Page History
OntoMapper Minutes
1/11/20114/10/12
On the call: Rob Wynden, Ketty Mobed, Prakash Lakshminarayanan, Vijay Rayanker, Aaron Mandel, Mark Weiner, Nive and Harsh at UAB
1) Further UETL testing at UAB. They need to use proxy MRNs and proxy Encounter Numbers. They did that and UETL is now working at UAB.
2) UAB has ICD9 and Labs In system now ... not mapped to main ontology
3) Prakash is working on Sybase IQ support last week. We are blocked on NCBO BioPortal for their bug fixes. We are importing all of our ontology there now...
4) Prakash will focus on LabNorm for now.
5) Vijay is loading more UCare data.
6) Vijay is making some enhancements after talking to UAB. To make the proxy list show up in the GUI to make it easier to maintain.
7) Ketty asked Mark about ICD9 and ICD10 support. Should we use an existing crosswalk or create our own?
1/4/2011
On the call: Rob Wynden, Aaron Mandel, Ketty Mobed, Harsh Taneja, Niveditha Thota, Vijay Rayanker, Prakash Lakshminarayanan, Mark Weiner, Peter Beninato
1) New site for our dev work is at community.i2b2.org
2) Harsh question on SVN site. UETL code is read only. Could not get HOM code however due to bad permissions on the SVN. We will fix that for her.
3) At UCSF we are working on production issues (we upgraded Sybase to 12.7). That is postponed for now.
4) BioPortal integration is now waiting on fixes from Stanford. So we are stuck for now. Ketty will make sure that we have a ticket opened at Stanford. The source terminology cannot be properly annotated at leaf nodes due to a bug in the BioPortal UI. We also need private NCBO sites working very soon (for license restriction).
5) We have a joint lab meeting (UCSF and Stanford) at Stanford on Thursday of this week.
6) At UAB the usage of UETL is working well. They seem to be clear of all exceptions and they can search for stuff.
7) Asma ICD9 455 and search by name in ICD9 tree (using Prakash's) and it works now! So UETL is running at UAB. BUT SEARCH BY CODE IS STILL GIVING AN ERROR.
8) UETL needs to have a check added for duplicate entries in the i2b2 table (this is a bug in UETL) - Vijay will work with them on this.
9) Ketty is working now with Peter's ICD9 mappings
10) Rob and Ketty are working on a paper about our integration with NCBO BioPortal
11) Regarding our work on ontologies... The NCBO Site: http://bioportal.bioontology.org/ontologies?filter=CTSA-HOM shows everything that our team has been working on so far. HOM has a LOT of terminologies available here already.
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
1) Prakash was doing the NorCal database update but IT seems to have shut down the servers - Rob to call the managing director on CELDAC (Janet Coffman)
2) Mark and Alice have been working with Ketty on setup for BioPortal for UPenn. They want to begin catching up with UCSF now. There does seem to be some instance data changes between demographics for UPenn and UCSF. Mark and Ketty are going to collaborate on differences like these to get them updated on BioPortal.
3) Vijay has been trying to get HOM accepting daily updates via CDC (change data capture)
4) Ketty has finished the ontologies for EPIC and CELDAC. Now working on demographics ontology.
5) ProxyGen is in test with Hillari and Radiology. Wyatt is trying to use it but Hillari's med ctr account has expired.
6) Peter at OHSU did a demo of i2b2 internally. They have some training scheduled over the next month. They have about 200 procedures loaded ... about 60% are falling out because they are not cpt based procedures.
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10/4/2011
On the call: Rob Wynden,Vijay Rayanker, Prakash, Ketty, Hillari, Bob, Peter, Mark, Alice
1) Prakash is working on load of EPIC data
2) Prakash got the maps done for OSHPD LA - there were some infrastructure issues after the load
3) UPenn is a bit on hold (Mark was on call last week). They need to rerun the EPIC data using UETL. Ketty would like to coordinate the detail data descriptions on BioPortal with UPenn. We want to do medications too.
