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OHDSI / OncologyWG

Oncology Working Group Repository
https://ohdsi.github.io/OncologyWG
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Reproduce the "Crosswalk from Cancer Registry to OMOP Oncology Module" #300

Closed YeechingTiger closed 2 years ago

YeechingTiger commented 4 years ago

Problem: Can not find the "Maps to" relationship between ICDO3 and SNOMED. The existing relationship is "is a".

Details: I have imported the vocabularies following the Oncology CDM Extension Installation tutorial (https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation). And when I tried to reproduce "Crosswalk from Cancer Registry to OMOP Oncology Module" (https://github.com/OHDSI/OncologyWG/blob/master/documentation/NAACCR%20-%20OMOP%20Diagnosis%20Crosswalk.pdf), the "Maps to" relationship did not exist.

Have I missed any steps to add the "Maps To" relationship? I have looked through the Wiki and issues but could not find the corresponding documents.

Screen Shot 2020-10-18 at 11 00 24 AM

Screen Shot 2020-10-18 at 11 00 32 AM

dimshitc commented 4 years ago

That's fine. Not all of the ICDO concepts have Maps TO SNOMED. if there's no equivalent in SNOMED, we build Is a relationship as a link to a closest hierarchical concept or concepts.

On Sun, 18 Oct 2020 at 18:05, Xing He notifications@github.com wrote:

Problem: Can not find the "Maps to" relationship between ICDO3 and SNOMED. The existing relationship is "is a".

Details: I have imported the vocabularies following the Oncology CDM Extension Installation tutorial ( https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation). And when I tried to reproduce "Crosswalk from Cancer Registry to OMOP Oncology Module" ( https://github.com/OHDSI/OncologyWG/blob/master/documentation/NAACCR%20-%20OMOP%20Diagnosis%20Crosswalk.pdf), the "Maps to" relationship did not exist.

Have I missed any steps to add the "Maps To" relationship? I have looked through the Wiki and issues but could not find the corresponding documents.

[image: Screen Shot 2020-10-18 at 11 00 24 AM] https://user-images.githubusercontent.com/18644687/96371751-5316b980-1131-11eb-97e1-9dd3610ecc2b.png

[image: Screen Shot 2020-10-18 at 11 00 32 AM] https://user-images.githubusercontent.com/18644687/96371753-58740400-1131-11eb-81f6-eb6ac6bc2c3a.png

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/OHDSI/OncologyWG/issues/300, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBMA73XUSPDTFNX77GHDM3SLL75BANCNFSM4SVENZDA .

YeechingTiger commented 4 years ago

Thanks! Does it mean that I could use the "is a" relationship to map the ICDO3 (Source Concept) to SNOMED (Standard Concept)? Just use it as "Maps To"? And it seems that I could only find ICDO3 "Maps To" itself for all the ICDO3 codes. Maybe I have missed something?

dimshitc commented 4 years ago

you need to use ICDO concept itself as a standard one (As a condition_concept_id).

On Sun, 18 Oct 2020 at 19:01, Xing He notifications@github.com wrote:

That's fine. Not all of the ICDO concepts have Maps TO SNOMED. if there's no equivalent in SNOMED, we build Is a relationship as a link to a closest hierarchical concept or concepts. … <#m7393812083150827978> On Sun, 18 Oct 2020 at 18:05, Xing He @.***> wrote: Problem: Can not find the "Maps to" relationship between ICDO3 and SNOMED. The existing relationship is "is a". Details: I have imported the vocabularies following the Oncology CDM Extension Installation tutorial ( https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation). And when I tried to reproduce "Crosswalk from Cancer Registry to OMOP Oncology Module" ( https://github.com/OHDSI/OncologyWG/blob/master/documentation/NAACCR%20-%20OMOP%20Diagnosis%20Crosswalk.pdf), the "Maps to" relationship did not exist. Have I missed any steps to add the "Maps To" relationship? I have looked through the Wiki and issues but could not find the corresponding documents. [image: Screen Shot 2020-10-18 at 11 00 24 AM] https://user-images.githubusercontent.com/18644687/96371751-5316b980-1131-11eb-97e1-9dd3610ecc2b.png [image: Screen Shot 2020-10-18 at 11 00 32 AM] https://user-images.githubusercontent.com/18644687/96371753-58740400-1131-11eb-81f6-eb6ac6bc2c3a.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#300 https://github.com/OHDSI/OncologyWG/issues/300>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBMA73XUSPDTFNX77GHDM3SLL75BANCNFSM4SVENZDA .

That's fine. Not all of the ICDO concepts have Maps TO SNOMED. if there's no equivalent in SNOMED, we build Is a relationship as a link to a closest hierarchical concept or concepts. … <#m7393812083150827978> On Sun, 18 Oct 2020 at 18:05, Xing He @.***> wrote: Problem: Can not find the "Maps to" relationship between ICDO3 and SNOMED. The existing relationship is "is a". Details: I have imported the vocabularies following the Oncology CDM Extension Installation tutorial ( https://github.com/OHDSI/OncologyWG/wiki/Oncology-CDM-Extension-Installation). And when I tried to reproduce "Crosswalk from Cancer Registry to OMOP Oncology Module" ( https://github.com/OHDSI/OncologyWG/blob/master/documentation/NAACCR%20-%20OMOP%20Diagnosis%20Crosswalk.pdf), the "Maps to" relationship did not exist. Have I missed any steps to add the "Maps To" relationship? I have looked through the Wiki and issues but could not find the corresponding documents. [image: Screen Shot 2020-10-18 at 11 00 24 AM] https://user-images.githubusercontent.com/18644687/96371751-5316b980-1131-11eb-97e1-9dd3610ecc2b.png [image: Screen Shot 2020-10-18 at 11 00 32 AM] https://user-images.githubusercontent.com/18644687/96371753-58740400-1131-11eb-81f6-eb6ac6bc2c3a.png — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#300 https://github.com/OHDSI/OncologyWG/issues/300>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBMA73XUSPDTFNX77GHDM3SLL75BANCNFSM4SVENZDA .

Thanks! Does it mean that I could use the "is a" relationship to map the ICDO3 (Source Concept) to SNOMED (Standard Concept)? Just use it as "Maps To"? And it seems that I could only find ICDO3 "Maps To" itself for all the ICDO3 codes. Maybe I have missed something?

— You are receiving this because you commented.

Reply to this email directly, view it on GitHub https://github.com/OHDSI/OncologyWG/issues/300#issuecomment-711253966, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACBMA77S5KPUYMW7QBGUJILSLMGMVANCNFSM4SVENZDA .