codelist comparison between outcome and pregnancy conceptsets

[RosaMGini]

dear @DavideMessinaARS

you can find in ARS' folder ConcePTIONcomponents\pregnancy\codelists\comparison_2209\1_input_six_codelists three pairs of spreadsheets

P_ELECTTERM_AESI - P_Interruption_PrA

P_SPONTABO_AESI - P_SpontaneousAbortion_PrA

P_STILLBIRTH_AESI - P_StillBirth_PrA

the first member of each pair contains two conceptsets (narrow and possible) for the clinical outcome; the second member of the pair contains juts one conceptset, which is less specific and refers to the 'type of end'. so we would ideally want that all codes of the second list are tagged like the first, but we hope that most of the work is already done, and just want to focus on what is missing

so: could you please compare in each pair the second spreadhseet to the first, and highlight which codes of the second are missing in the first? please note that unfortunately the first spreadsheet may contain some ranges and some stars, @giuhye can you perhaps have a look and try to clean before davide starts his work?

also, @AnnaGirardi22 can you provide davide with those few codes that were still missing from the work that was done in june? so we make sure that they are all also included in this comparison

thank! rosa

@clobart @GiorgioLimoncella @AnnaGirardi22 @JR-Farcli @cduransalinas @eimirh @giuhye

[DavideMessinaARS]

Script and results have been uploaded in ConcePTIONcomponents\pregnancy\codelists\comparison_2209

[eimirh]

Thanks Davide.

Apologies, Do I have access to that folder to have a look at the output? E

[RosaMGini]

@DavideMessinaARS can you post it on the VAC4EU Sharepoint?

[RosaMGini]

dear @eimirh @JR-Farcli @cduransalinas

find here in the folder 2_output_comparison 3 spreadsheets

in each spreadsheet you have the list of codes that are found in PrA but not in the corresponding AESI.

- interrpution: 69 codes
- spontaneous abortion: 30 codes
- stillbirth: 2 codes

can you please copy those spreadsheet in a new folder 3_reclassified and classify them according to the AESI standards?

[eimirh]

Dear all, Ive gone through the results of the comparison. Thanks a mill Davide for doing that.
I've commented on the three sheets I placed in folder 3. Not that many differences. please have a look when you get a chance.

There are a few concepts that were in the three PrA codelists that were not in the AESII lists. I added those I was confident about in CodeMpapper There are a few outstanding Concepts we need to resolve on our call on Thursday and then I'll update CodeMapper accordingly and upload the three final AESI lists to VAC4 EU then.

Were there other codes flagged by DAPS that are still missing form these three AESI lists?

Thanks all, e

[RosaMGini]

@AnnaGirardi22 and @giuhye can you check whether there is any code that was left out?

[AnnaGirardi22]

@AnnaGirardi22 and @giuhye can you check whether there is any code that was left out?

@RosaMGini @eimirh are you referring to all the codes we received from BIFAP, BIPS and BPE? We will consider than this document , correct? Thanks!

[eimirh]

Hi,

If we are going with the three AESI codelists below (which I believe we are), we need to check that the codes identified by the DAPS are also held within these codelists..

P_ELECTTERM_AESI rather than P_Interruption_PrA

P_SPONTABO_AESI rather than P_SpontaneousAbortion_PrA

P_STILLBIRTH_AESI rather P_StillBirth_PrA

Correct ?

E

[AnnaGirardi22]

@RosaMGini @eimirh aren't we considering for the task assigned (i.e. codes provided by DAPs possibly left out from the lists) the three sheets in folder 3_reclassified? Or the AESI codelist files (P_ELECTTERM_AESI, P_SPONTABO_AESI, P_STILLBIRTH_AESI)? thanks

[eimirh]

I would choose the later Anna.

If possible see if there are codes that the DAPs have flagged that are not in the three AESI sheets (in folder 1).

