OpenOmics: Presubmission Inquiry

[JonnyTran]

Submitting Author: Nhat Tran (@JonnyTran)
Package Name: OpenOmics One-Line Description of Package: Library for integration of multi-omics, annotation, and interaction data. Repository Link (if existing): https://github.com/BioMeCIS-lab/OpenOmics

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Description

OpenOmics is a Python library to assist integration of heterogeneous multi-omics bioinformatics data. By providing an API of data manipulation tools as well as a web interface (WIP), OpenOmics facilitates the common coding tasks when preparing data for bioinformatics analysis. It features support for:

• Genomics, Transcriptomics, Proteomics, and Clinical data.
• Harmonization with 20+ popular annotation, interaction, and disease-association databases (e.g. GENCODE, Ensembl, RNA Central, BioGRID, DisGeNet etc.)

OpenOmics also has an efficient data pipeline that bridges the popular data manipulation library like Pandas and distributed processing like Dask to the Dash web dashboard interface. With an intuitive web interface and easy-than-ever API, OpenOmics addresses the following use cases:

• Provides a standard pipeline for dataset indexing, table joining and querying, which are transparent to users.
• Multiple data types that supports both interactions and sequence data, and allows users to export to NetworkX graphs or down-stream machine learning.
• An easy-to-use API that works seamlessly with the Dash web interface.

Scope

• Please indicate which category or categories this package falls under:

  • [x] Data retrieval
  • [x] Data extraction
  • [x] Data munging
  • [ ] Data visualization
  • [ ] Data deposition
  • [x] Reproducibility
  • [ ] Geospatial
  • [ ] Education
  • [ ] Unsure/Other (explain below)

• Explain how the and why the package falls under these categories (briefly, 1-2 sentences). Please note any areas you are unsure of: OpenOmics' core functionalities are to provide a suite of tools for data preprocessing, data integration, and public database retrieval. Its main goal is to maximize the transparency and reproducibility in the process of multi-omics data integration.

• Who is the target audience and what are scientific applications of this package?
  OpenOmics' primary target audience are computational bioinformaticians, and the scientific application of this package is to facilitate the data prep tasks in multi-omics data integration in a reproducible manner. Also, we are currently developing interfaces to the Galaxy Tool Shed, disseminating the tool to biologists without a programming background.

• Are there other Python packages that accomplish the same thing? If so, how does yours differ? Existing PyPI Python packages within the scope of multi-omics data analysis are "pythomics" and "omics". Their functions appear to be lacking support for manipulation of integrated multi-omics dataset, retrieval of public databases, and extensible OOP design. OpenOmics aims to follow modern software best-practices and package publishing standards.

• Any other questions or issues we should be aware of?:

P.S. *Have feedback/comments about our review process? Leave a comment here

[NickleDave]

Hi @JonnyTran thank you for making this presubmission inquiry. Sorry we haven't gotten back to you sooner.

OpenOmics definitely looks like it is within scope for PyOpenSci, and I can see you have done a lot of work already to make sure the package adheres to our standards and guidelines, including your use of the pyopensci cookiecutter.

I am not sure if you saw that we're "on pause" for a bit while looking for further funding: https://pyopensci.discourse.group/t/on-pause-for-a-bit/224

In the meantime, I have been trying to help where I can. If @lwasser is okay with it, I could act as editor for this submission.

But realistically I won't be able to start that process until mid-January because of other obligations. Also, I want to make sure you're aware that currently our total total time for review has been 1-2 months.

I definitely want to do what I can to recognize all the hard work you've done on OpenOmics, and help you further develop the library via the PyOpenSci review process. But I also want to make sure we're on the same page about what the review process will look like because of those other factors. Please let us know if those timelines would be acceptable to you.

[lwasser]

@NickleDave if you are keen to serve as an editor here i can work on the other submission! i've been overwhelmed with conference things but havea bit more space now to support.

[JonnyTran]

But realistically I won't be able to start that process until mid-January because of other obligations. Also, I want to make sure you're aware that currently our total total time for review has been 1-2 months. Please let us know if those timelines would be acceptable to you.

Yes, I'm more than okay with the timeline. Thank you for the consideration of reviewing this work.

[NickleDave]

@NickleDave if you are keen to serve as an editor here i can work on the other submission! i've been overwhelmed with conference things but havea bit more space now to support.

Thank you @lwasser -- you mean Physcraper? I think I can handle this one and finish up that review as well.

Yes, I'm more than okay with the timeline. Thank you for the consideration of reviewing this work.

Great glad to hear it @JonnyTran Happy we can provide you a review and I'm looking forward to it. I will be able to start the week of Jan 11, got it in my calendar now

Please, whenever you are ready, go ahead and open a new issue that's a full submission review. If you can think of reviewers that would be appropriate, please also feel free to suggest them in the initial comment. I will also look for reviewers with relevant expertise when I start the process the week of Jan. 11. I can close this issue once you create the issue for full review. Thank you!!!

[JonnyTran]

@NickleDave Please, whenever you are ready, go ahead and open a new issue that's a full submission review. If you can think of reviewers that would be appropriate, please also feel free to suggest them in the initial comment. I will also look for reviewers with relevant expertise when I start the process the week of Jan. 11. I can close this issue once you create the issue for full review.

I've created a new issue for the full review at https://github.com/pyOpenSci/software-review/issues/31. I haven't think of any reviewers yet, but I'll update the issue if I find any.

[NickleDave]

whoops, forgot to close this

review already well under way in #31