[REVIEW]: OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases #3249

whedon · 2021-05-05T09:19:05Z

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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General checks

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Documentation

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Software paper

Summary: Has a clear description of the high-level functionality and purpose of the software for a diverse, non-specialist audience been provided?
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State of the field: Do the authors describe how this software compares to other commonly-used packages?
Quality of writing: Is the paper well written (i.e., it does not require editing for structure, language, or writing quality)?
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?

The text was updated successfully, but these errors were encountered:

whedon · 2021-05-05T09:19:09Z

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 🎉.

⚠️ JOSS reduced service mode ⚠️

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.

⭐ Important ⭐

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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For a list of things I can do to help you, just type:

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For example, to regenerate the paper pdf after making changes in the paper's md or bib files, type:

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arfon · 2021-05-05T09:20:49Z

Fast-tracking this submission because it has already been reviewed in pyOpenSci/software-submission#31 (comment)

whedon · 2021-05-05T09:22:23Z

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 · 2021-05-05T09:24:10Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

whedon · 2021-05-05T09:26:00Z

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 · 2021-05-05T15:39:57Z

@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 · 2021-05-05T16:00:26Z

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 · 2021-05-05T16:08:14Z

@whedon generate pdf

whedon · 2021-05-05T16:09:20Z

👉📄 Download article proof 📄 View article proof on GitHub 📄 👈

arfon · 2021-05-07T08:51:14Z

@whedon set 10.5281/zenodo.4731011 as archive

whedon · 2021-05-07T08:51:18Z

OK. 10.5281/zenodo.4731011 is the archive.

arfon · 2021-05-07T08:51:23Z

@whedon accept

whedon · 2021-05-07T08:51:26Z

Attempting dry run of processing paper acceptance...

whedon · 2021-05-07T08:52:39Z

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 · 2021-05-07T08:52:55Z

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 · 2021-05-07T08:57:14Z

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

JonnyTran · 2021-05-07T19:04:34Z

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

arfon · 2021-05-08T07:37:55Z

@whedon accept

whedon · 2021-05-08T07:37:58Z

Attempting dry run of processing paper acceptance...

whedon · 2021-05-08T07:39:05Z

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 · 2021-05-08T07:39:09Z

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

Check final proof 👉 openjournals/joss-papers#2287

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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 · 2021-05-08T07:52:31Z

@JonnyTran - please merge this PR which makes a number of small formatting fixes to your paper: JonnyTran/OpenOmics#164

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

JonnyTran · 2021-05-08T18:07:59Z

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 · 2021-05-09T13:05:35Z

@whedon accept

whedon · 2021-05-09T13:05:38Z

Attempting dry run of processing paper acceptance...

whedon · 2021-05-09T13:06:37Z

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 · 2021-05-09T13:06:47Z

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

Check final proof 👉 openjournals/joss-papers#2290

If the paper PDF and Crossref deposit XML look good in openjournals/joss-papers#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 · 2021-05-09T13:09:23Z

@whedon accept deposit=true

whedon · 2021-05-09T13:09:26Z

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

whedon · 2021-05-09T13:10:33Z

🐦🐦🐦 👉 Tweet for this paper 👈 🐦🐦🐦

whedon · 2021-05-09T13:10:33Z

🚨🚨🚨 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 👉 Creating pull request for 10.21105.joss.03249 joss-papers#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 · 2021-05-09T13:14:08Z

@JonnyTran - thanks for your submission to JOSS. Your paper is now accepted and published ⚡🚀💥

whedon · 2021-05-09T13:14:12Z

🎉🎉🎉 Congratulations on your paper acceptance! 🎉🎉🎉

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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whedon added the review label May 5, 2021

whedon assigned arfon May 5, 2021

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[PRE REVIEW]: OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases #3248

Closed

arfon mentioned this issue May 5, 2021

OpenOmics: Library for integration of multi-omics, annotation, and interaction data pyOpenSci/software-submission#31

Closed

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[REVIEW]: OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases #3249

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[REVIEW]: OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases #3249

[REVIEW]: OpenOmics: A bioinformatics API to integrate multi-omics datasets and interface with public databases #3249

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whedon commented May 5, 2021 • edited Loading

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