From 500ad873ce7665fc827a73ce668a4b60df1c83ea Mon Sep 17 00:00:00 2001 From: LianeHughes <68756672+LianeHughes@users.noreply.github.com> Date: Wed, 22 Nov 2023 13:30:58 +0100 Subject: [PATCH 1/6] Change email for edge and add latest national portals --- content/english/biobanks/_index.md | 2 +- content/english/biobanks/add_biobank.md | 5 +- content/english/biobanks/add_collection.md | 7 ++- content/english/contact/_index.md | 18 +++--- content/english/contribute.md | 14 ++--- content/english/data-management.md | 2 +- content/english/partners.md | 2 + content/english/privacy.md | 2 +- content/english/resources/_index.md | 2 +- content/english/share-data.md | 68 ++++++++++----------- content/english/support.md | 2 +- content/svenska/about/_index.md | 6 +- content/svenska/biobanks/_index.md | 2 +- content/svenska/contact/_index.md | 16 ++--- content/svenska/contribute.md | 15 ++--- content/svenska/partners.md | 2 + content/svenska/privacy.md | 2 +- content/svenska/share-data.md | 70 +++++++++++----------- content/svenska/support.md | 2 +- layouts/partials/footer.html | 2 +- 20 files changed, 124 insertions(+), 117 deletions(-) diff --git a/content/english/biobanks/_index.md b/content/english/biobanks/_index.md index d7e55c2db..be052c6af 100644 --- a/content/english/biobanks/_index.md +++ b/content/english/biobanks/_index.md @@ -20,7 +20,7 @@ As of May 2023, the Sample Collection Database contains information about **36 s ### 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 . +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 . ### Responsible organisations diff --git a/content/english/biobanks/add_biobank.md b/content/english/biobanks/add_biobank.md index 8350968d3..081aa58f4 100644 --- a/content/english/biobanks/add_biobank.md +++ b/content/english/biobanks/add_biobank.md @@ -3,9 +3,10 @@ title: Add a new biobank to the Swedish COVID-19 Sample Collection database toc: false recaptcha: true --- + The form below can be used to add a new biobank to the Swedish COVID-19 Sample Collection database which is part of the Swedish national COVID-19 data portal. All information provided in the form below will be displayed on the page of the biobank in the registry. Please fill in as many fields as possible so that the researchers have a good idea about what they can expect from the biobank. -Note that we distinguish between *biobanks* and *collections within biobanks*. Even if a biobank has a single collection, you should fill out both the form for adding a new biobank and the form for adding a new collection. If you would like to add a collection to a biobank that has already been registered, please fill out [the form for submitting a collection instead](/biobanks/add_collection/). +Note that we distinguish between _biobanks_ and _collections within biobanks_. Even if a biobank has a single collection, you should fill out both the form for adding a new biobank and the form for adding a new collection. If you would like to add a collection to a biobank that has already been registered, please fill out [the form for submitting a collection instead](/biobanks/add_collection/). {{< add_biobank_form >}} @@ -15,4 +16,4 @@ 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 . +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 . diff --git a/content/english/biobanks/add_collection.md b/content/english/biobanks/add_collection.md index 0c1d34a6e..167b3f01a 100644 --- a/content/english/biobanks/add_collection.md +++ b/content/english/biobanks/add_collection.md @@ -3,9 +3,10 @@ title: Add a new collection to the Swedish COVID-19 Sample Collection database toc: false recaptcha: true --- + The form below can be used to add a new collection to the Swedish COVID-19 Sample Collection database which is part of the Swedish national COVID-19 data portal. All information provided in the form below will be displayed on the page of the collection in the registry. Please fill in as many fields as possible so that the researchers have a good idea about what they can expect from the collection. -Note that we distinguish between *biobanks* and *collections within biobanks*. Even if a biobank has a single collection, you should fill out both the form for adding a new biobank and the form for adding a new collection. If you would like to add a new biobank, please fill out [the form for adding a new biobank](/biobanks/add_biobank/). The portal team will add new biobanks as quickly as possible after receiving that form. However, in order to prevent delays, please specify the 'new' biobank name by selecting 'other (please specify)' in the biobank name list and type the biobank name in the box that appears. +Note that we distinguish between _biobanks_ and _collections within