Submitting Entries for the Functional Assays Handbook

The RBK Consortium has developed the foundation for a collection of functional assays (with a current focus on physiological assays) that are both:

• critical for achieving our consortium mission - for glomerular function, tubular function and absorption, AND
• as transferable as possible for other labs in the consortium.

You can learn more about this resource here: Functional Assays Handbook

The following are instructions for updating this Handbook.

Requirement:

• Make sure you are in the correct Globus authentication group (follow the instructions on this page), and that you are logged in.

Overview

You are actually creating and connecting two types of records:

• the Functional Assay Handbook record, which populates the Handbook search with helpful information about targets and requirements for functional assays to help labs determine which assays are the best fit for their experiments and resources.

• the Protocol record, which is a standalone record with everything needed to reproduce a protocol and with the proper citations/authors and version number.

In the instructions below, we walk you through creating the Functional Assay record for the Handbook. If the protocol has not already been added to the system, we also describe the process for creating a protocol.

(You may also choose to create the Protocol record first and then create the Functional Assay Handbook record.)

We are still developing this documentation. If you have any questions, please reach out to help@rebuildingakidney.org.

Step 1: Create base Functional Assay record

First you must create the base record which is a container for all data related and linked to this functional assay record.

• Go to the Functional Assay Handbook page and log in: https://www.atlas-d2k.org/chaise/recordset/#2/Protocol:Functional_Assay_Handbook

• Click the Create button.

• Fill out the fields. Some notes:

  • Version: Please keep this the default and do not edit it.

  • Curation Status: Keep In Preparation while working on this assay. Then change to Release when it’s ready to be viewed by the public.

• When finished, click the Save button towards the top of the page.

Step 2: Link Kidney Structure

From the base record, look for the Kidney Structure field and click the Link records button. The intent is to focus on the major, higher-level structures instead of sub-segments.

Choose the structure from the anatomy terms. In the future, the Hub will narrow this list to those specifically appropriate for functional assays.

Until then, please refer to this list of term IDs (search using these ID numbers and look for the corresponding ID under the ID column). You may enter more than one. If you need a structure that is not listed, please contact help@rebuildingakidney.org.

Step 3: Link Technology

From the base record, look for the Technology field and click the Link records button.

Choose from the list. You may enter more than one.

If you do not see an existing technology that should be there, click Create New and fill out the short form to add a new technology term to the list.

Step 4: Link Protocol

From the base record, scroll down to the Protocols section and click the Link records button.

Choose from existing protocols or click Create New and create the protocol.

Protocols follow a similar pattern to functional assays where you create the base protocol record and then link further records afterwards. See directions in Step 5 below.

Step 5: Create Protocol (if not created already)

Overview of steps:

1. Note on Version field

2. Create the base Protocol record (Required).

3. Link at least one record each for Subject, Keyword, and Authors (Required)

4. Upload Figures and/or Videos (Optional)

Protocol records are based on the Nature Protocols format. Text fields accept Markdown formatting.

Note on Version field

If a protocol needs updating, create a new one and update the Version field.

Make sure that the Functional Assay Handbook records links to the correct version of a protocol.

Create the base Protocol record (Required)

From Step 4 (above), click Create New, fill out the appropriate fields and click Save.

Note that the following fields are required:

• Title: Please provide a concise but informative title that describes the protocol to unfamiliar users.

• Abstract: Add a short paragraph describing the protocol further

• Procedure: Enter the actual steps to perform the protocol.

• Data Provider: This is your lab’s institution. If you need to add an institution, please contact the Hub.

• Principal Investigator: Choose the contact PI from the list. If not available, contact help@rebuildingakidney.org.

• Curation Status: Use In Preparation while drafting, but when ready, click Submit. Cris from the Hub will review and approve.

We encourage you to include Anticipated Results in your protocol to help users know if it worked as intended.

Link records for Subject, Keyword, and Authors (Required)

On the Protocol record you just created, scroll down to each of the following sections and click Link records to add at least one of each (but you can add as many as applicable):

• Protocol Subject: These are subject categories related to the protocol (per Nature Protocols)

• Protocol Keyword: These are just helpful search terms. Either choose from the list or click Create new to create your own.

• Protocol Author: Click Add records for each protocol author. If they’re not already available, click Create New to add new people as authors.

Search through existing entries to find the best possible fit. But if you cannot find one, you can click the Create new button and make new entries.

Upload Attachments (for Images, Figures, Videos, etc) (Optional)

This section may be used for adding images to your protocol but is also useful for videos or other supplemental files.

To embed image files in your protocol: add the file to the Attachments section, copy the link and then embed it where desired in the base protocol. Important: You may only embed image files in .jpg or .png format.

• Scroll to the Attachments section and click Add records.

  • Use the Label field to describe the attachment.

  • Use the URI field to upload the file.

  • Click Save

• Embed Image: Note you can only embed an image file (in .jpg or .png format). For video files, you may only add a link to the URI for the figure (for information on how to add a link, see Formatting with Markdown).

  • In the record you just added, copy the URI field (the link to the image on our system).

  • Scroll back up to the top of the protocol and click Edit.

  • In the desired field, use the following Markdown format (similar to a markdown link but with an exclamation point at the beginning):

![alt text](URI-of-image-you-uploaded)