[REVIEW]: OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases

whedon commented 3 years ago

Submitting author: @JonnyTran (Nhat Tran) Repository: https://github.com/BioMeCIS-Lab/OpenOmics Version: v0.8.8 Editor: @arfon Reviewer: @arfon Archive: 10.5281/zenodo.4731011

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Status

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Markdown: [![status](https://joss.theoj.org/papers/aca43e3c2989a803b514faef72dd3294/status.svg)](https://joss.theoj.org/papers/aca43e3c2989a803b514faef72dd3294)

Reviewers and authors:

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Review checklist for @arfon

Conflict of interest

[x] I confirm that I have read the JOSS conflict of interest (COI) policy and that: I have no COIs with reviewing this work or that any perceived COIs have been waived by JOSS for the purpose of this review.

Code of Conduct

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General checks

[x] Repository: Is the source code for this software available at the repository url?
[x] License: Does the repository contain a plain-text LICENSE file with the contents of an OSI approved software license?
[x] Contribution and authorship: Has the submitting author (@JonnyTran) made major contributions to the software? Does the full list of paper authors seem appropriate and complete?
[x] Substantial scholarly effort: Does this submission meet the scope eligibility described in the JOSS guidelines

Functionality

[x] Installation: Does installation proceed as outlined in the documentation?
[x] Functionality: Have the functional claims of the software been confirmed?
[x] Performance: If there are any performance claims of the software, have they been confirmed? (If there are no claims, please check off this item.)

Documentation

[x] A statement of need: Do the authors clearly state what problems the software is designed to solve and who the target audience is?
[x] Installation instructions: Is there a clearly-stated list of dependencies? Ideally these should be handled with an automated package management solution.
[x] Example usage: Do the authors include examples of how to use the software (ideally to solve real-world analysis problems).
[x] Functionality documentation: Is the core functionality of the software documented to a satisfactory level (e.g., API method documentation)?
[x] Automated tests: Are there automated tests or manual steps described so that the functionality of the software can be verified?
[x] Community guidelines: Are there clear guidelines for third parties wishing to 1) Contribute to the software 2) Report issues or problems with the software 3) Seek support

Software paper

[x] Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
[x] A statement of need: Does the paper have a section titled 'Statement of Need' that clearly states what problems the software is designed to solve and who the target audience is?
[x] State of the field: Do the authors describe how this software compares to other commonly-used packages?
[x] Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
[x] References: Is the list of references complete, and is everything cited appropriately that should be cited (e.g., papers, datasets, software)? Do references in the text use the proper citation syntax?

whedon commented 3 years ago

Hello human, I'm @whedon, a robot that can help you with some common editorial tasks. @arfon it looks like you're currently assigned to review this paper :tada:.

:warning: JOSS reduced service mode :warning:

Due to the challenges of the COVID-19 pandemic, JOSS is currently operating in a "reduced service mode". You can read more about what that means in our blog post.

:star: Important :star:

If you haven't already, you should seriously consider unsubscribing from GitHub notifications for this (https://github.com/openjournals/joss-reviews) repository. As a reviewer, you're probably currently watching this repository which means for GitHub's default behaviour you will receive notifications (emails) for all reviews 😿

To fix this do the following two things:

Set yourself as 'Not watching' https://github.com/openjournals/joss-reviews:

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arfon commented 3 years ago

Fast-tracking this submission because it has already been reviewed in https://github.com/pyOpenSci/software-review/issues/31#issuecomment-832451199

whedon commented 3 years ago

Software report (experimental):

github.com/AlDanial/cloc v 1.88  T=0.86 s (156.7 files/s, 13359.7 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                          38           1044           1782           3615
Markdown                        21            292              0           1284
CSS                              5            197             87            982
TeX                              1             59              0            478
reStructuredText                61            426            704            127
YAML                             2             12             16             87
make                             2             24              6             78
XML                              2              0              0             71
DOS Batch                        1              8              1             27
TOML                             1              6              0             14
-------------------------------------------------------------------------------
SUM:                           134           2068           2596           6763
-------------------------------------------------------------------------------

Statistical information for the repository '36d4405885fdd6e8f1615832' was
gathered on 2021/05/05.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Jonny Tran                     930         16307          11528           34.34
JonnyTran                      457         27907          24256           64.35
Nhat Tran                        2           110             82            0.24
deepsource-autofix[b            12           624            252            1.08

Below are the number of rows from each author that have survived and are still
intact in the current revision:

Author                     Rows      Stability          Age       % in comments
Jonny Tran                 3618           22.2         10.5               11.08
JonnyTran                  2335            8.4          7.7               14.26
deepsource-autofix[b        488           78.2          2.3                0.00