biobanks_. Even if a biobank has a single collection, you should fill out both the form for adding a new biobank and the form for adding a new collection. If you would like to add a new biobank, please fill out [the form for adding a new biobank](/biobanks/add_biobank/). The portal team will add new biobanks as quickly as possible after receiving that form. However, in order to prevent delays, please specify the 'new' biobank name by selecting 'other (please specify)' in the biobank name list and type the biobank name in the box that appears. {{< add_collection_form >}} @@ -13,6 +14,6 @@ Note that we distinguish between *biobanks* and *collections within biobanks*. E The personal data you provide in this form, your name, email address and phone number, will be used to maintain the Swedish COVID-19 Sample Collection database where information about biobanks and sample collections relevant for COVID-19 research will be made available. The registry will be a part of the [Swedish COVID-19 Data Portal](https://covid19dataportal.se/). The Data Portal is a service run by the SciLifeLab Data Centre on assignment from Vetenskapsrådet. It serves to address [the government assignment to VR](https://www.regeringen.se/regeringsuppdrag/2020/05/uppdrag-om-svensk-samordning-och-deltagande-i-eu-kommissionens-covid-19-dataplattform/) to participate in the European open data platform for COVID-19 research. -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 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 . +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 . diff --git a/content/english/contact/_index.md b/content/english/contact/_index.md index e4cfceae7..107be3ef0 100644 --- a/content/english/contact/_index.md +++ b/content/english/contact/_index.md @@ -1,16 +1,16 @@ --- title: Contact and suggestions form menu: - navbar_top: - name: Contact - weight: 20 - identifier: contact - footer_about: - name: Support & Feedback - weight: 30 + navbar_top: + name: Contact + weight: 20 + identifier: contact + footer_about: + name: Support & Feedback + weight: 30 aliases: - - /suggestions/ + - /suggestions/ recaptcha: true --- -We welcome questions and suggestions regarding the *Swedish Pathogens Portal* and we can help with your data management or data sharing question (or at least point you to where your question can be answered). You can fill out the form below and the [the team behind the Portal](/about/) will be happy to help you find a good solution. Alternatively, you can send us an email: [datacentre@scilifelab.se](mailto:datacentre@scilifelab.se). +We welcome questions and suggestions regarding the _Swedish Pathogens Portal_ and we can help with your data management or data sharing question (or at least point you to where your question can be answered). You can fill out the form below and the [the team behind the Portal](/about/) will be happy to help you find a good solution. Alternatively, you can send us an email: [pathogens@scilifelab.se](mailto:pathogens@scilifelab.se). diff --git a/content/english/contribute.md b/content/english/contribute.md index ebdef5d07..0488919fa 100644 --- a/content/english/contribute.md +++ b/content/english/contribute.md @@ -1,13 +1,13 @@ --- title: Contribute menu: - top_actions: - name: Contribute - weight: 40 - pre: + top_actions: + name: Contribute + weight: 40 + pre: --- -The *Swedish Pathogens Portal* was built to serve the community of researchers working on relevant topics and we welcome any contributions from the community or suggestions on how the Portal can help the community. Whenever there is anything that you would like to share with your colleagues, do not hesistate to share it through the Portal. We welcome suggestions for new information or edits in all sections as well as ideas for new sections that could be launched. +The _Swedish Pathogens Portal_ was built to serve the community of researchers working on relevant topics and we welcome any contributions from the community or suggestions on how the Portal can help the community. Whenever there is anything that you would like to share with your colleagues, do not hesistate to share it through the Portal. We welcome suggestions for new information or edits in all sections as well as ideas for new sections that could be launched. For example, you can suggest a dataset that should be covered in the data highlights section or even write one, you can suggest an available dataset that would be useful to others in the community, add information about your own or your colleague's ongoing research project, share data from your project in a new [dashboard](/dashboards/), and so on. @@ -17,8 +17,8 @@ There are multiple ways to add/edit information on the Portal. Choose any method

