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Unverified Commit 0b1d88e5 authored by Weise, Martin's avatar Weise, Martin
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Updated nb

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.ipynb_checkpoints/analysis-checkpoint.ipynb
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Pipfile
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......@@ -8,6 +8,8 @@ pandas = "2.1.0"
numpy = "1.26.0"
matplotlib = "3.8.0"
jupyter = "*"
plotly = "*"
pycountry_convert = "*"
[requires]
python_version = "3.10"
Pipfile.lock 0 → 100644
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README.md
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[![Launch binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/git/https%3A%2F%2Fgitlab.tuwien.ac.at%2Fmartin.weise%2Ftres/HEAD?labpath=analysis.ipynb)
[![Apache 2 license](.gitlab/license.svg)](https://www.apache.org/licenses/LICENSE-2.0)
[![Release](https://gitlab.tuwien.ac.at/martin.weise/tres/-/badges/release.svg)](https://gitlab.tuwien.ac.at/martin.weise/tres/-/releases/)
[![Apache 2 license](.gitlab/cite.svg)](https://doi.org/10.48436/cv20m-sg117)
# Trusted Research Environments: Analysis of Characteristics and Data Availability
......
analysis.ipynb
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csv/access.csv
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ID,SUF,Physical Visit,External Physical Visit,Remote Visit
id,SUF,Physical Visit,External Physical Visit,Remote Visit
1,,,,1
2,,,,1
3,,,,
......@@ -59,4 +59,3 @@ ID,SUF,Physical Visit,External Physical Visit,Remote Visit
58,,,,1
59,,,,1
60,,1,,
61,,,,1
\ No newline at end of file
csv/countries.csv
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ID,Name,Code
id,Name,Code
1,Australia,AUS
2,Austria,AUT
3,Canada,CAN
......@@ -19,4 +19,3 @@ ID,Name,Code
18,Sweden,SWE
19,Great Britain,GBR
20,USA,USA
21,France,FRA
\ No newline at end of file
csv/inclusion.csv
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ID,Included,Exclusion Reason,Comment
id,Included,Exclusion Reason,Comment
1,1,,
2,1,,
3,0,peer review,
......@@ -59,4 +59,3 @@ ID,Included,Exclusion Reason,Comment
58,1,,
59,0,peer review,
60,1,,
61,1,,
\ No newline at end of file
csv/major_fields.csv
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ID,Life Sciences,"Physical Sciences, Mathematics, and Engineering",Arts and Humanities,Social and Behavioral Sciences
id,Life Sciences,"Physical Sciences, Mathematics, and Engineering",Arts and Humanities,Social and Behavioral Sciences
1,1,,,
2,1,,,
3,1,1,,
......@@ -59,4 +59,3 @@ ID,Life Sciences,"Physical Sciences, Mathematics, and Engineering",Arts and Huma
58,,1,,1
59,,,,
60,,,,
61,1,,,
\ No newline at end of file
csv/tres.csv
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ID,Name,Country ID,Structured Data,Data Level,Output Control,Inception Year,Records,Datatype,Statistics Office,Size,Source,Comment
id,Name,Country ID,Structured Data,Data Level,Output Control,Inception Year,Records,Datatype,Statistics Office,Size,Source,Comment
1,SURE,1,1,2,1,2017,0,2,0,,https://doi.org/10.1007/978-3-319-11257-2_23,Interview via mail
2,SeRP Australia,1,1,2,1,2011,0,2,0,,https://doi.org/10.1016/S0140-6736(16)32298-X,Interview via mail
3,Australian Research Environment,1,1,2,1,2021,995,1,0,13000,https://geonetwork.nci.org.au/geonetwork/srv/eng/catalog.search#/home,
......@@ -13,7 +13,7 @@ ID,Name,Country ID,Structured Data,Data Level,Output Control,Inception Year,Reco
12,National Bureau of Statistics China,5,1,2,1,2020,12144,1,1,,https://doi.org/10.3233/SJI-200754,
13,Statistics Denmark Remote Desktop,6,1,3,1,2008,2371,1,1,,https://doi.org/10.3233/sju-1995-12106,
14,EHDEN,7,0,2,0,2022,133,2,0,,https://doi.org/10.1016/j.cmpb.2018.03.024,
15,EJP RD Virtual Platform,7,0,2,1,2022,20,2,0,,https://doi.org/10.3233/SHTI210101,
15,EJP RD Virtual Platform,7,0,2,1,2023,20,2,0,,https://doi.org/10.3233/SHTI210101,
