BioModel Discussion Issue for eos81ew

[Zainab-ik]

Summary !!!

• BioModel Name: Williams2022 - Permeable compound selection using in vitro ADME data (PAMPA pH 5).

• BioModel Tag: fair AIML, Machine learning model

• Metadata Comments: Here are a few comments (from PAMPA 5 publication) ;

1. Oral permeability as a complex process that's dependent on membrane permeability, does that classify Oral permeability as a model property metadata?
2. The publication made mention of 2 models; a classifier and a neural network. While looking through the repo, I only see a Neural network .py file, are the models merged (is there a sort of model fusion like stacking), or only the Neural network model is implemeted?
3. There are 2 PAMPA models ( eos9tyg - PAMPA 7 & eos81ew - PAMPA 5). Both repository have same publication which describes only PAMPA 5. However, the publication for PAMPA 7.4.pdf attached is different even though I believe the model implementation and incorporation follows the same standard.
4. PAMPA 7 metadata is few compared to PAMPA 5 using their respective publication.
5. The PubChem bioassay dataset indicated in the NCATS website is also dfferent
6. In curating and annotating PAMPA 7.4 which is eos9tyg, which publication suits best; the publication in the repository which describes PAMPA 5 or the original publication?
7. There's a PAMPA-BBB model in NCATS, is that also incorporated in Ersilia? ---I checked, can't find.

• Contributor:

  roles	Names
  Curator	@Zainab-ik
  Modeller	Pauline-Banye
  Reviewer	@GemmaTuron

• Curation status : manually curated

• Annotation file: here

[Zainab-ik]

Errors

I noticed some errors in the eos81ew repository while looking through the model checkpoints and frameworks.

1. In eos81ew repo, there's a readme error in this folder - a mention of kinetic aqeous solubility which belongs to eos74bo

2. In the framework folder for eos81ew, there's also a readme description about eos74b0 and a github link about eos8ykt which doesn't seem to exist in Ersilia Model Hub.

[GemmaTuron]

Hi @Zainab-ik This readme file is not needed so it can be deleted, it was copied from other repos indeed. You can open a PR to eliminate it. The other questions:

• Oral permeability as a complex process that's dependent on membrane permeability, does that classify Oral permeability as a model property metadata? I don't think we should add oral availability as indeed this is a much more complex process
• The publication made mention of 2 models; a classifier and a neural network. While looking through the repo, I only see a - - Neural network .py file, are the models merged (is there a sort of model fusion like stacking), or only the Neural network model is implemeted? I don't understand the question. A neural network can be a classifier or a regressor, can you clarify?
• There are 2 PAMPA models ( eos9tyg - PAMPA 7 & eos81ew - PAMPA 5). Both repository have same publication which describes only PAMPA 5. However, the publication for PAMPA 7.4.pdf attached is different even though I believe the model implementation and incorporation follows the same standard. _I would cite the publication referenced in NCATS for each model, in the case of Pampa7.4 this one: https://opendata.ncats.nih.gov/adme/models/pampa_ph74 - also make a PR to change it if needed (editing the metadata.json file)_
• PAMPA 7 metadata is few compared to PAMPA 5 using their respective publication. indeed that seems the case
• The PubChem bioassay dataset indicated in the NCATS website is also dfferent different from where?
• In curating and annotating PAMPA 7.4 which is eos9tyg, which publication suits best; the publication in the repository which describes PAMPA 5 or the original publication? The publication on the NCATS website There's a PAMPA-BBB model in NCATS, is that also incorporated in Ersilia? ---I checked, can't find. It is not, we can add it to the model incorporation list

[Zainab-ik]

Hi @Zainab-ik This readme file is not needed so it can be deleted, it was copied from other repos indeed. You can open a PR to eliminate it.

I'd work on that.

• Oral permeability as a complex process that's dependent on membrane permeability, does that classify Oral permeability as a model property metadata? I don't think we should add oral availability as indeed this is a much more complex process
• The publication made mention of 2 models; a classifier and a neural network. While looking through the repo, I only see a - - Neural network .py file, are the models merged (is there a sort of model fusion like stacking), or only the Neural network model is implemeted? I don't understand the question. A neural network can be a classifier or a regressor, can you clarify?

You already clarified, thanks

• There are 2 PAMPA models ( eos9tyg - PAMPA 7 & eos81ew - PAMPA 5). Both repository have same publication which describes only PAMPA 5. However, the publication for PAMPA 7.4.pdf attached is different even though I believe the model implementation and incorporation follows the same standard. _I would cite the publication referenced in NCATS for each model, in the case of Pampa7.4 this one: https://opendata.ncats.nih.gov/adme/models/pampa_ph74 - also make a PR to change it if needed (editing the metadata.json file)_

Noted, Thanks for the clarification

• PAMPA 7 metadata is few compared to PAMPA 5 using their respective publication. indeed that seems the case
• The PubChem bioassay dataset indicated in the NCATS website is also dfferent different from where?

different from the one stated in the repository, i'd make a PR to fix that too.

• In curating and annotating PAMPA 7.4 which is eos9tyg, which publication suits best; the publication in the repository which describes PAMPA 5 or the original publication? The publication on the NCATS website

I worked with that.

There's a PAMPA-BBB model in NCATS, is that also incorporated in Ersilia? ---I checked, can't find. It is not, we can add it to the model incorporation list

NCATS - PAMPA BBB

[Zainab-ik]

Hi @GemmaTuron , PR opened here https://github.com/ersilia-os/eos81ew/pull/11 to fix the readme error