The codes supplied in tables 2b, 4b and 5c are SNOMED codes for procedures. Do you have a mapping to CPT or ICD procedure codes for these SNOMED codes?
Hi Barbara - thanks fot your comment. We are not aware of any mapping to CPT or ICD for these procedures. We also anticipate that some sites may not have access to these results. The algorithm is robust without them, but of course it is a plus if the data is available
We don't have a way of accessing the outlined SNOMED procedures if there aren't any ICD/CPT procedure mapping in place. However, Table 2/Table 4 are involved in ascertainment of a case. If I'm understanding correctly, you're saying we should be fine even without using these procedure codes when applying the logic to ascertain a case. Could you verify this? Thanks.
when we were uploading the file, the system kept showing "The value '-1' for 'AGE_AT_AD' (1st row) should be an integer, but appears to have non-numeric characters." So we replaced the '-1' with '0'.
Hi John, Thanks for answering. It's not 100% clear to us in the pseudocode which Tables/codes are for inclusion/exclusion criteria for cases &/or controls, vs. just data to capture. In the pseudocode, are only the tables that explicity say "case" or "control", and "incl/inclusion" or "exclusion" are the tables to use for inclusion & exclusion, & then do the data dictionary files list all the tables from which you want covariates for those dictionaries?
The relevant files (ICD, Meds etc.) have columns labeled case_incl/case_cov/case_excl/cont_cov/cont_excl. A "Y" (yes) on relevant columns gives you the classfification for each of the variables in the row.
Should we apply a trailing wildcard to all ICD10 and ICD9 codes listed, regardless of the underscore? I think that the summary indicates this, but would like to verify with you. Thanks! Dustin
The algorithm specifies we would like to capture behavioral health / clinical physchology visits associated with controls when there is exactly one of them. When we find such a visit for a control, is there information from the visit that needs to be recorded onto the data dictionaries?
Thanks for the question and sorry for the delayed response - we somehow missed this in the shuffle.
For controls with exactly one visit to behavioral health, please add this to to hx of diseases works. We can change the name of the column to be ICD_Code_or_Dept (we can parse out which entries are ICDs and which are department names further down the line).
How would you like us to handle combination therapies? If we determine that patient is on a combination therapy that includes a medication in one of the tables but that combination therapy hasn't been directly provided in the table itself, what should we do?
Thanks for the question, Ozan - if a combination therpay has its own unique code, it would be great to get that unique code (understanding we likely have not directly provided for it in the DD). Otherwise, it is acceptable to report the component that does match a medication in one of the tables.
Can you explain which meds you want in Anxiety meds.csv. Do you want the additional medications in table 5 and 8 or all the medication used to find the cases and controls. In the Anxiety hx of other diseases.csv you have a variable to see if it's a case or control, but you don't have that in the meds.csv which is why I wanted to double check on what you wanted to include.
In the document you also ask to 'capture the department visit for any control that has exactly 1 visit to a Behavioral Health/Clinical Psychology department at any age'. Where would you like us to note this in the data dictionary?
For the meds.csv, please report all the medications used to find cases and controls as well as the covariates.
For anxiety history, there is no need to report case/control status.
For controls with exactly one visit to behavioral health, please add this to to hx of diseases works. Thank you for catching this, and please note, we can change the name of the column to be ICD_Code_or_Dept (we can parse out which entries are ICDs and which are department names (further down the line).
Thank you John. I also wanted to confirm then that the data dictionary called anxiety hx of other diseases is just of the extra covariates you want us to find. Not of the inclusion codes?
I'd like to double check which Rx should we use to populate the meds.csv file for controls. I've included the table 8 covariate Rx. However, I can't think of any other meds related to controls that should populate meds.csv. For instance, by definition I believe there shouldn't be any Rx from Table 7. Would any other Rx from any of the tables go into meds.csv for controls? Thanks! Dustin
I noticed an error upon posting our demographic implemenation. It seems to occur for the race field when there are multiple races reported. In the event of multpile races reported we had created a comma delimited string of each instance. Let us know if we need to change the convention used. I didn't see any other errors. Thanks! Dustin
In anxiety_meds_mr.csv, there are rows that contain drug classes. Are these rows meant to aid in readability by grouping the meds (i.e. just a section header row), are do you specifically mean to include an entire drug class?