4) Vijay working on EPIC demographics loading
5) Ketty working on finishing the Cancer ontology (ICD03) ontology.
6) Ketty fixing some mis-mappings for EPIC
7) Peter is providing a demo to the health informatics folks at OHSU (has been talking to Explorys at Cleveland Clinic)
8) OHSU has been having performance problems in i2b2 with dead people (age in years is left as null)
9) Bob has finished the ProxyGen pretty much (it's in test). Just added docs for REST interface for Hillari
10) Hillari is testing ProxyGen and setting up scripting
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9/27/2011
Participants: Rob Wynden, Mark, Alice, Ketty, Vijay, Bob, Hillari, Peter, Prakash
1) Vijay has gotten one of the EPIC tables imported. They are short on memory.
2) Hillari may be able to test the first EPIC table now.
3) Ketty is working on the Cancer ontology.
4) Bob is in testing on the ProxyGen service now.
5) Mark and Alice at UPenn are now able to see Ketty's ontology on BioPortal. They now need to get Protege installed at UPenn. Also they are absorbing the EPIC data now also as UCSF is.
6) Peter is still working on the ETL side this week.
7) Prakash is running OSHPD maps - running very slow - 3 or 4 days
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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.
...
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
1) Vijay added support alpha-numeric support in UETL for support of EPIC. UPenn now has the same. Vijay is code complete and pushing this to Test and Hillari has documented the process already.
2) Prakash is adding support to HOM Interpreter for running multiple processes simultaneously for better performance. This is an issue on CELDAC.
3) Bob has ProxyGen started deploying into Test.
4) Ketty developing more ontologies as interesting targets.
5) Hillari waiting for UETL deployment to Test
6) Alice is still working on UETL for EPIC (we are working in with them).
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8/30/2011
Participants: Prakash, Hillari, Ketty, Vijay, Bob, Alice, Rob
* Ketty re-loaded new ontologies with additional nodes. To check with BioPortal folks if existing p2p mappings are not carried over to the new ones.
* Prakash ran CELDAC maps successfully on existing ontologies and would be running the same on Ketty's new ontologies.
* Vijay is extracting EPIC data using UETL command line.
* Hillari is documenting UETL process.
* Bob is encrypting the key for login using SHA-1 algorithm and packaging the web-services as WAR file.
* Alice is fine for now with UETL process.
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8/23/2011
On the call: Rob, Prakash, Ketty, Vijay, Peter, Bob
1) ProxyGen is getting setup with infrastructure so that QA can happen in about a day or so. Code is on Subversion. Thanks Bob!
2) Ketty is working her new demographics ontology and ready to start on labs. We need to talk about how to code the transitory regions. Time to load the Transplant database.
3) Prakash is working on BioPortal mappings. It's done now. Ready to start testing with CELDAC.
4) Vijay is doing an extract (Ketty and Mark W's 5 tables) from EPIC.
5) Vijay to give the Axium Dental bulk import files to Jeff Tan for reloading.
6) Peter is back from vacation and is working on their ETL approach. Setting up a staging server.
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8/16/2011
Participants: Rob, Prakash, Bob, Alice, Mark, Curtis, Ketty, Vijay, Hillari
* Bob setting up Test environment for proxygen
* Prakash finishing up and testing BioPortal maps
* Ketty uploading revised EPIC ontologies and verifying local BioPortal instance
* Vijay working on Clarity loads
* UPenn also working on data loads from Clarity
* UCSF to publish concept dimension files of EPIC
* Hillari to come up with change control docs for local BioPortal instance
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8/9/2011
On the call: Rob Wynden, Ketty Mobed, Hillari Allen, Mark, Alice, Prakash, Bob Hink, Hillari Allen
1) Alice is now running with UETL now. Can connect to Clarity and Oracle now and they are working now. Must enter schema name first in upper case and then select database from list after. You must choose the schema even though the UI suggests the opposite. If it is not done this way you need to restart the application. Also, can't use SQL Server with Windows Authentication unless you enter a DLL file into the same directory as the Jar File. Hillari will enter these tidbits into the documentation.
2) Ketty will send UPenn the table list we are using: PATIENT, PATIENT_RACE, CLAIM_INFO, CLAIM_INFO2 : UPenn started with these tables: PATIENT, PAT_ENC, ORDER_MEDICATION, CLARITY_MEDICATION : They are hoping to stratify the encounter by the clinic code that shows where the encounter happened.
3) UPenn will require access to UCSF's private BioPortal so that we can work in with them on figuring out the Clarity schema and UETL and HOM/Interpreter maps.
4) Ketty has figured out how to use BioPortal now. Both import and mapping is working now. She also has figured out how to load and map for i2b2 Primary and Secondary Diagnosis. She also can load very large ontologies at will...
5) Bob has V1 of ProxyGen completed and it is now checked into SVN. Deploying to our Test environment so that Hillari can do QA on it.
6) QA on the 4 HOM components: Hillari is working on a Test Plan.
7) Prakash is working on automated BioPortal mappings. Has been able to extract and load the data for processing. He should be done in about 2 weeks. Right now this is being tested for OSHPD.
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8/2/2011
On the call: many people...
1) Rob lost the minutes before they could be recorded here... sorry! I'll correct this if I find them...
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7/26/2011
On the call: Rob, Hari Rekapalli, Hillari Allen, Ketty Mobed, Peter, Prakash, Bob Hink
1) Prakash is working on automated mappings via BioPortal. It creates everything on the fly.
2) The 3char path enumeration is completed now.
3) Prakash is doing research on loading ontologies.
4) Ketty is working with Stanford on fixing problems with BioPortal 1-to-1 maps. Also we are pushing a new feature to support embedding ontologies within each other.
5) Bob is working on ProxyGen. Trying to wind up the alpha version. He is making a war file and dealing with threading issues.
6) Hillari can test ProxyGen after Bob is finished.
7) Peter got an incremental load working for i2b2. Used dates on his query. Looking at an August rollout plan.
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7/19/2011
On the call: Rob, Ketty, Mark W., Bob Hink, Prakash, Alice, Curtis H.
1) UPenn with Alice L. is working on installing UETL. Using UETL for HOMERUN and Clarity.
2) ProxyGen service now has logging and basic exception handling. Using the Apache Jersey REST framework. Ready for testing starting next week maybe.
3) Prakash has finished the 3character path enumeration algorithm now. It is collision free and deterministic! Can handle encoding of SNOMED!
4) Prakash is now working on mapping from BioPortal. Ketty has lots of maps staged there and ready for execution.
5) Ketty has been working on BioPortal and Protege getting target ontologies in place. She is working with Protege ontology insertion (so ICD9 inside of another ontology ontology for example). It seems to be based on copy and saves her lots of time.
6) On the source ontology end Ketty now can consume the UETL concept dimension file into BioPortal as a source ontology (using Mapping Master).
...
7/12/2011
On the call: Rob Wynden, Bob Hink, Hillari, Ketty, Prakash, Curtis
1) Prakash working on 3 character path enumeration algorithm. He has an alpha version too. It is both collision free and deterministic!
2) Ketty working several ontologies at once right now. She is curating source to target maps right now on BioPortal. Ray at the NCBO waiting for Rob's input so they can work in with us.
3) ProxyGen is working! :-) We have switch to MySQL for the Proxy Number table. He is working on the authentication now. Adding REST service calls.
4) UAB has data loaded and they are in testing phase now...
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7/5/2011
On the call: Rob, Prakash, Peter, Nivi, Ketty
1) The 1.6 port is completely done now. HOM interpreter also...
2) Prakash working on support for the 3 character path enumeration algorithm. (also Peter is adding a parent ID column in the concept path)
3) Ketty is working on ontologies. Lot's have been entered into BioPortal
4) We are running out of space in our ETL network where HOM/UETL runs... expanding hardware now...
