feat: new content cleanup (#2462) (#2463)

* feat: new content cleanup (#2462) * feat: added contribute data platforms image (#2462) --------- Co-authored-by: Fran McDade <franmcdade@Frans-MacBook-Pro.local>
DataBiosphere · Sep 27, 2024 · 252efb5 · 252efb5
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diff --git a/next/docs/contribute.mdx b/next/docs/contribute.mdx
@@ -7,33 +7,35 @@ title: "Contributing Data to the Human Cell Atlas"
 
 ## Overview
 
-The following instructions are for scientists wanting to contribute datasets to the Human Cell Atlas (HCA). For data to be included in atlases, data contributors must provide the following data and metadata. The data and metadata are stored in three platforms to ensure adequate protection is provided to sensitive information (e.g. FASTQ and Tier 2 metadata) and non-personal data is more openly available.
+The following instructions are for scientists wanting to contribute datasets to the Human Cell Atlas (HCA). For data to be included in atlases, data contributors must provide the following data and metadata. The data and metadata are stored in three platforms to ensure adequate protection is provided to sensitive information (e.g. FASTQ and Tier 2 metadata) and non-personal data is more openly available. For the list of metadata fields, click [here](/metadata).
+
+### Data Platforms
+
+<Figure alt="Data Platforms" hasBorder={false} src="/hca-bio-networks/contribute/data-platforms.png" />
 
 The [CellxGene Discover](https://cellxgene.cziscience.com/collections) platform stores matrices (in AnnData format) and Tier 1 metadata which are the core building blocks of atlases. Tier 1 metadata fields are typically ‘technical’ in nature (e.g. whether there was cell enrichment or depletion). For support creating an AnnData file, refer to this [tutorial](https://anndata.readthedocs.io/en/latest/index.html).
 
 The [HCA Data Repository]({browserURL}/projects) stores FASTQ files and the Tier 2 metadata which may contain personal information. To provide sufficient protection to this information, the HCA Data Repository operates a managed access service through the DUOS platform. Access to these datasets and metadata requires the submission of a Data Access Request which is reviewed by HCA’s global Data Access Committee.
 
 The [Cell Annotation Platform](https://celltype.info/) stores matrices and cell annotation metadata in a specially designed portal with features that allow members of the HCA community to jointly annotate data.
 
-For the list of metadata fields, click [here](/metadata).
-
 ## Inclusion Criteria
 
 HCA’s Biological Networks (open networks of scientists responsible for constructing atlases) are responsible for choosing the datasets that end up in HCA atlases. Not all datasets submitted to the HCA Data Portal will ultimately form part of an atlas.
 
 ## Contributing Unpublished Data
 
-**HCA welcomes the contribution of unpublished data to atlases**
+### HCA welcomes the contribution of unpublished data to atlases
 
 HCA welcomes the contribution of unpublished data to atlases and has put in place mechanisms to protect the data prior to the publication of atlases. Importantly, contributors of unpublished data are encouraged to make their data publicly available immediately via the HCA Data Repository, in accordance with the HCA Data Release Policy.
 
 If the data contributors are unable or decline to do so, they must, at minimum, agree to make their data publicly available via the HCA Data Repository (for raw sequence data and detailed Tier 2 metadata) and Chan Zuckerberg CELLxGENE (for gene expression matrices, Tier 1 metadata, and broad demographic metadata) as soon as the Atlas that incorporates it is published in a peer-reviewed scientific journal.
 
-**Embargoing unpublished data**
+### Embargoing unpublished data
 
 If you are contributing unpublished data, you may request that your data be “embargoed” in a private HCA data repository until the organ/tissue/system atlas you have contributed to is published. At that point, your data will be made available publicly via the HCA Data Explorer and linked to the corresponding Atlas page on the HCA Data Portal. Data contributors will be notified before their data is made public. Access to embargoed data will be restricted to HCA Data Wranglers, the corresponding Atlas integration team, and anyone else specified by the data contributor.
 
-**HCA’s Unpublished Data Policy**
+### HCA’s Unpublished Data Policy
 
 For more information, refer to HCA’s [Unpublished Data Policy](https://docs.google.com/document/d/1_afKJSStkN4lmGmKY23NhGWLZulALmgL3JgBcSGRD0c/edit).
 

diff --git a/next/docs/contribute/submitting-cell-annotation-metadata-to-cap.mdx b/next/docs/contribute/submitting-cell-annotation-metadata-to-cap.mdx
@@ -15,13 +15,15 @@ Data contributors will be notified once their datasets have been validated and u
 
 3. Data contributors will need to complete the cell annotation metadata fields for all cell labels using the CAP platform’s user interface. This can be done by an individual or by a group working within the private workspace.
 
-        a. Collaborators can be invited to contribute to the workspace by workspace owners and admins by clicking on Collaborators. 
+        a. Collaborators can be invited to contribute to the workspace by workspace owners and admins by clicking on Collaborators.
 
-4. Once the required fields have been completed, the draft publication will be submitted to review by CAP data curators and then published on the CAP website for others to view. 
+4. Once the required fields have been completed, the draft publication will be submitted to review by CAP data curators and then published on the CAP website for others to view.
 
         a. Should new annotation sets be added or edited, a new version of the annotations can be published.
 