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/nar/gky1079 is OK

MISSING DOIs

- 10.1093/nar/gkaa554 may be a valid DOI for title: The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2020 update
- 10.1093/bioinformatics/btz133 may be a valid DOI for title: Anduril 2: upgraded large-scale data integration framework
- 10.1074/mcp.m115.052381 may be a valid DOI for title: Integration of metabolomics and transcriptomics reveals major metabolic pathways and potential biomarker involved in prostate cancer
- 10.1371/journal.pcbi.1005752 may be a valid DOI for title: mixOmics: An R package for ‘omics feature selection and multiple data integration
- 10.1186/gm186 may be a valid DOI for title: Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
- 10.1093/nar/gkw377 may be a valid DOI for title: Enrichr: a comprehensive gene set enrichment analysis web server 2016 update
- 10.1038/nrg3606 may be a valid DOI for title: Long non-coding RNAs: new players in cell differentiation and development
- 10.1093/nar/gkr1175 may be a valid DOI for title: NONCODE v3. 0: integrative annotation of long noncoding RNAs
- 10.1093/nar/gks915 may be a valid DOI for title: LNCipedia: a database for annotated human lncRNA transcript sequences and structures
- 10.1101/gr.132159.111 may be a valid DOI for title: The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression
- 10.1093/nar/gku1173 may be a valid DOI for title: LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression
- 10.1093/nar/gky1051 may be a valid DOI for title: LncRNA2Target v2. 0: a comprehensive database for target genes of lncRNAs in human and mouse
- 10.1093/database/bav083 may be a valid DOI for title: LncReg: a reference resource for lncRNA-associated regulatory networks
- 10.1093/nar/gkq1138 may be a valid DOI for title: lncRNAdb: a reference database for long noncoding RNAs
- 10.1093/nar/gkw943 may be a valid DOI for title: DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants
- 10.1093/nar/gks1099 may be a valid DOI for title: LncRNADisease: a database for long-non-coding RNA-associated diseases
- 10.1093/nar/gkj112 may be a valid DOI for title: miRBase: microRNA sequences, targets and gene nomenclature
- 10.1093/nar/gkt1057 may be a valid DOI for title: NPInter v2. 0: an updated database of ncRNA interactions
- 10.1093/database/bav083 may be a valid DOI for title: LncReg: a reference resource for lncRNA-associated regulatory networks
- 10.1093/database/bat034 may be a valid DOI for title: lncRNome: a comprehensive knowledgebase of human long noncoding RNAs
- 10.1093/nar/gkj147 may be a valid DOI for title: The HUGO gene nomenclature database, 2006 updates
- 10.1017/cbo9780511546198.190 may be a valid DOI for title: Scale-free networks in cell biology
- 10.1093/nar/gkv1270 may be a valid DOI for title: DIANA-LncBase v2: indexing microRNA targets on non-coding transcripts
- 10.1093/nar/gkw1102 may be a valid DOI for title: The BioGRID interaction database: 2017 update
- 10.1093/nar/gkt1248 may be a valid DOI for title: starBase v2. 0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data
- 10.1371/journal.pcbi.1005752 may be a valid DOI for title: mixOmics: An R package for ‘omics feature selection and multiple data integration

INVALID DOIs

- None

arfon commented 3 years ago

@JonnyTran - while I check your paper over, please fix the DOIs in your references (noting that Whedon's suggestions are not always right), adding fields such as doi = 10.1093/nar/gkaa554 to your BibTeX file.

JonnyTran commented 3 years ago

I've just fixed the DOIs in the .bib file. By the way, the DOI for the openomics github repo is 10.5281/zenodo.4731011

Thanks!

JonnyTran commented 3 years ago

@whedon generate pdf

whedon commented 3 years ago

:point_right::page_facing_up: Download article proof :page_facing_up: View article proof on GitHub :page_facing_up: :point_left:

arfon commented 3 years ago

@whedon set 10.5281/zenodo.4731011 as archive

whedon commented 3 years ago

OK. 10.5281/zenodo.4731011 is the archive.

arfon commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

PDF failed to compile for issue #3249 with the following error:

 [WARNING] Citeproc: citation wolf2018scanpy not found
/app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:82:in `doi_citation': undefined method `encode' for nil:NilClass (NoMethodError)
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:64:in `make_citation'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:50:in `block in generate_citations'
    from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:149:in `each'
    from /app/vendor/bundle/ruby/2.6.0/gems/bibtex-ruby-5.1.6/lib/bibtex/bibliography.rb:149:in `each'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/bibtex_parser.rb:43:in `generate_citations'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/compilers.rb:248:in `crossref_from_markdown'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/compilers.rb:21:in `generate_crossref'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/lib/whedon/processor.rb:100:in `compile'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:88:in `compile'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/command.rb:27:in `run'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:in `invoke_command'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor.rb:387:in `dispatch'
    from /app/vendor/bundle/ruby/2.6.0/gems/thor-0.20.3/lib/thor/base.rb:466:in `start'
    from /app/vendor/bundle/ruby/2.6.0/bundler/gems/whedon-92346a0773a4/bin/whedon:131:in `<top (required)>'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `load'
    from /app/vendor/bundle/ruby/2.6.0/bin/whedon:23:in `<main>'

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/nar/gkaa554 is OK
- 10.3389/fonc.2020.00804 is OK
- 10.1093/bioinformatics/btz133 is OK
- 10.1371/journal.pcbi.1005752 is OK
- 10.1186/gm186 is OK
- 10.1093/nar/gkw377 is OK
- 10.1038/nrg3606 is OK
- 10.1093/nar/gkr1175 is OK
- 10.1093/nar/gks915 is OK
- 10.1101/gr.132159.111 is OK
- 10.1093/nar/gku1173 is OK
- 10.1093/nar/gky1051 is OK
- 10.1093/database/bav083 is OK
- 10.1093/nar/gkq1138 is OK
- 10.1093/nar/gks1099 is OK
- 10.1093/nar/gkj112 is OK
- 10.1093/nar/gkt1057 is OK
- 10.1093/database/bav083 is OK
- 10.1093/database/bat034 is OK
- 10.1093/nar/gkj147 is OK
- 10.1017/cbo9780511546198.190 is OK
- 10.1093/nar/gkv1270 is OK
- 10.1093/nar/gkw1102 is OK
- 10.1093/nar/gky1079 is OK
- 10.1093/nar/gkt1248 is OK
- 10.1371/journal.pcbi.1005752 is OK

MISSING DOIs

- 10.1074/mcp.m115.052381 may be a valid DOI for title: Integration of metabolomics and transcriptomics reveals major metabolic pathways and potential biomarker involved in prostate cancer

INVALID DOIs

- .1093/nar/gkw943 is INVALID

arfon commented 3 years ago

@JonnyTran - looks like your BibTeX file doesn't have a wolf2018scanpy entry. Could you take a look?

JonnyTran commented 3 years ago

Oops, I've missed those DOIs. I've just fixed them.

arfon commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/nar/gkaa554 is OK
- 10.1186/s13059-017-1382-0 is OK
- 10.3389/fonc.2020.00804 is OK
- 10.1093/bioinformatics/btz133 is OK
- 10.1074/mcp.M115.052381 is OK
- 10.1371/journal.pcbi.1005752 is OK
- 10.1038/nbt.3134 is OK
- 10.1093/bib/bbx080 is OK
- 10.1186/gm186 is OK
- 10.1093/nar/gkw377 is OK
- 10.1038/nrg3606 is OK
- 10.1093/nar/gkr1175 is OK
- 10.1093/nar/gks915 is OK
- 10.1101/gr.132159.111 is OK
- 10.1093/nar/gku1173 is OK
- 10.1093/nar/gky1051 is OK
- 10.1093/database/bav083 is OK
- 10.1093/nar/gkq1138 is OK
- 10.1093/nar/gkw943 is OK
- 10.1093/nar/gks1099 is OK
- 10.1093/nar/gkj112 is OK
- 10.1093/nar/gkt1057 is OK
- 10.1093/database/bav083 is OK
- 10.1093/database/bat034 is OK
- 10.1093/nar/gkj147 is OK
- 10.1017/cbo9780511546198.190 is OK
- 10.1093/nar/gkv1270 is OK
- 10.1093/nar/gkw1102 is OK
- 10.1093/nar/gky1079 is OK
- 10.1093/nar/gkt1248 is OK
- 10.1371/journal.pcbi.1005752 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2287

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2287, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 3 years ago

@JonnyTran - please merge this PR which makes a number of small formatting fixes to your paper: https://github.com/BioMeCIS-Lab/OpenOmics/pull/164

Also, please be sure to cite Dask and Pandas in your paper. You can find information on how to cite them here:

JonnyTran commented 3 years ago

Hi Arfon, I've just added pandas and dask citations.

