2019]]
 +
**[[ScrumSprint_DeepPheCR_2 | Sprint 2 DeepPhe-CR, Sept 19 - Oct 17, 2019]]
 +
**[[ScrumSprint_DeepPheCR_3 | Sprint 3 DeepPhe-CR, Oct 18 - Nov 14, 2019]]
 +
**[[ScrumSprint_DeepPheCR_4 | Sprint 4 DeepPhe-CR, Nov 14 - Jan 9, 2020]]
 +
**[[ScrumSprint_DeepPheCR_5 | Sprint 5 DeepPhe-CR, Jan 9 - Feb 6, 2020]]
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**[[ScrumSprint_DeepPheCR_6 | Sprint 6 DeepPhe-CR, Feb 7 - Mar 5, 2020]]
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**[[ScrumSprint_DeepPheCR_7 | Sprint 7 DeepPhe-CR, Mar 6 - Apr 2, 2020]]
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**[[ScrumSprint_DeepPheCR_8 | Sprint 8 DeepPhe-CR, Apr 3 - Apr 30, 2020]]
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**[[ScrumSprint_DeepPheCR_9 | Sprint 9 DeepPhe-CR, May 1 - May 28, 2020]]
 +
**[[ScrumSprint_DeepPheCR_10 | Sprint 10 DeepPhe-CR, May 29 - July 9, 2020]]
 +
 
 +
* [[Year2_goals_DeepPheCR | Goals DeepPhe-CR July 2020 - June 2021]]
 +
**[[ScrumSprint_DeepPheCR_11 | Sprint 11 DeepPhe-CR, July 16 - Aug 13, 2020]]
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**[[ScrumSprint_DeepPheCR_12 | Sprint 12 DeepPhe-CR, Aug 13 - Sept 10, 2020]]
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**[[ScrumSprint_DeepPheCR_13 | Sprint 13 DeepPhe-CR, Sept 10 - Oct 14, 2020]]
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**[[ScrumSprint_DeepPheCR_14 | Sprint 14 DeepPhe-CR, Oct 15 - Nov 12, 2020]]
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**[[ScrumSprint_DeepPheCR_15 | Sprint 15 DeepPhe-CR, Nov 13, 2020 - Jan 14, 2021]]
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**[[ScrumSprint_DeepPheCR_16 | Sprint 16 DeepPhe-CR, Jan 14 - Feb 18, 2021]]
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**[[ScrumSprint_DeepPheCR_17 | Sprint 17 DeepPhe-CR, Feb 18 - Mar 25, 2021]]
 +
**[[ScrumSprint_DeepPheCR_18 | Sprint 18 DeepPhe-CR, Mar 25 - April 28, 2021]]
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**[[ScrumSprint_DeepPheCR_19 | Sprint 19 DeepPhe-CR, Apr 29 - May 27, 2021]]
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**[[ScrumSprint_DeepPheCR_20 | Sprint 20 DeepPhe-CR, May 28 - Jun 30, 2021]]
 +
 
 +
* [[Year3_goals_DeepPheCR | Goals DeepPhe-CR July 2021 - June 2022]]
 +
**[[ScrumSprint_DeepPheCR_21 | Sprint 21 DeepPhe-CR, Aug 5 - Sept 8, 2021]]
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**[[ScrumSprint_DeepPheCR_22 | Sprint 22 DeepPhe-CR, Sept 9 - Oct 7, 2021]]
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**[[ScrumSprint_DeepPheCR_23 | Sprint 23 DeepPhe-CR, Oct 14 - Nov 11, 2021]]
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**[[ScrumSprint_DeepPheCR_24 | Sprint 24 DeepPhe-CR, Nov 12 - Dec 9, 2021]]
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**[[ScrumSprint_DeepPheCR_25 | Sprint 25 DeepPhe-CR, Dec 10, 2021 - Jan 13, 2022]]
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**[[ScrumSprint_DeepPheCR_26 | Sprint 26 DeepPhe-CR, Jan 14 - Feb 10, 2022]]
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**[[ScrumSprint_DeepPheCR_27 | Sprint 27 DeepPhe-CR, Feb 11 - Mar 10, 2022]]
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**[[ScrumSprint_DeepPheCR_28 | Sprint 28 DeepPhe-CR, Mar 11 - April 8, 2022]]
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**[[ScrumSprint_DeepPheCR_29 | Sprint 29 DeepPhe-CR, April 8 - May 5, 2022]]
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**[[ScrumSprint_DeepPheCR_30 | Sprint 30 DeepPhe-CR, May 6 - June 2, 2022]]
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**[[ScrumSprint_DeepPheCR_31 | Sprint 31 DeepPhe-CR, June 3 - 30, 2022]]
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 +
* [[Year4_goals_DeepPheCR | Goals DeepPhe-CR July 2022 - June 2023]]
 +
**[[ScrumSprint_DeepPheCR_32 | Sprint 32 DeepPhe-CR, July 1 - 28, 2022]]
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**[[ScrumSprint_DeepPheCR_33 | Sprint 33 DeepPhe-CR, July 29 - Aug 25, 2022]]
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**[[ScrumSprint_DeepPheCR_34 | Sprint 34 DeepPhe-CR, Aug 26 - Sept 22, 2022]]
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**[[ScrumSprint_DeepPheCR_35 | Sprint 35 DeepPhe-CR, Sept 23 - Oct 20, 2022]]
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**[[ScrumSprint_DeepPheCR_36 | Sprint 36 DeepPhe-CR, Oct 21 - Nov 24, 2022]]
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**[[ScrumSprint_DeepPheCR_37 | Sprint 37 DeepPhe-CR, Nov 25, 2022 - Jan 5, 2023]]
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**[[ScrumSprint_DeepPheCR_38 | Sprint 37 DeepPhe-CR, Jan 6 - Feb 2, 2023]]
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**[[ScrumSprint_DeepPheCR_39 | Sprint 39 DeepPhe-CR, Feb 3 - Mar 2, 2023]]
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**[[ScrumSprint_DeepPheCR_40 | Sprint 40 DeepPhe-CR, Mar 3 - 30, 2023]]
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**[[ScrumSprint_DeepPheCR_41 | Sprint 41 DeepPhe-CR, Mar 31 - Apr 27, 2023]]
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**[[ScrumSprint_DeepPheCR_42 | Sprint 42 DeepPhe-CR, Apr 28 - May 25, 2023]]
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**[[ScrumSprint_DeepPheCR_43 | Sprint 43 DeepPhe-CR, May 26 - June 30, 2023]]
 +
 