Thanks Anna E

On 21 Sep 2022 14:18, AnnaGirardi22 @.***> wrote:

@RosaMGinihttps://github.com/RosaMGini @eimirhhttps://github.com/eimirh aren't we considering for the task assigned (i.e. codes provided by DAPs possibly left out from the lists) the three sheets in folder 3_reclassified? Or the AESI codelist files (P_ELECTTERM_AESI, P_SPONTABO_AESI, P_STILLBIRTH_AESI)? thanks

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[AnnaGirardi22]

Perfect @eimirh ! many thanks, will update you as soon as we finish

[AnnaGirardi22]

results have been saved in ConcePTIONcomponents\pregnancy\codelists\comparison_2209\4_check with DAPs

[eimirh]

Hi,

Is it possible to share the link with me to check these?

Sorry!

Thanks a mill,

E

[AnnaGirardi22]

Hi,

Is it possible to share the link with me to check these?

Sorry!

Thanks a mill,

E

@eimirh we sent an email with the document some minutes ago Best

[eimirh]

Smashing. have it.

Tx

E

Eimir Hurley, PhD Researcher

(My name is Irish and is pronounced Ee-mer)

Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway

---

From: AnnaGirardi22 @.***> Sent: 22 September 2022 11:52:26 To: ARS-toscana/ConcePTIONAlgorithmPregnancies Cc: Eimir Hurley; Mention Subject: Re: [ARS-toscana/ConcePTIONAlgorithmPregnancies] codelist comparison between outcome and pregnancy conceptsets (Issue #35)

Hi,

Is it possible to share the link with me to check these?

Sorry!

Thanks a mill,

E

@eimirhhttps://github.com/eimirh we sent an email with the document some minutes ago Best

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[RosaMGini]

hi @eimirh @AnnaGirardi22 @JR-Farcli @cduransalinas @giuhye

we (myself, @clobart and @GiorgioLimoncella) donwloaded from the VAC4EU sharepoint the file

20220930_V2_ALL_full_codelist,csv

generated by @acidroyo-UMCU from the files you work in (@acidroyo-UMCU correct us if the file is the wrong one)

we found under 'type' PrA or AESI the list of conceptsets below, that we found, that we need to map to type_of_end (it is clearly the type of the end of the record, then the final type of end of the pregnancy is chosen according to the info carried by multiple records)

the current types of end are the following (UNF is the new one as suggested by @eimirh)

LB - live birth SB - still birth SA - spontaneous abortion T - termination ECT - ectopic pregnancy UNK - unknown (the pregnancy is ongoing at the moment when the record is recorded) UNF - (the pregnancy has ended at the moment when the recrod is recorded, and in an unfavorable undefined manner, may be ECT, SB, T, SA)

and the mapping between the file and the type of end is as specified below, note that there are some question marks, and pleae confirm that some conceptsets should no longer be included in the script

the list is also in this google spreadsheet that ww ask you to edit. once you this is done we can deploy the script

cheers, rosa, claudia, giorgio

event_definition	type	tag	type_of_end_recordwise
24weeks pregnancy	PrA	narrow	UKN
At term delivery	PrA		LB
Birth classified as narrow	PrA		LB
Birth classified as possible	PrA		UKN
Ectopic pregnancy	AESI	narrow	ECT
Ectopic pregnancy	AESI	possible	UKN or UNF ?
Ectopic Pregnancy	PrA		no longer used in the alg
Elective Termination Pregnancy	AESI	narrow	T
Elective Termination Pregnancy	AESI	possible	UKN or UNF ?
Fetal growth restriction	AESI	narrow	UKN or LB ?
Fetal growth restriction	AESI	possible	UKN or LB ?
Gestation 25 26 weeks	PrA		UKN
Gestation 27 28 weeks	PrA		UKN
Gestation 29 30 weeks	PrA		UKN
Gestation 31 32 weeks	PrA		UKN
Gestation 33 34 weeks	PrA		UKN
Gestation 35 36 weeks	PrA		UKN
Gestation 37 weeks	PrA		UKN
Gestation less than 24 weeks	PrA		UKN
Gestational diabetes	AESI	narrow	UKN
Gestational diabetes	AESI	possible	UKN
Interruption of pregnancy	PrA		no longer used in the alg
Livebirth	PrA		LB
Ongoing Pregnancy	PrA		UKN
Preeclampsia	AESI	narrow	UKN
Preeclampsia	AESI	possible	UKN
Pregnancy Bleeding	AESI	narrow	UKN
Pregnancy Bleeding	AESI	possible	UKN
Preterm Birth	AESI	narrow	LB
Preterm Birth	AESI	possible	UKN or LB ?
Preterm delivery	PrA		no longer used in the alg
Start of Pregnancy	PrA		UKN
Spontaneous abortion	PrA		no longer used in the alg
Spontaneous abortion	AESI	narrow	SA
Spontaneous abortion	AESI	possible	SA
Stillbirth	PrA		no longer used in the alg
Stillbirth	AESI	narrow	SB
Stillbirth	AESI	possible	UKN or UNF ?