Send us an e-mail

-

The easiest way to send a quick suggestion or start a conversation with the Portal team is to simply send us an email. Email us at datacentre@scilifelab.se where your ticket will be assigned to one of the members of the Portal team.

-

Contribute through e-mail

+

The easiest way to send a quick suggestion or start a conversation with the Portal team is to simply send us an email. Email us at pathogens@scilifelab.se where your ticket will be assigned to one of the members of the Portal team.

+

Contribute through e-mail

Send a GitHub pull request

diff --git a/content/english/data-management.md b/content/english/data-management.md index fcd69169f..5bc40742c 100644 --- a/content/english/data-management.md +++ b/content/english/data-management.md @@ -79,7 +79,7 @@ The Swedish National Data Service has put together guidelines on research data m ## Hands-on data management 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 Pathogens Portal_ team. Simply send an email to [data-management@scilifelab.se](mailto:data-management@scilifelab.se) or [datacentre@scilifelab.se](mailto: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 Pathogens Portal_ team. Simply send an email to [data-management@scilifelab.se](mailto:data-management@scilifelab.se) or [pathogens@scilifelab.se](mailto:pathogens@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. diff --git a/content/english/partners.md b/content/english/partners.md index 794c23470..2135f69f9 100644 --- a/content/english/partners.md +++ b/content/english/partners.md @@ -15,6 +15,8 @@ Besides [Sweden](https://www.pathogens.se), a number of other countries also lau - [COVID-19 Data Portal Greece](https://www.covid19dataportal.gr) - [COVID-19 Data Portal Italy](https://www.covid19dataportal.it) - [COVID-19 Data Portal Japan](https://covid19dataportal.jp) +- [COVID-19 Data Portal Luxembourg](https://covid19dataportal.lu) +- [COVID-19 Data Portal Netherlands](https://www.covid19dataportal.nl) - [COVID-19 Data Portal Poland](https://covid19dataportal.pl) - [COVID-19 Data Portal Slovenia](https://covid19dataportal.si) - [COVID-19 Data Portal Spain](https://www.covid19dataportal.es) diff --git a/content/english/privacy.md b/content/english/privacy.md index 9a68d68bf..7eb4f1418 100644 --- a/content/english/privacy.md +++ b/content/english/privacy.md @@ -26,7 +26,7 @@ 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 . +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 . ## Links to Other Sites diff --git a/content/english/resources/_index.md b/content/english/resources/_index.md index d7d2ec992..ec50727fb 100644 --- a/content/english/resources/_index.md +++ b/content/english/resources/_index.md @@ -11,7 +11,7 @@ This section of the Portal is dedicted to resources related to pandemic prepared The resources pages themselves are not static. They will be updated as soon as possible after more information becomes available on the resource(s).
- We welcome suggestions about relevant resources that could be included in this section. Those involved in the resources listed below are also invited to inform us of any updates. Please email us at datacentre@scilifelab.se or use our contact form to get in touch. + We welcome suggestions about relevant resources that could be included in this section. Those involved in the resources listed below are also invited to inform us of any updates. Please email us at pathogens@scilifelab.se or use our contact form to get in touch.
Section last updated: 2022.08.17 diff --git a/content/english/share-data.md b/content/english/share-data.md index 08f039180..e6d274b7d 100644 --- a/content/english/share-data.md +++ b/content/english/share-data.md @@ -2,9 +2,9 @@ title: Share data toc: true menu: - top_actions: - weight: 40 - pre: + top_actions: + weight: 40 + pre: aliases: - /data_types/genomics_transcriptomics/guidelines/ - /data_types/compound_and_target_data/guidelines/ @@ -29,15 +29,15 @@ For human data which needs to be stored in a safe environment with controlled ac Below are our data submission guidelines for each specific data type. You can also find