From cd590e4a4d14898b630341beef7dfbcfedff969c Mon Sep 17 00:00:00 2001 From: Jan Lorenz Date: Wed, 7 Jun 2023 09:54:26 +0200 Subject: [PATCH 01/10] Changed comment for Biobanks API --- layouts/topics/single.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/layouts/topics/single.html b/layouts/topics/single.html index 6a8a51f9..ce0651b4 100644 --- a/layouts/topics/single.html +++ b/layouts/topics/single.html @@ -83,7 +83,7 @@
{{ .Title }}
{{ if or (eq $page_topic "COVID-19") (eq $page_topic "Infectious diseases") }} -{{/* Doing this manually right now. Need to create expose an API from biobanks.covid19dataportal.se in the future to fetch this automatically. */}} +{{/* This needs to be updated manually. Usually once or twice per year. */}}

Sample collections (36)

From c68032bee1b867ba11444d4e4fa1cd8cf632463a Mon Sep 17 00:00:00 2001 From: Jan Lorenz Date: Mon, 12 Jun 2023 16:25:36 +0200 Subject: [PATCH 02/10] Updated data for May --- data/available_datasets.json | 191 ++++++++++++++++++++++++++++++++++- 1 file changed, 190 insertions(+), 1 deletion(-) diff --git a/data/available_datasets.json b/data/available_datasets.json index 0343a81c..faff1665 100644 --- a/data/available_datasets.json +++ b/data/available_datasets.json @@ -1,6 +1,195 @@ { - "last_updated": "2023-05-04", + "last_updated": "2023-06-12", "datasets": [ + { + "doi": "10.3389/fimmu.2023.1166924", + "available_items": [ + { + "type": "data", + "repo_name": "Protein Data Bank", + "accession_number": "7KRR", + "description": "Protein structures in PDBe", + "data_type": [ + "Protein data" + ], + "data_url": "https://www.ebi.ac.uk/pdbe/entry/pdb/7KRR" + }, + { + "type": "data", + "repo_name": "GenBank", + "accession_number": "NC_045512.2", + "description": "RefSeq - NCBI Reference Sequence Database", + "data_type": [ + "Genomics & transcriptomics data" + ], + "data_url": "https://www.ncbi.nlm.nih.gov/nuccore/NC_045512.2" + } + ], + "title": "A novel precision-serology assay for SARS-CoV-2 infection based on linear B-cell epitopes of Spike protein", + "issue": "", + "volume": "14", + "publisher": "Frontiers Media SA", + "published": "2023-05-12", + "author": [ + "Lundin S. B.", + "Kann H.", + "Fulurija A.", + "Andersson B.", + "Nakka S. S." + ] + }, + { + "doi": "10.3389/fpsyg.2023.1124627", + "available_items": [ + { + "type": "code", + "repo_name": "OSF", + "accession_number": "d99ed5ce0ed641ca80965e54c11afc81", + "description": "Data and script for re-analysis", + "data_type": [ + "Health data", + "Public health data" + ], + "data_url": "https://osf.io/f7ucb/?view_only=d99ed5ce0ed641ca80965e54c11afc81" + } + ], + "title": "Regional differences in personalities account for substantial heterogeneity of loneliness change from before to during the COVID-19", + "issue": "", + "volume": "14", + "publisher": "Frontiers Media SA", + "published": "2023-05-05", + "author": [ + "Xiao S.", + "Dang J." + ] + }, + { + "doi": "10.1007/s41669-023-00418-x", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "POETIC-COVID CEA PROJECT - R code that supports the findings of the study", + "data_type": [ + "Other data", + "Public health data" + ], + "data_url": "https://github.com/EECCnetwork/POETIC_CEA" + } + ], + "title": "Cost Effectiveness of Strategies for Caring for Critically Ill Patients with COVID-19 in Tanzania", + "issue": "", + "volume": "", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-05-13", + "author": [ + "Shah H. A.", + "Baker T.", + "Schell C. O.", + "Kuwawenaruwa A.", + "Awadh K." + ] + }, + { + "doi": "10.1038/s41467-023-38020-8", + "available_items": [ + { + "type": "data", + "repo_name": "", + "accession_number": "", + "description": "Data cannot be shared publicly, but