[eimirh]

Hi all.

Please see my comments on the doc: https://docs.google.com/spreadsheets/d/1TA1J9UGHsrbme49aP2j7CHUYd9xh1HUICPiBTyIs0s8/edit#gid=0

[RosaMGini]

thank you very much eimir!

i have now updated a new column, G, where i have incorporated eimir's comment. @AnnaGirardi22 @JR-Farcli @cduransalinas @giuhye do you have any additional comments?

in particular please note that all conceptsets specifiying length of pregnancy ( (Gestation_less24 Gestation_25_26 Gestation_27_28 Gestation_29_30 Gestation_31_32 Gestation_33_34 Gestation_35_36 Gestation_more37) are now set as 'unknown' end of pregnancy, because as such they don't imply that the pregnancy is over

we are today testing the script with such specifications on our internal data. please let us have your feedback by tomorrow!

[RosaMGini]

thanks @acidroyo-UMCU! is the 'V2' list still the good one? let us just check whether there are new conceptsets then, if so we need to update the spreadsheet

[giuhye]

thank you very much eimir!

i have now updated a new column, G, where i have incorporated eimir's comment. @AnnaGirardi22 @JR-Farcli @cduransalinas @giuhye do you have any additional comments?

in particular please note that all conceptsets specifiying length of pregnancy ( (Gestation_less24 Gestation_25_26 Gestation_27_28 Gestation_29_30 Gestation_31_32 Gestation_33_34 Gestation_35_36 Gestation_more37) are now set as 'unknown' end of pregnancy, because as such they don't imply that the pregnancy is over

we are today testing the script with such specifications on our internal data. please let us have your feedback by tomorrow!

Hi all,

Anna and i reviewed the google spreadsheet and we completely agree with eimir's indications.

Best,

Giulia and Anna

[RosaMGini]

guys, how complex would it be to split the concepts in

Gestation_less24 Gestation_25_26 Gestation_27_28 Gestation_29_30 Gestation_31_32 Gestation_33_34 Gestation_35_36 Gestation_more37

between those than mean that the pregnancy has ended in LB, those that mean that the pregnancy has ended in another manner, and those that don't imply that the pregnancy has ended?

@AnnaGirardi22 @giuhye

can you tell me if it's along or a short task?

cheers, rosa

[giuhye]

guys, how complex would it be to split the concepts in

Gestation_less24 Gestation_25_26 Gestation_27_28 Gestation_29_30 Gestation_31_32 Gestation_33_34 Gestation_35_36 Gestation_more37

between those than mean that the pregnancy has ended in LB, those that mean that the pregnancy has ended in another manner, and those that don't imply that the pregnancy has ended?

@AnnaGirardi22 @giuhye

can you tell me if it's along or a short task?

cheers, rosa

@cduransalinas can you please confirm that files mentioned by Rosa (i.e. "Gestation_less24", "Gestation_25_26", "Gestation_27_28", "Gestation_29_30", "Gestation_31_32", "Gestation_33_34", "Gestation_35_36", "Gestation_more37") are the excel files present in VAC4EU SP in the folder "AESI & Covariate definition forms & Algorithms"?

If so, they are not huge files and the task proposed by Rosa should not take long.

Best, Giulia

[cduransalinas]

Yes, those files are present in VAC4EU SP.

El mar, 4 oct 2022 a la(s) 12:28, giuhye @.***) escribió:

guys, how complex would it be to split the concepts in

Gestation_less24 Gestation_25_26 Gestation_27_28 Gestation_29_30 Gestation_31_32 Gestation_33_34 Gestation_35_36 Gestation_more37

between those than mean that the pregnancy has ended in LB, those that mean that the pregnancy has ended in another manner, and those that don't imply that the pregnancy has ended?

