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--- projects:workgroups:nlp-wg [2019/01/08 18:30]
anu_gururaj2 [Repository]
+++ projects:workgroups:nlp-wg [2023/05/10 01:37] (current)
vipina [Ongoing Projects]
@@ Line 5: / Line 5: @@
 The primary goal of the NLP working group is to promote the use of textual information from Electronic Health Records (EHRs) for observational studies under the OHDSI umbrella. To facilitate this objective, the group will develop methods and software that can be implemented to utilize clinical text for studies by the OHDSI community.
-==== Project Lead ====
+==== Workgroup Lead ====
-Hua Xu
+[[https://www.ohdsi.org/who-we-are/collaborators/hua-xu/|Hua Xu]]\\
-==== Project Co-leads ====
-Jon Duke, Nigam Shah, Noemie Elhadad
-==== Plan ====
+==== Project Coordinator ====
+ [[vipina.kuttichikeloth@yale.edu | Vipina K. Keloth ]]
+==== OHDSI NLP WG Monthly Meeting ====
+**When:** Second Wednesday of every month at 1 PM - 2 PM CT
+**Where:** [[https://teams.microsoft.com/dl/launcher/launcher.html?url=%2F_%23%2Fl%2Fmeetup-join%2F19%3Acd9841fec6df4f3d8eb6a6bf49ea305f%40thread.tacv2%2F1610663053273%3Fcontext%3D%257b%2522Tid%2522%253a%2522a30f0094-9120-4aab-ba4c-e5509023b2d5%2522%252c%2522Oid%2522%253a%252200626e72-b11c-482a-9dc4-d8eff51c5e5f%2522%257d%26anon%3Dtrue&type=meetup-join&deeplinkId=42431bac-788d-4a7b-8531-5eb2612224a6&directDl=true&msLaunch=true&enableMobilePage=true&suppressPrompt=true|Click here to join the meeting]]
+**Monthly Meeting:** Upcoming - May 9, 2023
+**Agenda**
+) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\
+**Title:** LeafAI: query generator for clinical cohort discovery rivaling a human programmer\\
+**Abstract:**  Identifying study-eligible patients within clinical databases is a critical step in clinical research. However, accurate query design typically requires extensive technical and biomedical expertise. We sought to create a system capable of generating data model-agnostic queries while also providing novel logical reasoning capabilities for complex clinical trial eligibility criteria. We incorporated hybrid deep learning and rule-based modules for these, as well as a knowledge base of the Unified Medical Language System (UMLS) and linked ontologies. To enable data-model agnostic query creation, we introduce a novel method for tagging database schema elements using UMLS concepts. To evaluate our system, called LeafAI, we compared the capability of LeafAI to a human database programmer to identify patients who had been enrolled in 8 clinical trials conducted at our institution. We measured performance by the number of actual enrolled patients matched by generated queries. LeafAI matched a mean 43% of enrolled patients with 27,225 eligible across 8 clinical trials, compared to 27% matched and 14,587 eligible in queries by a human database programmer. The human programmer spent 26 total hours crafting queries compared to several minutes by LeafAI. Finally, we introduce a novel multimodal user interface for interaction with LeafAI.\\
+) Updates on the progress of ongoing studies
+  - SDoH
+  - Psychiatry
+  - Oncology
+) NLP book chapter
-  - IRB for use of clinical text
-  - Clinical text data storage and representation schema
-  - NLP tools/pipelines for ETL
-  - Use cases, e.g, phenotyping for cohort selection using NLP outputs
 ==== Ongoing Projects ====
-  - Rules for defining term_exists – led by Stephane Meystre - COMPLETED
+  * Note type normalization
