Page History
4/10/12
On the call: Rob Wynden, Mark Weiner, Alice, Prakash
1) Send Mark a copy of UCSF's IRB for (ICD-10 and ICU Outcomes).
2) Mark wants prep of research by loading discharge summaries and run it himself for early concept testing. That way he can demo to Finance.
3) Prakash working SHRINE interface for Appliance. Still some problem with SHRINE Topic.
4) Ketty's Anti-hypertensives are now on BioPortal. Getting Meds into NCBO is now possible. Design query hierarchy. Use NCBO HOM features to merge that meds dictionary with another EPIC meds hierarchy. How about the VA meds hierarchy (terms are the same)? Mark will write up cross institutional queries on meds for finding meds of interest.
5) Rob and Ketty giving demo at ICBO in 2 weeks or so.
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4/3/12
NO HOM CALL TODAY
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3/27/12
On the call: Rob, Prakash, Mark, Alice, Ketty
1) We talked about the medication reconciliation need at a national level - Mark will write this up ... it may be very important for our drug-drug and off-label study work. Ketty has been working on this in BioPortal also.
2) Letter of Support from UPenn for our funders.
3) Prakash has been getting our SHRINE node up and running fully. Going well. Also working on SOW for our Puppet engineer for SHRINE configuration.
4) Ketty is working on the ICD-10 detail code HOM map.
5) Rob is working on re-entrance of the UETL code.
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3/20/2012
Participants: Ketty, Prakash, Alice
* Alice and Ketty discussed on NDC codes & Formulary.
* Prakash has set up SHRINE node at UCSF running on infiniDB.
* Lots of folks are at the AMIA CRI Summit this week...
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3/13/2012
On the call: Rob Wynden, Prakash Lakshminarayanan, Mark Weiner, Bob Hink
1) Mark and Rob's paper submission of Abstract is due Thursday
2) ProxyGen is done! Awesome. Going to try and use it for Radiology. Code is in CVS and emailed to Rob.
3) We need to get IRB approval for UPenn's Appliance. Mark will put in the IRB approval doc now.
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3/6/2012
Participants: Prakash, Peter
* No updates from OHSU.
* Prakash has deployed Ontology and CRC cells against infinidb and is fixing issues on the same.
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2/28/2012
On the call: Rob Wynden, Ketty Mobed, Prakash Lakshminarayanan, Hillari Allen, Peter Beninato, Mark Weiner
1) Mark getting IRB approval for UPenn for the Appliance
2) ICD-9 to ICD-10 Procedure mapping is completed by Ketty
3) Prakash completed the port to InfiniDB.
4) Prakash is installing PM Cell now.
5) Prakash will test the SHRINE cell with the Harvard test data
6) Mark met with 3M in Salt Lake last week. They hired 3M to do mapping for them for HDD (Health Data Dictionary) and mapped UPenn's medication data and SunRise data and translated it to HDD. Then mapped to RxNorm for them. 3M is thinking of open sourcing the HDD.
7) Mark wants to take the 3M maps (all in 1 self referential table leading to drug terms) and render that as an i2b2 ontology. Then they can use it for queries of the in-patient data. Then RxNorm data can be structured by drug class.
8) Hillari finishing testing on ProxyGen
9) Peter is working on cross training folks on ETL. Also working on encounters now.
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2/21/2012
On the call: Rob, Hillari, Bob, Prakash, Peter
1) Hillari continues with the ProxyGen testing. Final load test for ProxyGen is pretty good. It slows at the 50 user interval for 1000 MRNs.
2) Peter is mapping from the GPI (Medispan ID for drugs) in EPIC.
3) Prakash just finished the codebase for the port to InfiniDB. He is loading the demo data now and deploying cells.
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2/14/2012
Participants: Prakash, Peter, Hillari, Bob
* Peter discussed 1.602 issues that he has encountered and is concentrating on Labs and RxNorm. He's going to try HOM RxNorm map for resolving drugs in his Clarity database..
* Prakash is working on i2b2 1.602 codebase port to infinidb..
* Hillari is testing proxygen and it seems to be slow after 50 users..
* Bob is analysing the issue highlighted by Hillari and it seems to have been fixed in his Dev environment..
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2/7/2012
On the call: Rob, Prakash, Peter, Bob, Hillari
1) IDR units have started arrived.
2) Peter will work to coordinate with Rob S.
3) ProxyGen is under test. Hillari is waiting for software installation.
4) We are connecting the Appliance to SHRINE now.
5) Prakash is doing a port to InfiniDB. HOM is ported and he is working on i2b2 codebase port.