applications can be made for access.", + "data_type": [ + "Serology data", + "Health data" + ], + "data_url": "mailto:\"geldmacher@lrz.uni-muenchen.de\"" + } + ], + "title": "Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion", + "issue": "1", + "volume": "14", + "publisher": "Springer Science and Business Media LLC", + "published": "2023-05-24", + "author": [ + "Eser T. M.", + "Baranov O.", + "Huth M.", + "Ahmed M. I. M.", + "Deák F." + ] + }, + { + "doi": "10.1016%2Fj.lanepe.2023.100646", + "available_items": [ + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Data processing code is available on GitHub", + "data_type": [ + "Serology data", + "Health data" + ], + "data_url": "https://github.com/johanssonresearch/Correlate-of-vaccine-protection-against-fatal-COVID-19" + } + ], + "title": "Vaccine-induced correlate of protection against fatal COVID-19 in older and frail adults during waves of neutralization-resistant variants of concern: an observational study", + "issue": "", + "volume": "", + "publisher": "Elsevier BV", + "published": "2023-05-15", + "author": [ + "Vikström L.", + "Fjällström P.", + "Gwon Y.", + "Sheward D. J.", + "Wigren-Byström J." + ] + }, + { + "doi": "10.1128/jvi.01992-22", + "available_items": [ + { + "type": "data", + "repo_name": "zenodo", + "accession_number": "7826331", + "description": "Movies and data to accompany the study", + "data_type": [ + "Imaging data", + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://zenodo.org/record/7826331" + }, + { + "type": "code", + "repo_name": "GitHub", + "accession_number": "", + "description": "Image and time series analysis code written in MATLAB is available on GitHub", + "data_type": [ + "Imaging data", + "Biochemistry data", + "Genomics & transcriptomics data", + "Health data" + ], + "data_url": "https://github.com/kassonlab/micrograph-spot-analysis" + } + ], + "title": "Single-Virus Fusion Measurements Reveal Multiple Mechanistically Equivalent Pathways for SARS-CoV-2 Entry", + "issue": "5", + "volume": "97", + "publisher": "American Society for Microbiology", + "published": "2023-05-31", + "author": [ + "Sengar A.", + "Cervantes M.", + "Bondalapati S. T.", + "Hess T.", + "Kasson P. M." + ] + }, { "doi": "10.1038/s41598-023-33168-1", "available_items": [ From 191379b79e5a76a9e75d9ba6e25cfc9664bb9b8c Mon Sep 17 00:00:00 2001 From: Senthilkumar Panneerselvam Date: Tue, 13 Jun 2023 13:23:43 +0200 Subject: [PATCH 03/10] Change dckube to dc in URL --- content/english/dashboards/npc-statistics.md | 22 +++++++++---------- .../english/dashboards/serology-statistics.md | 6 ++--- .../covid_quantification/covid_quant_SLU.md | 2 +- .../historic_orebro_umea.md | 4 ++-- .../historic_stockholm.md | 2 +- content/english/privacy.md | 2 +- content/svenska/dashboards/npc-statistics.md | 22 +++++++++---------- content/svenska/dashboards/post_covid.md | 10 ++++----- .../svenska/dashboards/serology-statistics.md | 6 ++--- .../covid_quantification/covid_quant_SLU.md | 2 +- .../historic_orebro_umea.md | 4 ++-- .../historic_stockholm.md | 2 +- content/svenska/privacy.md | 2 +- layouts/contact/list.html | 2 +- layouts/events/list.html | 2 +- layouts/highlights/list.html | 2 +- layouts/index.html | 8 +++---- layouts/partials/footer.html | 2 +- layouts/shortcodes/add_biobank_form.html | 2 +- layouts/shortcodes/add_collection_form.html | 2 +- .../shortcodes/funding_suggestion_form.html | 2 +- .../pathogens_add_announcement.html | 2 +- .../pathogens_suggest_available_data.html | 2 +- .../shortcodes/serology_date_modified.html | 2 +- layouts/shortcodes/ww_dynamic_content.html | 2 +- 25 files changed, 58 insertions(+), 58 deletions(-) diff --git a/content/english/dashboards/npc-statistics.md b/content/english/dashboards/npc-statistics.md index 3f99ae14..9854c3a4 100644 --- a/content/english/dashboards/npc-statistics.md +++ b/content/english/dashboards/npc-statistics.md @@ -18,14 +18,14 @@ dashboards_topics: [COVID-19, Infectious diseases] KI Press Release