 +
* [[Year5_goals_DeepPheCR | Goals DeepPhe-CR July 2023 - June 2024]]
 +
**[[ScrumSprint_DeepPheCR_44 | Sprint 44 DeepPhe-CR, Jul 1 - Aug 3, 2023]]
 +
**[[ScrumSprint_DeepPheCR_45 | Sprint 45 DeepPhe-CR, Aug 3 - 31, 2023]]
 +
**[[ScrumSprint_DeepPheCR_46 | Sprint 46 DeepPhe-CR, Sept 1 - 28, 2023]]
 +
**[[ScrumSprint_DeepPheCR_47 | Sprint 47 DeepPhe-CR, Sept 29 - Oct 26, 2023]]
 +
**[[ScrumSprint_DeepPheCR_48 | Sprint 48 DeepPhe-CR, Oct 27 - Nov 30, 2023]]
 +
**[[ScrumSprint_DeepPheCR_49 | Sprint 49 DeepPhe-CR, Dec 1, 2023 - Jan 4, 2024]]
 +
**[[ScrumSprint_DeepPheCR_50 | Sprint 50 DeepPhe-CR, Jan 5 - Feb 1, 2024]]
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**[[ScrumSprint_DeepPheCR_51 | Sprint 51 DeepPhe-CR, Feb 2 - 29, 2024]]
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**[[ScrumSprint_DeepPheCR_52 | Sprint 52 DeepPhe-CR, Mar 1 - 29, 2024]]
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**[[ScrumSprint_DeepPheCR_53 | Sprint 53 DeepPhe-CR, Mar 29 - Apr 26, 2024]]
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**[[ScrumSprint_DeepPheCR_54 | Sprint 54 DeepPhe-CR, Apr 26 - May 30, 2024]]
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**[[ScrumSprint_DeepPheCR_55 | Sprint 55 DeepPhe-CR, May 31 - June 30, 2024]]
 +
 
 +
=== Project materials ===
 +
*[[UG3 Technical Details]]
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*[[Registry Integration User Stories]]
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*[[Technical Topics]]
 +
 
 +
=== Publications and presentations ===
 +
Peer-reviewed publications:
 +
#'''2023:''' Bitterman DS, Goldner E, Finan S, Harris D, Durbin EB, Hochheiser H, Warner JL, Mak RH, Miller T, Savova GK. An End-to-End Natural Language Processing System for Automatically Extracting Radiation Therapy Events From Clinical Texts. Int J Radiat Oncol Biol Phys. 2023 Sep 1;117(1):262-273. doi: 10.1016/j.ijrobp.2023.03.055. Epub 2023 Mar 27. PMID: 36990288; PMCID: PMC10522797.
 +
#'''2020:''' Durbin, Eric; Hochheiser , Harry; Petkov, Valentina; Rivera, Donna; Savova, Guergana; Warner, Jeremy. 2020. Tools and software to automate and normalize the cancer data abstraction workflow. Workshop at the annual North American Association of Cancer Registries (NAACCR). June 2020. Philadelphia, PA.
 +
#'''2020:''' Zhou Yuan, Sean Finan, Jeremy Warner, Guergana Savova, Harry Hochheiser 2019. Interactive Exploration of Longitudinal Cancer Patient Histories Extracted From Clinical Text. JCO Clin Cancer Inform. 2020 May;4:412-420. doi: 10.1200/CCI.19.00115
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#'''2019:''' Guergana Savova, Ioana Danciu, Folami Alamudun, Timothy Miller, Chen Lin, Danielle S Bitterman, Georgia Tourassi and Jeremy L Warner. 2019. Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records. Cancer Research. doi: 10.1158/0008-5472.CAN-19-0579
 +
 
 +
Pre-prints:
 +
#'''2023:''' Hochheiser H, Finan S, Yuan Z, Durbin EB, Jeong JC, Hands I, Rust D, Kavuluru R, Wu XC, Warner JL, Savova G. DeepPhe-CR: Natural Language Processing Software Services for Cancer Registrar Case Abstraction. medRxiv [Preprint]. 2023 Oct 26:2023.05.05.23289524. doi: 10.1101/2023.05.05.23289524. PMID: 37205575; PMCID: PMC10187451.
 +
 
 +
Presentations:
 +
#'''2019:''' Savova, Guergana and Hochheiser, Harry. “Cancer Deep Phenotype Extraction from Electronic Medical Records ”. Data Science Seminar Series. National Cancer Institute, National Institutes of Health. Oct 2019.
 +
#'''2019:''' Warner, Jeremy, Durbin, Eric, Petkov, Valentina and Savova, Guergana. 2019. Tools and Software to Automate and Normalize the Cancer Data Abstraction Workflow.  Workshop at 2019 Conference of the North American Association of Central Cancer Registries and the International Association of Cancer Registries. June 9-13, 2019. Vancouver, BC, Canada
  
 +
=== Websites ===
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* https://github.com/DeepPhe
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* https://github.com/DeepPhe/DeepPhe -- private code repository
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* https://github.com/DeepPhe/cr-neo4j-plugin
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* https://github.com/DeepPhe/docker
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* https://github.com/DeepPhe/cr-rest-api
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* https://github.com/DeepPhe/deepphe-owl
  
−
== Publications and presentations ==
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== Cancer Deep Phenotyping for Translational Science (DeepPhe) ==
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=== Publications and presentations ===
 
Peer-reviewed publications:
 
Peer-reviewed publications:
 
<ul>
 
<ul>
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</ol>
 
</ol>
 
</ul>
 
</ul>
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Other:
 
Other:
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# Warner, Jeremy. 2018. Improving Cancer Diagnosis and Care: Patient Access to Oncologic Imaging and Pathology Expertise and Technologies. the National Cancer Policy Forum of the National Academies of Sciences, Engineering, and Medicine. http://www.nationalacademies.org/hmd/Activities/Disease/NCPF/2018-FEB-12/Videos/Session%204%20Videos/32%20Warner.aspx -->
 
# Warner, Jeremy. 2018. Improving Cancer Diagnosis and Care: Patient Access to Oncologic Imaging and Pathology Expertise and Technologies. the National Cancer Policy Forum of the National Academies of Sciences, Engineering, and Medicine. http://www.nationalacademies.org/hmd/Activities/Disease/NCPF/2018-FEB-12/Videos/Session%204%20Videos/32%20Warner.aspx -->
  
