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Adding a project

How to add an eDNA project​

Author: Jennifer Kim Last update: Jul 18, 2023

Overview​

This document guides you through the process of uploading your own eDNA project. If you have not already, you will first need to create a profile before you can upload a project. If you have questions around privacy and sharing, read our data publishing FAQ. If you’re interested to learn more about how your data gets processed, read our data processing FAQ. During the process, if you encounter an error or have questions, feel free to contact our [help desk] or reach out to us on [Slack].

  • Add project details

  • Add metadata

  • Add sequence data (for metabarcoding projects)

  • Select lists to offer

  • View status and review

1. Add project details​

Note: You can start with either section 1 or 2. These sections are placed on the page in the location where the user will see the related data. The project details section lets you provide a brief summary of your project. The page will auto save as you add in your information. You can fill out the following information:

  • Project title

  • Create a title that will give users an idea of what the project is about before they open it. This will be displayed anywhere a thumbnail of your project is displayed and in search results.

  • Contributors

  • Type in the name of someone from your project team. If they have a profile created, they will appear in the dropdown. If they don’t have a profile, you can still add their name.

  • Project timeline

  • Choose the start and end dates your project was conducted. If it’s still ongoing, you can put a future end date or change it later. If it is a one day project, just enter in the start date.

  • DOI link

  • If you have already published this project elsewhere, you can provide the DOI link. This field can be left blank if you don’t have one.

  • Overview

  • Share a brief summary of your project. If you have published your research, you can use the abstract as a starting point. This will display as a snippet in search results.

  • Example: Arroyo Seco is an important tributary to the LA River, and a major canyon corridor for urban wildlife. Recent wildfires set by arsonists have put biodiversity and people living or working around Arroyo Seco at heightened risk. As the government is clearing flammable vegetation, we are asking how the watershed is possibly being affected by these activities. We are sharing data from monthly surveys of the watershed.

  • Methodology

  • This section will be auto-populated when you upload your metadata. You can then add more details or documents las needed. The only step that won’t be pre-populated is Extraction - you will have to fill out this information yourself.

  • The following is a list of steps that will be displayed in this section and an example of the type of content that will be populated in each step:

  • Study:

  • 06/08/19-06/08/19 in LA County (eDNA metabarcoding)

  • Sampling:

  • 55 samples, median 25 per site, across 3 sites

  • Extraction:

  • User enters something themselves - no default

  • Amplification:

  • 6 markers, 16S_bacteria, 18S_euk, CO_metazoa, ITS1_fungi, ITS2_plants, vert12sS

  • Sequencing:

  • Alumin MiSeq with read length of 300 base pairs

  • Quality control:

  • 3 negative controls, 0 mock communities

  • Taxon ID:

  • Processed with Tronko

2. Add metadata​

In this section, download and fill out our template spreadsheet(s) with your metadata and then upload for processing. For qPCR data, the spreadsheet should include your sample results. For Metabarcoding data, we will take your raw, unprocessed FastQ files and run them through our system to create organism lists so that all the data on our site is in a standardized format.

For more information on what happens with your data, read our data publishing FAQ

  • Pick the type of data in your project. We accept metabarcoding and qPCR.

  • Download the appropriate spreadsheet template. Please note that this spreadsheet is view only. You can make a copy in Google Sheets (File > Make a copy > save to a folder on your Drive) or download a copy in Excel format.

  • Fill out the spreadsheet with your project metadata. Each column in the spreadsheet has a description and value format to guide you. Some descriptions will include links to references you can use or notes on what is or isn’t acceptable.

  • Once the spreadsheet is complete, export the file as a CSV and upload it to eDNA Explorer.

  • If there are any errors or warnings, you will see a message appear on the file. You can click on it to see what the issues are. Although we can process the file with warnings if you believe the data is correct, any problems marked as errors will have to be corrected before processing. You can click on the warnings or errors message to view specific details.

  • The methodology are in the Project details section should populate from the metadata. You can add more information if you wish by clicking on “Add detail”.

3. Add sequence data (for Metabarcoding projects only)​

After you upload your metadata, the sequence data section will populate with your sample names. You can bulk upload your FastQ files with the “Upload files” button. If you want to upload individual files, you can use the “Add data” buttons for each line. The progress bar will indicate how far you are in your upload process. Once everything is complete, you can click “Start processing”. Tip: If this stalls at any point due to an internet connection issue, feel free to refresh the page and it will automatically pick up where it left off. Once all the files have uploaded, you can safely exit the page or continue on to selecting the default organism lists for your project. It will take 1-10 days for your data to process. [Add an image of the pop-up indicating the lists button once the pop-up is updated] If you have any questions about how your data gets processed, adding more samples to a project, or why you need to submit raw data, read our data processing FAQ.

4. Create and manage lists​

Select and customize the species lists people can use to view and filter your data once the data is analyzed. Use the search bar to look for a specific list or use one of the defaults provided.

5. View status and review your project​

When you’re data is done processing, you will receive an email notification. You can also check your profile page in the project section for the status. Once your data is processed, review your project page again to make sure all the details are correct. At this point, you can also view and download the charts and graphs with your data results to do further analysis on your own.

Publishing your project​

If you’d like to keep your project private, there is no further action required. If you want to make it public (and we strongly encourage this), you can hit the “Publish” button. Read more about privacy and data sharing in our data publishing FAQ. The project can be shared by clicking the “Copy link” button under the project on your profile page. If you want to add more samples or adjust your metadata in any way, just go to your project page and hit the “Add and manage data” button. [Add images here of the different status and processing states once they’re finalized]

Source document: Google Doc