5) Peter talked about Lori's project
6) Nivi making good progress at UAB
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6/28/2011
On the call: Rob Wynden, Bob Hink, Prakash, Ketty, Hillari
1) 1.6 port of HOM is completed.
2) Prakash now going to implement the 3 character concept path enumeration algorithm required for the support of SNOMED
3) Ketty's maps for EPIC are completed and on BioPortal (covers all basic maps for Harvard ontology)
4) ProxyGen, Bob working on code re-entrance and transaction issues
5) Hillari testing HOM Views
6) Ketty working on ICD9 upgrade
7) Everyone else is at the i2b2 and SHRINE conferences
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6/21/2011
On the call: Rob Wynden, Hillari Allen, Nivi, Bob, Ketty, Prakash, Peter, Mark
1) Nivi at UAB is loading in data right now. She tried static SQL inserts first. Now they have a 2 step process.
2) Prakash is working on 1.6 port. Code complete and works as well as 1.3 did. He is chasing down issues on new features now. We will see how we can cut down the feature set for now.
3) UETL now optionally working on command line. Hillari needs to run that through QA next. Hillari has network access. She needs to develop change control documentation.
4) Peter at OHSU is having trouble with escape characters in the incoming data stream for Microbiology. UETL does scrub those now...
5) UCSF has procedures loaded but we are now organizing it with Ketty's new procedure ontology on the BioPortal. She has it under "International Classification of Disease: ICD9".
6) Bob is working on the ProxyGen system: Finishing up a client test platform. Implementing a DB connection pool now. Working on concurrency.
7) UPenn will be assigning Alice to work on the further implementation of UETL at UPenn in a couple weeks from now...
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6/14/2011
On the call: Rob Wynden, Mark W, Prakash, Bob, Hillari, Peter B., Vijay
1) Bob and Prakash need a hand-off. Prakash just needs to get lined up. Also Hillari needs a hand-off too. Vijay splitting on vacation.
2) 1.6 port is code complete. Prakash is working on bugs right now. ViewCreator is running at UMass...
3) ProxyGen service (Bob) is working on it. Bob is updating the look-up algorithm and rest client for testing. Bob got an IP address for the network routing ... actually network routing is in progress now. Tomcat is used on his laptop for development.
4) Ketty has 4 bugs open with BioPortal. Stanford is working hard on those.
5) UPenn contact will call Prakash in about a week. They are interested in UETL against Clarity.
6) Mark to give drug name tests for RxNorm.
7) Both Rob and Mark are both working with UETL against Clarity.
8) Peter is still working on the microbiology data. They are meeting with Pharmacy group on use cases. Rob S. is putting a poster together for the AUG.
9) Ketty has a bunch of active EPIC related ontology work she is doing on BioPortal.
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6/7/2011
On the call: Rob Wynden, Peter, Ketty, Prakash, Bob, Nivi, Curtis, Mark
1) Bob is extending the ProxyGen service to include a data type so that two different types (like "SSN" and "MRN") don't inadvertently overlap.
2) Prakash just completed port to i2b2 1.6! He is in testing phase now...
3) Ketty is trying establish a standard demographics ontology. This would be something more advanced than the Harvard Demographics ontology. Should be done in a month or so.
4) Ketty is slowly working with Labs. Create a maps between our clinical labs and depts. It's pretty messy.
5) Nivi has mapped demographics, race, and added new terms to demographics from Harvard.
6) Rob is working on a new isomorphic mapping from ICD9 to ICD10 and back in order to map ICD10 to DRG codes.
7) ViewCreator is now working directly with Microsoft Excel 2010! Data extraction from i2b2 has never been so easy.
8) At UAB they are loading the rest of their patients. Inserts are taking a LONG time. Rob suggested using UETL.
9) Mark sending a medication dictionary to Rob for the RxNorm map. This could lead to a big improvement in RxNorm for the HOMERUN project.