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== DeepPhe Software ==
+
=== Information Extracted by DeepPhe ===
 +
* Cancer – body location, laterality, stage, clinical TNM, path TNM
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* Tumor – body location, laterality, diagnosis, tumor type, histologic type, cancer type, extend, grade
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* Specific to BrCA – clockface position, quadrant, ER/PR/HER2
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* Specific to OvCa – CA-125
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* Specific to melanoma – clarks level, Breslow depth
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* Specific to prostate cancer -- Gleason score, PSA
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* Medications
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* Procedures
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* Radiotherapy
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* Comorbidities
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* Episodes –
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** Pre-diagnostic: a tumor is mentioned PRIOR to a malignant diagnosis
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** Diagnostic: a tumor is mentioned WITH a malignant diagnosis
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** Decision making: discussion of potential treatments AFTER an established diagnosis
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** Treatment: a treatment is mentioned DURING the treatment episode
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** Follow-up: discussion appearing AFTER the treatment episode ends
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** Unknown: episode category unsettled
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 +
=== DeepPhe Software ===
 
<!-- The DeepPhe system will be available as part of Apache cTAKES at http://ctakes.apache.org/. It is now available at https://github.com/DeepPhe/DeepPhe-Release and https://github.com/DeepPhe/DeepPhe-Viz.
 
<!-- The DeepPhe system will be available as part of Apache cTAKES at http://ctakes.apache.org/. It is now available at https://github.com/DeepPhe/DeepPhe-Release and https://github.com/DeepPhe/DeepPhe-Viz.
  
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* [https://github.com/DeepPhe/DeepPhe-Release code]
 
* [https://github.com/DeepPhe/DeepPhe-Release code]
  
−
 
+
=== DeepPhe Gold Set ===
−
== DeepPhe Gold Set ==
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* [[Deidentification_Process | Process for Deidentification of Source Documents]].
 
* [[Deidentification_Process | Process for Deidentification of Source Documents]].
 
* [[Public_Deidentification_Process | Process for Deidentification of Source Documents]].
 
* [[Public_Deidentification_Process | Process for Deidentification of Source Documents]].
 
* [[Public:Deidentification_Process | Process for Deidentification of Source Documents]].
 
* [[Public:Deidentification_Process | Process for Deidentification of Source Documents]].
 
* [[Gold_Set_Selection | Process for Selection of Gold Set Source Documents]].
 
* [[Gold_Set_Selection | Process for Selection of Gold Set Source Documents]].
−
* DeepPhe UPMC Training/Development/Test splits
+
* DepPhe Training/Development/Test splits
 
** training set:  
 
** training set:  
 
*** all documents for Breast Cancer patients 03, 11, 92, 93 for a total of 48 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
 
*** all documents for Breast Cancer patients 03, 11, 92, 93 for a total of 48 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
−
*** all documents for Breast Cancer patients extended 04,05,06,09,10,12,13,14,18,19,20,22,23,26,27,30,31,32,33,34,35,40,41,42,43,38,39,46,47 for a total of 954 documents  (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
+
*** all documents for Breast Cancer patients extended 4,5,6,9,10,12,13,14,18,19,20,22,23,26,27,30,31,32,33,34,35,38,39,40,41,42,43,46,47 for a total of 954 documents  (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
 
*** all documents for Melanoma patients 05, 06, 18, 19, 25, 28, 30, 33, 34, 42, for a total of 233 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\trainSet\DeepPhe DevSet Phenotype Annotations.xlsm
 
*** all documents for Melanoma patients 05, 06, 18, 19, 25, 28, 30, 33, 34, 42, for a total of 233 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\trainSet\DeepPhe DevSet Phenotype Annotations.xlsm
 
*** all documents for Ovarian Cancer patients 3, 4, 7, 8, 12, 13, 16, 17, 18, 20, 24, 25, 26, 27, 30, 31, 32, 34, 37, 38, 41, 42, 43, 44, 46, 48 for a total of 1675 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\trainSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\trainSet\DeepPhe_ovCa_Train_Set_Phenotype_Annotations_GOLD.xlsm
 
*** all documents for Ovarian Cancer patients 3, 4, 7, 8, 12, 13, 16, 17, 18, 20, 24, 25, 26, 27, 30, 31, 32, 34, 37, 38, 41, 42, 43, 44, 46, 48 for a total of 1675 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\trainSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\trainSet\DeepPhe_ovCa_Train_Set_Phenotype_Annotations_GOLD.xlsm
 +
*** all documents for Colorectal cancer patients 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 set:  
 
** development set:  
 
*** all documents for Breast Cancer patients 02, 21 for a total of 42 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
 
*** all documents for Breast Cancer patients 02, 21 for a total of 42 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
−
*** all documents for Breast Cancer patients extended 01,15,16,17,28,29,36,37,44,45,07,08,24,25 for a total of 457 documents  (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
+
*** all documents for Breast Cancer patients extended 7,8,15,16,17,24,25,28,29,36,37,44,45 for a total of 457 documents  (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
 
*** all documents for Melanoma patients 07, 32, 43 for a total of 215 (processed only 211 docs) documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\devSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\devSet\DeepPhe DevSet Phenotype Annotations.xlsm
 
*** all documents for Melanoma patients 07, 32, 43 for a total of 215 (processed only 211 docs) documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\devSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\devSet\DeepPhe DevSet Phenotype Annotations.xlsm
 
*** all documents for Ovarian Cancer patients 9, 11, 19, 28, 29, 35, 39, 47 for a total of 562 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\devSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\devSet\DeepPhe_ovCa_Dev_Set_Phenotype_Annotations_GOLD.xlsm
 
*** all documents for Ovarian Cancer patients 9, 11, 19, 28, 29, 35, 39, 47 for a total of 562 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\devSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\devSet\DeepPhe_ovCa_Dev_Set_Phenotype_Annotations_GOLD.xlsm
 +
*** all documents for Colorectal cancer patients 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 set:  
 
** test set:  
 
*** all documents for Breast Cancer patients 01 (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\DeepPhe Test Phenotype Annotations v2.xlsm
 
*** all documents for Breast Cancer patients 01 (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\DeepPhe Test Phenotype Annotations v2.xlsm
−
*** all documents for Breast Cancer extended for patients 01, 02, 09,10,12,15,17,18,19,20,23,24,27,32,36,39,44,63, 76, 100, 101, 104, 106, 109, 111, 114, 115, 117, 118, 119, 120, 121, 123, 125, 126, 129, 130, 132, 136, 137, 138, 142, 143, 155, 156, 158, 174, 181, 189, 197 for phenotyping level testing use (\\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\DeepPhe Test Phenotype Annotations v2.xlsm
+
*** all documents for Breast Cancer extended for patients 01, 02, 63, 76, 100, 101, 104, 106, 109, 111, 114, 115, 117, 118, 119, 120, 121, 123, 125, 126, 129, 130, 132, 136, 137, 138, 142, 143, 155, 156, 158, 174, 181, 189, 197 for phenotyping level testing use (\\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\DeepPhe Test Phenotype Annotations v2.xlsm
 
