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Proposed Issue template for BioModels Annotation and Incorporation. #28

Open Zainab-ik opened 7 months ago

Zainab-ik commented 7 months ago

Hi @GemmaTuron @miquelduranfrigola

Here is an issue template for to incorporate BioModel annotations and information into Ersilia.

Below are the different sections ;

Model name: BioModel uses a one-liner approach to describe a model e.g. first author, year, model activity. Reference - or example; Swanson2023 - ADMET Properties Predictions Model Identifier; For each curated model incorporated or uploaded into the BioModels repository, an ID number is generated, e.g., BIOMD0000000100 Tag: All machine learning models in the BioModels repository have the FAIR AIML tag, this applies to the findability, accesibility, interoperability (model exchange) and reusability of the models. Metadata Information: This part describes the metadata extracted manually from the paper or auto-generated, challenges and clarification regarding its annotation. Contributor: The modeller, reviewer, and the curator of the model will be acknowledged. Curation Status: Metadata are curated either manually or AI generated. This section would identify that. Annotation file: The annotation files of the metadata should be linked to the model for accesibility BioModel Link: After uploading a model into the BioModels repository, a link is generated which should be attached to the Ersilia model. e.g., https://www.ebi.ac.uk/biomodels/MODEL1907310001

miquelduranfrigola commented 7 months ago

This looks good to me as a first iteration. Thanks @Zainab-ik ! @GemmaTuron what are your thoughts?

GemmaTuron commented 7 months ago

Hi @miquelduranfrigola , @Zainab-ik

I would say we need TWO different issues, one to discuss the data, where the -csv file in the Drive will be linked for example, and another final one that will collect the data we want from BioModels and be automatically incorporated into our database as well. The first one will serve as a discussion and the second will be parsable with a Git Action

miquelduranfrigola commented 7 months ago

Can we start with one, though?

Zainab-ik commented 7 months ago

Hi @miquelduranfrigola @GemmaTuron I've created the one for discussion linked here.

I'd open a new issue and start the discussion.

Zainab-ik commented 7 months ago

Hi @GemmaTuron I've replicated the same process here