Submitting Metadata in PHENO

This example based section will showcase how to submit your MIAPPE compliant Excel file in PHENO.

If you don’t have this file ready, start with the Fill a MIAPPE Template tutorial.

Go to the OntoBrAPI Submission page

1. Click on Submit Data.

This will take you to the OntoBrAPI submission tool.

Each of the following examples will showcase possible outcomes when trying to submit your file in PHENO.

Example 1 - Valid File

In the first example, the user has a simple MIAPPE compliant excel file:

📁 OntoBrAPI Example File 1 (Valid)

To submit your metadata:

1. Click on upload file, and select your file of choice ➡️ for this example, choose the Miappe_compliant_Excel.xlsx

A preliminary validation report will appear in the top right corner.

After a sucessfull validation check, the following prompt will appear:

Alongside the Mapping Section and a preview of the uploaded file:

2. After validation, the file needs to be mapped to the Plant Ontology. Click on Load Mapping

This will open a list of Predefined Mapping Templates.

3. Select the [JSON] MIAPPEV1.1 option

Since our input file is a standard MIAPPE file, this will automaticaly conclude the mapping.

The mapping success is seen on the color and number in the file sheet names, like shown bellow:

4. Lastly, click Run

That’s it! Your metadata was sucessfuly submitted in PHENO.

Example 2 - Invalid File

The second example will showcase working with an invalid input file:

📁 OntoBrAPI Example File 2 (Invalid)

Let’s try and submit this file and try to identify and fix eventual errors during submission.

1. Click Input File and select the Miappe_INCOMPLIANT_Excel.xlsx

As we can see, the loading failed due to an input file validation error.

By clicking in the FAIL button (Input validation menu), a message drop-down indicates a “CHECK FAILED - Invalid Input File Sheet Names” entry.

This means that one or more sheets in the Excel file are missing or have different names from the ones described in the MIAPPE standards.

Let’s take a closer look to the invalid file sheet names:

• The Person sheet name is not in English. Fix → “Pessoa” to Person.

• The Data file sheet name is incomplete. Fix → “Data” to Data file.

• In addition, the Environment sheet is missing. FIX → create a new sheet called Environment,

  and write Study unique ID*, Environment parameter* and Environment parameter value* in the first row

After fixing these problems, retry file submission:

2. Click Input File and select the fixed ``Miappe_INCOMPLIANT_Excel.xlsx``

Once again, upload fails. By looking at the validation report, we see a “CHECK FAILED - Invalid Investigation Sheet Names”.

In this case, by looking at the file, we see that the first two column headers within the Investigation sheet are incorrect.

• FIX → The column name “Investigation ID” should be Investigation unique ID*

• FIX → The column name “investigation title” should be Investigation title*.

Note

If you use the provided MIAPPE template, errors of this nature will be prevented.

For this last example, we will supply a valid Excel file, but use an incorrect mapping file (Invalid_Mapping_example.json).

Example 3 - Invalid Mapping

1. Click Input File and select the Miappe_compliant_Excel_file.xlsx

2. Click the Load Mapping option, and select the - Invalid_Mapping_example.json

3. Press Submit

As we can check by the warning, the supplied mapping was insufficient to properly connect the supplied Miappe metadata.

After Submission

The submitted dataset will be private, and only made public:

• Until the Public release date specified in the Investigation sheet is reached;

• After approval by a PHENO curator.

Once the dataset is made public, all phenotypic data associated with your submitted metadata will be readily accessible

in BrAPI compliant databases, such as the case of PHENO and FAIDARE.