-Note: As a tool that is open and available for use by the broader scientific community, CAP can also ingest datasets that are not being used for atlas assembly. To do this, contributors should visit the [CAP website](https://celltype.info/) and sign up or log in. Detailed instructions on how to submit, annotate, and then publish annotations are available [here](https://celltype.info/docs).  
+<Alert icon={false} severity="info">
+As a tool that is open and available for use by the broader scientific community, CAP can also ingest datasets that are not being used for atlas assembly. To do this, contributors should visit the [CAP website](https://celltype.info/) and sign up or log in. Detailed instructions on how to submit, annotate, and then publish annotations are available [here](https://celltype.info/docs).
+</Alert>
 
 ## Detailed guides on CAP
 
@@ -32,4 +34,4 @@ For more information on ingesting data into CAP and using the platform, please r
 - [Creating draft publications and uploading datasets](https://celltype.info/docs/creating-draft-publications-and-uploading-datasets)
 - [Anndata requirements for upload](https://celltype.info/docs/anndata-requirements-for-upload)
 - [Entering Cell Annotation Metadata](https://celltype.info/docs/entering-cell-annotation-metadata)
-- [Collaborating on the Workspace](https://celltype.info/docs/collaborating-on-the-workspace)
+- [Collaborating on the Workspace](https://celltype.info/docs/collaborating-on-the-workspace)
diff --git a/next/docs/contribute/submitting-hca-data-to-cellxgene-discover.mdx b/next/docs/contribute/submitting-hca-data-to-cellxgene-discover.mdx
@@ -76,7 +76,9 @@ In addition to the HCA obs fields above, there are an additional three fields th
     - index is Ensembl ID
     - preference is that gene have not been filtered in order to maximise future data integration efforts
 
+<Alert icon={false} severity="info">
 Should you require support creating an AnnData file or converting your file from another single cell file format click [here](https://github.com/cellgeni/sceasy) or reach out to [cellxgene@chanzuckerberg.com](mailto:cellxgene@chanzuckerberg.com) and mention that you are contributing to the HCA.
+</Alert>
 
 ## Tier 1 metadata fields
 

diff --git a/next/docs/guides/requesting-access-to-controlled-access-data.mdx b/next/docs/guides/requesting-access-to-controlled-access-data.mdx
@@ -62,15 +62,14 @@ The Datasets section of the Data Portal provides an interactive Data Explorer. P
 
 ![Data Access Request](/hca-bio-networks/guides/data-access-request.png)
 
-**Important Note:**
-
+<Alert icon={false} severity="info">
 - An NIH [eRA Commons](https://www.era.nih.gov/register-accounts/understanding-era-commons-accounts.htm) ID is required to submit a DUOS access request.
    - If you do not currently have an ID, contact your institution’s [signing official](https://www.era.nih.gov/erahelp/Commons/Commons/roles/SO.htm) to request one.
    - Any researcher (both within and outside of the US) can apply for an NIH eRA Commons ID, regardless of whether they belong to a NIH funded institution or not.
 - **Contact DUOS support** if you need help finding your signing official.
    - Before you can submit the data access request (DAR), you’ll need to have a signing official from your institution. If you don’t currently have a signing official on DUOS or do not know who that is, please [contact support](https://broad-duos.zendesk.com/hc/en-us/requests/new) for help.
-   - ![DUOS Navigation](/hca-bio-networks/guides/duos-nav.png)
 - If your onboarding signing official is already in DUOS, you don't need to contact support; proceed directly.
+</Alert>
 
 8. Complete the **Data Access Request** form. This form has four steps:
 

diff --git a/next/public/hca-bio-networks/contribute/data-platforms.png b/next/public/hca-bio-networks/contribute/data-platforms.png
diff --git a/next/public/hca-bio-networks/guides/duos-nav.png b/next/public/hca-bio-networks/guides/duos-nav.png
diff --git a/next/site-config/data-portal/dev/navigation/contribute.ts b/next/site-config/data-portal/dev/navigation/contribute.ts
@@ -16,10 +16,6 @@ export const CONTRIBUTE: NavigationEntry = {
       label: "Contribute",
       layoutStyle: LAYOUT_STYLE_CONTRAST_LIGHTEST,
       navigation: [
-        {
-          label: "Contribute",
-          url: "",
-        },
         {
           label: "Contributing Data to the Human Cell Atlas",
           selectedMatch: SELECTED_MATCH.EQUALS,
@@ -32,20 +28,20 @@ export const CONTRIBUTE: NavigationEntry = {
         },
         {
           label:
-            "Submitting Cell Annotation Metadata to the Cell Annotation Platform (CAP)",
-          url: `${ROUTES.CONTRIBUTE}/submitting-cell-annotation-metadata-to-cap`,
+            "Submitting FASTQs and Tier 2 metadata to the HCA Data Repository",
+          url: `${ROUTES.CONTRIBUTE}/submitting-fastqs-and-tier-2-metadata-to-the-hca-data-repository`,
         },
         {
           label:
-            "Submitting FASTQs and Tier 2 metadata to the HCA Data Repository",
-          url: `${ROUTES.CONTRIBUTE}/submitting-fastqs-and-tier-2-metadata-to-the-hca-data-repository`,
+            "Submitting Cell Annotation Metadata to the Cell Annotation Platform (CAP)",
+          url: `${ROUTES.CONTRIBUTE}/submitting-cell-annotation-metadata-to-cap`,
         },
       ],
       slugs: [
         "contribute",
-        "submitting-hca-data-to-cellxgene-discover",
         "submitting-cell-annotation-metadata-to-cap",
         "submitting-fastqs-and-tier-2-metadata-to-the-hca-data-repository",
+        "submitting-hca-data-to-cellxgene-discover",
       ],
       url: ROUTES.CONTRIBUTE,
       visible: VISIBLE.MD_DOWN,