ISA-Tab API for MIAPPE

[yelin Bei]

Hello everyone,

I'm doing some work on phenotypic data management. I learned about some of the ISA data models, which provide many tools such as ISA-Tab API,https://github.com/ISA-tools/isa-api, for creating and validating metadata fields.

The phenotypic data management community proposed that MIAPPE, the fields of phenotypic data and ISA data management need to correspond one-to-one, proposed a configuration file(https://github.com/MIAPPE/ISA-Tab-for-plant-phenotyping), I wonder how the profile technically replaces ISA fields with MIAPPE fields?

Thank you very much for any input,

Luna

[Philippe]

Hi Luna

Thank you for reaching out.  

You are right that the MIAPPE community create in ISA Configuration implementing MIAPPE checklist requirements: https://github.com/MIAPPE/ISA-Tab-for-plant-phenotyping.

Each of the configurations (one for greenhouse trials, one for field trials) overlays  MIAPPE requirements on the ISA grammar (ISA syntactic elements).

By "overlay", I mean that the MIAPPE requirements have been "mapped" or "cast" to ISA objects or ISA attributes (e.g. "Cultivar", can be assigned to ISA.Characteristics).

I will point to 3 resources you may want to look at for managing your data:

1. python ISA-API:

if using the python API, you'll need to invoke the MIAPPE configuration with the ISAvalidator function to ensure your instance data meet the requirement.

However, in its current implementation, the ISA configurations do not affect the object creation. We are looking into improving this.

2. java ISA4J

a java library under developmnet by IPK Gatersleben (Daniel Arend, cc-ed) and colleagues).

the library allows loading an ISAconfiguration and helps create ISA objects in java and include the new annotation requirements.

https://github.com/IPK-BIT/isa4j

https://f1000research.com/articles/9-1388

3. NFDI4Plants Datahub

This is a new addition to the ISA community with the following tools. It provides Excel templates to metadata description based on the ISA model, and place both data and metadata under version control

Please see:

ARC:

https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/implementation/ArcCommander.html

SWATE:

https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/tutorials/QuickStart_swate.html

This work is led by Timo Mühlhaus also cc-ed.

Hope this initial reply will guide you but if you need more help, follow up with us.

Kind regards

Philippe

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[yelin Bei]

Hi Philippe，

Thank you so much for your reply.

Please allow me to add some my working background. In fact, I am involved in and tracking the development of a phenotypic data management and analysis system, a simple websit where a phenometic experimental project can be created and the traits of the data set (image data) can be analyzed. The dataset is stored on the cloud server, and I hope that when the dataset is downloaded to the local, it can contain metadata information or metadata files that describe the dataset, and manage phenotype data in this way. I learned about MIAPPE in the field of phenotypic data management, a relatively well-described checklist of metadata information. ISA-Tab is the implementation format of MIAPPE. https://isa-tools.org/isa-api/content/creationtutorial.html In this file I learned some settings about ISA-API and the cases and instructions provided above.

My original idea was to make a data management interface for some of the fields of the MIAPPE Checklist by using ISA API (the user would fill in forms for some of the fields when creating a trial, and then these forms would be saved in a specific format to be attached to the original data set file).

Now a couple of questions appear:

1. The first one is about using the isa-api tool to apply to our metadata field. Is ISA-Tab just for describing local data (such as isa-api) and using interactive components to dynamically get field values is too bulky, even if I only need a few specific fields(Actually, I just need some definite fields)?

2. The second question is, from your last reply, I learned about the ISA validate function. It seems that it verifies the created ISA-Tab or ISA-JSON file, whether it conforms to the format specified by ISA. . https://isa-tools.org/isa-api/content/notebooks/reading-isa-tab-from-disk-exploring-and-validating.html, the picture below shows me verifying an isa-Tab file Results https://isa-tools.org/isa-api/content/validation.html

I don't understand what is the relationship between the configuration and the mapping of ISA metadata fields and MIAPPE metadata fields

3. The other is still about field mapping. From the example given by MIAPPE website(https://www.miappe.org/data/), the fields I see are still in the ISA data model. The example of dataset I have download by https://doi.ipk-gatersleben.de/DOI/c211b42e-b3ce-4a0c-9bf9-354ce3f35737/27824a03-903f-4a32-bef5-1b2e8d85800e/2

The following are their assay file and study file for the phenotype data set. Obviously, the original field is used, not the field of phenotype data, so I feel a little bit confused, the so-called MIAPPE field And the mapping of ISA fields, or what does the "overlay" refer to?

4. And finilly, for my work, for example, I have some datasets and I want to describe the data sets. I think the ISA data model and Tab format are a good idea, but in MIAPPE mapping here, I don't understand how the configuration can represent my dataset with metadata for phenotypic data, using Tab format. So I would like to know how to manage the data with this configuration, can you give some advice? Or is there some application for the ISA data model? Or the case for phenotypic data management?

Thank you so much for your reply to the cost of time and energy

Your sincerely,

Luna