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1/31/2012
On the call: Rob Wynden, Mark W, Alice L, Bob, Hillari, Peter B
1) We talked about the Appliance project
2) OSHPD Site announcement
3) Hillari is not getting QA done because central IT is pretty slow. No automated testing is available at present.
4) We talked about mapping to GPI from RxNorm and the troubles in achieving that. Peter B is very interested in that upgrade to the RxNorm map
5) 1.602 seems to be fairly stable (Peter B). Although the feedback from the field looks like large scale deployment may not be stable.
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1/24/2012
Participants: Prakash, Mark
Minutes:
* Alice is working with Ketty on EPIC data dictionary.
* UPenn is installing i2b2 1.6 on new hardware.
* Prakash has fixed the collision issue with path algorithm with 4 chars for each node.
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1/17/2012
Participants: Prakash, Peter, Mark, Alice
Minutes:
* Peter pointed out issues with i2b2 1.6.02 release.
* Mark is also having issues with i2b2 1.6.02 VM at his site.
* Prakash is fixing collision issues with path translator algorithm.
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1/10/2012
On the call: Rob Wynden, Bob Hink, Peter B, Alice L, Mark W
1) Peter is looking at 1.6.02 and looks pretty funny. Query re-use is messed up. Boolean operators work for some sites and not for others.
2) OHSU and UPenn interested in the appliance.
3) UPenn is stalled for a bit. They are busy and interested in the appliance.
4) ProxyGen has not yet been pushed through QA. Hillari is just now starting to load her test software onto the server.
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1/3/2012
On the call: Rob, Peter, Mark, Alice
1) Last week we had no call for the holidays ... this week is expected to be very light
2) Hillari is planning on QA scripts ... still waiting for her license to TestComplete
3) ICD9-10 work is semi-funded. UPenn is very interested
4) At UPenn, meds from in patient and outpatient dictionaries translated into other standardized meds ... work done with 3M. 3M did a proof of concept there. Interested in working with HOM on this too. Would require a license to the dictionary from 3M but that's fine on BioPortal now. The 3M dictionary is called the "HDD". A self-referential table, antibiotics has subclasses in the same table and it iterates like that with a drug name at the end. HOM would be great to create the exploding folders in i2b2 by reading the 3M dictionary.
5) OHSU had ICD9 codes in UMLS in November and they are about to run in production this afternoon. Peter can copy Ketty on that. The paths changed for a lot of concepts which creates problems.
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12/20/2011
On the call: Rob Wynden, Bob Hink, Ketty Mobed, Peter B, Prakash Lakshminarayanan, Mark and Alice,
1) Bob says that Hillari still has not gotten the software installed so she can test ProxyGen. Dealing with a licensing issue.
2) Prakash finished the ontology download feature. There are some collisions happening that needs help
3) Has set up 1.6 on his new laptop. Now running HOM against it and getting Oracle running.
4) Mark and Alice: compared the UPenn EPIC terminology to the UCSF EPIC terminology. Pretty much the same. Ketty is showing how the maps are built. Now they are exploring that.
5) At OHSU they had another training for 6 people. Had some feedback on the ontologies in use. Truncated zipcode for rural purposes. Zipcode truncation puts the zipcodes into the wrong states in EPIC because the truncated part leads to overlap on the zipcodes. Could use a map to address that...
6) Ketty is dealing with a BioPortal problem where it cannot deal with more than 65k terms ... ICD10 has more than that.
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12/13/2011
On the call: Rob Wynden, Ketty Mobed, Hillari Allen, Vijay, Bob Hink, Alice L.
1) Vijay is still figuring out the extraction for EPIC loading v2
2) Hillari has done some testing for ProxyGen. But that continues as the load testing software needs to be installed in the med ctr network and the PO is delayed
3) UPenn just started back in again with loading EPIC.
4) Ketty is just backed from leave. Continuing on demographics ontology work. Also waiting on some bug fixes in Protege which only can handle 62k rows and ICD10 has 80k rows.
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12/6/2011
On the call: Rob Wynden (UCSF), Vijay Rayanker, Mark & Alice (UPenn), Prakash, Bob Hink, Peter (OHSU), Hillari Allen
1) Prakash has been setting up a new system and finishing the ontology downloading code. The 3-char path enumeration may have some collisions and Prakash is looking into that.
2) Vijay is loading data for EPIC, working on full load again as well as CDC (change data capture) to bring in daily updates
3) Hillari is finally able to start testing on the ProxyGen service
4) Alice is back from Italy and can start back in with the EPIC load from UPenn. They are loading the UETL terminology to BioPortal.
