Re: loading I2B2 concepts: KUMC, MCW, UMN OK; struggles with MCRF, UTSW, WISC

For UTSW, I'm not seeing several of the terminologies I sent inside of Babel. I'm guessing they just need to be added to the table_access. Specifically, the following \Beacon\- Our Epic Beacon Staging information \CancerGeneConnect\ - A genetic database \caTissue\ - caTissue Samples

Re: optional columns in i2b2 dimension tables RE: Minutes of GPV-DEV call 20140128

My understanding is the same as Dan's with regard to the dimension tables. And with regard to modifiers, It looks like the modifier column was in 1.5, but i2b2 didn't know how to use it. "Introduced in Core i2b2 Version 1.6 In Version 1.6 of i2b2 we begin to use the modifier_cd column in the

Re: optional columns in i2b2 dimension tables RE: Minutes of GPV-DEV call 20140128

.edu>> Date: Tuesday, February 4, 2014 10:22 AM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "GPC-DEV@LISTSERV.KUMC.EDU<mailto:GPC-DEV@LISTSERV.KUMC.EDU>" mailto:GPC-DEV@LISTSERV.KUMC.EDU>> Subject: Re: optional columns in i2b2 dimensi

Re: optional columns in i2b2 dimension tables RE: Minutes of GPV-DEV call 20140128

he latter choice would seem likely to lead to inconsistencies in browsing the data once the ETLs are run. Jim From: Greater Plains Collaborative Software Development [mailto:GPC-DEV@LISTSERV.KUMC.EDU] On Behalf Of Phillip Reeder Sent: Tuesday, February 04, 2014 9:58 AM To: GPC-DEV@LISTS

[Gpc-dev] De-Identification Plan

Dan, With regard to de-identification plan, is there an example out there of what they are looking for? If not, I think we should write up something simple as a starting point to use for the discussion. I'm assuming that the majority of how we will de-identify our data sets will be easy to ag

Re: [Gpc-dev] GPC De-Identification Plan

>> Date: Tuesday, March 4, 2014 1:02 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:gpc-dev@listserv.kumc.edu>> Subject: RE: GPC De-Identification Plan The plan we submit is r

Re: [Gpc-dev] GPC De-Identification Plan - i2b2 re-identification process

aches have their pros and cons. -Keith From: gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> [mailto:gpc-dev-boun...@listserv.kumc.edu] On Behalf Of Phillip Reeder Sent: Tuesday, March 04, 2014 1:12 PM To: Dan Connolly; gpc-dev@listserv.kumc.edu<mailto:

Re: [Gpc-dev] GPC De-Identification Plan

aration of identified vs de-identified data. Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Tuesday, March 4, 2014 2:16 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:g

Re: [Gpc-dev] minutes gpc-dev 11 March 2014 for review

Tom/Umberto, Regarding the +/-30 days, is there any documentation that states that de-identifying dates with that offset is acceptable from a HIPAA perspective? That is what I think we are looking for as 365 seems to be the currently accepted standard for date shifting. Phillip On 3/11/14 1:54 P

Re: [Gpc-dev] de-identification - patients under 1 year old

The current plan is to shift the dates, then the true age at the time of the observation can be calculated using the shifted dates. Phillip From: Justin Dale mailto:jd...@umn.edu>> Date: Tuesday, March 18, 2014 9:04 AM To: "GPC-DEV@listserv.kumc.edu" mailto:GPC

Re: [gpc-informatics] #93: federated login using InCommon for GPC services such as babel

We federated an i2b2 client for a project down in Houston. We wrote a small wrapper that added a username into i2b2 database and set the password to be the session id. Then injected that into the i2b2 Ajax client dynamically to log the person into i2b2. When the person logged out or their seaso

Re: [gpc-informatics] #103: subject of observation (e.g. maternal findings relevant to child)

In general, I would link to the mother¹s medical record with a ³Child of² attribute. Currently, i2b2 doesn¹t allow that linking to be done through the query tool, but it could be queried through the backend database. Phillip On 4/7/14, 1:20 PM, "Dan Connolly" wrote: >On second thought... I s

Re: [gpc-informatics] #69: verify enterprise business concerns and constraints regarding summary publications of QA stats shared within network

The list seems like pretty reasonable values to be shared. But from reading it, I wasn¹t quite sure of the level of distribution we are looking at far as what is Public, vs PCORI Wide, vs GPC wide sharing of information. Also, how does this address the sharing of data quality metrics. For example

Re: [gpc-informatics] #118: ER/PR status in NAACCR tumor registry ETL

The ER/PR is a Site Specific Factor in the NAACCR file. Site Specific Factors vary by cancer site so SSF1 for Breast Cancer has a different meaning than SSF1 for Colon Cancer. To query for ER in i2b2, you can drag over ³SEER Site->Breast² and ³2880 CS Site-Specific Factor 1² and specify that the

Re: agreement on paths (c_fullname) is necessary and sufficient

I can do a short show and tell on concept paths in i2b2 and why the path is the most important piece on May 6th, if needed. On a related note, I've been playing with SHRINE recently and it might be a good tool to look at for holding our local mappings, even if we didn't link our nodes together.

Re: CPT metadata

We created our CPT hierarchy from the UMLS. Do you have a local copy of the UMLS that you can use? If so, I’m sure someone can send you the code needed to create the CPT metadata. Dan, Are you planning to create a GPC CPT hierarchy for procedures using the same script you used for the ICD9 hi

Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0

I think simply changing the query to be similar to the following would take care of Dan’s objection. We need a demographics tree structure created and added to Babel. Select count(*) from observation_fact join concept_dimension on observation_fact.concept_cd=concept_dimension.concept_cd and

Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0

The problem is that i2b2 does not query based on a code. It queries based on a path. For example, I may have a path for for Ethnicity of: \GPC\Demographics\Ethnicity\ aka LOINC:21838-8 \GPC\Demographics\Ethnicity\hispanic Ethnicity:Hisp \GPC\Demographics\Ethnicity\hispanic\Dominican Ethnicity:Do

Re: Boston i2b2

UT Southwestern will have a couple of people in Boston for the conference. Phillip From: , Angela mailto:b...@uthscsa.edu>> Date: Tuesday, June 10, 2014 at 12:19 PM To: "Apathy, Nate" mailto:nate.apa...@cerner.com>>, Russ Waitman mailto:rwait...@kumc.edu>>, 'MM Coady' mailto:coady...@umn.edu>>,

Re: [gpc-informatics] #114: Milestone 2.7 GPC harmonizes with PCORI CDM V1.0

Regarding specifically the PATIENTS section of document, do we have a proposed hierarchy for the patient demographics? Jim lists a path like: '\LP29694-4\LP7850-3\42784-9\%¹ (Ethnicity) But I¹m not sure where that path came from. I think if it were created on Babel and looked something like: \GP

PCORI Mapping

, or should we plan to write a SQL query outside of i2b2 to get the numbers for the GPC Site Population Data Summary? Thoughts? Phillip Reeder UT Southwestern UT Southwestern Medical Center The future of medicine, t

Re: PCORI Mapping

way to determine how accurate the birth_date is without it. Any thoughts here? Phillip From: , James R mailto:campb...@unmc.edu>> Date: Monday, July 28, 2014 at 8:51 AM To: "Hickman, Hubert B" mailto:huhick...@nebraskamed.com>>, Phillip Reeder mailto:phillip.ree

Re: i2b2 Queries

Jim, Are you asking about doing a query by value based on a birthdate calculation? So you would, for example, Search for patients > 90 days old using the query by value option in i2b2, and then it would calculate the age, compare it to 90 days, and return the patient set? I think the query by

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

mailto:dconno...@kumc.edu>> Date: Sunday, August 17, 2014 at 1:15 AM To: Lindsay Cowell mailto:lindsay.cow...@utsouthwestern.edu>> Cc: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:

Re: [gpc-informatics] #144: ETL Annotated Data Dictionary form required by PCORI

o populate it in our i2b2 dev environment while we work on getting it into production. Until/unless someone comes up with a better plan, that's the path I'm following. Phillip Reeder UT Southwestern Sent from my iPhone On Aug 20, 2014, at 4:34 PM, "Supreet Kathpalia" m

Encounter Provider IDs

add a provider_id column to the visit dimension of i2b2 and populate it. That way I can easily move it into the PCORI CDM with Nathan’s i2b2 to CDM code. What are others planning to do with the encounter provider id? — Phillip Reeder UT Southwestern UT

Re: Encounter Provider IDs

> * Visit > * Admitting > >- Glenn > > Medical Informatics Senior Analyst > CTSI ­ Clinical & Translational Science Institute > gbus...@mcw.edu > (414) 805-7239 > > >From: Phillip Reeder >mailto:phillip.ree...@utsouthwestern.ed >u>> &

Medication Mapping to RXNORM

I am looking at mapping our meds to RXNORM/NDFRT. Has anyone used the clarity RXNORM_CODES table for the rxnorm mapping, and generated an NDFRT i2b2 hierarchy? If so, could you send me your code to try out? I’ve used KU’s code to build the base NDFRT hierarchy, and now I’m trying to figure o

Re: PCORnet: DSSNI TF - CDRN Member Meeting Materials (Oct 7, 2014)

lissa; Parsa Mirhaji; Jeannette Linkquist (jeannette.lindqu...@einstein.yu.edu<mailto:jeannette.lindqu...@einstein.yu.edu>); mwy...@uabmc.edu<mailto:mwy...@uabmc.edu>; Michelle Smerek; Bakul Patel (bakul.pa...@fda.hhs.gov<mailto:bakul.pa...@fda.hhs.gov>); Maia Hansen (mhan...@nygen

Re: usable view of LOINC lab terms #158 (was: 10 Sites x N Domains ...)

Walter, If you have a way to map from LOINC codes to the hierarchy you are proposing, UTSW would be happy to test. We have the majority of our results coded to LOINC now, but we don't have the hierarchy to go along with it. Phillip Sent from my iPhone On Oct 7, 2014, at 2:27 PM, "Dan Connolly"

Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service

Delaying is OK with me as well. I¹d have to miss about 15 minutes in the middles, tarting at 3:00, if we do it today. Just let me know. Phillip On 10/16/14, 1:44 PM, "Alex Bokov" wrote: >Dan, how would you feel about postponing the VM demo? It sounds like >there was an unexpected incompatibil

Re: GPC Priority Data Types

the 10 sites as we would have a defined measuring point. Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Friday, October 3, 2014 at 1:10 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>> Cc: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.ku

Re: GPC Terminology V1

those as the initial modifier list. Phillip From: Bonnie Westra mailto:westr...@umn.edu>> Date: Thursday, October 30, 2014 at 10:54 AM To: Nathan Graham mailto:ngra...@kumc.edu>> Cc: Dan Connolly mailto:dconno...@kumc.edu>>, Phillip Reeder mailto:phillip.ree...@utsouthwester

Re: GPC Terminology V1

m to the list. Does that seem like a reasonable? Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Thursday, October 30, 2014 at 12:48 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, Bonnie Westra mailto:westr...@umn.edu>>, Nathan Graham mailto:ngra.

Re: GPC Terminology V1 (medication modifiers)

rescripts) data. Are there any other tables people are pulling medication from? How does this compare with what the non-epic sites have for medication sources? Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Thursday, October 30, 2014 at 1:47 PM To: Phillip Reede

Diagnosis Modifiers on Babel

The current terminology has the following for billing diagnosis modifiers: Admit Billing Diagnosis Principal Discharge Diagnosis Diagnosis Present on Admission Secondary Billing Diagnosis Based on some emails around the time of the modifiers were added, I think the terminology should be: Admit Di

Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution

Based on the emails I found, and what is on babel, this is what I think the modifiers should be. The only difference from Babel is in the Billing Diagnosis modifiers where I tried apply what was in the various emails. Cerner had Inactive and Canceled modifiers for the Problem List Diagnosis in on

Re: [gpc-informatics] #87: Deploy, document R Data Builder demo service

I was able to successfully install on a clean 1.7.03a VM. The new 1.7.04 VM did not work. On 1704, it looks like for some reason, it failed to add the line to the i2b2_loader.js file for the rdatabuilder plugin. Once I added it, it shows up in the client and I can run the plugin. And it¹s placin

Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution

I prefer the V1 as it most closely matches what had been discussed in the previous iteration of diagnosis modifiers, and it allows me to easily search for admit diagnosis or discharge diagnosis, etc. Additionally, I think it will be flexible for adding additional diagnosis types and for grouping t

Re: approving GPC terminologies: data-domains2 and group decision making

Regarding “How do you know when something is Final?”, Final doesn’t have to be set in stone, because there is always new information that can come along, but we can consider something final and freeze it, allowing for sites to take it and start implementing it. That’s the finalized I’m look

Re: vital status from EMR for breast cancer cohort characterization (#67, #32, #204)

I would definitely check the EMR vital status in addition to the tumor registry vital status. If you have both loaded into i2b2, it’s very easy to do a query to find how many patients are alive in one source, but deceased in the other. For our tumor registry, I typically run that report ever

Re: Installing DataBuilder

, if you have a dfbuild-extract.conf.example with an oracle driver info in it, I’ll probably need that too. Thanks, Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Tuesday, January 6, 2015 at 1:31 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>

Re: Installing DataBuilder

to configure my database and see if I can produce sqlite files. Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Tuesday, January 6, 2015 at 2:15 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>> Cc: "gpc-dev@listserv.kumc.edu<mailto:gpc-d

Re: Installing DataBuilder

How do I set the SID for the connection? sqlalchemy.exc.DatabaseError: (DatabaseError) ORA-12505: TNS:listener does not currently know of SID given in connect descriptor Phillip From: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>> Date: Friday, January 9, 2015 at 11:16 AM T

Re: Installing DataBuilder

PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>> Cc: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:gpc-dev@listserv.kumc.edu>> Subject: RE: Installing DataBuilder That's the database = line in the config file. -- Dan

Re: Due Monday, January 12th: Population characterization (parts A and B) for PCORNet LOI

join CLARITY.zc_fin_class fin on fin.fin_class_c = epm.financial_class group by pat_id ), … As a side note, a quick search of gpc-trac came up with a comment by Justin Dale<https://informatics.gpcnetwork.org/trac/Project/ticket/139#comment:5> indicating he used that table for some exploration

Vital Signs Hierarchy

. Thoughts? — Phillip Reeder UT Southwestern UT Southwestern Medical Center The future of medicine, today. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev

Re: Vital Signs Hierarchy

ut pretty good reason. -- Dan From: gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> [gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>] on behalf of Phillip Reeder [phillip.ree...@utsouthwestern.ed

IMO Terms in i2b2

Has anyone created a terminology for IMO terms in i2b2? A researcher here at UTSW was asking about the possibility of getting IMO terms in i2b2 and I was wondering if anyone had some code we could use as a base. Thanks, Phillip UT Southwestern Medical Center

Re: [gpc-informatics] #202: Deploy Data Builder at each GPC site

Check in the Apache error log as well. When I was having issues with permissions, the error was in there. Phillip Sent from my iPhone > On Jan 14, 2015, at 2:58 PM, GPC Informatics wrote: > > #202: Deploy Data Builder at each GPC site > --+--

Breast Cancer i2b2 XML Query Definition

Does anyone have an i2b2 XML query definition of the breast cancer query that they can share? I’d like to see if I get the same results using the PortQuery with an outside XML query definition as I do when I run the one we created locally. Thanks, Phillip UT

Re: RxNorm metadata

The modifiers on babel, in the GPC[PR] Medications, are the ones that I am proposing for the GPC. I think they are available for download on Central Desktop. The UTSW Medication modifiers are the ones that are currently supported by our local i2b2 install. We haven’t added in the additional m

Re: Medication Modifiers

RX|FILLED MED_DISPENSE/SureScripts Phillip From: , Angela mailto:b...@uthscsa.edu>> Date: Thursday, January 29, 2015 at 4:51 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mail

GPC Vital Signs

et us know your thoughts. It seems like a much more usable solution vs the entire LOINC Clinical Measures hierarchy. — Phillip Reeder UT Southwestern UT Southwestern Medical Center The future of medicine,

Medication Mapping Issue

We have medications in our clarity_medication table that are not as specific as the GPC Medication hierarchy. For example, we have a medication called “ZOLOFT ORAL” This has multiple GCNs associated with it for the 25MG, 50MG, and 100MG versions, and the oral concentrate version. And the cur

Re: Medication Mapping Issue

titute for Health Informatics Director, Center for Nursing Informatics Location - WDH 6-155 P - 612-625-4470, Fax - 612-625-7091 email - westr...@umn.edu<mailto:westr...@umn.edu> Mail - WDH 5-140, 308 Harvard St SE, Minneapolis, MN 55455 On Wed, Feb 18, 2015 at 12:18 PM, Phillip Reeder

Re: Medication Mapping Issue

atics Location - WDH 6-155 P - 612-625-4470, Fax - 612-625-7091 email - westr...@umn.edu<mailto:westr...@umn.edu> Mail - WDH 5-140, 308 Harvard St SE, Minneapolis, MN 55455 On Wed, Feb 18, 2015 at 12:18 PM, Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>> wrote: We have me

Re: Medication Mapping Issue

used their hierarchy and added my medication ids as leaf nodes under the mapped RXNorm term. Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Thursday, February 19, 2015 at 12:04 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "Apathy,Nate" ma

FW: PCORnet CDM Development Update

Just an FYI that CDM v3 is already being created and will be seeking comments next month. Phillip From: Jenny Ibarra mailto:jenny.iba...@duke.edu>> Date: Monday, March 16, 2015 at 12:56 PM To: Jenny Ibarra mailto:jenny.iba...@dm.duke.edu>> Subject: PCORnet CDM Development Update Dear PCORnet Co

Re: [gpc-informatics] #90: Diagnoses Modifiers for data attribution

I still feel that the source of the data is an important aspect that we need to be maintained. And the CDM Modifiers are not specific enough to describe the data. We could add a second modifier to every diagnosis. The negative being that a billing admit primary diagnosis requires three entries int

Re: CPT codes for procedures

I like Angela's plan as HCPCS is the superset of terms. If after we deploy, we find that we only need a smaller set, like HCPT, or CPT, we can drop down to the smaller set. But we will have the data behind the decision to do so. Phillip Sent from my iPhone On Mar 24, 2015, at 3:01 PM, Dan Con

Re: [gpc-informatics] #158: usable view of LOINC lab terms

I'm interested. Phillip Sent from my iPhone > On Mar 31, 2015, at 8:25 AM, Apathy,Nate wrote: > > Hi Jim, > > Yes, that's correct. We have a conversion table that holds the necessary > conversions from local units to the standard units as dictated by the > metadataxml and LOINC. Happy to disc

Re: Q1 2015 Quality Query

Has anyone re-written the queries for Oracle? Phillip From: Tom Mish mailto:m...@wisc.edu>> Date: Wednesday, March 25, 2015 at 8:53 AM To: "GPC-DEV@LISTSERV.KUMC.EDU" mailto:GPC-DEV@LISTSERV.KUMC.EDU>> Subject: Q1 2015 Quality Query Everyone, We releasing the

Re: Medication Mapping Issue (standardization measurement framework, milestone:data-quality3)

tom line is that when there is missing data, we ended up with a more generic RxNorm codes. When we had sufficient details, we were able to map to a more specific code. Bonnie Bonnie L. Westra, PhD, RN, FAAN, FACMI Associate Professor, University of Minnesota, School of Nursing & Institute for Healt

Re: Medication Mapping Issue (standardization measurement framework, milestone:data-quality3)

leaving the GPC standard as is for now. Phillip From: , Nate mailto:nate.apa...@cerner.com>> Date: Thursday, April 2, 2015 at 1:46 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, Dan Connolly mailto:dconno...@kumc.edu>>, Russ Waitman mailto:rwait...@kumc.

Re: Medication Mapping Issue (standardization measurement framework, milestone:data-quality3)

:34 PM To: "Apathy,Nate" mailto:nate.apa...@cerner.com>>, Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, Russ Waitman mailto:rwait...@kumc.edu>> Cc: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:gpc-dev@listserv.kumc.e

GPC_TERMS Table

I believe the GPC_TERMS table has the most current demographics, diagnosis, medications, and vital signs terminologies. For Diagnosis, I just moved over Hubert’s updated modifiers. I propose that this table become the home for the Approved GPC Terminologies. So, that would take care of Demogra

Re: [gpc-informatics] #103: subject of observation (e.g. maternal findings relevant to child)

The best way I can think of would be to add a concept that links to a parent or child patient_num. For example, if a child had an observation of: CHILD_OF VALUE= where is the patient_num of the mother. Or we could do the opposite with the mother¹s observation being: HAS_CHILD VALUE=22

Re: Your report "Surescripts Dispense Report ETL for i2b2" has been reviewed

The clarity.med_dispense table’s EXT_MED_ERX_ID is the clarity medication_id for the row so we simple brought over the fact as MED:medication_id into our i2b2 observation_fact table. It doesn’t give us the NDC codes so it’s probably not CDMv3 compatible, but it does allow us to query based on t

DataBuilder

Does the data builder plugin work with the 1.7.05 i2b2 web client? I migrated the plugin over and it shows up, but it’s not allowing me to drag anything into the plugin(concepts, patient sets, etc.). Just wanted to check if anyone else has had success before I start attempting to troubleshoot

Re: DataBuilder

: Dan Connolly mailto:dconno...@kumc.edu>> Date: Friday, August 7, 2015 at 10:30 AM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:gpc-dev@listserv.kumc.edu>> Subject: RE: Dat

Databuilder updates to handle duplicate patients in patient set

I’ve made changes to the following lines in the data builder.py file which create a distinct list of patients in a patient set, prior to dumping the observation_fact, patient_dimension, and visit_dimension. It seems to work for me. 287 pset = i2b2_star.t_qt_patient_set_collection.

Re: GPC and ACT synergy

I’m trying as best as possible to not have to deploy completely separate ETLs for ACT,GPC, and my local i2b2. I’m using the i2b2 ontology to handle the differences between the various terminologies. This allows me to keep the data consistent between my various i2b2 instances and use views, vs

ICD9 and CPT Procedures for GPC

Did we ever settle on a design for the ICD9 Procedures and CPT Procedures? The HCPCS hierarchy on the UTHSCSA tree on babel looks pretty good, using the AUI’s consistent with the ICD9 diagnosis. And I’m inclined to adopt that one for the CPT hierarchy. I’m not finding an equivalent ICD9 Procedu

Re: ICD9 and CPT Procedures for GPC

Any chance we can get the SCILHS terminologies loaded onto Babel so that we can all see it, along with the other GPC terminologies? Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Thursday, October 1, 2015 at 12:00 PM To: Phillip Reeder mailto:phillip.ree...@utsouthweste

Re: [gpc-informatics] #243: GPC Procedure Ontology: CPT, HCPCS

I¹d be curious to see what sort of coverage people are getting with the Harvard HCPCS terminology. San Antonio¹s terminology looks to have more stuff in it. For example, HCPCS Level 2 has 282K facts, which I think is what is built out in the PCORnet terminology, vs. 2.8M facts for the CPT hierarc

Re: [gpc-informatics] #160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO milestone 2.4)

Do we have a timeline for that evaluation? Phillip On 10/6/15, 12:21 PM, "GPC Informatics" wrote: >#160: reproducible GPC, CDM refresh at a critical mass of GPC sites (PMO >milestone 2.4) >-+ > Reporter: rwaitman | Owner: t

GPC Terminology on Central Desktop

I’ve uploaded the GPC Terminologies from Babel to Central Desktop to make it easier for people in the GPC to get/use the terminologies. Look for GPC_TERMS.zip under the GPC i2b2 metadata folder. There is one sql file that includes insert statements for the GPC terminologies on Babel, and anoth

Updated Medications on Babel

I updated the GPC Medications hierarchy on Babel to use the most recent version of RxNorm(10/5/2015). There have been a few changes in AUI’s since the terminology was originally added, but the vast majority of the paths remain the same. In addition, I have added the Semantic Clinical Drug lev

Re: GPC Medications and RXCUIs

I’ve updated babel and the GPC_TERMS.zip file on Central Desktop to make the c_dimcode equal to the c_fullname column for meds, and fixed a small issue with the demographics. Phillip From: Deborah Yoshihara mailto:dlyos...@wisc.edu>> Date: Friday, October 23, 2015 at 11:05 AM To: gpc-dev mailto

Re: RXNORM with RXCUIs

I put my internal medid concept as the leaf under the rxcui folder, then hide any empty folders. That allows me to use the same data with several different mapping, including being able to maintain the original hierarchy we pulled from epic, or potentially other hierarchies. It's the same way K

Re: [gpc-informatics] #263: Adaptable cohort query design and administration

Is the NCDR cath pci registry a fairly standard format, like the NAACCR file, and is this something all site should be working to gain access to? Or should we wait until the cohort query is more defined before we work on it. Phillip Sent from my iPhone > On Nov 17, 2015, at 2:46 PM, GPC Inform

Re: CDM v3 dependency on SCILHS code (#266, #381) RE: Agenda for GPC-DEV call tomorrow

I don’t know of anyone finding it not sufficient for CDMv3, but my main concern was that we don’t all have the SCILHS code. As far as I know, it hasn’t been released yet. If it is not released by Q1 2016, that is going to impact our expected timeline. Does SCILHS have an expected timeline for

Re: Q4 QA replacement files

In the code, there is a create for a table called Q4_2015_GPC_QA_NAACCR_BC_PATIENTS. This table is never used in the code. Are there some queries that were lost somewhere along the way? Phillip From: Debbie Yoshihara mailto:dlyos...@wisc.edu>> Date: Wednesday, December 9, 2015 at 12:29 PM To:

Oracle QA Queries

I believe this has all of the updates changed to merges and semicolons added where needed for it to run in Oracle. Phillip UT Southwestern Medical Center The future of medicine, today. qa_oracle.sql Description: qa_oracle.sql

Re: gpc-dev agenda and meeting notes for Feb 9 11am

Looking at the gpc lab terminology, it looks like we are missing lab units in the metadata. Does anyone have a complete set of lab metadata with units? Phillip From: Dan Connolly mailto:dconno...@kumc.edu>> Date: Monday, February 8, 2016 at 3:53 PM To: "gpc-dev@listserv.kumc.edu

SCILHS i2b2 to CDM on Oracle

Has anyone else attempted the SCILHS i2b2 to CDM code on Oracle? I'm focusing on the demographics table to start with have run into a few things I wanted to share. #1) SCILHS relies on the patient_dimension for the demographics, not the observation_fact. Just something to be aware of, not re

Re: SCILHS i2b2 to CDM on Oracle

I'm stuck. Phillip From: , Eric R mailto:larose.e...@mcrf.mfldclin.edu>> Date: Wednesday, February 10, 2016 at 1:13 PM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>>, "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:gpc-dev@l

Re: SCILHS i2b2 to CDM on Oracle

LL, [PROVIDERID] varchar(25) NULL Thanks, Eric LaRose x93591 From: Phillip Reeder [mailto:phillip.ree...@utsouthwestern.edu] Sent: Wednesday, February 10, 2016 1:19 PM To: Larose, Eric R; gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu> Subject: Re: SCILHS i2b2 to CDM on Oracle For t

Re: SCILHS i2b2 to CDM on Oracle

/github.com/SCILHS/i2p-transform> repository. -- Dan From: gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu> [gpc-dev-boun...@listserv.kumc.edu<mailto:gpc-dev-boun...@listserv.kumc.edu>] on behalf of Phillip Reeder [philli

Re: SCILHS i2b2 to CDM on Oracle

te: Wednesday, February 24, 2016 at 11:49 AM To: Phillip Reeder mailto:phillip.ree...@utsouthwestern.edu>> Cc: "gpc-dev@listserv.kumc.edu<mailto:gpc-dev@listserv.kumc.edu>" mailto:gpc-dev@listserv.kumc.edu>> Subject: RE: SCILHS i2b2 to CDM on Oracle Phillip

Re: gpc_terms --> pcornet_terms mapping

My only concern with the SCHILS version is that it seems we are having to deviate from the core source that SCHILS released with Nathan's fork vs the SCHILS(https://github.com/SCILHS/i2p-transform). Hopefully the two version will merge back together to make it easier so that sites don't have to

Re: question about obtaining LOINC codes for EMR data

We don't have loinc in our component table, but they are associated with the individual results. I used those to create our map from component to loinc. That left a large number of lab components still un-mapped so I used the common name field to map labs with the same common name to the same lo

CDMv3 ADMITTING_SOURCE

Where are you getting the ADMITTING_SOURCE column for the PCORI CDM v3? It looks like KUMC is getting their's from UHC data. Is anyone getting this from Epic? Thanks, Phillip UT Southwestern Medical Center The future of medicine, today. _

Re: [gpc-informatics] #473: PCORnet CDMv3 SAS prep-to-research Readiness

UTSW submitted Appendix B and ETL ADD as well. Phillip On 5/20/16, 1:54 PM, "gpc-dev-boun...@listserv.kumc.edu on behalf of GPC Informatics" wrote: >#473: PCORnet CDMv3 SAS prep-to-research Readiness >-+ > Reporter: bzschoche| Owner

Re: clarity latency period

That is my understanding as to how it works at UTSW as well. Phillip From: mailto:gpc-dev-boun...@listserv.kumc.edu>> on behalf of Mei Liu mailto:mei...@kumc.edu>> Date: Wednesday, June 22, 2016 at 11:49 AM To: "'gpc-dev@listserv.kumc.edu'" mailto:gpc-dev@listserv.kumc.edu>> Subject: clarity l

Re: DataBuilder installation instructions

Dan, Any chance someone from your site could go through the install of the current version so that other sites could be on the most recent version?I know we, at UTSW, would like to get to a more recent version as well. I know you have made numerous changes and enhancements in the past year

Re: GPC DEID Data Request: Immunoglobulin G Levels and the pattern of infection

Should there also be ICD10 codes for this? Phillip From: mailto:gpc-dev-boun...@listserv.kumc.edu>> on behalf of Tamara McMahon mailto:tmcma...@kumc.edu>> Date: Thursday, July 7, 2016 at 1:00 PM To: "'Verhagen, Laurel A'" mailto:verhagen.lau...@mcrf.mfldclin.edu>>, "Campbell, Walter S" mailto

Re: gpc-dev 2 Aug agenda and meeting notes

We received feedback/questions from PCORI. I have some questions for everyone regarding how refreshes/archiving should be done for it. Here are the questions from PCORI: 1)We would like to understand more about your processes for refreshing your DataMart and creating a locked/static version of

Re: struggles with alignment on diagnoses, labs in PI-CONNECT federated query

UTSW has Diagnosis and Procedures mapped to the GPC standard, they are just under a different project. We also have the majority of the PCORI terminology useable in i2b2. Due to different requirements of different project, ACT, GPC, PCORI, Local, it’s often necessary, or easier, to deploy mul

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