Merge branch 'master' into copilot/add-context-menu-to-section

Author: CodyCBakerPhD

docs/example-notebooks

@@ -18,21 +18,6 @@ To start using the archive, head over to the User Guide sections for [Sharing Da
 If are a developer and want to know how the project is organized, check out the [DANDI Ecosystem](./getting-started/dandi-ecosystem.md)
 page in the Getting Started section.
 
-
-## Where to Get Help
-
-You can communicate with the DANDI team in a variety of ways, depending on your needs:
-
-- You can ask questions, report bugs, or 
-request features [at our helpdesk](https://github.com/dandi/helpdesk/issues/new/choose).
-- For interacting with the global neuroscience community, post on https://neurostars.org
-and use the tag [dandi](https://neurostars.org/tag/dandi).
-- You can use the DANDI Slack workspace, which we will invite you to after approving your [registration on 
-  DANDI using GitHub](https://dandiarchive.org/) (this registration is required to upload data or to use the DANDI 
-  JupyterHub). See [here for details on how to
-  register](./getting-started/creating-account.md).
-- Email us: [info@dandiarchive.org](mailto: info@dandiarchive.org)
-
 ## Contributing and Feedback
 
 We are looking for people to give us feedback on this documentation. If anything

docs/img/dandi_api_key_reset.png

@@ -0,0 +1,12 @@
+# Support
+
+**For questions and support, we recommend using [GitHub Discussions](https://github.com/dandi/helpdesk/discussions/new?category=q-a)** 🙏
+
+Additional support channels:
+
+| Channel | Best For |
+|---------|----------|
+| ✨ [GitHub Issues](https://github.com/dandi/helpdesk/issues) | Report bugs and request features |
+| 💬 [Slack](https://dandiarchive.slack.com/) | Interact with the DANDI community (available after [registration](./getting-started/creating-account.md)) |
+| ✉️ [Email](mailto:help@dandiarchive.org) | Communicate privately |
+| 🌟 [NeuroStars with the `dandi` tag](https://neurostars.org/tag/dandi) | Interact with the global neuroscience community |

docs/index.md

@@ -1,4 +1,4 @@
-# General Policies v1.1.0
+# General Policies v1.2.0
 
 ## Content
 
@@ -47,6 +47,16 @@
   share access with other collaborators. These files will not be made publicly
   available till the end of the embargo period.
 
+## Collected Information
+
+We and our service providers collect a variety of information through the sites and by other means, which may include:
+
+- **Information you submit**: When you contact us, we collect information when you send us an email or send information to our servers. This may include your name, email address, the content of your communication, and any data you upload in association with the DANDI project. This does not include the research data, which is subject to any applicable research consent and applicable provisions of the Terms and Conditions.
+- **Information collected automatically**: We or our third-party service providers may automatically receive and record certain information when you use our Sites. For example, this may include your device's IP address, information about your use of the sites during your current session and over time (including the pages you view and your interactions with them, as well as what information you download), the date and time of your visit, links you click, searches conducted, the website visited before navigating to the website, social media referrals used to find the website (such as Facebook and LinkedIn), your software and hardware attributes (including browser and operating system type and version), and your general location inferred from IP address. To obtain such information, we or our third-party service providers may use the following technologies to recognize your device and collect information about your usage of the sites:
+  - _Server logs_: When you use the website, we automatically receive and record certain information from your computer (or other device) and your browser. To obtain such information, we may use server logs or applications that recognize your device and gather information about its online activity.
+
+We may combine information collected through the Sites with information that we collect in other contexts, such as information from email communications with you. We will treat such combined information in accordance with this General Policy.
+
 ## Removal
 
 - **Revocation:** Content not considered to fall under the scope of the repository

docs/support.md

@@ -6,6 +6,7 @@ Most of the data on DANDI is in Neurodata Without Borders (NWB), a data standard
 See [Converting data to NWB](./nwb/index.md) for guidance in how to convert your data to NWB and publish on DANDI.
 
