RE: [gpc-informatics] #44: portable HERON ETL for NAACCR
The query terms were chosen by the breast cancer team two months ago; see #204https://informatics.gpcnetwork.org/trac/Project/ticket/204, (with related discussion in #167https://informatics.gpcnetwork.org/trac/Project/ticket/167, and #32https://informatics.gpcnetwork.org/trac/Project/ticket/32). I don't see any new information that would motivate them to reconsider. For example, see discussion of the SEER Site Summary last Augusthttp://listserv.kumc.edu/pipermail/gpc-dev/2014q3/000399.html. To re-iterate: he SEER site recode is a function of not just the C50X primary site info but also histology. I suppose in theory it's possible to encode this in an i2b2 query, but that's not how the breast cancer team decided to do it. Digging into the references I provided... excerpt from seer_recode.sqlhttps://informatics.kumc.edu/work/browser/heron_load/seer_recode.sql: /* Breast */ when (site between 'C500' and 'C509') and not (histology between '9050' and '9055' or histology = '9140' or histology between '9590' and '9992') then '26000' excerpt from SEER Site Recode ICD-O-3 (1/27/2003) Definitionhttp://seer.cancer.gov/siterecode/icdo3_d01272003/,: Site Group ICD-O-3 SiteICD-O-3 Histology (Type)Recode Breast C500-C509 excluding 9590-9989, and sometimes 9050-9055, 9140 +http://seer.cancer.gov/siterecode/icdo3_d01272003/#_+ 26000 -- Dan From: gpc-dev-boun...@listserv.kumc.edu [gpc-dev-boun...@listserv.kumc.edu] on behalf of Nadkarni, Prakash [prakash-nadka...@uiowa.edu] Sent: Thursday, February 12, 2015 6:51 PM To: gpc-dev@listserv.kumc.edu Subject: RE: [gpc-informatics] #44: portable HERON ETL for NAACCR We did not include the SEER Site Summary. The ICD-O3 pattern (topography codes) for the site C50% (e.g., C508, C509 etc) identify the Breast cancer subtree unambiguously, and so we used this. I believe that the SEER summary is in fact derived from the topography codes, which are the primary data entered by the registry folks, and more finely granular - e.g., breast cancer has subtypes like paget's disease, etc. - but the use of English as opposed to numbers in the SEER field makes the output more human-comprehensible without having to use an ICD-O3 code book. To anyone who has implemented I2B2, however - I2B2 allows search by keyphrases corresponding to the codes - the SEER field is redundant, and does not add information over and above what the ICDO3 topography code provides. Prakash From: GPC Informatics [d...@madmode.com] Sent: Thursday, February 12, 2015 11:43 AM To: dconno...@kumc.edu; Nadkarni, Prakash; jd...@umn.edu Cc: ngra...@kumc.edu; ple...@uwhealth.org; gbus...@mcw.edu Subject: Re: [gpc-informatics] #44: portable HERON ETL for NAACCR #44: portable HERON ETL for NAACCR --+--- Reporter: dconnolly | Owner: prakashnadkarni Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: etl-dev | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking: 119, 227 | --+--- Comment (by dconnolly): Prakash, Did you include the SEER site recode in your ETL? We're not seeing any breast cancer diagnosis data (`\i2b2\naaccr\SEER Site\Breast\`) in what you submitted 02/11/2015 3:26pm. For reference: - [https://informatics.kumc.edu/work/wiki/TumorRegistry TumorRegistry] in the KUMC wiki - [https://informatics.kumc.edu/work/blog/2012/01/seer-recode-sql Adding SEER Site Recode to HERON Tumor Registry integration] Jan 2012 blog item -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/44#comment:17 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: [gpc-informatics] #44: portable HERON ETL for NAACCR