-  - Mapping of CUIs to standard terminology – Juan Banda - COMPLETED - [[https://github.com/thepanacealab/OHDSIananke]]
+  * Social Determinants of Health
-  - Mapping of Note Types to LOINC/standard vocabulary –Karthik Natarajan, Ruth Reeves, Jon Duke and Hua Xu– Report type list discussion
+  * Psychiatry - NLP for capturing administration of neuropsychiatric scales and their scores
-  - Landscape Analysis of section identifier systems and proposal of a standard terminology for use – Hua Xu, Karthik Natarajan
+  * Oncology - NLP for getting oncology data using Tumor Reg data as a gold standard for assessing the information obtained through the NLP algorithm
-  - Examples and rules for term_temporal – led by George Hripsack (Sunny)
+  * Book of OHDSI NLP Chapter
-  - Standardization of term_modifiers and values – Hua Xu
+==== Past Projects ====
+  * Note_NLP table
+  * COVID-19 testing normalization (TestNorm)
+  * Note type
+  * NLP tools: NLP Wrappers; THEIA; Ananke
 ==== Participants ====
-  * Hua Xu
+A noncomprehensive list of participants: [[ Click here ]]
-  * Nigam Shah
-  * Noemie Elhadad
-  * Jon Duke
-  * Alexandre Yahi
-  * Thomas Ginter
-  * Olga Patterson
-  * George Hripsack
-  * Vojtech Huser
-  * Mark Khayter
-  * Karthik Natarajan
-  * Min Jiang
-  * Scott DuVall
-  * Abraham Hartzema
-  * David Sontag
-  * Arnab Bose
-  * Anupama Gururaj
-  * Lian Hu
-  * Jan A Kors
-  * J van Der Lei
-  * Peter R Rijnbeek
-  * Vivienne Zhu
-  * Bob Patterson
-  * Michael Gurley
-  * Xiaoling Chen
-  * Hongfang Liu
-  * Hong Yu
-  * Stephane Meystre
-  * Timothy Miller
-  * Wendy Chapman
-  * Feifan Liu
-  * Paris Nicolas
-  * Mark Dredze
-  * Masoud Rouhizadeh
-  * Malcolm McRoberts
-  * Nishanth Parameshwar Pavinkurve
-  * Carol Friedman
-==== Upcoming Meeting Dates ====
-  * January 9th, 2019
+==== Upcoming Meeting Dates (2023) ====
-  * February 13th, 2019
-  * March 13th, 2019
+  * June 14
-  * April 10th, 2019
+  * July 12
-  * May 8th, 2019
+  * August 9
-  * June 12th, 2019
+  * September 13
-  * July 10th, 2019
+  * October 11
+  * November 8
+  * December 13
 ==== Repository ====
@@ Line 83: / Line 68: @@
   * OHDSIananke [[https://github.com/thepanacealab/OHDSIananke]]
-==== Proposal for concepts detected by NLP  ====
-create a new table called NOTE_NLP
-with the following columns
-  * **note_id** (integer) links to NOTE.note_id (foreign key)
-  * **note_concept_id** (integer) concept_id of a term found in the note
-  * **certainty** (real number 0-100) how certain is the NLP pipeline that this concept is present in the note
-  * **offset** position of where in the note was the concept  detected
-  * **span** (integer) number of characters from offset where the concept was detected
-  * **negation_flag** (string of length 1 (or boolean)) indicates if the concept is negated
-{{:projects:workgroups:16ohdsi_nlp_schema_updated.pdf|}}
-[[https://docs.google.com/document/d/1ykYVJTQ5MuI7eh_Nk7xzt44EzNjVs71nq2LIsC_RlOg/edit]]
+==== Past WG meetings (Agenda/Minutes/Recordings) ====
+**2023**\\
+  -[[WG_meeting_may_10_2023]]
+  -[[WG_meeting_apr_12_2023]]
+  -[[WG_meeting_mar_08_2023]]
+  -[[WG_meeting_feb_08_2023]]
+  -[[WG_meeting_jan_11_2023]]
+**2022**\\
+  -[[WG_meeting_dec_14_2022]]
+  -[[WG_meeting_nov_09_2022]]
+  -[[WG_meeting_sep_14_2022]]
+  -[[WG_meeting_aug_10_2022]]
+  -[[WG_meeting_jun_08_2022]]
+  -[[WG_meeting_may_11_2022]]
+  -[[WG_meeting_apr_13_2022]]
+  -[[WG_meeting_mar_09_2022]]
+  -[[WG_meeting_feb_09_2022]]
+  -[[WG_meeting_jan_12_2022]]
-==== Start Date ====
+**2021**\\
