[PRE REVIEW]: Adeft: Acromine-based Disambiguation of Entities from Text with applications to the biomedical literature

[whedon]

Submitting author: @johnbachman (John Bachman) Repository: https://github.com/indralab/adeft Version: 0.3.0 Editor: @brainstorm Reviewers: @GullyAPCBurns, @gbader, @GullyAPCBurns

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Thanks for submitting your paper to JOSS @johnbachman. Currently, there isn't an JOSS editor assigned to your paper.

@johnbachman if you have any suggestions for potential reviewers then please mention them here in this thread. In addition, this list of people have already agreed to review for JOSS and may be suitable for this submission.

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[whedon]

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This submission is currently in a pre-review state which means we are waiting for an editor to be assigned and for them to find some reviewers for your submission. This may take anything between a few hours to a couple of weeks. Thanks for your patience :smile_cat:

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[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1526 with the following error:

/app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:in parse': (tmp/1526/paper/paper.md): found unexpected document indicator while scanning a quoted scalar at line 2 column 8 (Psych::SyntaxError) from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:377:inparse_stream' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:325:in parse' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:252:inload' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:473:in block in load_file' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:inopen' from /app/vendor/ruby-2.4.4/lib/ruby/2.4.0/psych.rb:472:in load_file' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:95:inload_yaml' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon.rb:78:in initialize' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/processor.rb:36:innew' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/lib/whedon/processor.rb:36:in set_paper' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/bin/whedon:55:inprepare' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/command.rb:27:in run' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/invocation.rb:126:ininvoke_command' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor.rb:387:in dispatch' from /app/vendor/bundle/ruby/2.4.0/gems/thor-0.20.3/lib/thor/base.rb:466:instart' from /app/vendor/bundle/ruby/2.4.0/bundler/gems/whedon-18b9a37e7f54/bin/whedon:116:in <top (required)>' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:inload' from /app/vendor/bundle/ruby/2.4.0/bin/whedon:23:in `

'

[kyleniemeyer]

Hi @brainstorm, can you edit this submission?

[kyleniemeyer]

Hi @johnbachman, there was a missing close quotation mark in your paper's header that I fixed in https://github.com/indralab/adeft/pull/36, if you could merge that.

In this issue, we'll get an editor assigned to your submission, who will then assign two or more reviewers. If you have suggestions for who we might ask, either from the JOSS reviewer pool or from folks in your domain, that would be helpful.

[johnbachman]

Thanks very much! We've gone through the list of reviewers and suggest the following (based on listed experience in Python, NLP, and/or computational biology):

• bagheria
• ionlights
• nhejazi
• gweissman

[johnbachman]

The following also appear suitable but are fairly high up on the list:

• desilinguist
• jkahn

[kyleniemeyer]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

PDF failed to compile for issue #1526 with the following error:

Error reading bibliography ./paper.bib (line 26, column 4): unexpected "d" expecting space, ",", white space or "}" Error running filter pandoc-citeproc: Filter returned error status 1 Looks like we failed to compile the PDF

[johnbachman]

Found two missing commas in paper.bib, just fixed them and pushed again.

[johnbachman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[johnbachman]

Fixed missing references and misc formatting.

[johnbachman]

@whedon generate pdf

[whedon]

Attempting PDF compilation. Reticulating splines etc...

[whedon]

:point_right: Check article proof :page_facing_up: :point_left:

[johnbachman]

Proof looks good.

[brainstorm]

@kyleniemeyer happy to!

[brainstorm]

@whedon assign @brainstorm as editor

[whedon]

OK, the editor is @brainstorm

[brainstorm]

@vsoch, since you have done pretty rad stuff with wordvec/NLP before, would you mind helping me out on reviewing this submission? :)

[vsoch]

hey @brainstorm ! It's been a few years since I've looked at NLP, so I would suggest that we also find someone else that is actively practicing, and have me as a second reviewer? But this looks incredibly cool and it would be an honor! I may not have time until the weekend, but that's still pretty soon :)

[brainstorm]

Gotcha @vsoch, I'll take your offer as 2nd reviewer ;)

@mbod, would you like to assist us with this review?

