projects:workgroups:wg_meeting_01062016
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projects:workgroups:wg_meeting_01062016 [2016/01/06 17:01] anu_gururaj created |
projects:workgroups:wg_meeting_01062016 [2016/03/07 22:48] (current) anu_gururaj |
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| ==== Attendees ==== | ==== Attendees ==== | ||
| + | Hua Xu, Jon Duke, George Hripcsak, Karthik Natarajan, Anupama Gururaj, Mark Khayter, Min Jiang, Don Torok, Alexandre Yahi, Andrew Williams | ||
| ==== Agenda ==== | ==== Agenda ==== | ||
| Line 15: | Line 15: | ||
| ===Minutes=== | ===Minutes=== | ||
| - | - Presentation | + | - General IRB document for use of clinical text and approval from all contributors, post online - Almost completed |
| - | - IRB for use of clinical text | + | - Collect minimum set of modifiers for all clinical entities that support use of rule to derive clinical concepts: Alex |
| - | - Clinical text data storage and representation schema | + | * cTAKES is being run on clinical notes programmatically. Alex will present the minimal model in the next meeting. |
| - | - NLP tools/pipelines for ETL | + | - Aggregate and share note-type metadata from various sources: Karthik |
| - | - Use cases, e.g, phenotyping for cohort selection using NLP outputs | + | * LOINC note type mapping would be a very useful resource. We should generate hierarchical representation of note-types as an ontology. Karthik will present his work to date at the next meeting. |
| - | - Discussion | + | * Existing ontology for note types to be shared : Vanderbilt (Hua) and Regenstrief (Jon) |
| + | - Simple search set up for MT samples: MinPresentation | ||
| + | * Presentation {{:projects:workgroups:clinical_text_search_engine_01_06.pdf|}} | ||
| + | * The interface being developed should present a summary with visualization for patients/notes. | ||
| + | * We will add Boolean query options to improve the search | ||
| + | * We will implement a Ranking algorithm | ||
| + | * Assign fake patient ID's to the notes to generate the visualization portion. | ||
| + | * Generate a program like Circe to define the patient cohort | ||
| + | * Next steps: How to move the data from textual searches stored in a table outside of OMOP to the OMOP? | ||
| + | * Structured searches from CDW and textual searches can be combined using existing strategies. Jon will share the slides of his presentation on combining data from different searches | ||
| + | * Run NLP on the ElasticSearch to extract information | ||
| + | - Wrappers for cTAKES and Metamap | ||
| + | - Report on the WG - Hua will generate and share with the members for comments | ||
| + | - The best ways to represent textual data need to be determined | ||
| + | |||
| + | ===Action Items=== | ||
| + | |||
| + | - Minimal Model Presentation - Alex | ||
| + | - Note-type mapping Presentation - Karthink | ||
| + | - Share existing ontologies from Vanderbilt (Hua) and Regenstrief (Jon) | ||
| + | - Share strategies for combining data from different searches - Jon | ||
| + | - 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 | ||
projects/workgroups/wg_meeting_01062016.1452099706.txt.gz · Last modified: 2016/01/06 17:01 by anu_gururaj
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