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projects:workgroups:nlp-wg [2019/09/12 14:54] anu_gururaj2 [WG Agenda/Minutes/Recordings] |
projects:workgroups:nlp-wg [2023/05/10 01:34] vipina [OHDSI NLP WG Monthly Meeting] |
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==== Project Lead ==== | ==== Project 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 ==== |
- | - IRB for use of clinical text | + | [[vipina.kuttichikeloth@yale.edu | Vipina K. Keloth ]] |
- | - 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 ==== | + | ==== OHDSI NLP WG Monthly Meeting ==== |
+ | **When:** Second Wednesday of every month at 1 PM - 2 PM CT | ||
- | ===2018=== | + | **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]] |
- | - Rules for defining term_exists – led by Stephane Meystre - COMPLETED | + | **Monthly Meeting:** Upcoming - May 9, 2023 |
- | - Mapping of CUIs to standard terminology – Juan Banda - COMPLETED - [[https://github.com/thepanacealab/OHDSIananke]] | + | |
- | - Mapping of Note Types to LOINC/standard vocabulary –Karthik Natarajan, Ruth Reeves, Jon Duke and Hua Xu– Report type list discussion | + | **Agenda** |
- | - Landscape Analysis of section identifier systems and proposal of a standard terminology for use – Hua Xu, Karthik Natarajan | + | |
- | - Examples and rules for term_temporal – led by George Hripsack (Sunny) | + | 1) Presentation - **Nic Dobbins** (Principal Solutions Architect at UW Medicine Research IT; PhD Candidate in biomedical informatics at the University of Washington)\\ |
- | - Standardization of term_modifiers and values – Hua Xu | + | **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.\\ | ||
+ | |||
+ | 2) Updates on the progress of ongoing studies | ||
+ | - SDoH | ||
+ | - Psychiatry | ||
+ | - Oncology | ||
+ | 3) NLP book chapter | ||
+ | |||
+ | |||
+ | ==== Ongoing Projects ==== | ||
- | ===2019=== | + | * Note type normalization |
+ | * Social Determinants of Health | ||
+ | * Psychiatry - NLP for capturing administration of neuropsychiatric scales and their scores | ||
+ | * Oncology - NLP for getting oncology data using Tumor Reg data as a gold standard for assessing the information obtained through the NLP algorithm | ||
- | - Mapping of Note Types to LOINC/standard vocabulary –Karthik Natarajan, Ruth Reeves, Jon Duke and Hua Xu– Report type list discussion | + | ==== Past Projects ==== |
- | - Landscape Analysis of section identifier systems and proposal of a standard terminology for use – Hua Xu, Karthik Natarajan | + | |
- | - Examples and rules for term_temporal – led by George Hripsack (Sunny) | + | |
- | - Standardization of term_modifiers and values – Hua Xu | + | |
- | - Evaluate and revise textual CDM tables by sharing practical issues and lessons learnt during ETL for processing textual data into CDM, Usecases – Ruth Reeves, | + | |
- | - Develop tools (within Atlas) to facilitate uses of NLP data for cohort building/phenotyping : Collaborate with eMERGE consortium: | + | |
- | - Conduct cross-site studies that use textual data | + | |
- | - Continue developing other NLP resources | + | |
+ | * Note_NLP table | ||
+ | * COVID-19 testing normalization (TestNorm) | ||
+ | * Note type | ||
+ | * NLP tools: NLP Wrappers; THEIA; Ananke | ||
==== Participants ==== | ==== Participants ==== | ||
- | * Hua Xu | + | A noncomprehensive list of participants: [[ Click here ]] |
- | * Anupama Gururaj | + | |
- | * 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 | + | |
- | * 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 | + | |
- | * Miao Chen | + | |
- | * Jianlin Shi | + | |
- | * Vassilis Koutkias | + | |
- | * Dan Schlegel | + | |
- | * Mark V Mai | + | |
- | * Todd Lingren | + | |
- | * Jose Posada | + | |
- | * Andrew E Williams | + | |
- | * Vignesh Srinivasan | + | |
- | * Yuan Luo | + | |
- | * Kelly Peterson | + | |
- | * Xiao Dong | + | |
- | * Ning Shang | + | |
- | * Nishanth Parameshwar Pavinkurve | + | |
- | * Jessie Tenenbaum | + | |
- | * Elizabeth Marshall | + | |
- | * Kathleen Nogueira | + | |
- | ==== Upcoming Meeting Dates ==== | + | |
- | * September 11th, 2019 | + | ==== Upcoming Meeting Dates (2023) ==== |
- | * October 9th, 2019 | + | |
- | * November 13th, 2019 | + | * March 8 |
- | * December 11th, 2019 | + | * April 12 |
+ | * May 10 | ||
+ | * June 14 | ||
+ | * July 12 | ||
+ | * August 9 | ||
+ | * September 13 | ||
+ | * October 11 | ||
+ | * November 8 | ||
+ | * December 13 | ||
==== Repository ==== | ==== Repository ==== | ||
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* OHDSIananke [[https://github.com/thepanacealab/OHDSIananke]] | * 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_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]] |
- | -[[WG_meeting_01092019]] | + | -[[WG_meeting_03092016]] |
- | -[[WG_meeting_02132019]] | + | -[[WG_meeting_02032016]] |
- | -[[WG_meeting_03132019]] | + | -[[WG_meeting_01062016]] |
- | -[[WG_meeting_04102019]] | + | |
- | -[[WG_meeting_05082019]] | + | **2015**\\ |
- | -[[WG_meeting_07102019]] | + | -[[WG_meeting_11042015]] |
- | -[[WG_meeting_08142019]] | + | -[[projects:workgroups:minutes|WG_meeting_10072015]] |
- | -[[WG_meeting_09112019]] | + | |
- | ==== Meetings ==== | + | |
- | Schedule: Second Wednesday of every month at 2pm Eastern Time | + | ===== Microsoft Teams meeting ===== |
- | + | ||
- | The next meeting will be on September 11th, 2019 | + | |
- | + | ||
- | Meetings in 2019: | + | |
- | + | ||
- | * September 11th, 2019 | + | |
- | * October 9th, 2019 | + | |
- | * November 13th, 2019 | + | |
- | * December 11th, 2019 | + | |
- | + | ||
- | Call-in: | + | |
- | OHDSI NLP WG | ||
- | Occurs the second Wednesday of every month effective 5/8/2019 from 1:00 PM to 2:00 PM, (UTC-06:00) Central Time (US & Canada) | + | **Join on your computer or mobile app** |
- | Meeting number: **807 541 523** | ||
- | Password: **ohdsi** | + | [[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]] |
- | [[https://uthealth.webex.com/uthealth/j.php?MTID=m9d5511fc2cf5b3b7bc64b92096cf6c74]] | + | [[https://aka.ms/JoinTeamsMeeting|Learn More]] |
- | Join by video system | ||
- | Dial 807541523@uthealth.webex.com | ||
- | You can also dial 173.243.2.68 and enter your meeting number. | ||
- | Join by phone | ||
- | +1-415-655-0001 US Toll | ||
- | 1-844-621-3956 United States Toll Free | ||
- | Access code: 807 541 523 |