5) Peter added new grouping to department tree along with specialty. Looking at code for i2b2 1.6. (UCSF has 1.6rc3 in Dev ... needs testing)
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11/29/2011
Attendees: Hillari, Vijay, Bob, Prakash, Ketty, Rob, Peter (OHSU), Mark (UPenn)
- Hillari still has problems connecting to MedCtr. She has tried all avenues possible. Rob will try to get this resolved.
- Vijay has resolved the column problems
- Bob is in waiting mode for Hillari to do the testing
- Prakash is working on the ontology extraction (ICD9-10, SNOMedCT) in Bioportal
- Ketty has worked on the ICD9-10 overlay and is waiting for issue resolution in Protégé; she is also further developing the demographics ontology. To get some clearer guidance and support, she will contact Don Dunkin.
- Peter is working on the RXNorm and will get help from Rob to overcome some of the issues on his end.
- Mark is waiting for Alice to come back from vacation so they can start working on their ontology in BP; will get back to Ketty if needed.
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11/22/2011
Participants: Rob, Bob, Ketty, Peter, Vijay
1) Vijay is fixing documentation of process for de-identification, proxied MRNs are working properly. Column names show even if not pulled in... may need to update code for that
2) Peter is assigning patient counts at the folder level and not at the leaf level
3) Bob is still not in test for ProxyGen
4) Ketty working on ICD9 and ICD10 ontologies a lot
5) Peter has had a light system launch and they are servicing real users now, working with AHFS drug hierarchy which is a proprietary coding from HL7
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11/15/2011
Participants: Prakash, Bob, Peter, Hillari, Vijay, Nivi, Mark Weiner
Minutes
* Rob is on vacation this week.
* Vijay completed the first end to end dry on EPIC data including mapping.
* Hillari is testing the first dry run on EPIC data.
* Prakash is testing Ontology Retrieval functionality.
* Bob is awaiting Proxygen testing by Hillari.
* UAB intends to migrate to 1.6 from 1.3.
* Peter discussed 1.6 migration issues.
* Mark reported that Alice is on vacation.
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11/8/2011
On the call: Rob Wynden, Ketty Mobed, Bob Hink, Vijay Rayanker, Prakash Lakshminarayanan, Ketty Mobed, Alice L., Peter B, Deb B (Children's Hospital Colorado), Hillari
1) EPIC data has all been loaded at UCSF we have run HOM maps on demographics. Then will run on claim info etc...
2) Prakash working on the loading of an ontology tree from BioPortal using HOM. Pulls entire tree!
3) Ketty is working on a new demographics ontology. Work on GEMS mappings from ICD9-ICD10
4) Hillari is trying to build a test suite on Vijay's EPIC maps
5) Hillari does not have access to the test ProxyGen because she does not have network access
6) Alice still working on loading EPIC at UPenn
7) Colorado Children's new HOM resource (Craig) will be starting next week
8) OHSU had their second training last week. Did a cohort selection for a neurology study and it worked! Also talked about a 1.6 bug regarding clearing an old query out.
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11/1/2011
On the call: Participants: Prakash, Ketty, Peter, Alice, Curtis, Debb, Vijay, Bob, Rob
* Vijay has completed uploading EPIC data and is now running HOM maps on the same.
* Prakash is back from paternity leave and is transitioning HOM stuff to Vijay.
* Peter informed that new set of ICD codes have been added in UMLS this October.
* Bob is waiting for QA to be completed on his stuff.
* Discussed i2b2 1.6 install issues pertaining to user creation and LDAP.
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10/25/2011
On the call: Rob, Alice, Bob, Vijay
1) Light attendance today due to AMIA.
2) The ProxyGen is still sitting in QA right now.
3) Alice at UPenn is looking at Ketty's materials. They are comparing our Clarity mappings to theirs.
4) Vijay is doing Clarity data loading. Hoping to have all 5 tables done today.
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10/18/2011
On the call: Rob Wynden, Vijay, Bob, Ketty, Mark, Alice, Peter, Hillari
1) Prakash is on leave for 3 weeks or so
2) Vijay is setting up the HOM Interpreter on his desktop
3) ProxyGen still in test with Hillari and Wyatt. Hillari has campus connectivity issues
4) Mark and Alice had a call with Ketty yesterday and they are learning the BioPortal upload process
5) Peter is doing another run of his ETL process. Now he is flagging clear CPT procedures
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10/11/2011
On the call: Rob Wynden, Ketty, Prakash, Hillari, Bob Hink, Alice, Mark, Vijay, Peter
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9/20/2011
Participants: Prakash, Peter, Vijay, Mark, Alice, Rob, Ketty
* Vijay is extracting EPIC data.
* Prakash completed running OSHPD maps for Northern California. Subsequently focusing on Southern California maps..
* Peter is working on the ETL process.