 DANDI also supports the [Brain Imaging Data Structure (BIDS)](https://bids.neuroimaging.io/). For more information, see:
+
 - [Getting Started with BIDS](https://bids.neuroimaging.io/getting_started/index.html)
 - [BIDS converters](https://bids.neuroimaging.io/tools/converters.html) for conversion of raw data to a BIDS dataset
 - [BIDS specification](https://bids-specification.readthedocs.io)

docs/terms-policies/policies.md

@@ -46,6 +46,9 @@ Make sure to inspect the metadata for each institution on the ror.org website, a
 (e.g. many different countries have an "NIH"). Make sure to select the role `dcite:Funder` to list the contributor
 under the "Funding information" section.
 
+If there is more than one award number associated with a funding agency, you should enter the organization multiple times,
+once for each award number.
+
 ### Subject Matter
 
 The Subject Matter section allows you to annotate the Dandiset with links to terms in ontologies. Use `Generic Type`
@@ -66,3 +69,17 @@ It is highly recommended to add links to the following resources (if they exist)
   * A data analysis library associated with the publication that can take this data as input
   * An example notebook submitted to http://github.com/dandi/example-notebooks that demonstrates how to use the data
   * Associated datasets published on DANDI or on other archives.
+
+#### Related Resource Relation
+
+Related Resources include a relation attribute.
+The relation tag describes the relationship FROM the Dandiset TO the resource.
+In other words, this relation should satisfy: dandiset `<relation>` resource.
+
+If the resource is a journal article or preprint, the "repository" should be the name of the journal or preprint server.
+
+Some common relations include:
+
+* For a publication or preprint that is the primary account of the data being deposited, use "dcite:isDescribedBy".
+* For a data descriptor paper, e.g. as is common in the journal Scientific Data, use "dcite:IsDocumentedBy".
+* To associate a new paper that analyzes the data in this Dandiset, use "dcite:IsCitedBy".

docs/user-guide-sharing/converting-data/index.md

@@ -4,7 +4,7 @@ Once you create a Dandiset, DANDI will automatically create a `draft` version
 of the Dandiset that can be changed as many times as needed by editing the 
 metadata or uploading new files.
 
-When the draft version is ready, you can *publish* your Dandiset. This results
+When the draft version is ready, you should *publish* your Dandiset. This results
 in an immutable snapshot of your Dandiset with its own unique version number
 that others can cite. If you need to change the data or metadata, you can do
 so by continuing to modify the draft version and publishing a new version

docs/user-guide-sharing/dandiset-metadata.md

@@ -71,6 +71,13 @@ There are two options for storing your DANDI access credentials:
 
 - Note that there are no spaces around the "=".
 
+- If your `DANDI_API_KEY` needs to be reset (for example, because it was publicly exposed), you can cycle your API key by following the instructions below:
+
+   1. Log in to DANDI Archive
+   2. Click on your user initials in the top-right corner
+   3. Click the circular arrow
+   ![dandi_api_key_reset](../img/dandi_api_key_reset.png)
+
 ### 2. `keyring` Library
 
 If the `DANDI_API_KEY` environment variable is not set, the CLI will look up the API key using the [keyring](https://github.com/jaraco/keyring) library, which supports numerous backends, including the system keyring, an encrypted keyfile, and a plaintext (unencrypted) keyfile.

docs/user-guide-sharing/publishing-dandisets.md

@@ -45,4 +45,8 @@ Passing all of these levels of validation can sometimes be tricky. If you have a
 
 ## Validating BIDS Files
 
-Once your files are converted to the BIDS standard, perform validation of the files using the [BIDS validator](https://bids.neuroimaging.io/tools/validator.html).
+Once your files are converted to the BIDS standard,
+
+  - ensure that you have a [`dataset_description.json`](https://bids-specification.readthedocs.io/en/stable/modality-agnostic-files/dataset-description.html#dataset_descriptionjson) file at the top-level of your dataset directory;
+  - ensure that you have a `.bidsignore` file containing `dandiset.yaml`, since that DANDI-specific file is not part of the BIDS specification;
+  - perform validation of the files using [`dandi validate`](https://dandi.readthedocs.io/en/latest/cmdline/validate.html) to ensure your data is compliant with the BIDS and/or NWB standards. Alternatively, you could independently validate your files using the [BIDS Validator](https://bids.neuroimaging.io/tools/validator.html) and/or [NWB Inspector](https://nwb.org/tools/core/nwbinspector/). Note that [`dandi upload`](https://dandi.readthedocs.io/en/latest/cmdline/upload.html) will also perform validation during upload.