Merge pull request #105 from ScilifelabDataCentre/dev

Preparing new release

LICENSE.md

@@ -0,0 +1,59 @@
+## Website content
+
+Unless specified otherwise, the content (text and images) of this website is
+licensed [Creative Commons Attribution 4.0 International
+License](https://creativecommons.org/licenses/by/4.0/). This is a human-readable
+summary of (and not a substitute for) [the
+license](https://creativecommons.org/licenses/by/4.0/legalcode).
+
+### You are free to:
+
+- **Share** — copy and redistribute the material in any medium or format
+- **Adapt** — remix, transform, and build upon the material for any purpose,
+  even commercially.
+
+The licensor cannot revoke these freedoms as long as you follow the license terms.
+
+### Under the following terms:
+
+- **Attribution** — You must give appropriate credit, provide a link to the
+  license, and indicate if changes were made. You may do so in any reasonable
+  manner, but not in any way that suggests the licensor endorses you or your
+  use.
+- **No additional restrictions** — You may not apply legal terms or
+  technological measures that legally restrict others from doing anything the
+  license permits.
+
+### Notices:
+
+You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation.
+
+No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material.
+
+## Software
+
+Except where otherwise noted, any software in this repository are made available under the [OSI](https://opensource.org/)-approved [MIT license](https://opensource.org/licenses/mit-license.html).
+
+### For the rest of the code
+
+Copyright (c) 2025 SciLifeLab Data Centre
+
+### The MIT License (MIT)
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

@@ -138,3 +138,8 @@ If in doubt, you can ask for help by emailing [datacentre@scilifelab.se](mailto:
 
 The portal was built by the DDLS Precision Medicine Data Science Node with colleagues at SciLifeLab.
 
+# License
+
+This project is licensed under the terms of the MIT license.
+
+Copyright © 2025 SciLifeLab Data Centre