-The dataset visualised in the graphs on this page is available [here](https://datagraphics.dckube.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418). The numbers reported here were compiled automatically and, as such, might not correspond to +The dataset visualised in the graphs on this page is available [here](https://datagraphics.dc.scilifelab.se/dataset/bbbaf64a25a1452287a8630503f07418). The numbers reported here were compiled automatically and, as such, might not correspond to the numbers reported through other sources for different reasons. #### Total NPC test numbers The total number of SARS-CoV-2 (COVID-19) tests conducted at the national Pandemic Centre (NPC) since the start of the pandemic, separated according to whether the results were positive, negative, or invalid/inconclusive. -Source code for the below graph is available [here](https://datagraphics.dckube.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1). +Source code for the below graph is available [here](https://datagraphics.dc.scilifelab.se/graphic/ba0b27320fe74ad0aef59a26be6c37f1).
Scroll the plot sideways to view all data. @@ -39,7 +39,7 @@ Source code for the below graph is available [here](https://datagraphics.dckube. The number of SARS-CoV-2 (COVID-19) tests ran daily or weekly, divided according to whether results were positive, negative, or invalid/inconclusive. -Source code is available for both the [daily](https://datagraphics.dckube.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc) and [weekly](https://datagraphics.dckube.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf) graphs below. +Source code is available for both the [daily](https://datagraphics.dc.scilifelab.se/graphic/ddb1119aefce47d58d0b3a49e98b4fcc) and [weekly](https://datagraphics.dc.scilifelab.se/graphic/1f2322f4301c4773878c956c578e8caf) graphs below.
- +
diff --git a/layouts/shortcodes/pathogens_suggest_available_data.html b/layouts/shortcodes/pathogens_suggest_available_data.html index 324ae690..76fb8fcd 100644 --- a/layouts/shortcodes/pathogens_suggest_available_data.html +++ b/layouts/shortcodes/pathogens_suggest_available_data.html @@ -15,7 +15,7 @@
You are welcome to submit information about your own dataset or a suggestion for a dataset published by someone else that you think may be useful on this page. Information about both openly available and restricted access datasets can be submitted. In the latter case we ask for a clear description of access conditions - who will be granted access, what is the procedure, and what are are expections.
- +
diff --git a/layouts/shortcodes/serology_date_modified.html b/layouts/shortcodes/serology_date_modified.html index 5c5285b9..a5555b44 100644 --- a/layouts/shortcodes/serology_date_modified.html +++ b/layouts/shortcodes/serology_date_modified.html @@ -6,6 +6,6 @@ document.getElementById("last_modified").innerText = String(dataset_info.modified).substring(0,10); } }; -xmlhttp.open("GET", "https://datagraphics.dckube.scilifelab.se/api/dataset/6d6f551abc10413a97a6ab64ebac46bd", true); +xmlhttp.open("GET", "https://datagraphics.dc.scilifelab.se/api/dataset/6d6f551abc10413a97a6ab64ebac46bd", true); xmlhttp.send(); diff --git a/layouts/shortcodes/ww_dynamic_content.html b/layouts/shortcodes/ww_dynamic_content.html index 9a907e40..b258ba85 100644 --- a/layouts/shortcodes/ww_dynamic_content.html +++ b/layouts/shortcodes/ww_dynamic_content.html @@ -1,7 +1,7 @@