arfon
commented
6 years ago I don’t know to be honest. In the Whedon gem we use a BibTeX library that validates these entries. Perhaps you could do the same?
On 9/27/18, 8:04 AM, "Vanessa Sochat" notifications@github.com wrote:
hey
@arfon <https://github.com/arfon> ! What would you consider the minimum required fields for references (meaning present and defined?) so far I have a type (e.g., article) and title, month, and year. But we might want some additional checks, like giving a warning if missing a doi,
or requiring a journal OR url? Let me know your thoughts! Just for perusing, here are the listing of fields for the current references I'm testing with. I'm not saying this is right / wrong, but rather a "real world" example:
['title', 'abstract', 'publisher', 'month', 'year']
['title', 'affiliation', 'abstract', 'journal', 'volume', 'number', 'pages', 'month', 'year', 'language']
['title', 'booktitle', 'abstract', 'month', 'year', 'howpublished', 'note']
['title', 'abstract', 'institution']
['title', 'abstract', 'journal', 'publisher', 'volume', 'month', 'year', 'keywords']
['title', 'abstract', 'howpublished', 'note']
['title', 'abstract', 'journal']
['title', 'abstract', 'journal', 'volume', 'number', 'pages', 'month', 'year']
['title', 'month', 'year', 'note', 'doi', 'url']
['title', 'year']
['title', 'affiliation', 'abstract', 'journal', 'volume', 'number', 'pages', 'month', 'year']
['title', 'publisher', 'series', 'year']
['title', 'journal', 'publisher', 'volume', 'number', 'month', 'year', 'address']
['title', 'abstract', 'journal', 'publisher', 'pages', 'doi', 'month', 'year', 'language']
['title', 'affiliation', 'abstract', 'journal', 'publisher', 'volume', 'pages', 'month', 'year', 'keywords', 'language', 'doi']
['title', 'affiliation', 'abstract', 'journal', 'publisher', 'volume', 'pages', 'month', 'year', 'doi', 'keywords', 'language']
['title', 'abstract', 'month', 'year', 'archivePrefix', 'primaryClass', 'doi', 'eprint']
['title', 'abstract', 'journal', 'publisher', 'volume', 'month', 'year', 'doi']
['title', 'abstract', 'month', 'year', 'archivePrefix', 'primaryClass', 'eprint']
And given my validation, the simple test passes for all of the above:
Testing bibliography entry Stodden2010-cu
type: article
title: The Scientific Method in Practice: Reproducibility in the Computational Sciences
Testing bibliography entry Ram2013-km
type: article
title: Git can facilitate greater reproducibility and increased transparency in science
Testing bibliography entry noauthor_2015-ig
type: misc
title: Docker-based solutions to reproducibility in science - Seven Bridges
Testing bibliography entry noauthor_undated-pi
type: misc
title: expfactory-docker
Testing bibliography entry Sochat2016-pu
type: article
title: The Experiment Factory: Standardizing Behavioral Experiments
Testing bibliography entry noauthor_undated-sn
type: misc
title: Science is in a reproducibility crisis: How do we resolve it?
Testing bibliography entry Baker_undated-bx
type: article
title: Over half of psychology studies fail reproducibility test
Testing bibliography entry Open_Science_Collaboration2015-hb
type: article
title: {PSYCHOLOGY}. Estimating the reproducibility of psychological science
Testing bibliography entry vanessa_sochat_2017_1059119
type: misc
title: {expfactory/expfactory: The Experiment Factory (v3.0) Release}
Testing bibliography entry McDonnell2012-ns
type: misc
title: psiTurk (Version 1.02)[Software]. New York, {NY}: New York University
Testing bibliography entry De_Leeuw2015-zw
type: article
title: jsPsych: a {JavaScript} library for creating behavioral experiments in a Web browser
Testing bibliography entry Smith2005-kg
type: book
title: Virtual Machines: Versatile Platforms for Systems and Processes
Testing bibliography entry Merkel2014-da
type: misc
title: Docker: Lightweight Linux Containers for Consistent Development and Deployment
Testing bibliography entry Ali2016-rh
type: article
title: The Case for Docker in Multicloud Enabled Bioinformatics Applications
Testing bibliography entry Moreews2015-dy
type: article
title: {BioShaDock}: a community driven bioinformatics shared Docker-based tools registry
Testing bibliography entry Belmann2015-eb
type: article
title: Bioboxes: standardised containers for interchangeable bioinformatics software
Testing bibliography entry Boettiger2014-cz
type: article
title: An introduction to Docker for reproducible research, with examples from the {R} environment
Testing bibliography entry Santana-Perez2015-wo
type: article
title: Towards Reproducibility in Scientific Workflows: An {Infrastructure-Based} Approach
Testing bibliography entry Wandell2015-yt
type: article
title: Data management to support reproducible research
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vsoch
hey @arfon ! What would you consider the minimum required fields for references (meaning present and defined?) so far I have a type (e.g., article) and title, month, and year. But we might want some additional checks, like giving a warning if missing a doi, or requiring a journal OR url? Let me know your thoughts! Just for perusing, here are the listing of fields for the current references I'm testing with. I'm not saying this is right / wrong, but rather a "real world" example:
And given my validation, the simple test passes for all of the above: