documentation:oncology:development_schedule

Anonymous (anonymous@undisclosed.example.com) — 2021-09-22T17:50:11+0000

Every Other Wednesday, 10 am ET Join Team Meeting using the link below:

documentation:oncology:forum

Anonymous (anonymous@undisclosed.example.com) — 2019-01-17T02:12:23+0000

[ International Classification of Diseases for Oncology (ICD-O)] [AACR presentations on Cancer Research Data Commons(CRDC)] [Genomic Data in the CDM] [Oncology/Episode of Care Proposal] [Oncology data use cases] [Oncology radiology imaging integration into CDM]

documentation:oncology:genomic_schedule

Anonymous (anonymous@undisclosed.example.com) — 2021-09-22T17:50:58+0000

Every Tuesday, 9 am ET. Join Team Meeting using link below:

documentation:oncology:leadership_schedule

Anonymous (anonymous@undisclosed.example.com) — 2019-10-22T21:39:15+0000

Every 4th Tuesday, 10 am ET. Join Zoom Meeting Meeting ID: 988 206 409 Password: 027729 One tap mobile +16465588656,,988206409# US (New York) +14086380968,,988206409# US (San Jose)

documentation:oncology:meeting_2010

Anonymous (anonymous@undisclosed.example.com) — 2019-06-12T13:59:22+0000

Meeting 11-JUN-2019 Meeting notes Meeting 12-MAR-2019 Meeting notes

documentation:oncology:meeting_2017

Anonymous (anonymous@undisclosed.example.com) — 2019-01-16T18:02:36+0000

Meeting 12-Dec-2017 Meeting notes Meeting 28-Nov-2017 Meeting notes Meeting 14-Nov-2017 Meeting notes Meeting 31-Oct-2017 Meeting notes Face-to-Face Meeting 19-Oct-2017 Meeting notes Meeting 19-Sep-2017 Meeting notes Meeting 5-Sep-2017 Meeting notes Meeting 8-Aug-2017 Meeting notes Meeting 25-Jul-2017 Meeting notes Meeting 11-Jul-2017 Meeting notes Meeting 27-Jun-2017

documentation:oncology:meeting_2018

Anonymous (anonymous@undisclosed.example.com) — 2019-01-16T18:00:43+0000

Meeting 19-Jun-2018 Meeting notes Face-to-Face Meeting 02-May-2018 Meeting notes Meeting 17-Apr-2018 Meeting notes Meeting 3-Apr-2018 Meeting notes Meeting 20-Mar-2018 Meeting notes Meeting 5-Feb-2018 Meeting notes Meeting 23-Jan-2018 Meeting notes Meeting 9-Jan-2018 Meeting notes

documentation:oncology:meeting_info

Anonymous (anonymous@undisclosed.example.com) — 2019-05-27T22:33:43+0000

Meeting URL Meeting ID 348 727 294 Want to dial in from a phone? Dial one of the following numbers: +1.408.740.7256 (US (San Jose)) +1.408.317.9253 (US (Primary, San Jose)) (see all numbers - ) Enter the meeting ID and passcode followed by # Connecting from a room system? Dial: bjn.vc or 199.48.152.152 and enter your meeting ID & passcode

documentation:oncology:meeting_notes_2017_apr_04

Anonymous (anonymous@undisclosed.example.com) — 2017-04-10T03:36:14+0000

The group agreed to explore the onco domains in the following order: * Diagnosis * Treatment * Outcomes survival * Molecular biomarkers * Pathology reports * Imaging * Performance status Existing standards · Tumor Registry, CDISC and SEER are the existing standards and efforts in harmonizing the data collection.

documentation:oncology:meeting_notes_2017_apr_18

Anonymous (anonymous@undisclosed.example.com) — 2017-04-27T03:16:57+0000

* · We had a recap of the ICD-O 3 vocabulary and agreed upon using a temporary pre-coordinated terms which would collapse the ICD-O 3 three axes to a single axis. Similar to the approach of transforming LOINC to CDM model. Rimma to document the mapping/proposal and route to group by next week.

