From db33b8b78be0c604b8471b9900ec38a720851105 Mon Sep 17 00:00:00 2001 From: Susheel Varma Date: Sun, 7 Feb 2021 21:02:11 +0000 Subject: [PATCH 1/3] Adding gender codelists --- ...heel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD.csv | 5 +++ ...eel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD.csv | 3 ++ _data/data_sources.yml | 11 +++++-- _layouts/phenotype.html | 6 +++- .../susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md | 31 +++++++++++++++++++ 5 files changed, 52 insertions(+), 4 deletions(-) create mode 100644 _data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD.csv create mode 100644 _data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD.csv create mode 100644 _phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md diff --git a/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD.csv b/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD.csv new file mode 100644 index 00000000..436b6f19 --- /dev/null +++ b/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD.csv @@ -0,0 +1,5 @@ +System,Code,Description +dm+d,1,Male +dm+d,2,Female +dm+d,9,Indeterminate (unable to be classified as either male or female) +dm+d,X,Not Known (not recorded) \ No newline at end of file diff --git a/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD.csv b/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD.csv new file mode 100644 index 00000000..40a0ac13 --- /dev/null +++ b/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD.csv @@ -0,0 +1,3 @@ +System,Code,Description +gprd,1,Male +gprd,2,Female \ No newline at end of file diff --git a/_data/data_sources.yml b/_data/data_sources.yml index 7645cee7..40880367 100644 --- a/_data/data_sources.yml +++ b/_data/data_sources.yml @@ -50,7 +50,12 @@ Office of National Statistics (ONS): name: Office for National Statistics (ONS) id: 487222b7-5c13-4a92-8b41-044796048720 url: https://web.www.healthdatagateway.org/dataset/487222b7-5c13-4a92-8b41-044796048720 - - - +National Neonatal Research Database: + name: National Neonatal Research Database + id: 67020745-9def-4c6e-b5ac-bb273bd0a20e + url: https://web.www.healthdatagateway.org/dataset/67020745-9def-4c6e-b5ac-bb273bd0a20e +Maternity Services Data Set: + name: Maternity Services Data Set + id: 11d3cf0f-ae5d-42f4-a756-b98c3eff46bc + url: https://web.www.healthdatagateway.org/dataset/11d3cf0f-ae5d-42f4-a756-b98c3eff46bc diff --git a/_layouts/phenotype.html b/_layouts/phenotype.html index af0cc331..9ce19f36 100644 --- a/_layouts/phenotype.html +++ b/_layouts/phenotype.html @@ -79,7 +79,11 @@

Metadata

{% elsif codelist contains 'UKBIOBANK' %} + + {% elsif codelist contains 'GPRD' %} + {% endif %} diff --git a/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md b/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md new file mode 100644 index 00000000..6dbb30b7 --- /dev/null +++ b/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md @@ -0,0 +1,31 @@ +--- +layout: phenotype +title: Gender +phenotype_id: Lbc3RUsSRuRK5qQBPvdV89 +name: Gender +type: Lifestyle Risk Factor +group: Demographics +data_sources: + - National Neonatal Research Database + - Maternity Services Data Set +validation: +codelists: + - susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD.csv + - susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD.csv +clinical_terminologies: + - NHS Data Model and Dictionary + - GPRD Local Classification +author: Susheel Varma +status: DRAFT +date: 2021-02-07 +modified_date: 2021-02-07 +version: Revision 1 +--- + +### Primary Care + +{% include csv.html csvdata=site.data.codelists.susheel_gender_gprd_Lbc3RUsSRuRK5qQBPvdV89_Local %} + +### Secondary Care + +{% include csv.html csvdata=site.data.codelists.susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD %} \ No newline at end of file From af404e38e1647dcd0fc84a5a43b9b0143dfb8c36 Mon Sep 17 00:00:00 2001 From: Susheel Varma Date: Sun, 7 Feb 2021 23:51:14 +0000 Subject: [PATCH 2/3] Correcting Primary care GPRD codelist link --- _phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md b/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md index 6dbb30b7..26d64d34 100644 --- a/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md +++ b/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md @@ -24,7 +24,7 @@ version: Revision 1 ### Primary Care -{% include csv.html csvdata=site.data.codelists.susheel_gender_gprd_Lbc3RUsSRuRK5qQBPvdV89_Local %} +{% include csv.html csvdata=site.data.codelists.susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD %} ### Secondary Care From 444829909dac13c794446bcd8881812275cbbe3d Mon Sep 17 00:00:00 2001 From: Susheel Varma Date: Mon, 8 Feb 2021 12:41:45 +0000 Subject: [PATCH 3/3] Adding NHS Scotland ISD Data Dictionary --- .../codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_ISD.csv | 5 +++++ _layouts/phenotype.html | 6 +++++- _phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md | 6 +++++- 3 files changed, 15 insertions(+), 2 deletions(-) create mode 100644 _data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_ISD.csv diff --git a/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_ISD.csv b/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_ISD.csv new file mode 100644 index 00000000..7cd24fe7 --- /dev/null +++ b/_data/codelists/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_ISD.csv @@ -0,0 +1,5 @@ +System,Code,Description +isd,0,"Not Known (i.e. Indeterminate sex, includes 'Intersex')" +isd,1,Male +isd,2,Female +isd,9,"Not Specificed (includes not stated by patient, or not recorded)" \ No newline at end of file diff --git a/_layouts/phenotype.html b/_layouts/phenotype.html index 9ce19f36..53fc3524 100644 --- a/_layouts/phenotype.html +++ b/_layouts/phenotype.html @@ -83,7 +83,11 @@

Metadata

{% elsif codelist contains 'GPRD' %} + + {% elsif codelist contains 'ISD' %} + {% endif %} diff --git a/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md b/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md index 26d64d34..13a5561d 100644 --- a/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md +++ b/_phenotypes/susheel_gender_Lbc3RUsSRuRK5qQBPvdV89.md @@ -12,9 +12,11 @@ validation: codelists: - susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD.csv - susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_GPRD.csv + - susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_ISD.csv clinical_terminologies: - NHS Data Model and Dictionary - GPRD Local Classification + - NHS Scotland ISD Data Dictionary author: Susheel Varma status: DRAFT date: 2021-02-07 @@ -28,4 +30,6 @@ version: Revision 1 ### Secondary Care -{% include csv.html csvdata=site.data.codelists.susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD %} \ No newline at end of file +{% include csv.html csvdata=site.data.codelists.susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_DMD %} + +{% include csv.html csvdata=site.data.codelists.susheel_gender_Lbc3RUsSRuRK5qQBPvdV89_ISD %} \ No newline at end of file