similar recommendations per data type on [The European COVID-19 Data Portal data submission information](https://www.covid19dataportal.org/submit-data). -* ##### Genomics & transcriptomics data +- ##### Genomics & transcriptomics data - We suggest that raw virus sequence data as well as assembled and annotated genomes are submitted to [ENA](https://www.ebi.ac.uk/ena). In order to provide further support to users, the Swedish Pathogens Portal team has also produced a [detailed tutorial on submission to ENA](/support_services/tutorial_ena/tutorial_ena_intro). ENA also provide their own documentation to help with submission at [SARS-CoV-2 submission](https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html). + We suggest that raw virus sequence data as well as assembled and annotated genomes are submitted to [ENA](https://www.ebi.ac.uk/ena). In order to provide further support to users, the Swedish Pathogens Portal team has also produced a [detailed tutorial on submission to ENA](/support_services/tutorial_ena/tutorial_ena_intro). ENA also provide their own documentation to help with submission at [SARS-CoV-2 submission](https://ena-browser-docs.readthedocs.io/en/latest/help_and_guides/sars-cov-2-submissions.html). - Before submission of raw sequence data (e.g. shotgun sequencing) it is necessary to remove contaminating human reads. Host (human) sequence data requires restricted access, and NBIS is building a local federated version of the European Genome-phenome Archive (EGA) in Sweden (EGA-SE), allowing for the publication of sensitive personal data within a legal framework. Until local EGA is available, the dataset should remain in the secure analysis environment (e.g., at Bianca on [UPPMAX](https://www.uppmax.uu.se/)). SciLifeLab [can help with publishing and access control](https://www.scilifelab.se/data/humandata/). In any case, we recommend to make a metadata-only record in the [SciLifeLab Data Repository](/support_services/general_data_repository/) with contact details on how to get access, and for which a DOI (i.e., a persistent identifier) can be issued. The DOI can then be used in the article to refer to the dataset. Once the Swedish EGA is operational, and the dataset is deposited there, the access information can be changed to point to the EGA ID. See [DOI: 10.17044/scilifelab.12292778](https://doi.org/10.17044/scilifelab.12292778.v1) for an example. + Before submission of raw sequence data (e.g. shotgun sequencing) it is necessary to remove contaminating human reads. Host (human) sequence data requires restricted access, and NBIS is building a local federated version of the European Genome-phenome Archive (EGA) in Sweden (EGA-SE), allowing for the publication of sensitive personal data within a legal framework. Until local EGA is available, the dataset should remain in the secure analysis environment (e.g., at Bianca on [UPPMAX](https://www.uppmax.uu.se/)). SciLifeLab [can help with publishing and access control](https://www.scilifelab.se/data/humandata/). In any case, we recommend to make a metadata-only record in the [SciLifeLab Data Repository](/support_services/general_data_repository/) with contact details on how to get access, and for which a DOI (i.e., a persistent identifier) can be issued. The DOI can then be used in the article to refer to the dataset. Once the Swedish EGA is operational, and the dataset is deposited there, the access information can be changed to point to the EGA ID. See [DOI: 10.17044/scilifelab.12292778](https://doi.org/10.17044/scilifelab.12292778.v1) for an example. - * [The European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena) - * [ENA SARS-CoV-2 submission tutorial](https://covid19dataportal.se/support_services/tutorial_ena/tutorial_ena_intro/) - * [SciLifeLab Data Repository for metadata records of sequence data with restricted access](https://scilifelab.se/data/repository) + - [The European Nucleotide Archive (ENA)](https://www.ebi.ac.uk/ena) + - [ENA SARS-CoV-2 submission tutorial](https://covid19dataportal.se/support_services/tutorial_ena/tutorial_ena_intro/) + - [SciLifeLab Data Repository for metadata records of sequence data with restricted access](https://scilifelab.se/data/repository)
