Jan 09, 2024

Public workspaceExperiment Data Depot (EDD) Data Import

 Forked from Experiment Data Depot (EDD) Study Creation
DOI
https://dx.doi.org/10.17504/protocols.io.bp2l6bd15gqe/v1
Experiment Data Depot (EDD) Data Import
  • Jennifer Gin1,
  • Christopher Petzold1
  • 1Lawrence Berkeley National Laboratory
  • LBNL omics
  • Agile BioFoundry
Christopher J Petzold
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DOI: https://dx.doi.org/10.17504/protocols.io.bp2l6bd15gqe/v1
External link: https://public-edd.agilebiofoundry.org/
Protocol Citation: Jennifer Gin, Christopher 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, data into an edd study, experiment data depot, software tool for biological experimental data storage, data import, biological experimental data storage, experiment data depot google site, edd study, more information about the edd visit, data, edd visit, edd, csv file, acs synthetic biology, exported csv file, based software tool, synthetic biology, protocol detail
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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.

For more information about the EDD visit: Experiment Data Depot Google Site.

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:
https://public-edd.agilebiofoundry.org/
https://public-edd.agilebiofoundry.org/s/example-data-quality-study-2/overview/


Materials
Example proteomics data import file:
Download Example Proteomics data (1).xlsxExample Proteomics data (1).xlsx

Troubleshooting
Before start
The following instructions show you how to import data for proteomics and metabolomics.

Create an EDD study (EDD Study Creation protocol) before you start the data import process.
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.
ABCDE
Line NameMeasurement TypeTimeValueUnits
181-aceF-R1sp|B1X8I1|XYLA_ECODH122795counts
181-aceF-R2sp|B1X8I1|XYLA_ECODH122611counts
181-aceF-R3sp|B1X8I1|XYLA_ECODH122155counts
Proteomics Example Data File
Download Example Proteomics data.xlsxExample Proteomics data.xlsx

ABCDE
Line NameMeasurement TypeTimeValueUnits
181-aceF-R1CID:440917 D-Limonene120.079585069mM
181-aceF-R2CID:440917 D-Limonene123.712638406mM
181-aceF-R3CID:440917 D-Limonene120.416450273mM
Metabolomics Example Data File
Download Example Metabolomics data.xlsxExample Metabolomics data.xlsx

ABCDE
Line NameMeasurement TypeTimeValueUnits
181-aceF-R1CID:5793 D-Glucose1222.07066865g/L
181-aceF-R2CID:5793 D-Glucose1221.84441193g/L
181-aceF-R3CID:5793 D-Glucose1221.45756405g/L
HPLC Example Data File
Download Example HPLC aceF.xlsxExample 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.