next-app/src/app/accessclinicaldata/page.tsx

@@ -34,46 +34,63 @@ export default function AboutPage(): ReactElement {
         </ul>
       </div>
       <div className="flex flex-col gap-y-4">
-        <Title level={1}>How to access clinical data</Title>
+        <Title level={1}>Access data for precision medicine research</Title>
         <p>
-          Human data for research can be accessed from several sources such as:
-          medical records, quality registries, research databases, etc. If
-          sensitive personal data (
+          Researchers can access human data for research from various national
+          and international sources, such as research databases, quality
+          registries, patient or medical records, biobanks, and more. However,
+          human data is often not freely available. Researchers seeking access
+          to human data must submit an application outlining their project and
+          its requirements. The responsible institution, typically a healthcare
+          region or university, will release the data only after conducting harm
+          and confidentiality assessments.
+        </p>
+        <div className="flex flex-row items-center">
+          <Title level={2}>Swedish research projects or databases</Title>
+          <Link href="/swedishresearchprojects">
+            <svg
+              className="ml-2 fill-primary w-7 h-7"
+              xmlns="http://www.w3.org/2000/svg"
+              viewBox="0 0 32 32"
+            >
+              <g data-name="19-Arrow Right">
+                <path d="M16 0a16 16 0 1 0 16 16A16 16 0 0 0 16 0zm0 30a14 14 0 1 1 14-14 14 14 0 0 1-14 14z" />
+                <path d="m26.71 15.29-7-7-1.42 1.42 5.3 5.29H5v2h18.59l-5.29 5.29 1.41 1.41 7-7a1 1 0 0 0 0-1.41z" />
+              </g>
+            </svg>
+          </Link>
+        </div>{" "}
+        <p>
+          It is possible to request existing data from several research projects
+          or research databases in Sweden. Projects can be found, for example,
+          on the website of the project’s entity responsible for the research,
+          the{" "}
           <a
-            href="https://www.imy.se/en/individuals/data-protection/introduktion-till-gdpr/what-is-actually-meant-by-personal-data/what-is-meant-by-sensitive-personal-data/"
+            href="https://snd.se/en/catalogue/search"
             target="_blank"
             className="text-primary hover:text-black underline"
           >
-            definition
+            Swedish National Data Service (SND)
           </a>
-          ) will be used, the research project must be approved by the{" "}
+          , or the{" "}
           <a
-            href="https://etikprovningsmyndigheten.se/en/"
+            href="https://precision-medicine-portal.scilifelab.se/swedishresearchprojects"
             target="_blank"
             className="text-primary hover:text-black underline"
           >
-            Swedish Ethical Review Authority
+            Precision Medicine Portal
           </a>
-          . This applies even if all the sensitive personal data being processed
-          is pseudonymised. Moreover, necessary legal measures must be in place
-          before the data can be transferred from the agency or organisation
-          that provides the source data. Exactly how the procedures for
-          requesting data for research and how the data is disclosed differ
-          between various authorities or organisations.
+          .
         </p>
-        <Title level={2}>Patient records and medical records</Title>
         <p>
-          Healthcare staff document patient interactions, and after a
-          confidentiality assessment, this information can be requested for
-          medical research. In Sweden, the 21 regions are responsible for most
-          healthcare services, while municipalities handle services like home
-          care, and private practitioners manage their own records.
-          Consequently, to conduct research using patient records from across
-          the country, it may be necessary to request data from multiple
-          sources.
+          In the research data catalogue at SND, it is possible to search for
+          research projects and data from several disciplines. Some data and
+          metadata can be downloaded directly from the catalogue. SND also
+          provides information about data management and a service for data
+          sharing.
         </p>
         <div className="flex flex-row items-center">
-          <Title level={2}>Quality registers</Title>
+          <Title level={2}>Quality registries</Title>
           <Link href="/registries">
             <svg
               className="ml-2 fill-primary w-7 h-7"
@@ -180,8 +197,110 @@ export default function AboutPage(): ReactElement {
             </a>
           </li>
         </ul>
+        <p></p>
+        <Title level={2}>Patient and medical records</Title>
+        <p>
+          Healthcare staff document patient interactions, and after a
+          confidentiality assessment, this information can be requested for
+          medical research by lämna in en begäran om utlämnande av patientdata.
+          In Sweden, the 21 regions are responsible for most healthcare
+          services, while municipalities handle services like home care, and
+          private practitioners manage their own records. Consequently, to
+          conduct research using patient records from across the country, it may
+          be necessary to request data from multiple sources.
+        </p>
+        <Title level={2}>Research data management</Title>
+        <p>
+          SciLifeLab provides general research data management (RDM) guidelines,{" "}
+          <a
+            href="https://data-guidelines.scilifelab.se/"
+            target="_blank"
+            className="text-primary hover:text-black underline"
+          >
+            available here
+          </a>
+          , and specific information about the ethical, legal, and societal
+          implications (ELSI) for research involving human data,{" "}
+          <a
+            href="https://data-guidelines.scilifelab.se/topics/research-involving-human-data/"
+            target="_blank"
+            className="text-primary hover:text-black underline"
+          >
+            available here
+          </a>
+          . They also offer guidance on{" "}
+          <a
+            href="https://data-guidelines.scilifelab.se/topics/sharing-human-data/"
+            target="_blank"
+            className="text-primary hover:text-black underline"
+          >
+            sharing sensitive human data
+          </a>
+          .
+        </p>
+        <p>
+          More information and tailored research support can be found at
+          universities, colleges, and healthcare regions or hospitals. A
+          selection of links:
+        </p>
+        <ul className="list-disc pl-4">
+          <li>
+            <a
+              href="https://www.oru.se/english/research/research-support/"
+              target="_blank"
+              className="text-primary hover:text-black underline"
+            >
+              Örebro University
+            </a>
+          </li>
+          <li>
+            <a
+              href="https://www.oru.se/english/research/research-support/"
+              target="_blank"
+              className="text-primary hover:text-black underline"
+            >
+              Karolinska University Hospital
+            </a>
+          </li>
+          <li>
+            <a
+              href="https://www.staff.lu.se/research-and-education/research-support"
+              target="_blank"
+              className="text-primary hover:text-black underline"
+            >
+              Lund University
+            </a>
+          </li>
+          <li>
+            <a
+              href="https://www.umu.se/en/research-support-and-collaboration-office/"
+              target="_blank"
+              className="text-primary hover:text-black underline"
+            >
+              Umeå University
+            </a>
+          </li>
+          <li>
+            <a
+              href="https://www.uu.se/en/staff/gateway/research/research-handbook/uppsala-universitys-research-support/the-medfarm-research-support"
+              target="_blank"
+              className="text-primary hover:text-black underline"
+            >
+              Uppsala University
+            </a>
+          </li>
+          <li>
+            <a
+              href="https://staff.ki.se/research-support"
+              target="_blank"
+              className="text-primary hover:text-black underline"
+            >
+              Karolinska Universitetet
+            </a>
+          </li>
+        </ul>
+        <LastUpdated date="13-01-2025" />
       </div>
-      <LastUpdated date="11-11-2024" />
     </div>
   );
 }

