Hello human, I'm @whedon, a robot that can help you with some common editorial tasks.

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

@whedon commands

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

@whedon generate pdf

Software report (experimental):

github.com/AlDanial/cloc v 1.84  T=0.04 s (226.7 files/s, 40348.1 lines/s)
-------------------------------------------------------------------------------
Language                     files          blank        comment           code
-------------------------------------------------------------------------------
Python                           4            183            129            757
Markdown                         3             51              0            166
TeX                              1             11              0            127
-------------------------------------------------------------------------------
SUM:                             8            245            129           1050
-------------------------------------------------------------------------------


Statistical information for the repository '2140' was gathered on 2020/03/04.
The following historical commit information, by author, was found:

Author                     Commits    Insertions      Deletions    % of changes
Samantha Pendleton              15          1135             66          100.00

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
Samantha Pendleton         1069           94.2          0.2               11.23

Reference check summary:

OK DOIs

- None

MISSING DOIs

- https://doi.org/10.1093/database/bau033 may be missing for title: tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles
- https://doi.org/10.3115/v1/p14-5010 may be missing for title: The Stanford CoreNLP natural language processing toolkit
- https://doi.org/10.1093/nar/gkr972 may be missing for title: Disease Ontology: a backbone for disease semantic integration
- https://doi.org/10.1016/j.ajhg.2008.09.017 may be missing for title: The Human Phenotype Ontology: a tool for annotating and analyzing human hereditary disease
- https://doi.org/10.1093/bib/bbv011 may be missing for title: The role of ontologies in biological and biomedical research: a functional perspective

INVALID DOIs

- None

👉 Check article proof 📄 👈

@sap218 thanks for submitting this work. This appears to be a re-submission of this work which was previously rejected by JOSS: #2054. Can you tell us in detail how the functionality of project has been significantly expanded with respect to the previously submitted version?

@Kevin-Mattheus-Moerman Thanks!

Previously I submitted Jabberwocky with a single command, which allowed users to retrieve key elements from a text corpus using an ontology’s terms. Jabberwocky is the first tool to use an ontology directly. However, I understand the feedback that Jabberwocky was a minor-utility package and so I significantly expanded to include more functionality that demonstrates its utility in developing and maintaining ontologies, as well as querying text. This updated version of Jabberwocky includes two new subcommands, which together combine to make a workflow for users. Jabberwocky can now perform a tf-idf analysis on textual data to select key terms, and annotate those key terms in the ontology. Users can iteratively use these commands to identify and incrementally add new synonyms to expand their ontology.

Dear authors and reviewers

We wanted to notify you that in light of the current COVID-19 pandemic, JOSS has decided to suspend submission of new manuscripts and to handle existing manuscripts (such as this one) on a "best efforts basis". We understand that you may need to attend to more pressing issues than completing a review or updating a repository in response to a review. If this is the case, a quick note indicating that you need to put a "pause" on your involvement with a review would be appreciated but is not required.

Thanks in advance for your understanding.

Arfon Smith, Editor in Chief, on behalf of the JOSS editorial team.

@whedon invite @majensen as editor

@majensen has been invited to edit this submission.

@whedon assign @majensen as editor

OK, the editor is @majensen

@wdduncan -- would you be willing to review this software for JOSS? Information about reviewing is available here. Please let me know here or via other channels - thanks for considering! --@majensen