We did not include the SEER Site Summary. The ICD-O3 pattern (topography codes) for the site C50% (e.g., C508, C509 etc) identify the Breast cancer subtree unambiguously, and so we used this. I believe that the SEER summary is in fact derived from the topography codes, which are the primary data entered by the registry folks, and more finely granular - e.g., breast cancer has subtypes like paget's disease, etc. - but the use of English as opposed to numbers in the SEER field makes the output more human-comprehensible without having to use an ICD-O3 code book. To anyone who has implemented I2B2, however - I2B2 allows search by keyphrases corresponding to the codes - the SEER field is redundant, and does not add information over and above what the ICDO3 topography code provides. Prakash From: GPC Informatics [d...@madmode.com] Sent: Thursday, February 12, 2015 11:43 AM To: dconno...@kumc.edu; Nadkarni, Prakash; jd...@umn.edu Cc: ngra...@kumc.edu; ple...@uwhealth.org; gbus...@mcw.edu Subject: Re: [gpc-informatics] #44: portable HERON ETL for NAACCR #44: portable HERON ETL for NAACCR --+--- Reporter: dconnolly | Owner: prakashnadkarni Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: etl-dev | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking: 119, 227 | --+--- Comment (by dconnolly): Prakash, Did you include the SEER site recode in your ETL? We're not seeing any breast cancer diagnosis data (`\i2b2\naaccr\SEER Site\Breast\`) in what you submitted 02/11/2015 3:26pm. For reference: - [https://informatics.kumc.edu/work/wiki/TumorRegistry TumorRegistry] in the KUMC wiki - [https://informatics.kumc.edu/work/blog/2012/01/seer-recode-sql Adding SEER Site Recode to HERON Tumor Registry integration] Jan 2012 blog item -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/44#comment:17 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics Notice: This UI Health Care e-mail (including attachments) is covered by the Electronic Communications Privacy Act, 18 U.S.C. 2510-2521, is confidential and may be legally privileged. If you are not the intended recipient, you are hereby notified that any retention, dissemination, distribution, or copying of this communication is strictly prohibited. Please reply to the sender that you have received the message in error, then delete it. Thank you. ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: [gpc-informatics] #44: portable HERON ETL for NAACCR
Thx again guys, very helpful, many blind alleys avoided. ;) -Original Message- From: Dan Connolly [mailto:dconno...@kumc.edu] Sent: Monday, January 05, 2015 3:28 PM To: Lenon Patrick; 'gpc-dev@listserv.kumc.edu' Cc: Nathan Graham; Mish Thomas F Subject: RE: [gpc-informatics] #44: portable HERON ETL for NAACCR 1) I don't remember any waiting period, but it was 2 years ago, so who knows. 2) yes 3) No; ICD-10 isn't relevant to NAACCR ETL. -- Dan From: Lenon Patrick [ple...@uwhealth.org] Sent: Monday, January 05, 2015 2:17 PM To: 'gpc-dev@listserv.kumc.edu'; Dan Connolly Cc: Nathan Graham; Lenon Patrick; Mish Thomas F Subject: RE: [gpc-informatics] #44: portable HERON ETL for NAACCR Thx, some additional questions: 1) I have not heard back from the WHO person, and my membership seems to be pending or something, so no downloads show as available for now. Did you have to go through some waiting period like this? (Maybe I mistakenly got in the commercial license queue instead of the research license queue?) 2) In your naaccr_concepts_load.sql, you refer to tables who.topo, who.morph2, and who.morph3. Do those correspond to the ICD-O-3_CSV-metadata.zip and ICD-O-2_CSV.zip you refer to below? 3) Did you not download ICD-10? Thanks as always for your assistance. -Original Message- From: GPC Informatics [mailto:d...@madmode.com] Sent: Monday, January 05, 2015 12:59 PM To: dconno...