- *** + *** -* ##### Protein data +- ##### Protein data - For a curated list of relevant proteomics repositories see [FAIRsharing](https://fairsharing.org/) using the query ’[proteomics](https://fairsharing.org/search/?q=proteomics&content=biodbcore&name=&taxonomies=&organisations=&shortname=&description=&supportlinks=&licenses=&countries=&maintainers=&expanded_onto_domains=&expanded_onto_disciplines=&user_defined_tags=&record_id=&miriam_id=&search_state=hidden)’. + For a curated list of relevant proteomics repositories see [FAIRsharing](https://fairsharing.org/) using the query ’[proteomics](https://fairsharing.org/search/?q=proteomics&content=biodbcore&name=&taxonomies=&organisations=&shortname=&description=&supportlinks=&licenses=&countries=&maintainers=&expanded_onto_domains=&expanded_onto_disciplines=&user_defined_tags=&record_id=&miriam_id=&search_state=hidden)’. - We recommend to use the [PRIDE](https://www.ebi.ac.uk/pride/) repository provided by the [ProteomeXchange](http://www.proteomexchange.org/) Consortium. The repository admits protein and peptide identification/quantification data with the accompanying mass spectra evidence and any other related data types. Submission is done using the [PX Submission Tool](https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool). + We recommend to use the [PRIDE](https://www.ebi.ac.uk/pride/) repository provided by the [ProteomeXchange](http://www.proteomexchange.org/) Consortium. The repository admits protein and peptide identification/quantification data with the accompanying mass spectra evidence and any other related data types. Submission is done using the [PX Submission Tool](https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool). - Other types of proteomics data should also be made available, we recommend [SciLifeLab Data Repository](/support_services/general_data_repository/). In order to make the data useful and ready for analyses and integration, a detailed description of the data format and how the variables are organized should be provided. Each protein variable should come with a unique identifier such as UniProt ID or ENGS ID (and stating the versions used to link the data). + Other types of proteomics data should also be made available, we recommend [SciLifeLab Data Repository](/support_services/general_data_repository/). In order to make the data useful and ready for analyses and integration, a detailed description of the data format and how the variables are organized should be provided. Each protein variable should come with a unique identifier such as UniProt ID or ENGS ID (and stating the versions used to link the data). - Metadata: For proteomics, use the minimal information model specified in [MIAPE](https://doi.org/10.25504/FAIRsharing.8vv5fc), and fill them using the controlled vocabularies specified by the Proteomics Standards Initiative: [PSI CVs](https://doi.org/10.25504/FAIRsharing.sxh2dp). + Metadata: For proteomics, use the minimal information model specified in [MIAPE](https://doi.org/10.25504/FAIRsharing.8vv5fc), and fill them using the controlled vocabularies specified by the Proteomics Standards Initiative: [PSI CVs](https://doi.org/10.25504/FAIRsharing.sxh2dp). - * [PRIDE repository](https://www.ebi.ac.uk/pride/) and [PX Submission Tool](https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool) - * [SciLifeLab Data Repository for other types of proteomics data](https://scilifelab.se/data/repository) + - [PRIDE repository](https://www.ebi.ac.uk/pride/) and [PX Submission Tool](https://www.ebi.ac.uk/pride/markdownpage/pridesubmissiontool) + - [SciLifeLab Data Repository for other types of proteomics data](https://scilifelab.se/data/repository) - *** + *** -* ##### Imaging data +- ##### Imaging data - Depending on the type of image data you have, different public repositories are available, please see the table at [BioImage Archive](https://www.ebi.ac.uk/bioimage-archive/). + Depending on the type of image data you have, different public repositories are available, please see the table at [BioImage Archive](https://www.ebi.ac.uk/bioimage-archive/). - * [BioImage Archive](https://www.ebi.ac.uk/bioimage-archive/) + - [BioImage Archive](https://www.ebi.ac.uk/bioimage-archive/) - *** + *** -* ##### Biochemistry +- ##### Biochemistry - We suggest that users submit data to [ChEMBL](https://www.ebi.ac.uk/chembl/) which is a manually curated database of bioactive molecules with drug-like properties run by EMBL-EBI. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. + We suggest that users submit data to [ChEMBL](https://www.ebi.ac.uk/chembl/) which is a manually curated database of bioactive molecules with drug-like properties run by EMBL-EBI. It brings together chemical, bioactivity and genomic data to aid the translation of genomic information into effective new drugs. - * [ChEMBL](https://www.ebi.ac.uk/chembl/) + - [ChEMBL](https://www.ebi.ac.uk/chembl/) - *** + *** -* ##### Health data +- ##### Health data - In cases where data cannot be deposited into a public repository due to privacy restrictions we suggest creating a metadata-only record on the [SciLifeLab Data Repository](https://scilifelab.se/data/repository) ((submissions accepted from all life science researchers in Sweden)) with information about what data is available upon request and how such a request can be made. The repository is managed locally by the SciLifeLab Data Centre, and it allows to obtain a DOI which can then be referred to in the publication. + In cases where data cannot be deposited into a public repository due to privacy restrictions we suggest creating a metadata-only record on the [SciLifeLab Data Repository](https://scilifelab.se/data/repository) ((submissions accepted from all life science researchers in Sweden)) with information about what data is available upon request and how such a request can be made. The repository is managed locally by the SciLifeLab Data Centre, and it allows to obtain a DOI which can then be referred to in the publication. - * [SciLifeLab Data Repository](https://scilifelab.se/data/repository) + - [SciLifeLab Data Repository](https://scilifelab.se/data/repository) - *** + *** -* ##### General data repositories +- ##### General data repositories - Most life science data types can be published as raw or processed data in repositories at the [EMBL-EBI](https://www.ebi.ac.uk). When no archive is suitable, use a general purpose repository such as the [SciLifeLab Data Repository](https://scilifelab.se/data/repository) (submissions accepted from all life science researchers in Sweden), [Figshare](https://figshare.com) or [Zenodo](https://zenodo.org). Besides scientific data, here you can publish documents, presentations, figures, protocols, or other information that you want to make public at any stage in the research process. A publication here is permanent, and provides a Digital Object Identifier, DOI. + Most life science data types can be published as raw or processed data in repositories at the [EMBL-EBI](https://www.ebi.ac.uk). When no archive is suitable, use a general purpose repository such as the [SciLifeLab Data Repository](https://scilifelab.se/data/repository) (submissions accepted from all life science researchers in Sweden), [Figshare](https://figshare.com) or [Zenodo](https://zenodo.org). Besides scientific data, here you can publish documents, presentations, figures, protocols, or other information that you want to make public at any stage in the research process. A publication here is permanent, and provides a Digital Object Identifier, DOI. - *** + *** ## 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 Pathogens Portal* team. Simply send an email to . 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 Pathogens Portal_ team. Simply send an email to . 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. diff --git a/content/english/support.md b/content/english/support.md index 228f087f3..82649129e 100644 --- a/content/english/support.md +++ b/content/english/support.md @@ -14,7 +14,7 @@ Below is an overview of relevant support services (free or against a fee) provid

