[PRE REVIEW]: Ontology for the Avida digital evolution platform

[editorialbot]

Submitting author: !--author-handle-->@miguelfortuna<!--end-author-handle-- (Miguel A. Fortuna) Repository: https://gitlab.com/fortunalab/ontoavida Branch with paper.md (empty if default branch): development Version: v2022-03-15 Editor: Pending Reviewers: Pending Managing EiC: Daniel S. Katz

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[editorialbot]

Checking the BibTeX entries failed with the following error:

Failed to parse BibTeX on value "--4468" (NAME) ["@", #<BibTeX::Entry >, {:author=>["{Adami} C. and {Ofria} C. and {Collier} T.~C."], :title=>["Evolution of biological complexity"], :journal=>["PNAS"], :volume=>"97", :pages=>"4463"}]

[editorialbot]

Software report:

github.com/AlDanial/cloc v 1.88  T=2.21 s (16.7 files/s, 237485.9 lines/s)
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Language                     files          blank        comment           code
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XML                             27         124057          31436         368419
Markdown                         9            322              0            925
TeX                              1             35              0            282
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SUM:                            37         124414          31436         369626
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gitinspector failed to run statistical information for the repository

[editorialbot]

Wordcount for paper.md is 3261

[editorialbot]

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

[danielskatz]

👋 @miguelfortuna - I'm the track editor for this submission to JOSS. As I look at the repo, I'm unsure if this is a software package or an ontology. JOSS is for review and publication of short papers and associated software, and in this case, I see a longish paper and no software, which makes me suspect that this might not be in scope for JOSS. Can you comment on this?

[danielskatz]

👋 @miguelfortuna - I would appreciate your reply to the question above☝️

[miguelfortuna]

Dear Daniel, sorry for the delay in my response. Ontoavida is an ontology that formalizes the vocabulary of Avida (i.e., a software platform for performing evolution experiments in silico). This ontology is required to retrieve data on digital organisms from avidaDB (an RDF database containing the genomes, transcriptomes, and phenotypes of more than a million digital organisms). In this sense, it's software that was built using tools from the OBO Foundry (e.g., ROBOT). This paper describes both the workflow for developing the ontology and the way of querying avidaDB. The software is available at the OBO Foundry website (https://obofoundry.org/ontology/ontoavida.html) and its development can be tracked at our gitlab repository (https://gitlab.com/fortunalab/ontoavida). Here is the link (https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1581) to the thread that we had with the OBO Foundry when requesting the acceptance of Ontoavida in its repository. We really think this submitted paper is the last essential part for completing our open source software project.

[miguelfortuna]

@editorialbot generate pdf

[editorialbot]

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

[miguelfortuna]

suggestions for potential reviewers: tpoisot dombennett KonradHoeffner ProfTuan

[danielskatz]

@miguelfortuna - JOSS practice is to include the software paper in the repo with the software. Can you perhaps do this?

[miguelfortuna]

The software is already there (the final product, i.e., the ontology, is named ontoavida.owl). Note that the paper is located in the development branch. Since OWL files are meant to be read by machines, I have now uploaded a friendly HTML version of the ontology (i.e., file ontoavida.html). This easy-to-read version created by pyLODE is also explained in the paper and is accesible from here.

[danielskatz]

@miguelfortuna - an ontology is not software for JOSS. Can you explain what you mean by software? I don't see what I think of as software in https://obofoundry.org/ontology/ontoavida.html

[miguelfortuna]

You're right. I think there is a fine line where an ontology ends and a knowledge base software begins. Ontoavida comprises the vocabulary needed to access and retrieve data from avidaDB database. In fact, we provide an example of querying avidaDB using the ontology (pages 7-8). The ontology we describe here is a requirement to get knowledge from a semantic database. We still think it can be considered an important part of a knowledge base software and hence, it might be suitable for publication in JOSS.

[danielskatz]

@miguelfortuna - I don't mean to imply that this isn't important, but it is not research software in JOSS's definition, so I'm going to reject this submission. I hope you can find another, better suited place to publish it.

[danielskatz]

@editorialbot reject

[editorialbot]

Paper rejected.