next-app/src/app/datasources/page.tsx

@@ -82,10 +82,13 @@ export default function DataPage(): ReactElement {
   async function getData() {
     try {
       const response = await axios.get(dataSourcesURI);
-      const tmpDataSourcesJSON = response.data.filter(
-        (element: IDataSourcesDC) =>
+      const tmpDataSourcesJSON = response.data
+        .filter((element: IDataSourcesDC) =>
           element.ddls.includes("Precision Medicine and Diagnostics")
-      );
+        )
+        .filter(
+          (element: IDataSourcesDC) => element.name !== "SCAPIS database"
+        ); // Exclude "SCAPIS"
       setDataSourcesJSON(tmpDataSourcesJSON);
     } catch (error) {
       console.error("Error fetching data:", error);
@@ -197,12 +200,10 @@ export default function DataPage(): ReactElement {
       <div className="lg:grid lg:grid-cols-4 lg:gap-8 pt-8">
         <div className="lg:col-span-1 mb-8 lg:mb-0">
           <div className="space-y-8">
-            {/* Disclaimer */}
             <div className="w-full max-w-lg bg-muted border border-neutral rounded-lg p-4 text-sm text-muted-foreground text-left mx-auto">
               To access data, researchers may need to obtain ethical approval,
               submit data requests and set up data management agreements.
             </div>
-            {/* Search */}
             <div className="space-y-4">
               <label
                 htmlFor="search"
@@ -220,7 +221,6 @@ export default function DataPage(): ReactElement {
                 className="bg-muted"
               />
             </div>
-            {/* Data Type Filters */}
             <div className="space-y-4">
               <h2 className="font-bold text-2xl text-foreground">Data Type</h2>
               <Card>
@@ -248,7 +248,6 @@ export default function DataPage(): ReactElement {
                 </CardContent>
               </Card>
             </div>
-            {/* Disease Type Filters */}
             <div className="space-y-4">
               <h2 className="font-bold text-2xl text-foreground">
                 Disease Type
@@ -293,17 +292,17 @@ export default function DataPage(): ReactElement {
             .map((item, index) => (
               <Card key={index}>
                 <CardHeader className="bg-muted">
-                  <CardTitle className="flex flex-col sm:flex-row justify-between items-start sm:items-center gap-4">
+                  <CardTitle className="flex flex-row justify-between items-center gap-4 sm:flex-row">
                     <a
                       href={sanitizeURL(item.url)}
                       target="_blank"
                       rel="noopener noreferrer"
-                      className="text-xl text-primary hover:underline"
+                      className="text-xl text-primary hover:underline flex-grow"
                     >
                       {item.name}
                     </a>
                     <img
-                      className="float-right w-62 h-12 object-scale-down object-right pl-2"
+                      className="w-40 h-10 object-contain object-right"
                       src={`/img/datasources/${sanitizeString(
                         item.thumbnail.split("/").pop()?.split(".")[0] || ""
                       )}.png`}
@@ -318,7 +317,7 @@ export default function DataPage(): ReactElement {
             ))}
         </div>
       </div>
-      <LastUpdated date="11-11-2024" />
+      <LastUpdated date="18-12-2024" />
     </div>
   );
 }