[brainstorm]

@whedon assign @vsoch as reviewer

[brainstorm]

@whedon start review

[whedon]

It looks like you don't have an editor and reviewer assigned yet so I can't start the review. Try one or more of these commands:

# Change editorial assignment
@whedon assign @username as editor

# Assign a GitHub user as the sole reviewer of this submission
@whedon assign @username as reviewer

# Add a GitHub user to the reviewers of this submission
@whedon add @username as reviewer

[vsoch]

Do we have a primary reviewer?

[brainstorm]

No replies and couldn't get hold of any in private :/

[brainstorm]

@Gweissman, would you like to assist JOSS with this review?

[brainstorm]

:wave: @adammichaelwood, would you like to assist JOSS with this review?

[adammichaelwood]

Thanks for asking. I don't have time for this at the moment.

On Sun, Jul 21, 2019, 5:13 PM Roman Valls Guimera notifications@github.com wrote:

👋 @adammichaelwood https://github.com/adammichaelwood, would you like to assist JOSS with this review?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1526?email_source=notifications&email_token=AANRU4KF3PLI75TWB2JYKTTQAT3SJA5CNFSM4H3M6U5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD2OOS3Q#issuecomment-513599854, or mute the thread https://github.com/notifications/unsubscribe-auth/AANRU4PQUFZYAKJP4NH7N3DQAT3SJANCNFSM4H3M6U5A .

[gweissman]

@brainstorm Thanks for thinking of me. I am unavailable until October.

[brainstorm]

👋 @desilinguist Would you mind helping me out with this review? Thanks!

[bgyori]

Hi @brainstorm, is there some way we can help move the review process forward? Should we suggest outside reviewers not listed in the JOSS spreadsheet?

[brainstorm]

@bgyori Yes please! I'm having a hard time finding suitable reviewers for this one.

[johnbachman]

@gbader and @GullyBurns would be great choices.

[GullyAPCBurns]

Happy to help

[brainstorm]

@whedon assign @GullyAPCBurns as reviewer

[whedon]

OK, the reviewer is @GullyAPCBurns

[brainstorm]

This is great, thanks @GullyAPCBurns and @bgyori... if @gbader is up for the task, we can get this started (respecting @vsoch preference to defer this review to more NLP-centric folks).

[gbader]

sure, I can help, though I may be delayed.

[brainstorm]

@whedon add @gbader as reviewer

[whedon]

OK, @gbader is now a reviewer

[brainstorm]

@whedon start review

[whedon]

OK, I've started the review over in https://github.com/openjournals/joss-reviews/issues/1708. Feel free to close this issue now!

[brainstorm]

Alright, off we go!: https://github.com/openjournals/joss-reviews/issues/1708

[GullyBurns]

Question about conflict of interest: I worked in the same DARPA program as the authors and entered into collaborative discussions although we never published or actively worked together. Just wanted to check that this never rose to the level of a COI?

On Wed, Sep 4, 2019 at 7:36 PM Roman Valls Guimera notifications@github.com wrote:

Alright, off we go!: #1708 https://github.com/openjournals/joss-reviews/issues/1708

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/openjournals/joss-reviews/issues/1526?email_source=notifications&email_token=AK4AALUYHBT2XLC7GLJABPTQIBWDBA5CNFSM4H3M6U5KYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD55T46Y#issuecomment-528170619, or mute the thread https://github.com/notifications/unsubscribe-auth/AK4AALRAIR6WEOHMLE4G5ELQIBWDBANCNFSM4H3M6U5A .

--

• Gully Burns, D.Phil.
• Research Scientist,
• Meta, Science Initiative.
• c: +1 650-208-8426
• gully.burns@chanzuckerberg.com

[brainstorm]

@GullyBurns The JOSS editorial team reckons this does not qualify as a COI, so thanks for raising it up but you are free to proceed, no worries.