10) Peter is looking at microbiology data and figuring out to combine organism and antibiotic to sustainability. A few hundred thousand records at present.
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5/31/2011
On the call: Rob, Ketty, Hillari, Bob, Vijay, Prakash, Peter, Nivi
1) HOM ViewCreator 1.1 now working with Microsoft Excel 2010 (works very well... very easy data extracts)
2) Vijay is just about done with command line update for UETL. Got code completed and is now alpha test phase
3) Bob is just getting started with ProxyGen
4) Ketty has been working on the labs ontology
5) Prakash is working on port to i2b2 1.6
6) Nivi loading 1.5 Million patients (labs, icd9 and cpt)
7) Peter working on Clarity Pharm class for medications
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5/24/2011
On the call: Rob Wynden, Vijay, Prakash, Nivi, Peter, Bob Hink, Hillari
1) Vijay is working on UETL Command Line support.
2) Bob is now starting a ProxyGen project. The SOW for this has been added to the files section.
3) Both Vijay and Bob will need to deal with concurrency. Coordination is required for the build process, merging the branches.
4) Prakash is working on our port to i2b2 1.6rc3. First support for Sybase then handling port to HOM second.
5) ViewCreator 1.1 going into production. Need to move 1.2 to Test very soon. Hillari will handle coordination.
6) UAB has about 1000 patients up with ICD9 and Lab Codes. Search by value is not working yet. Labs are not working in i2b2 yet anywhere that we can tell.
7) Ketty is working with the Labs and OHSU terminology for such. Peter is working on a crosswalk for about 300 labs or so.
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5/17/2011
On the call: Rob Wynden, Prakash, Ketty, Hillari, Curtis, Nivi, Mark
1) We had a HOM ViewCreator demo
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5/10/2011
On the call: Rob Wynden, Prakash, Vijay, Nivi, Hillari, Peter, Mark
1) Prakash V1.2 of HOM View
2) Hillari will test V1.1 now and then V1.2 later
3) Porting to i2b2 1.6 rc3 now (there may be problems with this version ... we will see) rc4 will support modifier codes also so we may want to track in rc4
4) Vijay is still working on the command line operation feature of UETL
5) Ketty has been working a lot on the labs terminology - Rob will ask Ketty to present early prelim results next week
6) UAB does not have encounter numbers for labs - they are generating fake encounters
7) Prakash to demo HOM View next week
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5/3/2011
On the call: Rob, Prakash, Vijay, Ketty, Curtis, Peter, Hillari, Mark
1) HOM Views, Prakash is finishing up the pivot version. Java program talks to i2b2 over jdbc. Could we use web services (REST) over SSL? Would be better than a file based CSV. Also, Prakash wants to re-use the i2b2 password for the HOM Views interface for pivot.
2) Command line operation for UETL. This feature is in process. UETL also needs to be re-entrant. Need web service to allow access to the proxy MRNs.
3) Local instance of BioPortal is now working. We are loading maps and terminologies now...
4) Curtis on labs: created a simple ontology that's only 2 or 3 levels. They may be able to get a LOINC mapped set from Cerner but don't know for sure.
5) Peter on labs: again mapped to internal approach. They have a hierarchy that covers 300 most common lab types. Ketty to follow up with Peter and will look at existing BioPortal content also.
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04/26/2011
Participants: Prakash, Nivi, Vijay, Ketty, Peter, Mark Weiner, Curtis, Ishani
* UAB is working on labs based on Peter's work. Peter to share his latest work on labs.
* Prakash has released version 1.1 of ViewCreator that has procedures for pagination ported to Oracle.
* Vijay is working on UETL Command line execution.
* Ketty is testing Bioportal VM at UCSF; has created ICD9 owl file for upload onto the same.
* UCLA had issues querying by dates and Peter explained the procedure for the same.
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HOM Team Meeting Minutes
4/19/2011
On the call: Rob Wynden, Prakash, Ketty, Nivi, Vijay, Peter
1) Vijay made some changes for Hari. We can now import text with UETL that contains escape sequences. We are building an NLP capability into HOM UETL. We can now tag the text with SNOMED terms and DeID it with PhysioNet.
2) The HOM Views work (with Prakash) now pages data and we are adding pivot functionality. This is ODBC or JDBC access to i2b2.
3) Ketty will try and test the UCSF local version of NCBO BioPortal
4) Peter is evaluating the i2b2 RC3 1.6 version. Looks rough so far.
5) Peter has some data for labs from Rob Schuff for us to load into BioPortal. Rob to send Peter the path enumeration algorithm.
6) We talked a lot about the upgrade path to 1.6 rc3
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4/12/2011
On the call: Rob, Vijay, Prakash, Mark, Peter, Ketty
1) Vijay has been helping Ishani (UCLA) and Adrian (UChicago). They seem to have what they need for now.
2) Prakash has just implemented paging into HOM Views (with paging) and also has a prototype pivot function as well. Currently running on Oracle and IQ.
3) Rob is documenting the new concept path algorithm for Lori Phillips.
4) Mark still thinks that the i2b2 backend is still useful and necessary for HOMERUN. Rob will write up a draft for tomorrow.
5) We do have an instance of NCBO BioPortal for UCSF that can house proprietary terminologies.
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4/5/2011
Roll call: Mark W, Rob W, Prakash, Vijay, Ishani, Peter, Curtis, Nivi
1) Talk about new concept path algorithm
2) Rob will send concept path algo to Lori Phillips
3) Talked about HOM Views – i2b2 access by SAS, STATA, SPSS and R (and maybe Excel). The biostats scripts will run in an interoperable fashion relative to the same interface and concept paths as defined above.
4) We are working on paging data (sort of like a cursor) and a pivot function for HOM Views now. Prakash will continue to copy builds over to Peter B for review.
5) Talked about lab data paths.
6) Ishani needs help with UETL.. Vijay will help out.
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3/29/2011: Rob Wynden, Peter (OHSU), Adrian (UChicago), Vijay, Prakash, Ishami (UCLA), Mark, Nivi (UAB)
1) Loading CPTs at UAB and working with OHSU and Peter's scripts. CPTs will be local encoding in the UAB section of the trees.
2) U Chicago was looking for updated of UETL. Have not gotten the link yet.
3) UCLA is now working with UETL. They seem to be moving forward well.
4) Described the 3 char combinatorial method of building concept paths (a derivative of Path Enumeration). This will handle 42,000 terms per level with a depth of 42 levels.
5) Is the c_dim code and c_fullname the same with the combinatorial path enumeration? Prakash will include that.
6) The UETL will generate concept codes that now include the data source name as well. Prakash has further restrictions on the lengths that will be given to Prakash. This is important for downstream biostats environments just as SAS.
7) Talked about HOM view for SAS access to i2b2.
8) Talk about lab data normalization and we are ready to prototype this work.
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3/22/2011
Participants: Rob Wynden, Prakash, Peter, Lori Phillips, Vijay Rayanker, Ketty Mobed, Nivi (UAB), Mark W, Curtis, Adrian Walts (U Chicago), Ishami (UCLA)
1) Talked about the %like% operator and the restrictions on concept path length
2) Vijay will send Lori the code for Path Enumeration. But for UMLS we need to traverse 22 LEVELS!!!! (post UMLS rms files ... a csv format ... on BioPortal?)
3) Curtis suggested an alternative (Depth First Traversal) method to using trees. Should we switch to that?
4) Adrian needs updated version of UETL. Vijay will provide that.
5) Ishami had a talk with Prakash on i2b2 setup project.
6) Nivi had problems with CPT from BioPortal due to license issue. Talked about BioPortal VM and troubles getting the legal license to CPT.
7) We have a joint lab meeting scheduled with Stanford on content mgmt for BioPortal
8) We are in prototyping mode on lab data normalization now
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3/15/2011
Participants: Rob Wynden, Vijay Rayanker, Peter Beninato, Ketty Mobed, Nivi, Mark Weiner
1) Talked about labs, got script from Peter and code from Prakash
2) UAB starting with CPT codes first and basic structure (they are on BioPortal and some LOINC work is there also)
3) Rob met with Rob Schuff at AMIA about this. Will starting working more closely with OHSU
4) BioPortal now supports private terminologies
5) Under the HOM section in BioPortal we have CPT metathesaurus hierarchical terms
6) We need to get Shawn's team on this call each each - especially as it relates to ICD9
7) Number labs, text based labs, text number (3 types?) - query-by-value the tvalchar supports an operand (2.2E for example) - Peter can describe this - so we need to know this for mapping and the HOM View?
8) Our RxNorm paper is due on Thursday
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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
* UAB is working on labs, to load them onto Bioportal.
* Prakash to work on HOM map for UAB labs.
* Peter to share lab map table with the group
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2/23/2011
Participants: Prakash, Nive, Harsh, Vijay, Aaron Mandel, Peter, Mark
1) UAB working on bringing in Lab data into i2b2
2) Vijay working on making UETL accessible from command line
3) Prakash working on port of View creator onto Oracle
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2/15/2011
| No Format |
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Participants: Prakash, Vijay, Ishani (UCLA), Peter, Curtis (UAB), Nive (UAB)
* UCLA has minor issues with UETL imports probably due to wrong usage, another screen-share to be scheduled.
* Vijay is working on UETL updates.
* Diagnoses and procedures have been implemented at UAB.
* View Creator deployed at UCSF with an additional view for Visits.
* Discussed on bringing in Lab data into i2b2 at UAB.
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2/8/2011
On the call: Rob Wynden, Ketty, Prakash, Vijay, Nive, Harsh (UAB), Ishani and Khy (UCLA), Peter B, Curtis H
1) We had a demo for U Chicago and sent them the executable
2) UAB i2b2 in Production had trouble but now it is working correctly now
3) UAB still using demo data ... need to do the Oracle Server SQL load bulk load step
4) We need password for SVN from Aaron Mandel.
5) UCLA needs the biostats view
6) Vijay working on making command line execution
7) Prakash is working on the View implemention/optimization
8) Ketty is working on Protege mapping process into BioPortal
9) We had a very successful with Shawn's team
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2/1/2011
On the call: Rob, Prakash, Ketty, Vijay, Nive, Harsh, Dave Hau (from NCI), Khy, Shani (UCLA), Adrian (U Chicago), Mark Weiner, Curtis
1) UCSF created a View structure. This allows access to i2b2 from SAS, STATA, R and SPSS
2) Site updates
3) Ketty working with Lori at partners on the scripts. Automation of the UETL concept paths.
4) There is a webinar on RxNorm and meds tomorrow
5) UAB having some build problems in production. They are working through the AUG now.
6) Demo with Curtis
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1/25/2011
On the call: Rob Wynden, Prakash Lakshminarayanan, Ketty Mobed, Aaron Mandel, Vijay Rayanker, Nive and Harsh, Peter B., Khy, Adrian from U. Chicago, Mark Weiner, Curtis H.
1) Khy at UCLA has i2b2 running now and now they need ETL help. Now installing HOM and working Vijay.
2) UAB is working on main production database now. They are configuring the VM in a more efficient manner now. Using test data still for now. After test will use real patient data.
3) Vijay has made the changes to support not generating proxy MRNs. Change made by UAB and posted in main code base now.
4) U. Chicago has i2b2 running and needs UETL help with cancer registry.
5) Rob working with Matt Wyatt at UAB on submitting an admin supplement related to this work from UAB.
6) Still changes on BioPortal changes. Due this week
7) We have been running many maps off of BioPortal, Disposition and working on Formulary.
8) UAB is working on lab mapping now
9) UCSF working a stored proc that allows you to extract all data associated with a patient
10) We have a demo of HOM / BioPortal for Shawn Murphy's team today at noon.
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1/18/2011
On the call: Rob Wynden, Prakash, Vijay, Mark W, Nive and Harsh, Ketty, Khy (UCLA), Aaron Mandel, Mark W., Curtis H.,
1) We are still waiting on BioPortal to make our bug fixes
2) Vijay has loaded all UCare data. Allowing users to avoid making proxies of MRNs or Birth Date etc... for UAB
3) Nive: UAB is now working on loading real data (they had been using test data). They had been working on a VM instance with Oracle ... but now they want to use the main database.
4) Vijay to start working with Khy at UCLA
5) Vijay will work on integrating UAB support for Views into UETL
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11/16/2011
Participants: Prakash, Peter, Vijay, Curtis
* Prakash is finishing up the map for Patient and Encounter mapping. Another map that exclusively supports Patient mapping alone needs to be developed since UCare Discharge table has only patient reference.
* Vijay is loading UCare and AXIUM data.
* Peter talked about long and unpredicatbale execution time of i2b2 queries at his site.
* UAB is doing prep work on i2b2 install.
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1/11/2011
On the call: Rob Wynden, Ketty Mobed, Prakash Lakshminarayanan, Vijay Rayanker, Aaron Mandel, Mark Weiner, Nive and Harsh at UAB
1) Further UETL testing at UAB. They need to use proxy MRNs and proxy Encounter Numbers. They did that and UETL is now working at UAB.
2) UAB has ICD9 and Labs In system now ... not mapped to main ontology
3) Prakash is working on Sybase IQ support last week. We are blocked on NCBO BioPortal for their bug fixes. We are importing all of our ontology there now...
4) Prakash will focus on LabNorm for now.
5) Vijay is loading more UCare data.
6) Vijay is making some enhancements after talking to UAB. To make the proxy list show up in the GUI to make it easier to maintain.
7) Ketty asked Mark about ICD9 and ICD10 support. Should we use an existing crosswalk or create our own?
8) RxNorm updates are not getting handled fast enough in BioPortal
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1/4/2011
On the call: Rob Wynden, Aaron Mandel, Ketty Mobed, Harsh Taneja, Niveditha Thota, Vijay Rayanker, Prakash Lakshminarayanan, Mark Weiner, Peter Beninato
1) New site for our dev work is at community.i2b2.org
2) Harsh question on SVN site. UETL code is read only. Could not get HOM code however due to bad permissions on the SVN. We will fix that for her.
3) At UCSF we are working on production issues (we upgraded Sybase to 12.7). That is postponed for now.
4) BioPortal integration is now waiting on fixes from Stanford. So we are stuck for now. Ketty will make sure that we have a ticket opened at Stanford. The source terminology cannot be properly annotated at leaf nodes due to a bug in the BioPortal UI. We also need private NCBO sites working very soon (for license restriction).
5) We have a joint lab meeting (UCSF and Stanford) at Stanford on Thursday of this week.
6) At UAB the usage of UETL is working well. They seem to be clear of all exceptions and they can search for stuff.
7) Asma ICD9 455 and search by name in ICD9 tree (using Prakash's) and it works now! So UETL is running at UAB. BUT SEARCH BY CODE IS STILL GIVING AN ERROR.
8) UETL needs to have a check added for duplicate entries in the i2b2 table (this is a bug in UETL) - Vijay will work with them on this.
9) Ketty is working now with Peter's ICD9 mappings
10) Rob and Ketty are working on a paper about our integration with NCBO BioPortal
11) Regarding our work on ontologies... The NCBO Site: http://bioportal.bioontology.org/ontologies?filter=CTSA-HOM shows everything that our team has been working on so far. HOM has a LOT of terminologies available here already.
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.12) Next week we will see a demo of the UAB ACE (Aggregate Cohort Estimator) query interface
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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
...
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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