BOSC_cofest2019_log.md

1. Zotero connector browser plugin:

1. Fetch reference from github repository

1. From bibtex file
2. From .cff file
3. From zenodo/doi badge on github

2. Explore crossref and eventdata

1. Crossref DOI -> metadata: https://search.crossref.org/
2. Datacite DOI -> metadata: https://search.datacite.org/

1. How is this different from altmetrics?

1. Open source, not mystery algorithm

3. Other ways people publish software (can we fetch reference information from them)

1. Journal of Open Source Software
2. Journal of Open Research Software
3. SoftwareX
4. GigaScience

4. Generate CITATION.cff based on GH info

1. what can we get from API

Notes:

Datacite v4.2 scheme: https://schema.datacite.org/meta/kernel-4.2/doc/DataCite-MetadataKernel_v4.2.pdf

https://blog.datacite.org/doi-registrations-software/

“As of May 16, 2018, 58,301 DOIs have been registered for software. We can break down this number by repository where the software source code is hosted – most DOIs for software have been registered at Zenodo.”

CERN.ZENODO - ZENODO - Research. Shared.        41346

FIGSHARE.ARS - figshare Academic Research System        4226

PURDUE.NCIB - National Cancer Institute, Bioconductor        2769

PURDUE.EZID - Purdue University        2463

OSTI.DOE - DOE Generic        736

INIST.INRA - Institut National de Recherche Agronomique        223

OCEAN.OCEAN - Code Ocean        206

CRUI.INFNCNAF - Istituto Nazionale di Fisica Nucleare. Centro Nazionale Analisi Fotogrammi        190

CDL.UCI - UC Irvine Library        120

ETHZ.DA-RD - ETHZ Data Archive - Research Data

FORCE11 Software Citation Implementation Working Group (SCIWG): https://github.com/force11/force11-sciwg

• Challenges Preprint: https://arxiv.org/abs/1905.08674v1 (or Github https://github.com/force11/force11-sciwg/tree/master/Challenges)

RDA software source code identification WG: https://www.rd-alliance.org/groups/software-source-code-identification

Browser plugin:

https://github.com/zotero/zotero-connectors

Github API

REST API endpoints

users/

• name
• company
• location

repos/

• name
• full_name : [org]/[reponame]
• Created_at

Github - CFF mapping

CFF Key	CFF Data Type	Description	Github	Github query
abbreviation	String	The abbreviation of the work	-	-
abstract	String	The abstract of a work	Repo description	https://api.github.com/repos/org/repo field is ‘description”
authors	Collection of entity or person objects	The author of a work	Contributor names?	https://api.github.com/repos/org/repo  ‘contributors_url’
collection-doi	String	The DOI of a collection containing the work
collection-title	String	The title of a collection or proceedings
collection-type	String	The type of a collection
commit	String	The (e.g., Git) commit hash or (e.g., Subversion) revision number of the work	Git commit hash
conference	Entity object	The conference where the work was presented
contact	Collection of entity or person objects	The contact person, group, company, etc. for a work
copyright	String	The copyright information pertaining to the work
data-type	String	The data type of a data set
database	String	The name of the database where a work was accessed/is stored
database-provider	Entity object	The provider of the database where a work was accessed/is stored
date-accessed	Date	The date the work has been last accessed
date-downloaded	Date	The date the work has been downloaded
date-published	Date	The date the work has been published
date-released	Date	The date the work has been released
department	String	The department where a work has been produced
doi	String	The DOI of the work
edition	String	The edition of the work
editors	Collection of entity or person objects	The editors of a work
editors-series	Collection of entity or person objects	The editors of a series in which a work has been published
end	Integer	The end page of the work
entry	String	An entry in the collection that constitutes the work
filename	String	The name of the electronic file containing the work
format	String	The format in which a work is represented
institution	Entity object	The institution where a work has been produced or published
isbn	String	The ISBN of the work
issn	String	The ISSN of the work
issue	Integer	The issue of a periodical in which a work appeared
issue-date	String	The publication date of the issue of a periodical in which a work appeared - see note below
issue-title	String	The name of the issue of a periodical in which the work appeared
journal	String	The name of the journal/magazine/newspaper/periodical where the work was published
keywords	Collection of strings	Keywords pertaining to the work
languages	Collection of ISO 639 language strings	The language of the work
license	License string	The license under which a work is licensed	License
license-url	String (URL)	The URL of the license text under which a work is licensed	License-URL?
location	Entity object	The location of the work
loc-start	Integer	The line of code in the file where the work starts
loc-end	Integer	The line of code in the file where the work ends
medium	String	The medium of the work
month	Integer	The month in which a work has been published
nihmsid	String	The NIHMSID of a work
notes	String	Notes pertaining to the work
number	String	The accession number for a work
number-volumes	Integer	The number of volumes making up the collection in which the work has been published
pages	Integer	The number of pages of the work
patent-states	Collection of strings	The states for which a patent is granted
pmcid	String	The PMCID of a work
publisher	Entity object	The publisher who has published the work
recipients	Collection of entity or person objects	The recipient of a personal communication
repository	String (URL)	The repository where the work is stored	Repo URL
repository-code	String (URL)	The version control system where the source code of the work is stored	Github?
repository-artifact	String (URL)	The repository where the (executable/binary) artifact of the work is stored
scope	String	The scope of the reference, e.g., the section of the work it adheres to
section	String	The section of a work that is referenced
senders	Collection of entity or person objects	The sender of a personal communication
status	Status string	The publication status of the work
start	Integer	The start page of the work
term	String	The term being referenced if the work is a dictionary or encyclopedia
thesis-type	String	The type of the thesis that is the work
title	String	The title of the work	Repo name
translators	Collection of entity or person objects	The translator of a work
type	Reference types string	The type of the work
url	String (URL)	The URL of the work	Repo URL
version	String	The version of the work	release/version?
volume	Integer	The volume of the periodical in which a work appeared
volume-title	String	The title of the volume in which the work appeared
year	Integer	The year in which a work has been published	created_at -> extract year?
year-original	Integer	The year of the original publication	created_at -> extract year?

Person object

CFF keys	CFF property	Github	Github query
family-names	String
given-names	String
name-particle	String
name-suffix	String
affiliation	String	User company	https://api.github.com/users/yochannah Field is “company”
address	String
city	String	User location	https://api.github.com/users/yochannah Field is “location”
region	String
post-code	String
country	String
orcid	String (ORCID URL)
email	String	User email	https://api.github.com/users/yochannah Field is “email”
tel	String
fax	String
website	String (URL)	User blog	https://api.github.com/users/yochannah Field is “blogl”

Citation.js

• https://citation.js.org/demo Try out: Can generate various citation formats from a DOI or another ID or citation format.
• https://citation.js.org Promises also CFF, but for now it can’t be found it in the code or the docs.
• Any new input formats with parsers can be added as plugins, and built-in ones can be overridden
• https://doi.org/10.7287/peerj.preprints.27466v2 (Lars G. Willighagen 2019, PeerJ Preprints)
• https://doi.org/10.5281/zenodo.1005176 (Willighagen & Willighagen et al. 2017-2018, Zenodo)
• Issue (just like Zotero): It DOES NOT retrieve the version of software from Zenodo :-(
• Open question: Is it possible to plug in also new serialisations == output formats? That could solve the above issue

Future work - at eLife sprint:

• Deprecate node app and consider converting to a flask app, because there are helper apps

• Use doi2cff - works ok
• https://github.com/citation-file-format/github2cff doesn’t install on python 2 or 3 machines. Maybe pick it up and fix it.
• Don’t think Citation.js is needed– unless someone wants to build this in js
• CFF TO ZENODO?

• Extend zenodo to pull good cff data, make the artifact deposit, and then zenodo says

•  “we suggest you update your cff to include this DOI - download the new file here

• Could also contain your orcid if not present.

• or copy/paste your creds into the file
• Auto-add to cff ON github. Seems a bit scary.