documentation:oncology:meeting_notes_2017_aug-08

Anonymous (anonymous@undisclosed.example.com) — 2017-09-10T04:28:04+0000

Agenda: * Update on the cancer diagnosis mapping POC implementation - Dmytry/Anna * Surgical treatments continued - Rimma [ Surgical treatment ovreview] * Radiation treatments - Michael [ Radiation treatment overview] To-do list: * Dima/Anna: continue with ICD-O to SNOMED mappings * Rimma: share current OMOP mappings of cancer surgery CPT codes to SNOMED with Dmytry for QA

documentation:oncology:meeting_notes_2017_dec-12

Anonymous (anonymous@undisclosed.example.com) — 2018-04-30T18:44:39+0000

* * * Next steps: testing the diagnosis vocabulary - touch base * Additional diagnostic features representation continued - Rimma Belenkaya * Treatment representation proposal - Michael Gurley *

documentation:oncology:meeting_notes_2017_jul-09

Anonymous (anonymous@undisclosed.example.com) — 2017-07-18T13:37:16+0000

Agenda: * Ordered List ItemBrief update on the cancer diagnosis mapping POC implementation - Dmitri * Review of immunotherapy, targeted and hormonal therapies- Don * Treatments, next steps Review of chemotherapy treatment options for breast cancer (Guoqian) and Review of surgical treatments (Rimma) didn’t happen because last minute meeting conflicts.

documentation:oncology:meeting_notes_2017_jul-25

Anonymous (anonymous@undisclosed.example.com) — 2017-07-30T20:37:02+0000

Agenda: * Update on the cancer diagnosis mapping POC implementation - Dima/Anna * Review of immunotherapy, targeted and hormonal therapies details - Don [Exploration of NCI oncology drug mappings to OHDSI vocabulary] [Current mappings of NCI oncology drugs to OHDSI vocabulary] * Review of chemotherapy treatment options for breast cancer - Guoqian Cancer Chemotherapy Drugs * Review of surgical treatments - Rimma

documentation:oncology:meeting_notes_2017_jun_13

Anonymous (anonymous@undisclosed.example.com) — 2017-06-15T03:19:25+0000

* 1 Follow-up to our meeting with NCI terminology group * 2 Overview of ICD-O - NCIt mapping results - Rimma * * 3 Overview of ICD-O - SNOMED mapping results - Michael * * 4 Next steps in cancer diagnosis mapping and representation * Guoqian suggested using SNOMED post-coordinated expressions, will explore and present this option

documentation:oncology:meeting_notes_2017_jun_27

Anonymous (anonymous@undisclosed.example.com) — 2017-07-08T03:01:21+0000

* Plan for POC for cancer diagnosis mapping to SNOMED - Rimma [Proposal] * Presentation of SNOMED post-coordination by Harold Solbrig, Mayo [snomed_cg.pdf]

documentation:oncology:meeting_notes_2017_may_02

Anonymous (anonymous@undisclosed.example.com) — 2017-05-10T07:18:04+0000

* [Cancer diagnosis proposal] was revisited with a demo from Christian Reich via mapping SNOMED à NCI Metathesaurus à ICD-O per suggestions from Iker. [ the full list of SNOMED codes that are descendants of “Malignant Neoplastic Disease”, and their crosswalk to NCI codes through UMLS.] [ Forum discussion] * Michael Gurley will generate the list of valid site/histology combinations based on the SEER validation list and then attempt to query the NCI Metathesaurus to find a SNOMED code for…

documentation:oncology:meeting_notes_2017_may_16

Anonymous (anonymous@undisclosed.example.com) — 2017-06-11T22:41:24+0000

1. Discussion with NCI vocabulary team is scheduled for May 30th. Only people who signed up for doodle would be sent invites. 2. Volunteers to look up cancer treatment domain as below: Michael: Radiation therapy/ Active Surveillance Guoqian: Chemotherapy Don