*** all documents for Melanoma patients 02, 03, 11, 12, 14, 16, 24, 27, 41, 44 for a total of 229 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\testSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\testSet\DeepPhe TestSet Phenotype Annotations.xlsm
 
*** all documents for Melanoma patients 02, 03, 11, 12, 14, 16, 24, 27, 41, 44 for a total of 229 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\testSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\testSet\DeepPhe TestSet Phenotype Annotations.xlsm
 
*** all documents for Ovarian Cancer patients 15, 21, 33, 36, 40, 45, 49, 50 for a total of 559 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\testSet); gold annotations are in \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\testSet\DeepPhe_ovCa_Test_Set_Phenotype_Annotations_GOLD.xlsm
 
*** all documents for Ovarian Cancer patients 15, 21, 33, 36, 40, 45, 49, 50 for a total of 559 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\testSet); gold annotations are in \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\testSet\DeepPhe_ovCa_Test_Set_Phenotype_Annotations_GOLD.xlsm
 +
*** all documents for Colorectal cancer patients 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
 
** use the training set for developing the algorithms and the development set to report results and error analysis. The test set will be used only for the final evaluation to go in publications.
 
** use the training set for developing the algorithms and the development set to report results and error analysis. The test set will be used only for the final evaluation to go in publications.
 
* [[SEER_Project_Splits| SEER Project Train/Dev/Test Splits]]
 
* [[SEER_Project_Splits| SEER Project Train/Dev/Test Splits]]
 
* [[Clinical Genomics Gold Set | Clinical Genomics Gold Set ]]
 
* [[Clinical Genomics Gold Set | Clinical Genomics Gold Set ]]
  
−
 
+
=== Qualitative Interviews ===
−
== Qualitative Interviews ==
+
 
* [[User_Personae | Detailed Stakeholder Descriptions]].  
 
* [[User_Personae | Detailed Stakeholder Descriptions]].  
 
* [[Interview_Protocol | Interview Protocol]]
 
* [[Interview_Protocol | Interview Protocol]]
Line 209: Line 336:
  
  
−
== Project materials/ WIKIs to tasks ==
+
=== Software Development Goals: Phase 2 ===
 +
* [[phase_2_user_software_goal | Software development goals for the 2nd phase of funding (2020-2025)]]
 +
* [[Expert_informant_feedback | Feedback from Clinical Informants regarding visualization  ]]
 +
* [[phase_2_user_stories | Phase 2 user stories for visualization]]
 +
* [[DeepPhe-Viz-Tasks_Phase 2 | DeepPhe-Viz Tasks]]
 +
* [[dpv_design_suggestions| Other Design Suggestions]]
 +
* [[Unresolved Visualization Design Questions]]
 +
 
 +
=== Scrum Sprints ===
 +
* [[Previous sprints]]
 +
*[[Year1_goals_DeepPhe_Sept2020_Aug2021 | Goals DeepPhe Sept 2020 - Aug 2021]]
 +
**[[Sprint_1_DeepPhe | Sprint 1 DeepPhe, Dec 3, 2020 - Jan 6, 2021]]
 +
**[[Sprint_2_DeepPhe | Sprint 2 DeepPhe, Jan 7 - Feb 25, 2021]]
 +
**[[Sprint_3_DeepPhe | Sprint 3 DeepPhe, Feb 25 - Mar 25, 2021]]
 +
**[[Sprint_4_DeepPhe | Sprint 4 DeepPhe, Mar 25 - Apr 28, 2021]]
 +
**[[Sprint_5_DeepPhe | Sprint 5 DeepPhe, Apr 29 - May 27, 2021]]
 +
**[[Sprint_6_DeepPhe | Sprint 6 DeepPhe, May 28 - Jun 24, 2021]]
 +
**[[Sprint_7_DeepPhe | Sprint 7 DeepPhe, Jun 25 - Jul 22, 2021]]
 +
**[[Sprint_8_DeepPhe | Sprint 8 DeepPhe, Jul 23 - Aug 19, 2021]]
 +
**[[Sprint_9_DeepPhe | Sprint 9 DeepPhe, Aug 20 - Sept 16, 2021]]
 +
*[[Year2_goals_DeepPhe_Sept2021_Aug2022 | Goals DeepPhe Sept 2021 - Aug 2022]]
 +
**[[Sprint_10_DeepPhe | Sprint 10 DeepPhe, Sept 17 - Oct 14, 2021]]
 +
**[[Sprint_11_DeepPhe | Sprint 11 DeepPhe, Oct 14 - Nov 11, 2021]]
 +
**[[Sprint_12_DeepPhe | Sprint 12 DeepPhe, Nov 12 - Dec 9, 2021]]
 +
**[[Sprint_13_DeepPhe | Sprint 13 DeepPhe, Dec 10, 2021 - Jan 13, 2022]]
 +
**[[Sprint_14_DeepPhe | Sprint 14 DeepPhe, Jan 14 - Feb 10, 2022]]
 +
**[[Sprint_15_DeepPhe | Sprint 15 DeepPhe, Feb 11 - Mar 10, 2022]]
 +
**[[Sprint_16_DeepPhe | Sprint 16 DeepPhe, Mar 11 - April 8, 2022]]
 +
**[[Sprint_17_DeepPhe | Sprint 17 DeepPhe, April 8 - May 5, 2022]]
 +
**[[Sprint_18_DeepPhe | Sprint 18 DeepPhe, May 12 - June 9, 2022]]
 +
**[[Sprint_19_DeepPhe | Sprint 19 DeepPhe, June 10 - July 7, 2022]]
 +
**[[Sprint_20_DeepPhe | Sprint 20 DeepPhe, July 8 - Aug 5, 2022]]
 +
**[[Sprint_21_DeepPhe | Sprint 21 DeepPhe, Aug 5 - Sept 1, 2022]]
 +
*[[Year3_goals_DeepPhe_Sept2022_Aug2023 | Goals DeepPhe Sept 2022 - Aug 2023]]
 +
**[[Sprint_22_DeepPhe | Sprint 22 DeepPhe, Sept 2 - 30, 2022]]
 +
**[[Sprint_23_DeepPhe | Sprint 23 DeepPhe, Sept 30 - Nov 30, 2022]]
 +
**[[Sprint_24_DeepPhe | Sprint 24 DeepPhe, Dec 1, 2022 - Jan 5, 2023]]
 +
**[[Sprint_25_DeepPhe | Sprint 25 DeepPhe, Jan 6 - Feb 2, 2023]]
 +
**[[Sprint_26_DeepPhe | Sprint 26 DeepPhe, Feb 3 - Mar 2, 2023]]
 +
**[[Sprint_27_DeepPhe | Sprint 27 DeepPhe, Mar 3 - 30, 2023]]
 +
**[[Sprint_28_DeepPhe | Sprint 28 DeepPhe, Mar 31 - Apr 27, 2023]]
 +
**[[Sprint_29_DeepPhe | Sprint 29 DeepPhe, Apr 28 - May 25, 2023]]
 +
**[[Sprint_30_DeepPhe | Sprint 30 DeepPhe, May 26 - June 30, 2023]]
 +
**[[Sprint_31_DeepPhe | Sprint 31 DeepPhe, Jul 1 - Aug 3, 2023]]
 +
**[[Sprint_32_DeepPhe | Sprint 32 DeepPhe, Aug 3 - 31, 2023]]
 +
*[[Year4_goals_DeepPhe_Sept2023_Aug2024 | Goals DeepPhe Sept 2023 - Aug 2024]]
 +
**[[Sprint_33_DeepPhe | Sprint 33 DeepPhe, Aug 31 - Sep 28, 2023]]
 +
**[[Sprint_34_DeepPhe | Sprint 34 DeepPhe, Sep 29 - Oct 26, 2023]]
 +
**[[Sprint_35_DeepPhe | Sprint 35 DeepPhe, Oct 27 - Nov 30, 2023]]
 +
**[[Sprint_36_DeepPhe | Sprint 36 DeepPhe, Nov 30, 2023 - Jan 4, 2024]]
 +
**[[Sprint_37_DeepPhe | Sprint 37 DeepPhe, Jan 5 - Feb 1, 2024]]
 +
**[[Sprint_38_DeepPhe | Sprint 38 DeepPhe, Feb 2 - 29, 2024]]
 +
**[[Sprint_39_DeepPhe | Sprint 39 DeepPhe, Mar 1 - 28, 2024]]
 +
**[[Sprint_40_DeepPhe | Sprint 40 DeepPhe, Mar 29 - Apr 26, 2024]]
 +
**[[Sprint_41_DeepPhe | Sprint 41 DeepPhe, Apr 26 - May 30, 2024]]
 +
**[[Sprint_42_DeepPhe | Sprint 42 DeepPhe, May 31 - Jun 27, 2024]]
 +
**[[Sprint_43_DeepPhe | Sprint 43 DeepPhe, Jun 28 - Aug 1, 2024]]
 +
**[[Sprint_44_DeepPhe | Sprint 44 DeepPhe, Aug 1 - 29, 2024]]
 +
*[[Year5_goals_DeepPhe_Sept2024_Aug2025 | Goals DeepPhe Sept 2024 - Aug 2025]]
 +
**[[Sprint_45_DeepPhe | Sprint 45 DeepPhe, Aug 30 - Sept 26, 2024]]
 +
**[[Sprint_46_DeepPhe | Sprint 46 DeepPhe, Sept 27 - Oct 24, 2024]]
 +
 