Support on using the Portal

-If you have questions or suggestions for the _Swedish Pathogens Portal_, you can get in touch with the Portal team either by filling out [our contact form](/contact/) or by sending an email to . +If you have questions or suggestions for the _Swedish Pathogens Portal_, you can get in touch with the Portal team either by filling out [our contact form](/contact/) or by sending an email to . Get in touch with the Portal team diff --git a/content/svenska/about/_index.md b/content/svenska/about/_index.md index 1433a8c85..c39fef0a0 100644 --- a/content/svenska/about/_index.md +++ b/content/svenska/about/_index.md @@ -8,7 +8,7 @@ menu: name: Om dataportalen weight: 10 navbar_about: - name: "Översikt

" + name: "Översikt

" weight: 10 layout: about_navbar --- @@ -21,7 +21,7 @@ Portalen drivs av [SciLifeLab Data Centre](https://scilifelab.se/data/) och sama Den här webbplatsen är byggd med hjälp av [Hugo](https://gohugo.io/) och använder [Bootstrap](https://getbootstrap.com/) ramverket, [DataTables](https://datatables.net/) används för att skapa tabeller, [Vega/Vega-Lite](https://vega.github.io/vega-lite/) och [Plotly](https://plotly.com/) för interaktiv grafik. Koden är öppen källkod ([MIT-licens](https://choosealicense.com/licenses/mit/)) och [finns tillgänglig på GitHub](https://github.com/ScilifelabDataCentre/covid-portal). Vi välkomnar att Portalens källkod återanvänds och att forskare bidrar till webbsidans källkod. -Om du vill bidra med innehåll eller har förslag på förbättringar av webbplatsen, vänligen kontakt oss på +Om du vill bidra med innehåll eller har förslag på förbättringar av webbplatsen, vänligen kontakt oss på #### Portalens historia @@ -33,7 +33,7 @@ Från 2022 har Portalen utvidgats till att även inkluderar forskningsämnen med Från starten har Portalen drivits av SciLifeLab Data Centre och samarbetspartners, med stöd och input av forskarsamhället. Många personer har varit involverade i uppbyggnad, drift och utvecklingsarbete av webbsidans källkod och Portalens innehåll. En ofullständig lista över dessa personer som bidragit finns tillgänglig på GitHub. Det nuvarande dedikerade teamet som aktivt arbetar med Portalen visas nedan. -Vi hjälper er gärna med support, tar emot förslag på förbättringar av nuvarande sektioner eller förslag på nya sektioner samt svarar på frågor relaterade till datahantering, datadelning och Portalens innehåll. Maila oss på . +Vi hjälper er gärna med support, tar emot förslag på förbättringar av nuvarande sektioner eller förslag på nya sektioner samt svarar på frågor relaterade till datahantering, datadelning och Portalens innehåll. Maila oss på .
diff --git a/content/svenska/biobanks/_index.md b/content/svenska/biobanks/_index.md index d30b1fb7e..eca241ab2 100644 --- a/content/svenska/biobanks/_index.md +++ b/content/svenska/biobanks/_index.md @@ -22,7 +22,7 @@ I Maj 2023 innehåller det svenska Covid-19 Provsamlingsregistret **36 provs ### Registrera en provsamling i Covid-19 Provsamlingsregistret -För att registrera en provsamling i Covid-19 Provsamlingsregistret [kontaktas Biobank Sverige](https://biobanksverige.se/provsamlingar-publicerade-i-covid-19-data-portal-sweden-underlattar-forskning-om-covid-19/) (på denna sida finner du länkar för att registrera olika typer av provsamlingar). För frågor, kommentarer, eller förslag om provsamlingsregistret kontakta . +För att registrera en provsamling i Covid-19 Provsamlingsregistret [kontaktas Biobank Sverige](https://biobanksverige.se/provsamlingar-publicerade-i-covid-19-data-portal-sweden-underlattar-forskning-om-covid-19/) (på denna sida finner du länkar för att registrera olika typer av provsamlingar). För frågor, kommentarer, eller förslag om provsamlingsregistret kontakta . ### Ansvariga organisationer diff --git a/content/svenska/contact/_index.md