projects:workgroups:wg_meeting_02032016
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projects:workgroups:wg_meeting_02032016 [2016/03/07 21:18] anu_gururaj created |
projects:workgroups:wg_meeting_02032016 [2016/03/07 21:53] anu_gururaj |
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| - | ====== Minutes_Meeting_01062016 ====== | + | ====== Minutes_Meeting_02032016 ====== |
| ==== Attendees ==== | ==== Attendees ==== | ||
| - | Hua Xu, Jon Duke, George Hripcsak, Karthik Natarajan, Anupama Gururaj, Mark Khayter, Min Jiang, Don Torok, Alexandre Yahi, Andrew Williams | + | Hua Xu, Jon Duke, George Hripcsak, Karthik Natarajan, Anupama Gururaj, Mark Khayter, Min Jiang, Alexandre Yahi, Noemie Elhadad, Juan M Banda, Olga Patterson, Lian |
| ==== Agenda ==== | ==== Agenda ==== | ||
| - | -IRB for use of clinical text | + | - Minimal Model Presentation – Alex |
| - | -Clinical text data storage and representation schema | + | - Note-type mapping Presentation – Karthik |
| - | -NLP tools/pipelines for ETL | + | - Share existing ontologies from Vanderbilt (Hua) and Regenstrief (Jon) |
| - | -Use cases, e.g, phenotyping for cohort selection using NLP outputs | + | - Share strategies for combining data from different searches – Jon |
| - | -Discussion | + | - Report on WG for commenting – Hua |
| + | - Wrappers for cTAKES and Metamap – Min | ||
| + | - Improvements to search engine set up using MT samples – Min | ||
| + | - Textual Data Representation – Discussion | ||
| + | - Goals of 2016 | ||
| + | - Change of meeting time | ||
| ===Minutes=== | ===Minutes=== | ||
| - | - General IRB document for use of clinical text and approval from all contributors, post online - Almost completed | + | - Minimal model presentation - Alex |
| - | - Collect minimum set of modifiers for all clinical entities that support use of rule to derive clinical concepts: Alex | + | - the model is based on the SHARE-N model and adapted to the current data structure. This model incorporates other semantic types and all of the modifiers are not available in cTAKES yet. |
| - | * cTAKES is being run on clinical notes programmatically. Alex will present the minimal model in the next meeting. | + | - the notes were processed from eMERGE cohort at Columbia with about 60,000 notes encompassing 1700 patients. The original patient number was 3200. |
| + | - In theory, a set containing the combination of minimal modifiers can be generated. Practically, can we trust the data enough to add it into OHDSI tables? - only highest confidence data (with maximum PPV) should be added to the tables. | ||
| + | - Next steps: | ||
| + | - Look at the note sections to determine the errors. | ||
| + | - Work with Sunny to generate the NLP outputs for the phenotyping data | ||
| + | - Evaluate by comparisons with structured data | ||
| + | - Make the system more robust | ||
| + | - Generate a protocol and/or annotation guidelines | ||
| + | - Share the data as a Gold standard with manually annotated CUIs | ||
| + | - Alex's script is to be tried on different datasets and evaluated across notes from different institutions | ||
| + | - Identify minimal set of notes to work with when recommending to the OHDSI community | ||
| - Aggregate and share note-type metadata from various sources: Karthik | - Aggregate and share note-type metadata from various sources: Karthik | ||
| * LOINC note type mapping would be a very useful resource. We should generate hierarchical representation of note-types as an ontology. Karthink will present his work to date at the next meeting. | * LOINC note type mapping would be a very useful resource. We should generate hierarchical representation of note-types as an ontology. Karthink will present his work to date at the next meeting. | ||
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| - Improvements to search engine set up using MT samples - Min | - Improvements to search engine set up using MT samples - Min | ||
| - Textual Data Representation - Discussion | - Textual Data Representation - Discussion | ||
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projects/workgroups/wg_meeting_02032016.txt · Last modified: 2016/03/09 20:31 by anu_gururaj
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