documentation:oncology:meeting_notes_2017_nov-14

Anonymous (anonymous@undisclosed.example.com) — 2017-11-28T23:47:58+0000

* Update on cancer diagnosis features and treatment modeling - Rimma/Michael * Update on diagnosis mapping - Dmytry Dymshyts * Cancer data modeling and challenges at Outcomes Insights, Inc - Mark Danese

documentation:oncology:meeting_notes_2017_nov-28

Anonymous (anonymous@undisclosed.example.com) — 2017-11-29T00:16:49+0000

Meeting recording 1. Statement of a problem, diagnosis Caisis mapping use case - Patrick Mergler [Presentation] 2. Implementation of the cancer diagnosis vocabulary in OMOP: extension of the ICD-0 to SNOMED mappings and improvement of SNOMED cancer diagnosis representation - Dmytry Dymshyts

documentation:oncology:meeting_notes_2017_oct-19

Anonymous (anonymous@undisclosed.example.com) — 2017-10-30T15:17:48+0000

[Face-to-Face Oncology Meeting Notes] Next steps I. Tasks to generate the minimal viable product 1. Diagnosis a. Vocabulary Mapping * Rely only on pre-coordination of SNOMED morphology and anatomy corresponding to ICD-O histology and topography. If a pre-coordinated SNOMED diagnosis does not exist, create OMOP-generated one.

documentation:oncology:meeting_notes_2017_oct-31

Anonymous (anonymous@undisclosed.example.com) — 2017-11-28T23:46:48+0000

* CancerLinQs implementation of the OMOP model - Andrew Stewart * Staging, grading, extent of disease and tumor characteristics - Michael Gurley

documentation:oncology:meeting_notes_2017_sep-05

Anonymous (anonymous@undisclosed.example.com) — 2017-09-10T19:45:06+0000

Agenda 1. Updates (5 min each) for the current efforts in progress: Mapping ICD-O diagnoses to SNOMED - Dmitry Dymshyts and Anna Ostropolets Identifying cancer drug regimens - Michael Gurley and Don O'Hara Mapping surgical procedures - Rimma Belenkaya Identifying vocabulary/standards to represent radiation regimens - Michael Gurley Developing oncology model in OMOP CDM - Michael Gurley and Rimma Belenkaya

documentation:oncology:meeting_notes_2017_sep-19

Anonymous (anonymous@undisclosed.example.com) — 2017-10-03T00:08:05+0000

Agenda 1. Project planning - Rimma Project plan 2. Updates from Michael * Asking the group's experience on the prevalence of using ICD9/ICD10 procedure codes to identify procedures

documentation:oncology:meeting_notes_2018_apt-03

Anonymous (anonymous@undisclosed.example.com) — 2018-04-30T18:30:03+0000

Move the Treatment Proposal to vote. Review data examples and finalize the following structural changes: * Replace high level Treatment-Condition with FACT_RELATIONSHIP * Make relationship to the lower level tables optional * Introduce TREATMENT_MODIFIER table to both low and high-level treatments (similar to condition modifiers)

documentation:oncology:meeting_notes_2018_apt-17

Anonymous (anonymous@undisclosed.example.com) — 2018-04-30T18:27:03+0000

1. Treatment proposal a. Close voting by the end of the week: b. Give both options, A and B, to the CDM WG and community to fully understand the ETL and queering implications of each 2. Vocabulary tasks a. Full description of the tasks and workforce is here:

documentation:oncology:meeting_notes_2018_feb-05

Anonymous (anonymous@undisclosed.example.com) — 2018-04-30T18:37:18+0000

* Quick review of the voting results for the diagnostic features proposal - Rimma Belenkaya * Cancer treatment representation proposal - Michael Gurley

documentation:oncology:meeting_notes_2018_jan-09

Anonymous (anonymous@undisclosed.example.com) — 2018-04-30T18:41:51+0000

* Discussing the Cancer Diagnostic features proposal: * Feedback:

documentation:oncology:meeting_notes_2018_jan-23

Anonymous (anonymous@undisclosed.example.com) — 2018-04-30T18:39:25+0000

* Finalize diagnostic features proposal and prepare for CDM workgroup presentation - Rimma Belenkaya * Testing of cancer diagnosis mappings and hierarchy - group discussion *

documentation:oncology:meeting_notes_2018_jun-19

Anonymous (anonymous@undisclosed.example.com) — 2018-06-21T18:18:18+0000

Save the dates * Diagnosis and Treatment proposal presentations to the CDM WG have been scheduled for August 7th and September 4th at 1 pm EST * Cancer Data Standardization Panel has been accepted for the 2018 AMIA Symposium in San Francisco. It will take place on November 6, at 1:45 pm.

documentation:oncology:meeting_notes_2018_mar-20

Anonymous (anonymous@undisclosed.example.com) — 2018-04-30T18:33:59+0000

* 1. Review data/SQL examples for abstraction of cancer treatments - Michael Gurley * 2. Review results of Cancer Registry diagnosis ETL at Columbia, problems and solutions - Ray/Dmytry - tentatively * 3. Plan next steps: * Finalizing and Presenting Diagnosis and Treatment Proposal to the larger CDM WG

documentation:oncology:meeting_notes_2018_may-02

Anonymous (anonymous@undisclosed.example.com) — 2018-05-10T04:35:33+0000

Participants Christian, Eldar, Michael, Shantha, Ray, Andrew, Mui, Rimma, Ben, Hamed, Rachel, Chan Topics [Outline] * Detailed planning of vocabulary tasks * Comprehensive review of Cancer Registry and integration of NAACCR into OMOP vocabulary * Priorities and use cases

documentation:oncology:meeting_notes_2019_aug-06

Anonymous (anonymous@undisclosed.example.com) — 2019-09-16T04:40:28+0000

Meeting Notes August 6, 2019 Here is a link to a recording of the meeting: recording. Topics * Michael Gurley shared updated DDL for the OMOP Oncology CDM extension. DDL. The update included DDL for the CONCEPT_NUMERIC table and a CSV file and script to load the new table.

documentation:oncology:meeting_notes_2019_aug-13

Anonymous (anonymous@undisclosed.example.com) — 2019-08-19T01:46:12+0000

Meeting Notes August 13, 2019 Here is a link to a recording of the meeting: recording. Topics * Robert Miller shared and explained his code to convert NAACCR flat file-formatted data to the input format necessary for the generic ETL SQL. See here generic ETL SQL .

documentation:oncology:meeting_notes_2019_aug-27

Anonymous (anonymous@undisclosed.example.com) — 2019-08-28T14:51:41+0000

Meeting Notes August 27, 2019 Topics * Seng Chan You from Ajou University told the group about the code he and his colleagues have developed for extracting treatment cycle from single medication records in CDM databases from OMOP data. See here:

documentation:oncology:meeting_notes_2019_aug-29

Anonymous (anonymous@undisclosed.example.com) — 2019-08-30T13:50:32+0000

Meeting Notes August 29, 2019 Topics * Robert Miller asked about how code that prepares data for the common ETL input format should deal with ambiguous ICDO site/histology combination in multiple NAACCR schemas. * It was decided that pre-reprocessing code should not consider the ambiguity and rely ETL code to skip ambigious ICDO site/histology combinations. SQL for identifying NAACCR ambiguities is here:

documentation:oncology:meeting_notes_2019_jul-02

Anonymous (anonymous@undisclosed.example.com) — 2019-07-03T11:28:23+0000

Meeting Notes June 19, 2019 Topics Attendees: Rimma, Dmytry, Christian, Michael We went over the backlog of milestone items to prepare us for beta testing. See here: * We discussed scoping NAACCR items to schemas. This is the requirement that all the necessary NAACCR items to diagnose a site/histology combination are linked and represented within the OMOP vocabulary. Example:…

documentation:oncology:meeting_notes_2019_jul-09

Anonymous (anonymous@undisclosed.example.com) — 2019-07-11T19:05:30+0000

Meeting Notes July 9, 2019 Topics * Hokyun Jeon from AJOU University gave a [ Presentation] titled “Implementation of Episode-based Oncology OMOP-CDM In Electronic Health Record”. This presentation gave an overview of the first attempt by a group to implement the population of the OMOP Oncology CDM extension.