 +
=== Project materials/ WIKIs to tasks ===
 
* [[Archive]]
 
* [[Archive]]
 +
<!-- *[[UG3 Technical Details]]-->
  
−
 
+
=== Communication ===
−
== Communication ==
+
 
* Weekly team meetings
 
* Weekly team meetings
 
* Tools we use for communication are listed in our [[Communications_Plan |Communications Plan ]].
 
* Tools we use for communication are listed in our [[Communications_Plan |Communications Plan ]].
  
−
== Scrum Sprints ==
+
=== Meeting Notes ===
−
* [[Previous sprints]]
+
* [[Meeting notes]]
 +
<!-- == Scrum Sprints == -->
 +
<!-- * [[Previous sprints]]-->
  
−
*[[ScrumSprint_47 | Sprint 47, May 9 - June 5, 2019]]
+
<!-- *[[Year1_goals_DeepPheCR | Goals DeepPhe-CR July 2019 - June 2020]]-->
−
 
+
<!-- *[[ScrumSprint_DeepPheCR | Sprint 1 DeepPhe-CR, August 2019]]-->
−
== Meeting Notes ==
+
<!-- *[[ScrumSprint_DeepPheCR_2 | Sprint 2 DeepPhe-CR, Sept 19 - Oct 17, 2019]]-->
−
* [[Meeting notes]]
+
<!-- *[[ScrumSprint_DeepPheCR_3 | Sprint 3 DeepPhe-CR, Oct 18 - Nov 14, 2019]]-->
 +
<!-- *[[ScrumSprint_DeepPheCR_4 | Sprint 4 DeepPhe-CR, Nov 14 - Jan 9, 2020]]-->
 +
<!-- *[[ScrumSprint_DeepPheCR_5 | Sprint 5 DeepPhe-CR, Jan 9 - Feb 6, 2020]]-->
 +
<!-- *[[ScrumSprint_DeepPheCR_6 | Sprint 6 DeepPhe-CR, Feb 7 - Mar 5, 2020]]-->
 +
<!-- *[[ScrumSprint_DeepPheCR_7 | Sprint 7 DeepPhe-CR, Mar 6 - Apr 2, 2020]]-->
 +
<!-- *[[ScrumSprint_DeepPheCR_8 | Sprint 8 DeepPhe-CR, Apr 3 - May 1, 2020]]-->
  
 
== Contact ==
 
== Contact ==
 +
<!-- If you need assistance or if you have further questions about the project, contact us at the [https://groups.google.com/forum/#!forum/deepphe DeepPhe group].-->
 +
If you have further questions about the project, contact guergana dot savova at childrens dot harvard dot edu.
  
−
If you need assistance or if you have further questions about the project, contact us at the [https://groups.google.com/forum/#!forum/deepphe DeepPhe group].
 