16,European Genome-phenome Archive,7,0,2,1,2008,10495,1,0,,https://doi.org/10.1038/ng.3312,
17,Health-X dataLOFT,7,1,2,1,2023,0,2,0,,https://doi.org/10.1109/MMUL.2022.3153121,
18,HONEUR,7,1,2,1,2018,44000,2,0,,https://doi.org/10.1111/ejh.13780,
......@@ -54,10 +54,8 @@ ID,Name,Country ID,Structured Data,Data Level,Output Control,Inception Year,Reco
53,Clinical Practice Research Datalink,19,1,2,1,1993,24,2,0,,https://doi.org/10.1093/ije/dyv098,
54,QResearch,19,1,2,1,2004,15,1,0,,http://doi.org/10.14236/jhi.v12i1.108,
55,eDRIS,19,1,2,1,2013,86,2,0,,http://doi.org/10.17061/phrp2541541,
56,SHAIP,19,0,2,1,2022,0,2,0,,https://doi.org/10.23889%2Fijpds.v7i3.2056,
57,FSRD,20,1,1,1,,,1,1,,https://doi.org/10.1177/0002716210374014,
56,SHAIP,19,0,2,1,2022,95,2,0,,https://doi.org/10.23889/ijpds.v7i3.2056,
57,FSRDC,20,1,1,1,1982,,1,1,,https://doi.org/10.1177/0002716210374014,
58,SRE,20,1,2,1,2019,4,2,0,,https://doi.org/10.1007/s10552-022-01571-0,
59,SCRE UC Santa Barbara,20,,2,1,2020,0,2,0,,https://www.it.ucsb.edu/secure-compute-research-environment/secure-compute-research-environment-user-guide,
60,"Secure Research Infrastructure
",20,1,1,1,2021,0,2,0,,https://doi.org/10.1145/3437359.3465577,
61,Health Data Hub,21,1,2,1,2019,0,2,0,,https://doi.org/10.1055/s-0039-1677917 ,
\ No newline at end of file
60,Secure Research Infrastructure,20,1,1,1,2021,0,2,0,,https://doi.org/10.1145/3437359.3465577,
sql/schema.sql
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-- TABLES
CREATE TABLE countries
(
id BIGINT PRIMARY KEY NOT NULL,
name VARCHAR(255) NOT NULL,
code VARCHAR(100)
) WITH SYSTEM VERSIONING;
CREATE TABLE tres
(
id BIGINT PRIMARY KEY NOT NULL,
name VARCHAR(255) NOT NULL,
country_id BIGINT NOT NULL,
structured_data BOOLEAN,
data_level INT,
output_control BOOLEAN,
inception_year YEAR,
records BIGINT,
datatype INT,
statistics_office BOOLEAN,
size INT,
source TEXT,
comment TEXT,
FOREIGN KEY (country_id) REFERENCES countries (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE major_fields
(
id BIGINT NOT NULL,
life_sciences BOOLEAN,
physical_sciences BOOLEAN,
arts_and_humanities BOOLEAN,
social_sciences BOOLEAN,
FOREIGN KEY (id) REFERENCES tres (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE inclusion
(
id BIGINT NOT NULL,
included BOOLEAN NOT NULL,
exclusion_reason ENUM ('peer review', 'environment', 'duplicate'),
comment TEXT,
FOREIGN KEY (id) REFERENCES tres (id)
) WITH SYSTEM VERSIONING;
CREATE TABLE access
(
id BIGINT NOT NULL,
suf BOOLEAN,
physical_visit BOOLEAN,
external_physical_visit BOOLEAN,
remote_visit BOOLEAN,
FOREIGN KEY (id) REFERENCES tres (id)
) WITH SYSTEM VERSIONING;
-- VIEWS
CREATE VIEW tres_included AS
(
SELECT t.`id`,
t.`name`,
c.`name` as country_name,
c.`code`,
t.`structured_data`,
t.`data_level`,
t.`output_control`,
t.`inception_year`,
t.`records`,
t.`datatype`,
t.`statistics_office`,
f.`life_sciences`,
f.`physical_sciences`,
f.`arts_and_humanities`,
f.`social_sciences`
FROM `tres` t
JOIN `countries` c ON t.`country_id` = c.`id`
JOIN `major_fields` f ON f.`id` = t.`id`
WHERE EXISTS (SELECT 1
FROM `inclusion` i
WHERE i.`included` = true
AND i.`id` = t.`id`)
ORDER BY country_name ASC);
CREATE VIEW tres_excluded AS
(
SELECT t.`id`,
t.`name`,
c.`name` as country_name,
c.`code`,
i.`exclusion_reason`
FROM `tres` t
JOIN `countries` c ON t.`country_id` = c.`id`
JOIN `inclusion` i ON i.`id` = t.`id`
WHERE EXISTS (SELECT 1
FROM `inclusion` i
WHERE i.`included` = false
AND i.`id` = t.`id`)
ORDER BY country_name ASC);
CREATE VIEW tres_access AS
(
SELECT t.`id`,
t.`name`,
t.`inception_year`,
t.`statistics_office`,
t.`data_level`,
t.`datatype`,
c.`code` as country_code,
a.`suf`,
a.`physical_visit`,
a.`external_physical_visit`,
a.`remote_visit`
FROM `tres` t
JOIN `access` a ON t.`id` = a.`id`
JOIN `countries` c ON c.`id` = t.`country_id`
WHERE EXISTS (SELECT 1
FROM `inclusion` i
WHERE i.`included` = true
AND i.`id` = t.`id`));
\ No newline at end of file
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