* UPenn is extracting EPIC data using UETL. Vijay to send updated code..
* Ketty is working on Southern California OSHPD maps.
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On the call: Rob Wynden, Bob Hink, Prakash, Mark Weiner, Vijay, Ketty, Peter B., Hillari
1) Vijay loaded core EPIC tables (5 core ones for now). Loaded 3 tables on Test. Hillari wants the other 2 tables in Test also. We will load all 5-core tables into Test.
2) The SCP copy method is very slow and we are switching over to GridFTP now to improve performance. Jeff is transferring files and will run the load script.
3) Ketty working on more ontology development – Transplant, Cancer Registry, Demographics. Rob would like to see our LOINC work in motion now also.
4) Prakash just loaded OSHPD for 2005 northern California into i2b2. Looks very good. We also have ICD9 diagnosis codes loaded also. We also need to add CPT support. Also loading 2 additional years for OSHPD. Adding Ketty's new primary/secondary diagnosis ontology.
5) UPenn has now loaded obs fact from the Picard data warehouse. They hit a snag on terms that are not automatically made into a hierarchy. They need to see Ketty's work on BioPortal. Ketty to help Mark with arranging physician hierarchy as extension of UHC.
6) Peter has a new database server up now for all of their ETL processes. They are running within about 5 hours now. Working on presentation internally now for their rollout.
7) Diagnosis can be shown on the patients problem list and it's not necessarily shown on the encounter (just associated with the patient ID). That can make patient count matching challenging.
8) Bob on ProxyGen: migrating over to the Test environment now. He has a database set up for testing without messing with the production database. Adding encounter and composite key.
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9/6/2011
On the call: Rob, Ketty, Vijay, Alice, Prakash, Bob, Hillari
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3/8/2011
Prakash, Nivi (UAB), Vijay, Peter
- UAB - UETL code changes committed to SVN, custom loader scripts to be shared with UCSF
- ViewCreator released to i2b2 wiki, documentation pending
- Peter's lab work to be shared with UAB
3/1/2011
Participants: Prakash, Aaron Mandel, Vijay, Nive, Rob Wynden, Peter, Curtis
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12) Next week we will see a demo of the UAB ACE (Aggregate Cohort Estimator) query interface
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12/21/2011
Ketty, Prakash, Harsh, Peter, Curtis, Nevi, Aaron
Prakash – updating Sybase
Ketty – more uploads and annotations in NCBO BioPortal. One UCare table (DISCH) is there. While proprietary, it was put there to the public site for our group to review and give comments back to Ketty. We are still waiting on the public site from Stanford.
Nevi (UAB) – have used UETL to import files to the i2b2 sql loader. They encountered some issues with some nodes and database. Also an issue with the drag and drop option showed nulls at the tool tip. They were able to resolve most issues. Prakash discussed some of the items with them, but some of the unresolved issues will wait until Vijay comes back in 2 weeks.
Curtis (UAB) – while they have to wait on the UETL issues, they want to get started on HOM. Prakash will set up a call for tomorrow (12/22) pm and get things started for them.
Aaron – HOM wiki has been relocated to Harvard (wiki.i2b2.org). Only he, Prakash and Rob have access to it right now. Won't be available until Rob gives his okay.
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12/14/2010
On the call: Rob Wynden, Harsh, Ketty, Peter, Prakash, Mark Weiner, Curtis and John from UAB also
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On the call: Rob Wynden, Prakash Lakshminarayanan, Marco Casale, Tim Thimman, Nick Anderson, Justin Prosser, Prakash Lakshminarayanan, Matvey Palchuk, Mike Klumpenaar
1) All sites should rebuild on the most current build of HOM
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3. Rob is continuing forth on the SHRIMP UI redesign to add a Mapping Workbench Tab for OntoMapper
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11/24/2009
On the call - Nick Anderson, Prakash Lakshminarayanan, Aaron Mandel, Mark Weiner, Matvey Palchuk, Mike Klumpenaar
1. Nick was interested in progress of RxNorm API for Ontomapper and Prakash reported that this is being initiated at UCSF.
2. Aaron Mandel checked on the status of Ontomapper documentation. Prakash said that it's is not yet ready and would be taken up shortly.
3. Prakash said that Ontomapper has been tested on HSDB maps. Aaron queried on the type of medications supported by HSDB. Prakash explained HSDB maps were simple and based on raw HSDB data. Prakash also said that RxNorm maps would be a good benchmark for Ontomapper.
4. We discussed on various RxNorm medications.
5. Rob and team would work on leveraging SHRIMP UI for Ontomapper work.
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11/17/2009
1) There was NO ONTOMAPPER MEETING today because so many people are at the AMIA conference... we reconvene next week.
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