The query terms were chosen by the breast cancer team two months ago; see #204<https://informatics.gpcnetwork.org/trac/Project/ticket/204>, (with related discussion in #167<https://informatics.gpcnetwork.org/trac/Project/ticket/167>, and #32<https://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 August<http://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.sql<https://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) Definition<http://seer.cancer.gov/siterecode/icdo3_d01272003/>,: Site Group ICD-O-3 Site ICD-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: [email protected] [[email protected]] on behalf of Nadkarni, Prakash [[email protected]] Sent: Thursday, February 12, 2015 6:51 PM To: [email protected] 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 [[email protected]] Sent: Thursday, February 12, 2015 11:43 AM To: [email protected]; Nadkarni, Prakash; [email protected] Cc: [email protected]; [email protected]; [email protected] 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 [email protected] http://listserv.kumc.edu/mailman/listinfo/gpc-dev
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