@AnnaGirardi22 https://github.com/AnnaGirardi22 @giuhye https://github.com/giuhye

can you tell me if it's along or a short task?

cheers, rosa

@cduransalinas https://github.com/cduransalinas can you please confirm that files mentioned by Rosa (i.e. "Gestation_less24", "Gestation_25_26", "Gestation_27_28", "Gestation_29_30", "Gestation_31_32", "Gestation_33_34", "Gestation_35_36", "Gestation_more37") are the excel files present in VAC4EU SP in the folder "AESI & Covariate definition forms & Algorithms"?

If so, they are not huge files and the task proposed by Rosa should not take long.

Best, Giulia

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[giuhye]

Dear @cduransalinas @eimirh @JR-Farcli and @RosaMGini ,

Anna and i completed the review of concepts suggested by Rosa. All changes were made in the relevant files in the SP folder "AESI & Covariate definition forms & Algorithms". In particular, we split the original file into two files named UNK and LB.

Best,

Giulia and Anna

[clobart]

Dear all @acidroyo-UMCU @cduransalinas @eimirh and @JR-Farcli,

Giorgio and I have changed manually the splitted concept sets into a new version of the codelist for the pregnancy algorithm, so we can start to test the script on our data.

So this task of producing an updates codelist is not a priority! But for completeness, when you are free @acidroyo-UMCU, can you please produce the list and put it in SP?

Many thanks to all for the great effort!!

Claudia and @GiorgioLimoncella @giuhye @AnnaGirardi22

[eimirh]

Thanks a million all for all your work on this.

Its really appreciated.

With kind regards,

Eimir

Eimir Hurley, PhD Researcher

(My name is Irish and is pronounced Ee-mer)

Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway

---

From: Claudia @.***> Sent: 05 October 2022 16:16:37 To: ARS-toscana/ConcePTIONAlgorithmPregnancies Cc: Eimir Hurley; Mention Subject: Re: [ARS-toscana/ConcePTIONAlgorithmPregnancies] codelist comparison between outcome and pregnancy conceptsets (Issue #35)

Dear all @acidroyo-UMCUhttps://github.com/acidroyo-UMCU @cduransalinashttps://github.com/cduransalinas @eimirhhttps://github.com/eimirh and @JR-Farclihttps://github.com/JR-Farcli,

Giorgio and I have changed manually the splitted concept sets into a new version of the codelist for the pregnancy algorithm, so we can start to test the script on our data.

So this task of producing an updates codelist is not a priority! But for completeness, when you are free @acidroyo-UMCUhttps://github.com/acidroyo-UMCU, can you please produce the list and put it in SP?

Many thanks to all for the great effort!!

Claudia and @GiorgioLimoncellahttps://github.com/GiorgioLimoncella @giuhyehttps://github.com/giuhye @AnnaGirardi22https://github.com/AnnaGirardi22

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[RosaMGini]

dear @acidroyo-UMCU

don' worry and take your time in producing the new codelist: the final changes were included today and @clobart was able to tweak manually the codelist you produced yesterday - so we can now test and if everything is ok we can release

then when you have time to update formally the codelist just drop us a notification here and we will include it. thx!!!

cheers, rosa&team

[RosaMGini]

this issue is followed up by this one

[RosaMGini]

@acidroyo-UMCU an additional code revision is ongoing, so the generation of the codelist will only be needed at some point next week

[eimirh]

Hi,

Is it possible to share the link with me to check these?

Sorry!

Thanks a mill,

E

Eimir Hurley, PhD Researcher

(My name is Irish and is pronounced Ee-mer)

Pharmacoepidemiology and Drug Safety Research Group, Department of Pharmacy, Faculty of Mathematics and Natural Sciences, University of Oslo, Norway

---

From: AnnaGirardi22 @.***> Sent: 21 September 2022 20:39:17 To: ARS-toscana/ConcePTIONAlgorithmPregnancies Cc: Eimir Hurley; Mention Subject: Re: [ARS-toscana/ConcePTIONAlgorithmPregnancies] codelist comparison between outcome and pregnancy conceptsets (Issue #35)

Closed #35https://github.com/ARS-toscana/ConcePTIONAlgorithmPregnancies/issues/35 as completed.

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