I opted for the bibtex with author names,

@InProceedings{ matthew_rocklin-proc-scipy-2015, author = { Matthew Rocklin }, title = { Dask: Parallel Computation with Blocked algorithms and Task Scheduling }, booktitle = { Proceedings of the 14th Python in Science Conference }, pages = { 130 - 136 }, year = { 2015 }, editor = { Kathryn Huff and James Bergstra } }

rather than team authors,

@Manual{, title = {Dask: Library for dynamic task scheduling}, author = {{Dask Development Team}}, year = {2016}, url = {https://dask.org}, }

because Whedon will pick up the last name as (Team, 2016) inline citation.

Thanks for checking this over. I hope I didn't miss anything else.

arfon commented 3 years ago

@whedon accept

whedon commented 3 years ago

Attempting dry run of processing paper acceptance...

whedon commented 3 years ago

Reference check summary (note 'MISSING' DOIs are suggestions that need verification):

OK DOIs

- 10.1093/nar/gkaa554 is OK
-  10.25080/Majora-92bf1922-00a  is OK
- 10.25080/Majora-7b98e3ed-013 is OK
- 10.1186/s13059-017-1382-0 is OK
- 10.3389/fonc.2020.00804 is OK
- 10.1093/bioinformatics/btz133 is OK
- 10.1074/mcp.M115.052381 is OK
- 10.1371/journal.pcbi.1005752 is OK
- 10.1038/nbt.3134 is OK
- 10.1093/bib/bbx080 is OK
- 10.1186/gm186 is OK
- 10.1093/nar/gkw377 is OK
- 10.1038/nrg3606 is OK
- 10.1093/nar/gkr1175 is OK
- 10.1093/nar/gks915 is OK
- 10.1101/gr.132159.111 is OK
- 10.1093/nar/gku1173 is OK
- 10.1093/nar/gky1051 is OK
- 10.1093/database/bav083 is OK
- 10.1093/nar/gkq1138 is OK
- 10.1093/nar/gkw943 is OK
- 10.1093/nar/gks1099 is OK
- 10.1093/nar/gkj112 is OK
- 10.1093/nar/gkt1057 is OK
- 10.1093/database/bav083 is OK
- 10.1093/database/bat034 is OK
- 10.1093/nar/gkj147 is OK
- 10.1017/cbo9780511546198.190 is OK
- 10.1093/nar/gkv1270 is OK
- 10.1093/nar/gkw1102 is OK
- 10.1093/nar/gky1079 is OK
- 10.1093/nar/gkt1248 is OK
- 10.1371/journal.pcbi.1005752 is OK

MISSING DOIs

- None

INVALID DOIs

- None

whedon commented 3 years ago

:wave: @openjournals/joss-eics, this paper is ready to be accepted and published.

Check final proof :point_right: https://github.com/openjournals/joss-papers/pull/2290

If the paper PDF and Crossref deposit XML look good in https://github.com/openjournals/joss-papers/pull/2290, then you can now move forward with accepting the submission by compiling again with the flag deposit=true e.g.

@whedon accept deposit=true

arfon commented 3 years ago

@whedon accept deposit=true

whedon commented 3 years ago

Doing it live! Attempting automated processing of paper acceptance...

whedon commented 3 years ago

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon commented 3 years ago

🚨🚨🚨 THIS IS NOT A DRILL, YOU HAVE JUST ACCEPTED A PAPER INTO JOSS! 🚨🚨🚨

Here's what you must now do:

Check final PDF and Crossref metadata that was deposited :point_right: https://github.com/openjournals/joss-papers/pull/2291
Wait a couple of minutes, then verify that the paper DOI resolves https://doi.org/10.21105/joss.03249
If everything looks good, then close this review issue.
Party like you just published a paper! 🎉🌈🦄💃👻🤘

Any issues? Notify your editorial technical team...

arfon commented 3 years ago

@JonnyTran - thanks for your submission to JOSS. Your paper is now accepted and published :zap::rocket::boom:

whedon commented 3 years ago

:tada::tada::tada: Congratulations on your paper acceptance! :tada::tada::tada:

If you would like to include a link to your paper from your README use the following code snippets:

Markdown:
[![DOI](https://joss.theoj.org/papers/10.21105/joss.03249/status.svg)](https://doi.org/10.21105/joss.03249)

HTML:
<a style="border-width:0" href="https://doi.org/10.21105/joss.03249">
  <img src="https://joss.theoj.org/papers/10.21105/joss.03249/status.svg" alt="DOI badge" >
</a>

reStructuredText:
.. image:: https://joss.theoj.org/papers/10.21105/joss.03249/status.svg
   :target: https://doi.org/10.21105/joss.03249

This is how it will look in your documentation:

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