  
 
== Getting started ==
 
== Getting started ==

Latest revision as of 15:59, 9 October 2024


Welcome to the Cancer Deep Phenotype Extraction project

Our goal is to develop novel methods for information extraction to facilitate automatic/unsupervised/minimally supervised extraction of specific discrete cancer-related data from various types of unstructured electronic medical records. Our two main use cases are cancer deep phenotyping for translational science (DeepPhe) and a platform for cancer surveillance by the cancer registries (DeepPhe*CR)


Who We Are

Boston Children's Hospital/Harvard Medical School

  • Guergana Savova (MPI for DeepPhe and DeepPhe*CR)
  • Timothy Miller
  • Sean Finan
  • David Harris
  • Chen Lin
  • past members -- Dmitriy Dligach (currently faculty at Loyola University, Chicago), James Masanz

University of Pittburgh

  • Harry Hochheiser (MPI for DeepPhe and DeepPhe*CR)
  • Zhou Yuan
  • John Levander
  • past members - through June 2017: Rebecca Crowley Jacobson (MPI), Roger Day, Adrian Lee, Robert Edwards, John Kirkwood, Kevin Mitchell, Eugene Tseytlin, Girish Chavan, Melissa Castine; Liz Legowski (through Jan 2015), Olga Medvedeva, Mike Davis

Rhode Island Hospital (Brown University)

University of Kentucky/Kentucky Cancer Registry

  • Eric Durbin (MPI for DeepPhe*CR)
  • Isaac Hands
  • Jong Jeong
  • Ramakanth (Rama) Kavuluru
  • David Rust
  • Lisa Witt

Dana-Farber Cancer Institute

University of Minnesota

  • Piet de Groen

Vanderbilt University

Funding

The project described is supported by the National Cancer Institute at the US National Institutes of Health. It is part of the National Cancer Institute's Informatics Technology for Cancer Research (ITCR) Initiative (http://itcr.nci.nih.gov/) and the Surveillance, Epidemiology, and End Results Program (SEER; https://seer.cancer.gov/) at the US National Cancer Institute (NCI). The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.


Cancer Deep Phenotyping for Cancer Surveillance (DeepPhe*CR)

Scrum Sprints

Project materials

Publications and presentations

Peer-reviewed publications:

  1. 2023: Bitterman DS, Goldner E, Finan S, Harris D, Durbin EB, Hochheiser H, Warner JL, Mak RH, Miller T, Savova GK. An End-to-End Natural Language Processing System for Automatically Extracting Radiation Therapy Events From Clinical Texts. Int J Radiat Oncol Biol Phys. 2023 Sep 1;117(1):262-273. doi: 10.1016/j.ijrobp.2023.03.055. Epub 2023 Mar 27. PMID: 36990288; PMCID: PMC10522797.
  2. 2020: Durbin, Eric; Hochheiser , Harry; Petkov, Valentina; Rivera, Donna; Savova, Guergana; Warner, Jeremy. 2020. Tools and software to automate and normalize the cancer data abstraction workflow. Workshop at the annual North American Association of Cancer Registries (NAACCR). June 2020. Philadelphia, PA.
  3. 2020: Zhou Yuan, Sean Finan, Jeremy Warner, Guergana Savova, Harry Hochheiser 2019. Interactive Exploration of Longitudinal Cancer Patient Histories Extracted From Clinical Text. JCO Clin Cancer Inform. 2020 May;4:412-420. doi: 10.1200/CCI.19.00115
  4. 2019: Guergana Savova, Ioana Danciu, Folami Alamudun, Timothy Miller, Chen Lin, Danielle S Bitterman, Georgia Tourassi and Jeremy L Warner. 2019. Use of Natural Language Processing to Extract Clinical Cancer Phenotypes from Electronic Medical Records. Cancer Research. doi: 10.1158/0008-5472.CAN-19-0579

Pre-prints:

  1. 2023: Hochheiser H, Finan S, Yuan Z, Durbin EB, Jeong JC, Hands I, Rust D, Kavuluru R, Wu XC, Warner JL, Savova G. DeepPhe-CR: Natural Language Processing Software Services for Cancer Registrar Case Abstraction. medRxiv [Preprint]. 2023 Oct 26:2023.05.05.23289524. doi: 10.1101/2023.05.05.23289524. PMID: 37205575; PMCID: PMC10187451.

Presentations:

  1. 2019: Savova, Guergana and Hochheiser, Harry. “Cancer Deep Phenotype Extraction from Electronic Medical Records ”. Data Science Seminar Series. National Cancer Institute, National Institutes of Health. Oct 2019.
  2. 2019: Warner, Jeremy, Durbin, Eric, Petkov, Valentina and Savova, Guergana. 2019. Tools and Software to Automate and Normalize the Cancer Data Abstraction Workflow. Workshop at 2019 Conference of the North American Association of Central Cancer Registries and the International Association of Cancer Registries. June 9-13, 2019. Vancouver, BC, Canada

Websites

Cancer Deep Phenotyping for Translational Science (DeepPhe)

Publications and presentations

Peer-reviewed publications:

    1. Lin, Chen; Miller, Timothy; Dligach, Dmitriy; Amiri, Hadi; Bethard, Steven and 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. Oct 31-Nov 1, 2018. Brussels, Belgium. https://aclanthology.coli.uni-saarland.de/papers/W18-5619/w18-5619
    2. Malty, Andrew M., Jain, Sandeep K., Yang, Peter C., Harvey, Krysten, Warner, Jeremy L. Computerized approach to creating a systematic ontology of hematology/oncology regimens. JCO Clinical Cancer Informatics. 2018 May 11. http://ascopubs.org/doi/full/10.1200/CCI.17.00142
    3. Miller, Timothy; Dligach, Dmitriy; Bethard, Steven; Lin, Chen; Savova, Guergana. 2017. Towards Generalizable Entity-Centric Clinical Coreference Resolution. Journal of Biomedical Informatics. Vol. 69, May 2017, pp. 251-258. https://doi.org/10.1016/j.jbi.2017.04.015; http://www.sciencedirect.com/science/article/pii/S1532046417300850
    4. Castro SM, Tseytlin E, Medvedeva O, Mitchell K, Visweswaran S, Bekhuis T, Jacobson RS. 2017. Automated annotation and classification of BI-RADS assessment from radiology reports. J Biomed Inform. 2017 May;69:177-187. doi: 10.1016/j.jbi.2017.04.011. PMID: 28428140; PMCID: PMC5706448 [Available on 2018-05-01] DOI:10.1016/j.jbi.2017.04.011 https://www.sciencedirect.com/science/article/pii/S1532046417300813
    5. 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. https://aclanthology.coli.uni-saarland.de/papers/W17-2341/w17-2341
    6. Miller, T; Bethard, S; Amiri, H; Savova, G. 2017. Unsupervised Domain Adaptation for Clinical Negation Detection. BioNLP workshop at the Association for Computational Linguistics conference. Vancouver, Canada, Friday August 4, 2017 https://aclanthology.coli.uni-saarland.de/papers/W17-2320/w17-2320
    7. Savova, G., Tseytlin, E., Finan, S., Castine, M., Miller, T., Medvedeva, O., Haris, D., Hochheiser, H., Lin, C., Chavan, G., Jacobson R. 2017. DeepPhe - A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records. Annual Symposium of the American Medical Informatics Association (AMIA). Nov 2017. Washington DC https://amia2017.zerista.com/event/member/389439
    8. Savova, G., Tseytlin, E., Finan, S., Castine, M., Miller, T., Medvedeva, O., Haris, D., Hochheiser, H., Lin, C., Chavan, G., Jacobson R. 2017. DeepPhe: A Natural Language Processing System for Extracting Cancer Phenotypes from Clinical Records. Cancer Research 77(21), November 2017 DOI: 10.1158/0008-5472.CAN-17-0615. https://www.ncbi.nlm.nih.gov/pubmed/29092954
    9. 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. https://aclanthology.coli.uni-saarland.de/papers/E17-2118/e17-2118
    10. Chen, Lin; 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 https://aclanthology.coli.uni-saarland.de/papers/W16-2914/w16-2914
    11. Hochheiser, Harry; Castine, Melissa; Harris, David; Savova, Guergana; Jacobson, Rebecca. 2016. An Information Model for Computable Cancer Phenotypes. BMC Medical Informatics and Decision Making. https://bmcmedinformdecismak.biomedcentral.com/articles/10.1186/s12911-016-0358-4 https://www.ncbi.nlm.nih.gov/pubmed/27629872
    12. Ethan Hartzell, Chen Lin. 2016. Enhancing Clinical Temporal Relation Discovery with Syntactic Embeddings from GloVe. International Conference on Intelligent Biology and Medicine (ICIBM 2016). Medical Informatics Thematic Track. December 2016, Houston, Texas, USA
    13. Dmitriy Dligach, Timothy Miller, Guergana K. Savova. 2015. Semi-supervised Learning for Phenotyping Tasks. AMIA Annual Symposium. Nov 2015, San Francisco, CA. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4765699/
    14. Chen, Lin; Dligach, Dmitriy; Miller, Timothy; Bethard, Steven; Savova, Guergana. 2015. Multilayered temporal modeling for the clinical domain. Journal of the American Medical Informatics Association. 2016 Mar;23(2):387-95. doi: 10.1093/jamia/ocv113 https://www.ncbi.nlm.nih.gov/pubmed/26521301

Peer-reviewed other:

    1. Beeghly-Fadiel, Alicia; Warner, Jeremy; Finan, Sean; Masanz, James; Hochheiser, Harry; Savova, Guergana. (under review). Deep Phenotype Extraction to Facilitate Cancer Research: Extending DeepPhe to Ovarian Cancer. American Association for Cancer Research (AACR) 2019. March 29-April 3, 2019. Atlanta, GA.
    2. Yuan, Zhou; Finan, Sean; Warner, Jeremy; Savova, Guergana; Hochheiser, Harry. 2018. Toward Longitudinal Visual Analytics for Cancer Patient Trajectories Extracted from Clinical Text. 2018 Workshop on Visual Analytics and Healthcare, Demonstration Presentation. AMIA 2018, Nov 3-7, 2018. San Francisco, CA.
    3. Chen Lin, Timothy A. Miller, Hadi Amiri, David Harris, Samuel M. Rubinstein, Jeremy Warner, Guergana K. Savova, Ph.D. 2018. Classification of electronic medical records of breast cancer and melanoma patients into clinical episodes. 30th Anniversary AACR Special Conference Convergence: Artificial Intelligence, Big Data, and Prediction of Cancer. Oct 14-17, 2018. Newport, RI, USA.
    4. Warner, Jeremy; Elhadad, Noemie; Bastarache, Lisa; Gotz, David; Savova, Guergana. 2018. Panel - Didactic: Computable Longitudinal Patient Trajectories. Annual Symposium of the American Medical Informatics Association. November, 2018. San Francisco, CA. (peer-reviewed panel)
    5. Savova G, Tseytlin E, Finan S, Castine M, Miller T, Medvedeva O, Harris D, Hochheiser H, Lin C, Chavan G, Warner JL, Jacobson R. DeepPhe – a natural language processing system for extracting cancer phenotypes from clinical records. Annual conference of the North American Association of Central Cancer Registries (NAACCR). Pittsburgh, PA.
    6. Warner JL, Harris D, Rubinstein S, Finan S, Lin C, Miller T, Amiri H, Hochheiser H, Savova G. Capturing high-resolution temporal cancer phenotypes using DeepPhe. Annual conference of the North American Association of Central Cancer Registries (NAACCR). Pittsburgh, PA.
    7. Yang PC, Malty A, Jain SK, Harvey K, Finan S, Warner JL. 2018. A Comprehensive Ontology of Hematology/Oncology Regimens. Annual conference of the North American Association of Central Cancer Registries (NAACCR). Pittsburgh, PA.
    8. Hochheiser H; Jacobson R; Washington N; Denny J; Savova G. 2015. Natural language processing for phenotype extraction: challenges and representation. AMIA Annual Symposium. Nov 2015, San Francisco, CA. (peer-reviewed panel)

Invited presentations:

    1. Savova, Guergana. 2019. Cancer Deep Phenotype Extraction from Electronic Medical Records. Molecular Med Tri-con. March 10-15, 2019. San Francisco, CA, USA
    2. Savova G. 2018. Software and Research Challenges for Clinical NLP. Dana Farber Cancer Institute; 2018 October; Boston, MA, USA.
    3. Savova, Guergana. 2018. Cancer Deep Phenotype Extraction form Electronic Medical Records (DeepPhe). College of American Pathologists Pathology Electronic Reporting meeting (CAP PERT). July 29, 2018. Montreal, QB, CA.
    4. Warner, Jeremy. 2018. A Comprehensive Ontology of Hematology/Oncology Regimens. College of American Pathologists Pathology Electronic Reporting meeting (CAP PERT). July 29, 2018. Montreal, QB, CA.
    5. Savova, G; Miller, T. 2018. DeepPhe and Extraction of Oncology Patient Phenotypes from Unstructured Text Using NLP and Other AI Tools. Presentation to Dana Farber Cancer Institute. January 24 2018. Boston, MA.
    6. Warner, Jeremy. 2017. Supporting cancer registries through automated extraction of pathology and chemotherapy regimen information.” CDC/NCI/FDA/VA Clinical Natural Language Processing Workshop. Atlanta, GA.
    7. Savova, Guergana. 2017. Select Applications of Natural Language Processing in Biomedicine. Natural Language Processing Symposium, Boston University, Boston, MA. November, 2017.
    8. Jacobson, Rebecca. 2017. Invited presentation at Ohio State University James Cancer Center Grand Rounds, January 20th, 2017
    9. Jacobson, Rebecca. 2017. Invited presentation at Case Western University Comprehensive Cancer Center Seminar Series, March 10th, 2017
    10. Jacobson, Rebecca. 2016. Invited presentation of cTAKES and DeepPhe to NCI in January, 2016. Gaithersburg, MD
    11. Jacobson, Rebecca. 2016. Invited presentation in CBIIT Speaker Series, February 17, 2016. Gaithersburg, MD
    12. Jacobson, Rebecca. 2016. Invited presentation at University of Pittsburgh Cancer Informatics (UPCI) External Advisory Board, March 8, 2016
    13. Finan, Sean. 2016. cTAKES/deepPhe presentation at the ITCR workshop at CI4CC in Napa, CA
    14. Jacobson, Rebecca. 2016. Invited presentation at SEER PI meeting in New Mexico, March 16, 2016
    15. Jacobson, Rebecca. 2016. Invited presentation at University of Michigan Department of Learning Health Sciences, April 6th, 2016
    16. Jacobson, Rebecca. 2016. Invited presentation at Pathology Informatics 2016, Pittsburgh PA, May 24th, 2016
    17. Jacobson, Rebecca. 2016. Invited presentation at University of Pittsburgh Cancer Institute Scientific Retreat, Greensburg, PA, June 16th, 2016
    18. Jacobson, Rebecca and Savova, Guergana. 2016. Invited presentation at SEER meeting in Gaithersburg, MD, December 10, 2016
    19. Jacobson, Rebecca and Savova, Guergana. Invited presentation of cTAKES/DeepPhe to NCI in October, 2015

Other:


Information Extracted by DeepPhe

  • Cancer – body location, laterality, stage, clinical TNM, path TNM
  • Tumor – body location, laterality, diagnosis, tumor type, histologic type, cancer type, extend, grade
  • Specific to BrCA – clockface position, quadrant, ER/PR/HER2
  • Specific to OvCa – CA-125
  • Specific to melanoma – clarks level, Breslow depth
  • Specific to prostate cancer -- Gleason score, PSA
  • Medications
  • Procedures
  • Radiotherapy
  • Comorbidities
  • Episodes –
    • Pre-diagnostic: a tumor is mentioned PRIOR to a malignant diagnosis
    • Diagnostic: a tumor is mentioned WITH a malignant diagnosis
    • Decision making: discussion of potential treatments AFTER an established diagnosis
    • Treatment: a treatment is mentioned DURING the treatment episode
    • Follow-up: discussion appearing AFTER the treatment episode ends
    • Unknown: episode category unsettled

DeepPhe Software

DeepPhe release is available in

DeepPhe Gold Set

  • Process for Deidentification of Source Documents.
  • Process for Deidentification of Source Documents.
  • Process for Deidentification of Source Documents.
  • Process for Selection of Gold Set Source Documents.
  • DepPhe Training/Development/Test splits
    • training set:
      • all documents for Breast Cancer patients 03, 11, 92, 93 for a total of 48 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
      • all documents for Breast Cancer patients extended 4,5,6,9,10,12,13,14,18,19,20,22,23,26,27,30,31,32,33,34,35,38,39,40,41,42,43,46,47 for a total of 954 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
      • all documents for Melanoma patients 05, 06, 18, 19, 25, 28, 30, 33, 34, 42, for a total of 233 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\trainSet\DeepPhe DevSet Phenotype Annotations.xlsm
      • all documents for Ovarian Cancer patients 3, 4, 7, 8, 12, 13, 16, 17, 18, 20, 24, 25, 26, 27, 30, 31, 32, 34, 37, 38, 41, 42, 43, 44, 46, 48 for a total of 1675 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\trainSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\trainSet\DeepPhe_ovCa_Train_Set_Phenotype_Annotations_GOLD.xlsm
      • all documents for Colorectal cancer patients 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 set:
      • all documents for Breast Cancer patients 02, 21 for a total of 42 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
      • all documents for Breast Cancer patients extended 7,8,15,16,17,24,25,28,29,36,37,44,45 for a total of 457 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedDev\DeepPhe Gold Phenotype Annotations_v2.xlsm
      • all documents for Melanoma patients 07, 32, 43 for a total of 215 (processed only 211 docs) documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\devSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\devSet\DeepPhe DevSet Phenotype Annotations.xlsm
      • all documents for Ovarian Cancer patients 9, 11, 19, 28, 29, 35, 39, 47 for a total of 562 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\devSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\devSet\DeepPhe_ovCa_Dev_Set_Phenotype_Annotations_GOLD.xlsm
      • all documents for Colorectal cancer patients 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 set:
      • all documents for Breast Cancer patients 01 (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\DeepPhe Test Phenotype Annotations v2.xlsm
      • all documents for Breast Cancer extended for patients 01, 02, 63, 76, 100, 101, 104, 106, 109, 111, 114, 115, 117, 118, 119, 120, 121, 123, 125, 126, 129, 130, 132, 136, 137, 138, 142, 143, 155, 156, 158, 174, 181, 189, 197 for phenotyping level testing use (\\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\breast\UPMCextendedTest\DeepPhe Test Phenotype Annotations v2.xlsm
      • all documents for Melanoma patients 02, 03, 11, 12, 14, 16, 24, 27, 41, 44 for a total of 229 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\testSet); gold annotations are \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\melanoma\testSet\DeepPhe TestSet Phenotype Annotations.xlsm
      • all documents for Ovarian Cancer patients 15, 21, 33, 36, 40, 45, 49, 50 for a total of 559 documents (in BCH \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\testSet); gold annotations are in \\rc-fs\chip-nlp\Public\DeepPhe\DeepPheDatasets\ovarian\final_dataset\testSet\DeepPhe_ovCa_Test_Set_Phenotype_Annotations_GOLD.xlsm
      • all documents for Colorectal cancer patients 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
    • use the training set for developing the algorithms and the development set to report results and error analysis. The test set will be used only for the final evaluation to go in publications.
  • SEER Project Train/Dev/Test Splits
  • Clinical Genomics Gold Set

Qualitative Interviews


Software Development Goals: Phase 2

Scrum Sprints

Project materials/ WIKIs to tasks

Communication

Meeting Notes


Contact

If you have further questions about the project, contact guergana dot savova at childrens dot harvard dot edu.


Getting started

Consult the User's Guide for information on using the wiki software.

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