@kumc.edu; Lenon Patrick Cc: ngra...@kumc.edu Subject: Re: [gpc-informatics] #44: portable HERON ETL for NAACCR #44: portable HERON ETL for NAACCR --+--- Reporter: dconnolly | Owner: lenonpat Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: etl-dev | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking: 119 | --+--- Changes (by dconnolly): * owner: dconnolly = lenonpat Comment: Patrick, I found my (30 Jan 2013) notes on downloading materials from WHO... The pointer in my notes is http://www.who.int/classifications/icd/adaptations/oncology/en/index.html (along with http://apps.who.int/classifications/apps/icd/ClassificationDownloadNR/license.htm ) and I recorded the md5sums of what I downloaded - `b088c4e4bd2d685c9dd04e3b3c14c98b` ICD-O-3_CSV-metadata.zip - `1308ce6f4ef93c67137154cc6a723fc6` ICD-O-2_CSV.zip -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/44#comment:8 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
RE: [gpc-informatics] #44: portable HERON ETL for NAACCR
1) I don't remember any waiting period, but it was 2 years ago, so who knows. 2) yes 3) No; ICD-10 isn't relevant to NAACCR ETL. -- Dan From: Lenon Patrick [ple...@uwhealth.org] Sent: Monday, January 05, 2015 2:17 PM To: 'gpc-dev@listserv.kumc.edu'; Dan Connolly Cc: Nathan Graham; Lenon Patrick; Mish Thomas F Subject: RE: [gpc-informatics] #44: portable HERON ETL for NAACCR Thx, some additional questions: 1) I have not heard back from the WHO person, and my membership seems to be pending or something, so no downloads show as available for now. Did you have to go through some waiting period like this? (Maybe I mistakenly got in the commercial license queue instead of the research license queue?) 2) In your naaccr_concepts_load.sql, you refer to tables who.topo, who.morph2, and who.morph3. Do those correspond to the ICD-O-3_CSV-metadata.zip and ICD-O-2_CSV.zip you refer to below? 3) Did you not download ICD-10? Thanks as always for your assistance. -Original Message- From: GPC Informatics [mailto:d...@madmode.com] Sent: Monday, January 05, 2015 12:59 PM To: dconno...@kumc.edu; Lenon Patrick Cc: ngra...@kumc.edu Subject: Re: [gpc-informatics] #44: portable HERON ETL for NAACCR #44: portable HERON ETL for NAACCR --+--- Reporter: dconnolly | Owner: lenonpat Type: enhancement | Status: assigned Priority: major | Milestone: bc-survey-cohort-def Component: etl-dev | Resolution: Keywords: breast-cancer-cohort | Blocked By: Blocking: 119 | --+--- Changes (by dconnolly): * owner: dconnolly = lenonpat Comment: Patrick, I found my (30 Jan 2013) notes on downloading materials from WHO... The pointer in my notes is http://www.who.int/classifications/icd/adaptations/oncology/en/index.html (along with http://apps.who.int/classifications/apps/icd/ClassificationDownloadNR/license.htm ) and I recorded the md5sums of what I downloaded - `b088c4e4bd2d685c9dd04e3b3c14c98b` ICD-O-3_CSV-metadata.zip - `1308ce6f4ef93c67137154cc6a723fc6` ICD-O-2_CSV.zip -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/44#comment:8 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
Re: [gpc-informatics] #44: portable HERON ETL for NAACCR
#44: portable HERON ETL for NAACCR -+ Reporter: dconnolly| Owner: dconnolly Type: enhancement | Status: assigned Priority: major| Milestone: data-agg1 Component: etl-dev | Resolution: Keywords: | Blocked By: Blocking: 119 | -+ Changes (by dconnolly): * milestone: = data-agg1 -- Ticket URL: http://informatics.gpcnetwork.org/trac/Project/ticket/44#comment:3 gpc-informatics http://informatics.gpcnetwork.org/ Greater Plains Network - Informatics ___ Gpc-dev mailing list Gpc-dev@listserv.kumc.edu http://listserv.kumc.edu/mailman/listinfo/gpc-dev