b/content/svenska/contact/_index.md index 335eb6f85..3e58ac22f 100644 --- a/content/svenska/contact/_index.md +++ b/content/svenska/contact/_index.md @@ -1,14 +1,14 @@ --- title: Kontakta oss menu: - navbar_top: - name: Kontakt - weight: 20 - identifier: contact - footer_about: - name: Support och Feedback - weight: 30 + navbar_top: + name: Kontakt + weight: 20 + identifier: contact + footer_about: + name: Support och Feedback + weight: 30 recaptcha: true --- -Om du har förslag på Portalens innehåll eller har ett dataset du vill dela i ett öppet datarepositorie men behöver support eller har frågor rörande datahantering relaterat till ett covid-19 eller pandemisk beredskap forskningsprojekt hjälper [teamet som arbetar med dataportalen](/sv/about/) dig gärna. Fyll i formuläret nedan eller maila oss på [datacentre@scilifelab.se](mailto:datacentre@scilifelab.se). +Om du har förslag på Portalens innehåll eller har ett dataset du vill dela i ett öppet datarepositorie men behöver support eller har frågor rörande datahantering relaterat till ett covid-19 eller pandemisk beredskap forskningsprojekt hjälper [teamet som arbetar med dataportalen](/sv/about/) dig gärna. Fyll i formuläret nedan eller maila oss på [pathogens@scilifelab.se](mailto:pathogens@scilifelab.se). diff --git a/content/svenska/contribute.md b/content/svenska/contribute.md index 5aaa5e71e..365743534 100644 --- a/content/svenska/contribute.md +++ b/content/svenska/contribute.md @@ -2,12 +2,13 @@ title: Bidra till Portalen toc: false menu: - top_actions: - name: Bidra till Portalen - weight: 40 - pre: + top_actions: + name: Bidra till Portalen + weight: 40 + pre: --- -Den *Patogens Portal Sverige* har som syfte att stödja forskare som arbetar inom de forskningsområden som Portalen specifikt är inriktade på. Vi välkomnar både förslag på och bidrag till Portalens innehåll och förslag på hur Portalen kan utvecklas för att bättre stödja forskningen. Som forskare uppmanar vi dig att interagera med Portalen, exempelvis genom att dela data eller information genom Portalen. Vi tar även gärna emot förslag på nytt innehåll, nya sektioner samt förslag på hur nuvarande sektioner kan utvecklas och förnyas. + +Den _Patogens Portal Sverige_ har som syfte att stödja forskare som arbetar inom de forskningsområden som Portalen specifikt är inriktade på. Vi välkomnar både förslag på och bidrag till Portalens innehåll och förslag på hur Portalen kan utvecklas för att bättre stödja forskningen. Som forskare uppmanar vi dig att interagera med Portalen, exempelvis genom att dela data eller information genom Portalen. Vi tar även gärna emot förslag på nytt innehåll, nya sektioner samt förslag på hur nuvarande sektioner kan utvecklas och förnyas. Förslag på som du exempelvis kan inkomma med. Tipsa oss om du har förslag på nya publikationer som delar dataset eller källkod öppet och som kunde passa som en ”Data Highlight”. Vi tar även emot färdigskrivna förslag på texter. Ge förslag på nya dataset som vi kan lyfta fram i ”Tillgängliga data”-sektionen. Uppdatera information om pågående projekt, ditt eget eller andras. Dela dina data öppet i nya [dashboards på Portalen](/sv/dashboards/) osv. @@ -17,8 +18,8 @@ Det finns flera sätt att ge förslag på eller redigera informationen som ligge

Skicka ett bidrag genom epost

-

Det enklaste sättet att skicka oss ett förslag eller få kontakt med oss i Portalenteamet är helt enkelt att skicka oss epost. Skicka epost till datacentre@scilifelab.se så kommer ditt ärende får ett ärendenummer och tilldelas en a oss i Portalenteamet.

-

Bidra med epost

+

Det enklaste sättet att skicka oss ett förslag eller få kontakt med oss i Portalenteamet är helt enkelt att skicka oss epost. Skicka epost till pathogens@scilifelab.se så kommer ditt ärende får ett ärendenummer och tilldelas en a oss i Portalenteamet.

+

Bidra med epost