projects:workgroups:nlp-wg
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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 01:30] vipina [Past WG meetings (Agenda/Minutes/Recordings)] |
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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 - March 8, 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 - Dr. Daniel G. Smith, Emory University\\ |
| - | - Standardization of term_modifiers and values – Hua Xu | + | **Abstract:** Implementing an NLP process into production is an often challenging task, with considerable requirements for accuracy prior to being relied upon in a clinical workflow. However, including other local members of the clinical and research community in the process at each stage of model selection and development could provide considerable advantages. At Winship Cancer Institute, we’re starting to bring NLP to our research abstractors, as well as our tumor registrars, so that they can provide critical feedback on dictionary curation, NER label verification, and final accuracy of the models in development. We seek feedback from the NLP working group regarding our model of the current process, as well as discuss your experiences in bringing clinical and research staff into the NLP process.\\ |
| + | |||
| + | 2) Updates on the progress of ongoing studies | ||
| + | - SDoH | ||
| + | - Psychiatry | ||
| + | - Oncology | ||
| + | 3) NLP book chapter and other OKRs | ||
| + | |||
| + | |||
| + | ==== 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 ==== | ||
| Line 110: | Line 69: | ||
| * 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 | ||
projects/workgroups/nlp-wg.txt · Last modified: 2023/05/10 01:37 by vipina
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