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Markdown lint fix for email address
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senthil10 committed May 4, 2023
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2 changes: 1 addition & 1 deletion content/english/biobanks/_index.md
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Expand Up @@ -20,7 +20,7 @@ As of September 2021, the Sample Collection Database contains information about

### Submit information about sample collections

Those wishing to submit information about their sample collections to the database should [contact Biobank Sverige](https://biobanksverige.se/provsamlingar-publicerade-i-covid-19-data-portal-sweden-underlattar-forskning-om-covid-19/) (the linked page also contains forms for adding new collections to the database). Questions, comments, or suggestions regarding the database itself can be sent to datacentre@scilifelab.se.
Those wishing to submit information about their sample collections to the database should [contact Biobank Sverige](https://biobanksverige.se/provsamlingar-publicerade-i-covid-19-data-portal-sweden-underlattar-forskning-om-covid-19/) (the linked page also contains forms for adding new collections to the database). Questions, comments, or suggestions regarding the database itself can be sent to <datacentre@scilifelab.se>.

### Responsible organisations

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2 changes: 1 addition & 1 deletion content/english/biobanks/add_biobank.md
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Expand Up @@ -15,4 +15,4 @@ The personal data you provide in this form, your name, email address and phone n

The information you provide will be processed for research purposes, i.e. using the lawful basis of public interest and following the Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 (General Data Protection Regulation) on the protection of natural persons about the processing of personal data and on the free movement of such data.

The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using datacentre@scilifelab.se.
The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using <datacentre@scilifelab.se>.
2 changes: 1 addition & 1 deletion content/english/biobanks/add_collection.md
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Expand Up @@ -15,4 +15,4 @@ The personal data you provide in this form, your name, email address and phone n

The information you provide will be processed for research purposes, i.e. using the lawful basis of public interest and following the Regulation (EU) 2016/679 of the European Parliament and of the Council of 27 April 2016 (General Data Protection Regulation) on the protection of natural persons about the processing of personal data and on the free movement of such data.

The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using datacentre@scilifelab.se.
The following parties will have access to processing your personal data: SciLifeLab Data Centre, Uppsala University and Biobank Sverige, Region Uppsala. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using <datacentre@scilifelab.se>.
2 changes: 1 addition & 1 deletion content/english/dashboards/wastewater/covid_quant_GU.md
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## Dataset

**Download the data:** [Quantification of SARS-CoV-2 and enteric viruses in wastewater](https://blobserver.dckube.scilifelab.se/blob/wastewater_data_gu_allviruses.xlsx). Results are available for SARS-CoV-2 from week 7 of 2020 (with a small gap over winter 2022-2023), and for enteric viruses from week 2 of 2023. Updated weekly.\
**Contact:** helene.norder@gu.se
**Contact:** <helene.norder@gu.se>

**How to cite the dataset:** Norder, H., Nyström, K. Patzi Churqui, M., Tunovic, T., Wang, H. (2023). Detection of SARS-CoV-2 and other human enteric viruses in wastewater from Gothenburg. [https://doi.org/10.17044/scilifelab.22510501](https://doi.org/10.17044/scilifelab.22510501).

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2 changes: 1 addition & 1 deletion content/english/dashboards/wastewater/covid_quant_KTH.md
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Expand Up @@ -90,7 +90,7 @@ Please also note that although the same methods are used for all cities shown on
## Dataset

**Download the data:** [N3-gene copy number per PMMoV gene copy number; Excel file](https://blobserver.dckube.scilifelab.se/blob/stockholm_wastewater_method_Sep_2021.xlsx). Results are available (partially) starting from week 16 of 2020 for Stockholm and starting from week 39 of 2021 for Malmö; updated weekly.\
**Contact:** zeynepcg@kth.se
**Contact:** <zeynepcg@kth.se>

**How to cite dataset:**
Cetecioglu, Z. G., Williams, C., Khatami, K., Atasoy, M., Nandy, P., Jafferali, M. H., Birgersson, M. (2021). SARS-CoV-2 Wastewater Data from Stockholm, Sweden. [https://doi.org/10.17044/scilifelab.14315483](https://doi.org/10.17044/scilifelab.14315483).
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2 changes: 1 addition & 1 deletion content/english/dashboards/wastewater/covid_quant_SLU.md
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Expand Up @@ -111,7 +111,7 @@ The group provide reports to summarise their latest findings. The latest report

## Dataset

**Contact:** anna.szekely@slu.se and maja.malmberg@slu.se
**Contact:** <anna.szekely@slu.se> and <maja.malmberg@slu.se>

**Download the data:** [N1-gene copy number per PMMoV gene copy number, CSV file.](https://datagraphics.dckube.scilifelab.se/dataset/0ac8fa02871745048491de74e5689da9.csv). Data are available from week 38 of 2020; updated weekly.

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This page displays data on the amount of SARS-CoV-2 in Umeå and Örebro wastewater between October 2020 and June 2021. After June 2021, a new method is used for analyses of wastewater, and [the most recent data can be found here](../).

The data displayed here were collected as part of a research project led by associate professor Maja Malmberg (SLU, Swedish University of Agricultural Sciences; maja.malmberg@slu.se) in collaboration with the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and associate professor Mette Myrmel at the Norwegian University of Life Sciences. The amount of SARS-CoV-2 virus in the wastewater of Umeå is measured using samples taken from the wastewater treatment facilities in Umeå and Örebro. Please [consult this map for the exact catchment area of the wastewater collection channels in Umeå](/wastewater/map_umeaa.jpg). Please [consult this map for the exact catchment area of the wastewater collection channels in Örebro](/wastewater/map_orebro.pdf).
The data displayed here were collected as part of a research project led by associate professor Maja Malmberg (SLU, Swedish University of Agricultural Sciences; <maja.malmberg@slu.se>) in collaboration with the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and associate professor Mette Myrmel at the Norwegian University of Life Sciences. The amount of SARS-CoV-2 virus in the wastewater of Umeå is measured using samples taken from the wastewater treatment facilities in Umeå and Örebro. Please [consult this map for the exact catchment area of the wastewater collection channels in Umeå](/wastewater/map_umeaa.jpg). Please [consult this map for the exact catchment area of the wastewater collection channels in Örebro](/wastewater/map_orebro.pdf).

After preparation, the viruses were extracted using ultra filtration and analyzed using qPCR technique for SARS CoV-2 RNA. Primers were used to detect the SARS-COV-2 gene (previously used and verified by [Corman and colleagues (2020)](https://doi.org/10.2807/1560-7917.ES.2020.25.3.2000045)). qPCR samples were normalized against PMMV. Until January 2021, three samples per week were taken and their results were pooled to provide a weekly estimate. From February 2021, samples were instead collected weekly.

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This page displays data on the amount of SARS-CoV-2 in Stockholm between April 2020 and August 2021 calculated as Gene copy number/week (raw wastewater) with bovine + PMMoV factor. From September 2021 onwards, the method was changed. Please [see this page for the most recent data](./).

This project, led by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology; zeynepcg@kth.se), is a collaboration between the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and the [SEED](https://www.kth.se/en/seed) and [Chemical Engineering](https://www.kth.se/ket/chemical-engineering-1.784196) departments at KTH, in close collaboration with Stockholm Vatten och Avfall and the Käppala Association. The sampling of wastewater, started in mid-April 2020, from Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from a population of approximately 360,000; 860,000 and 500,000, respectively. Please consult [this map for the exact catchment area of the wastewater collection channels in Käppala](/wastewater/map_Kappala.pdf) and [this map for the exact catchment area of the wastewater collection channels in Bromma and Henriksdal](/wastewater/map_Bromma_Henriksdal.pdf).
This project, led by associate professor Zeynep Cetecioglu Gurol and colleagues (KTH Royal Institute of Technology; <zeynepcg@kth.se>), is a collaboration between the [SciLifeLab COVID-19 National Research Program](https://www.scilifelab.se/covid-19) and the [SEED](https://www.kth.se/en/seed) and [Chemical Engineering](https://www.kth.se/ket/chemical-engineering-1.784196) departments at KTH, in close collaboration with Stockholm Vatten och Avfall and the Käppala Association. The sampling of wastewater, started in mid-April 2020, from Bromma, Henriksdal, and Käppala wastewater treatment plants (WWTP). These treatment plants receive wastewater from a population of approximately 360,000; 860,000 and 500,000, respectively. Please consult [this map for the exact catchment area of the wastewater collection channels in Käppala](/wastewater/map_Kappala.pdf) and [this map for the exact catchment area of the wastewater collection channels in Bromma and Henriksdal](/wastewater/map_Bromma_Henriksdal.pdf).

After concentration, filtering, and preparation, the samples are analyzed using qPCR technique for SARS CoV-2 RNA. Primers of the nucleocapsid (N) gene were used to detect the SARS-COV-2 gene (previously used and verified by [Medema and colleagues (2020)](https://doi.org/10.1016/j.scitotenv.2020.142939)). In some cases, the raw wastewater has been frozen at –20 degrees, and concentrated wastewater or purified RNA have been stored at -80 C before the next analysis step was carried out. The concentration method used by prof. Zeynep Cetecioglu Gurol and her colleagues is based on their published study ([Jafferali and colleagues, 2021](https://doi.org/10.1016/j.scitotenv.2020.142939)) comparing four different concentration methods. The study concluded that the double ultrafiltration method adapted by KTH has a significantly higher efficiency compared to single filtration and adsorption methods. For detailed information about the concentration method, see the publication.

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2 changes: 1 addition & 1 deletion content/english/pathogens/mpox.md
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Expand Up @@ -20,7 +20,7 @@ Information regarding mortality rate is limited, but there is significant variat

In this section, we present announcements about ongoing research efforts primarily by (but not limited to) researchers and institutions based in Sweden. The intention is to 'highlight' these efforts as soon as possible, so that we can maximise their usefulness to researchers.

Please feel free to submit an announcement using the form below or by sending an e-mail to datacentre@scilifelab.se.
Please feel free to submit an announcement using the form below or by sending an e-mail to <datacentre@scilifelab.se>.

Lists of data, tools, publications, and other potentially useful information are provided further down on the page and likely to be more complete.

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8 changes: 4 additions & 4 deletions content/english/pathogens/voc/omicron.md
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On this page we have compiled current knowledge on Omicron, the latest SARS-CoV-2 variant to be designated as a Variant of Concern (VOC). This includes available data, ongoing research efforts, initial findings, among other things related to Omicron. Please see [this page for information on other VOCs](../).

We make all possible efforts to track preprints, publications, and other resources related to Omicron and link them below. Researchers and organisations from around Sweden are also welcome to submit their datasets and to make relevant announcements on this page. If you feel like something is missing that should be included, or you wish to make a submission/announcement, please use the forms below or email us at datacentre@scilifelab.se. The team behind the COVID-19 Data Portal continuously monitors incoming suggestions, and new items are published as soon as possible.
We make all possible efforts to track preprints, publications, and other resources related to Omicron and link them below. Researchers and organisations from around Sweden are also welcome to submit their datasets and to make relevant announcements on this page. If you feel like something is missing that should be included, or you wish to make a submission/announcement, please use the forms below or email us at <datacentre@scilifelab.se>. The team behind the COVID-19 Data Portal continuously monitors incoming suggestions, and new items are published as soon as possible.

## Available data

This section presents a list of the available data related to Omicron (or related work that could benefit research into this variant) shared by researchers affiliated to a Swedish research institute. We welcome the submission of suggestions for additional datasets, either using the form below or by e-mail: datacentre@scilifelab.se. All submissions will be moderated by the Portal team before they appear on the page.
This section presents a list of the available data related to Omicron (or related work that could benefit research into this variant) shared by researchers affiliated to a Swedish research institute. We welcome the submission of suggestions for additional datasets, either using the form below or by e-mail: <datacentre@scilifelab.se>. All submissions will be moderated by the Portal team before they appear on the page.

{{< pathogens_suggest_available_data origin="omicron" >}}

Expand Down Expand Up @@ -59,7 +59,7 @@ Recent data highlights related to *Omicron* variant. All *Omicron* related data

## Ongoing research efforts

In this section, we present announcements about ongoing research efforts from researchers and organisations in Sweden. Please feel free to share what you are currently working on and/or your results, to seek collaborators to aid with aspects of your work (e.g. data, equipment, reagents, etc.). Any announcement useful for advacing research on Omicron is welcome. Feel free to submit the information either by using the form below or by sending us an e-mail to datacentre@scilifelab.se.
In this section, we present announcements about ongoing research efforts from researchers and organisations in Sweden. Please feel free to share what you are currently working on and/or your results, to seek collaborators to aid with aspects of your work (e.g. data, equipment, reagents, etc.). Any announcement useful for advacing research on Omicron is welcome. Feel free to submit the information either by using the form below or by sending us an e-mail to <datacentre@scilifelab.se>.

{{< pathogens_add_announcement origin="omicron" >}}

Expand Down Expand Up @@ -114,6 +114,6 @@ Here we list a number of useful resources related to the new *SARS-CoV-2 Omicron

## Get in touch with us

Do you have suggestions or other feedback? Get in touch with us by e-mailing datacentre@scilifelab.se.
Do you have suggestions or other feedback? Get in touch with us by e-mailing <datacentre@scilifelab.se>.

{{< omicron_page_form_scripts >}}
2 changes: 1 addition & 1 deletion content/english/privacy.md
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Expand Up @@ -22,7 +22,7 @@ You can opt out of your Log Data being collected below:

Our **Service** contains a number of forms through which the website visitors may choose to get in touch with us or send us suggestions. The website visitors may choose to provide their personal information such as, for example, their name and e-mail address, through these forms.

The following parties will have access to processing the personal data provided through the forms: SciLifeLab Data Centre, Uppsala University. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using datacentre@scilifelab.se.
The following parties will have access to processing the personal data provided through the forms: SciLifeLab Data Centre, Uppsala University. Your personal data will be deleted when no longer needed, or when stipulated by the archival rules for the university as a government authority. If you want to update or remove your personal data please contact the controller SciLifeLab Data Centre at Uppsala University using <datacentre@scilifelab.se>.

## Links to Other Sites

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Expand Up @@ -95,6 +95,6 @@ Below are our data submission guidelines for each specific data type. You can al

## Data sharing support

All researchers affiliated with a university or research institute in Sweden working on research topics relevant to pandemic preparedness can receive free individual consultations and hands-on help within reasonable bounds from the *Swedish COVID-19 & Pandemic Preparedness Portal* team. Simply send an email to datacentre@scilifelab.se. Your question will be assigned to a data steward with relevant expertise who can either help you directly or point you to the correct tool or service.
All researchers affiliated with a university or research institute in Sweden working on research topics relevant to pandemic preparedness can receive free individual consultations and hands-on help within reasonable bounds from the *Swedish COVID-19 & Pandemic Preparedness Portal* team. Simply send an email to <datacentre@scilifelab.se>. Your question will be assigned to a data steward with relevant expertise who can either help you directly or point you to the correct tool or service.

You are welcome to send both general questions about best approaches to research data management, data management plans (DMPs), reproducibility, FAIR, and open science as well as specific questions about your research projects such as which repository to choose to deposit data, what the suitable metadata standards would be, which file formats to use, etc. In some cases the data stewards can act as brokers and submit data to repositories on your behalf.
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