Jan 09, 2024
Experiment Data Depot (EDD) Data Import
Forked from Experiment Data Depot (EDD) Study Creation
- 1Lawrence Berkeley National Laboratory
External link: https://public-edd.agilebiofoundry.org/
Protocol Citation: Jennifer Gin, Christopher J Petzold 2024. Experiment Data Depot (EDD) Data Import . protocols.io https://dx.doi.org/10.17504/protocols.io.bp2l6bd15gqe/v1
Manuscript citation:
Morrell, William C., et al. "The experiment data depot: a web-based software tool for biological experimental data storage, sharing, and visualization." ACS synthetic biology 6.12 (2017): 2248-2259.
License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: January 11, 2021
Last Modified: January 09, 2024
Protocol Integer ID: 46196
Keywords: EDD, Metadata, Synthetic Biology, Experiment Data Depot, Metabolic Engineering, REST API
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Abstract
This protocol details how to import data into an EDD Study. Data can be shared with collaborators via exported CSV files or through the REST API.
Citation:
Morrell, William C., et al. "The experiment data depot: a web-based software tool for biological experimental data storage, sharing, and visualization." ACS synthetic biology 6.12 (2017): 2248-2259. (link to publication)
Example Links:
Materials
Example proteomics data import file:
Example Proteomics data (1).xlsx Before start
The following instructions show you how to import data for proteomics and metabolomics.
Click the Import Data button on the top right.
Import Data
Go through the set of data import steps:
Identify what protocol was used. Click Shotgun (Discovery) Proteomics.
Select the layout of your data. Click Generic.
Click Start Import on the bottom right.
Note
Repeat for each data type you want to import into the EDD.
Example data layouts:
Here, we have measured the amount of protein "XYLA_ECODH", metabolite "D-Limonene", and extracellular "D-Glucose" for sample "181-aceF" in triplicates at time "12" hours.
| A | B | C | D | E | |
| Line Name | Measurement Type | Time | Value | Units | |
| 181-aceF-R1 | sp|B1X8I1|XYLA_ECODH | 12 | 2795 | counts | |
| 181-aceF-R2 | sp|B1X8I1|XYLA_ECODH | 12 | 2611 | counts | |
| 181-aceF-R3 | sp|B1X8I1|XYLA_ECODH | 12 | 2155 | counts |
Proteomics Example Data File
Example Proteomics data.xlsx | A | B | C | D | E | |
| Line Name | Measurement Type | Time | Value | Units | |
| 181-aceF-R1 | CID:440917 D-Limonene | 12 | 0.079585069 | mM | |
| 181-aceF-R2 | CID:440917 D-Limonene | 12 | 3.712638406 | mM | |
| 181-aceF-R3 | CID:440917 D-Limonene | 12 | 0.416450273 | mM |
Metabolomics Example Data File
Example Metabolomics data.xlsx | A | B | C | D | E | |
| Line Name | Measurement Type | Time | Value | Units | |
| 181-aceF-R1 | CID:5793 D-Glucose | 12 | 22.07066865 | g/L | |
| 181-aceF-R2 | CID:5793 D-Glucose | 12 | 21.84441193 | g/L | |
| 181-aceF-R3 | CID:5793 D-Glucose | 12 | 21.45756405 | g/L |
HPLC Example Data File
Example HPLC aceF.xlsx Drag-and-drop to upload data file into the dropzone box.
Drag data file (.xlsx) to the dropzone
After the EDD interprets the file it will calculate the number of records to save. Check that this is correct, then click the Save button.
Once the data is uploaded, the EDD will bring you to the Data page in the Line graph view. You can toggle to the Bar Graphs.
Repeat the Data Import process for other data types.