+  -[[WG_meeting_dec_08_2021]]
+  -[[WG_meeting_nov_10_2021]]
+  -[[WG_meeting_oct_13_2021]]
+  -[[WG_meeting_sep_08_2021]]
+  -[[WG_meeting_aug_11_2021]]
-August 2015
+**2019**\\
-==== WG Agenda/Minutes/Recordings ====
+  -[[WG_meeting_10092019]]
+  -[[WG_meeting_09112019]]
+  -[[WG_meeting_08142019]]
+  -[[WG_meeting_07102019]]
+  -[[WG_meeting_05082019]]
+  -[[WG_meeting_04102019]]
+  -[[WG_meeting_03132019]]
+  -[[WG_meeting_02132019]]
+  -[[WG_meeting_01092019]]
+**2018**\\
+  -[[WG_meeting_11142018]]
+  -[[WG_meeting_09122018]]
+  -[[WG_meeting_06132018]]
+  -[[WG_meeting_05092018]]
+  -[[WG_meeting_04142018]]
+  -[[WG_meeting_03142018]]
+  -[[WG_meeting_02142018]]
+  -[[WG_meeting_01102018]]
-  -[[projects:workgroups:minutes|WG_meeting_10072015]]
+**2017**\\
-  -[[WG_meeting_11042015]]
-  -[[WG_meeting_01062016]]
-  -[[WG_meeting_02032016]]
-  -[[WG_meeting_03092016]]
-  -[[WG_meeting_04132016]]
-  -[[WG_meeting_04202016]]
-  -[[WG_meeting_06142017]]
-  -[[WG_meeting_07122017]]
-  -[[WG_meeting_09132017]]
-  -[[WG_meeting_10112017]]
   -[[WG_meeting_12122017]]
-  -[[WG_meeting_01102018]]
+  -[[WG_meeting_10112017]]
-  -[[WG_meeting_02142018]]
+  -[[WG_meeting_09132017]]
-  -[[WG_meeting_03142018]]
+  -[[WG_meeting_07122017]]
-  -[[WG_meeting_04142018]]
+  -[[WG_meeting_06142017]]
-  -[[WG_meeting_05092018]]
-  -[[WG_meeting_06132018]]
+**2016**\\
-  -[[WG_meeting_09122018]]
+  -[[WG_meeting_04202016]]
-  -[[WG_meeting_11142018]]
+  -[[WG_meeting_04132016]]
-==== Meetings ====
+  -[[WG_meeting_03092016]]
+  -[[WG_meeting_02032016]]
+  -[[WG_meeting_01062016]]
+**2015**\\
+  -[[WG_meeting_11042015]]
+  -[[projects:workgroups:minutes|WG_meeting_10072015]]
+===== Microsoft Teams meeting =====
+**Join on your computer or mobile app**
+[[https://teams.microsoft.com/dl/launcher/launcher.html?url=%2F_%23%2Fl%2Fmeetup-join%2F19%3Acd9841fec6df4f3d8eb6a6bf49ea305f%40thread.tacv2%2F1610663053273%3Fcontext%3D%257b%2522Tid%2522%253a%2522a30f0094-9120-4aab-ba4c-e5509023b2d5%2522%252c%2522Oid%2522%253a%252200626e72-b11c-482a-9dc4-d8eff51c5e5f%2522%257d%26anon%3Dtrue&type=meetup-join&deeplinkId=42431bac-788d-4a7b-8531-5eb2612224a6&directDl=true&msLaunch=true&enableMobilePage=true&suppressPrompt=true|Click here to join the meeting]]
-    Schedule: Second Wednesday of every month at 2pm Eastern Time
+[[https://aka.ms/JoinTeamsMeeting|Learn More]]
-    THE DECEMBER MEETING IS CANCELLED
-    The next meeting will be on January 9th, 2019
-    Meetings in 2019:
-      * February 13th
-      * March 13th
-      * April 10th
-      * May 8th
-      * June 12th
-      * July 10th
-    Call-in:
-) Dial +1 (571) 317-3122 (United States)
-       Please see below for international call-in numbers
-) Enter conference ID: 707-196-421
-    Screen Sharing: [[https://global.gotomeeting.com/join/707196421]]
-    More phone numbers
-    * Australia : +61 2 8355 1039
-    * Austria : +43 7 2088 2172
-    * Belgium : +32 (0) 42 68 0180
-    * Canada : +1 (647) 497-9379
-    * Denmark : +45 89 88 05 39
-    * Finland : +358 (0) 931 58 4588
-    * France : +33 (0) 170 950 589
-    * Germany : +49 (0) 692 5736 7301
-    * Ireland : +353 (0) 15 360 757
-    * Italy : +39 0 294 75 15 37
-    * Netherlands : +31 (0) 108 080 116
-    * New Zealand : +64 9 801 0294
-    * Norway : +47 21 51 81 86
-    * Spain : +34 911 23 4248
-    * Sweden : +46 (0) 852 500 516
-    * Switzerland : +41 (0) 435 0824 41
-    * United Kingdom : +44 (0) 330 221 0099

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