documentation:oncology:meeting_notes_2019_jul-16

Anonymous (anonymous@undisclosed.example.com) — 2019-07-21T23:02:55+0000

Meeting Notes July 16, 2019 Topics * Joseph Plasek from Advocate Aurora Health University gave a [ Presentation] titled “Common Data Model for harmonizing heterogenous data”. This presentation gave an overview of Aurora Health's, UW Health and Advocate Health Care transformation of Non-Muscle Invasive Blander Cancer data into the OMOP CDM. In the absence of the completed OMOP CDM Oncology Extension, this effort worked within the current OMOP CDM. Joseph pointed out some gaps in the propos…

documentation:oncology:meeting_notes_2019_jul-23

Anonymous (anonymous@undisclosed.example.com) — 2019-07-26T10:59:24+0000

Meeting Notes July 23, 2019 Here is a link to a recording of the meeting: recording. Topics * Michael Gurley shared updated DDL for the OMOP Oncology CDM extension. DDL. The update renamed a column 'episode_event_event_id' to 'event_id' in the EPISODE_EVENT table. This had been decided a while back but not been implemented. The update also renamed constraints/indexes to be in line with current OMOP naming conventions.

documentation:oncology:meeting_notes_2019_jul-30

Anonymous (anonymous@undisclosed.example.com) — 2019-08-07T13:00:28+0000

Meeting Notes July 30, 2019 Topics * Rimma Belenkaya reviewed the latest draft of the ETL documentation including coverage for NAACCR numeric concepts. * The group discussed how to handle NAACCR items codes that represent numeric ranges. There is no current mechanism or convention within OMOP covering this use case. See forum discussion here:

documentation:oncology:meeting_notes_2019_jun-11

Anonymous (anonymous@undisclosed.example.com) — 2019-08-18T13:31:45+0000

Meeting Notes June 11, 2019 Topics * The group reviewed the following presentation: [ Presentation] * The group discussed SQL showing how to map ICDO Site/Histology combinations to pre-coordinated Condition concepts. * The group discussed SQL showing how to find all Site/Histology combinations containing a particular ICDO site or histology.

documentation:oncology:meeting_notes_2019_jun-18

Anonymous (anonymous@undisclosed.example.com) — 2019-06-20T11:16:03+0000

Meeting Notes June 18, 2019 Topics * The group reviewed the following presentation: [ Presentation] * The group discussed the following questions: * Should representation of cancer staging within the OMOP vocabulary preserve the differences in possible values for cancer staging across anatomic site? Or should the list of possible values be collapsed across anatomic sites?

documentation:oncology:meeting_notes_2019_jun-19

Anonymous (anonymous@undisclosed.example.com) — 2019-06-20T11:45:09+0000

Meeting Notes June 19, 2019 Topics Attendees: Dmytry, Christian, Michael * Dmytry can assign NAACCR Secondary diagnoses concepts non-standard as we expect to get this information from EHR. Don't create answers as separate codes for concepts with ICD10CM ranges as it is already a ICD10CM codes present in the OHDSI vocabulary.

documentation:oncology:meeting_notes_2019_jun-25

Anonymous (anonymous@undisclosed.example.com) — 2019-06-27T14:10:58+0000

Meeting Notes June 25, 2019 Topics * Rimma Belenkaya went over the ETL instructions for ETLing oncology diagnosis modifiers from NAACCR formatted tumor registry date into the OMOP Oncology CDM extension. See draft document here: * Maxim Moinat raised the issue of whether he should map European tumor registry data to NAACCR or go directly to SNOMED and/or LOINC…