Barbara Benoit
SNOMED codes for procedures
Fri, 2018-12-21 11:34The codes supplied in tables 2b, 4b and 5c are SNOMED codes for procedures. Do you have a mapping to CPT or ICD procedure codes for these SNOMED codes?
Barbara
John Connolly
SNOMED codes for procedures
Fri, 2018-12-21 12:08Hi Barbara - thanks fot your comment. We are not aware of any mapping to CPT or ICD for these procedures. We also anticipate that some sites may not have access to these results. The algorithm is robust without them, but of course it is a plus if the data is available
Best,
John
Ozan Dikilitas
SNOMED issue
Mon, 2019-01-21 08:51Hello John,
We don't have a way of accessing the outlined SNOMED procedures if there aren't any ICD/CPT procedure mapping in place. However, Table 2/Table 4 are involved in ascertainment of a case. If I'm understanding correctly, you're saying we should be fine even without using these procedure codes when applying the logic to ascertain a case. Could you verify this? Thanks.
Ozan
John Connolly
SNOMED issue
Tue, 2019-01-22 14:23Many thanks for checking, Ozan - you are correct.
Best,
John
Wei-Qi Wei
Age_at_AD in the demo DD
Thu, 2019-01-03 12:41when we were uploading the file, the system kept showing "The value '-1' for 'AGE_AT_AD' (1st row) should be an integer, but appears to have non-numeric characters." So we replaced the '-1' with '0'.
John Connolly
Age_at_AD in the demo DD
Thu, 2019-01-03 12:45Hi Wei-Qi - many thanks and that is a good workaround. I will ask Lyam to update the DD.
Best,
John
Anika Ghosh
genetics/chromosomal abnormalities
Wed, 2019-01-16 09:41Hi, Are there certain codes or ways you want us to find genetic or chromosomal abnormalities?
Thanks,
Anika
John Connolly
genetics/chromosomal abnormalities
Thu, 2019-01-17 08:14Hi Anika,
We have listed chromosomal abnormality ICD codes in the DD - are you having trouble locating them?
Best,
John
Jen Pacheco
case/ctl. exclusions vs. just DD data in pseudocode
Thu, 2019-01-17 18:09Hi John, Thanks for answering. It's not 100% clear to us in the pseudocode which Tables/codes are for inclusion/exclusion criteria for cases &/or controls, vs. just data to capture. In the pseudocode, are only the tables that explicity say "case" or "control", and "incl/inclusion" or "exclusion" are the tables to use for inclusion & exclusion, & then do the data dictionary files list all the tables from which you want covariates for those dictionaries?
John Connolly
case/ctl. exclusions
Fri, 2019-01-18 07:52Hi Jen,
The relevant files (ICD, Meds etc.) have columns labeled case_incl/case_cov/case_excl/cont_cov/cont_excl. A "Y" (yes) on relevant columns gives you the classfification for each of the variables in the row.
Thanks,
John
Dustin Key
ICD Wildcard verification
Tue, 2019-01-22 11:17Hi John,
Should we apply a trailing wildcard to all ICD10 and ICD9 codes listed, regardless of the underscore? I think that the summary indicates this, but would like to verify with you. Thanks! Dustin
John Connolly
ICD Wildcard verification
Tue, 2019-01-22 14:18Hi Dustin,
Thanks for checking - yes, go ahead and apply the trailing wildcard.
Best,
John
Dustin Key
Department Visits associated with controls
Tue, 2019-01-22 17:11Hi John,
The algorithm specifies we would like to capture behavioral health / clinical physchology visits associated with controls when there is exactly one of them. When we find such a visit for a control, is there information from the visit that needs to be recorded onto the data dictionaries?
Thanks!
Dustin
John Connolly
Department Visits associated with controls
Fri, 2019-02-15 15:44Thanks for the question and sorry for the delayed response - we somehow missed this in the shuffle.
For controls with exactly one visit to behavioral health, please add this to to hx of diseases works. We can change the name of the column to be ICD_Code_or_Dept (we can parse out which entries are ICDs and which are department names further down the line).