documentation:oncology:meeting_notes_2019_mar-12

Anonymous (anonymous@undisclosed.example.com) — 2019-03-13T13:38:58+0000

Participants Christian Reich, Rimma Belankaya, Dmytry Dymshyts, Andrew Williams, Robert Miller, Michael Gurley Topics * Reviewed Dmytry's latest progress on the NAACCR ingestion script. * Discussed the possibility of moving NAACCR schemas into a new structure to keep the CONCEPT.concept_code clean (not contain anything NOT in NAACCR source data). But we decided for version 1 we would include NAACCR schemas in the vocabulary, and include NAACCR schema IDs in site-dependent NAACCR items a…

documentation:oncology:meeting_notes_2019_sep-03

Anonymous (anonymous@undisclosed.example.com) — 2019-09-05T17:23:47+0000

Meeting Notes September 03, 2019 Topics * Mike Gurley pointed out the script written by Dymytry Dymshyts to populate missing metadata concepts. For the following issue: See here: * Rimma Belenkaya asked that logic for the SQL ETL should skip any schema with an ambiguous site/histology combination in more than one NAACCR schema. Not just ambiguous site/histology…

documentation:oncology:models

Anonymous (anonymous@undisclosed.example.com) — 2017-04-27T02:12:39+0000

The CAP Cancer Protocols: for useful prior work that needs to be normalized to standard vocabularies. CDISC therapeutic areas: NAACCR Standards for Cancer Registries LOINC NAACER v11 and v12 mapping HL7_CDA_Pilot_Project_Protocol

documentation:oncology:outreach_schedule

Anonymous (anonymous@undisclosed.example.com) — 2021-09-22T17:49:15+0000

Every 1st and 3rd Tuesday of the month; 3PM EST Here is the link to the Team Meeting:

documentation:oncology:participants

Anonymous (anonymous@undisclosed.example.com) — 2017-07-11T18:13:45+0000

{{:documentation:oncology:oncologygroupcontactlist.xlsx|Participant List}}

documentation:oncology:previous_discussions

Anonymous (anonymous@undisclosed.example.com) — 2019-10-22T19:07:44+0000

Meeting 15-Oct-2019 Meeting notes

documentation:oncology:proposals

Anonymous (anonymous@undisclosed.example.com) — 2019-12-06T21:42:14+0000

Documentation Planning * [ Oncology Documentation Scope (Word document)] PROJECT PLANNING * [ Current Task List] * [ List of Use Cases] ONCOLOGY WG PRODUCTS OMOP CDM Oncology Module * [ OMOP CDM Oncology Extension (Complete PDF)] * [ Part 1: "Oncology Extension Summary" (Power Point presentation)] * [ Part 2: "Oncology Extension Detailed" (Word document)] OMOP CDM Extension Implementing Oncology Module * [DDL for EPISODE, EPISODE_EVENT and MEASUREMENT tables] ETL Instruc…

documentation:oncology:test

Anonymous (anonymous@undisclosed.example.com) — 2019-10-22T21:25:03+0000

Test

documentation:oncology:use_case_repo.xlsx

Anonymous (anonymous@undisclosed.example.com) — 2019-10-22T21:29:29+0000

Outreach Repository:

documentation:oncology:vocabularies

Anonymous (anonymous@undisclosed.example.com) — 2017-04-10T03:41:04+0000

ICD-O-3 Online version of ICD-O from International Agency of Research on Cancer (IARC) Link to SEER ICD-O-3. SEER provides validation lists for “coherent” topography/morphology or site/histology combinations [ICD-O-3 Validation List] Online downloadable CSV version of ICD-O-3 from WHO (does not contain 2011 ICD-O-3.1 updates) Guidance documents from NAACCR on now to implement ICD-O-3.1 History of ICD-O Mapping to ICD-10 Mapping of oncology diagnosis using NCI Metathesaurus Memo…

documentation:oncology:vocabulary_schedule

Anonymous (anonymous@undisclosed.example.com) — 2021-09-22T17:46:42+0000

Every Thursday, 1pm ET. Here is the Teams Link:

Observational Health Data Sciences and Informatics documentation:oncology

documentation:oncology:archive

documentation:oncology:data_source.xlsx