Ozan Dikilitas
Medication
Wed, 2019-01-23 08:47Hello John,
How would you like us to handle combination therapies? If we determine that patient is on a combination therapy that includes a medication in one of the tables but that combination therapy hasn't been directly provided in the table itself, what should we do?
Best,
Ozan
John Connolly
Medication
Wed, 2019-01-23 16:01Thanks for the question, Ozan - if a combination therpay has its own unique code, it would be great to get that unique code (understanding we likely have not directly provided for it in the DD). Otherwise, it is acceptable to report the component that does match a medication in one of the tables.
Best,
John
Anika Ghosh
Inclusion Codes - inpatient
Mon, 2019-02-11 17:32Hello,
I wanted to confirm that for the cases, we want the inclusion codes to come from only inpatient visits? The code can't be from an outpatient visit?
Thanks,
Anika
John Connolly
Inclusion Codes - inpatient
Tue, 2019-02-12 12:22Hi Anika,
Inclusion codes should come from BOTH inpatient and outpatient visits. (Note, restrictions are/were for in-PERSON versus in-patient visits)
Best,
John
Anika Ghosh
Thank you John. I should have
Tue, 2019-02-12 14:29Thank you John. I should have read the description closer.
Anika Ghosh
Data Dictionaries
Wed, 2019-02-13 13:59Hi,
Can you explain which meds you want in Anxiety meds.csv. Do you want the additional medications in table 5 and 8 or all the medication used to find the cases and controls. In the Anxiety hx of other diseases.csv you have a variable to see if it's a case or control, but you don't have that in the meds.csv which is why I wanted to double check on what you wanted to include.
In the document you also ask to 'capture the department visit for any control that has exactly 1 visit to a Behavioral Health/Clinical Psychology department at any age'. Where would you like us to note this in the data dictionary?
Thanks,
Anika
John Connolly
Data Dictionaries
Thu, 2019-02-14 13:08Hi Anika,
For the meds.csv, please report all the medications used to find cases and controls as well as the covariates.
For anxiety history, there is no need to report case/control status.
For controls with exactly one visit to behavioral health, please add this to to hx of diseases works. Thank you for catching this, and please note, we can change the name of the column to be ICD_Code_or_Dept (we can parse out which entries are ICDs and which are department names (further down the line).
Best regards,
John
Anika Ghosh
Thank you John. I also wanted
Fri, 2019-02-15 09:51Thank you John. I also wanted to confirm then that the data dictionary called anxiety hx of other diseases is just of the extra covariates you want us to find. Not of the inclusion codes?
Thanks,
Anika
John Connolly
Thank you for the question.,
Fri, 2019-02-15 15:45Thank you for the question., Anika Yes, just the extra covariates.
Dustin Key
Rx for controls
Fri, 2019-02-15 11:14Hi John,
I'd like to double check which Rx should we use to populate the meds.csv file for controls. I've included the table 8 covariate Rx. However, I can't think of any other meds related to controls that should populate meds.csv. For instance, by definition I believe there shouldn't be any Rx from Table 7. Would any other Rx from any of the tables go into meds.csv for controls? Thanks! Dustin
John Connolly
Rx for controls
Fri, 2019-02-15 15:44Thank you for the question. Yes, just the table 8 meds for the controls.
Dustin Key
Demog table error when posted implementation
Tue, 2019-02-19 13:42Hi John,
I noticed an error upon posting our demographic implemenation. It seems to occur for the race field when there are multiple races reported. In the event of multpile races reported we had created a comma delimited string of each instance. Let us know if we need to change the convention used. I didn't see any other errors. Thanks! Dustin
John Connolly
Demog table error when posted implementation
Tue, 2019-02-19 13:57Thanks Dustin, and that works just fine.
John Connolly
Demog table error when posted implementation
Tue, 2019-02-19 13:56Thanks Dustin, and that works just fine.
Ken Borthwick
med clarification
Mon, 2019-03-04 11:36Hi John,
In anxiety_meds_mr.csv, there are rows that contain drug classes. Are these rows meant to aid in readability by grouping the meds (i.e. just a section header row), are do you specifically mean to include an entire drug class?
Thanks, Ken
Frank Mentch
drug classes are meant as section headers in meds file
Mon, 2019-03-04 11:48Ken, thanks for the clarifying question. Yes, the drug class names in the file are meant to be section headers and not search terms.