Scientific Software Registry Collaboration Workshop

One goal of this workshop was to complete the development of best practices for discipline-specific software registries and repositories started in earlier virtual task force meetings. The deliverable for this goal is Nine Best Practices for Research Software Registries and Repositories: A Concise Guide. These practices are also listed below, as are examples of them and the author list for the above document.

Best Practices

Provide a public scope statement
Provide guidance for users
Provide guidance to software contributors
Establish an authorship policy
Share your metadata schema
Stipulate conditions of use
State a privacy policy
Provide a retention policy
Disclose your end-of-life policy

Policy examples: Scope Statement

Astrophysics Source Code Library. (n.d.). Editorial policy. https://ascl.net/wordpress/submissions/editiorial-policy/
bio.tools. (n.d.). Curators Guide. https://biotools.readthedocs.io/en/latest/curators_guide.html
Caltech Library. (2017). Terms of Deposit. https://data.caltech.edu/terms
Caltech Library. (2019). CaltechDATA FAQ. Caltech Library. https://www.library.caltech.edu/caltechdata/faq
Computational Infrastructure for Geodynamics. (n.d.). Code Donation. https://geodynamics.org/cig/dev/code-donation/
CoMSES Net Computational Model Library. (n.d.). Frequently Asked Questions. https://www.comses.net/about/faq/#model-library
ORNL DAAC for Biogeochemical Dynamics. (n.d.). Data Scope and Acceptance Policy. https://daac.ornl.gov/submit/
RDA Registry and Research Data Australia. (2018). Collection. ARDC Intranet. https://intranet.ands.org.au/display/DOC/Collection
Remote Sensing Code Library. (n.d.). Submit. https://rscl-grss.org/submit.php
SciCrunch. (n.d.). Curation Guide for SciCrunch Registry. https://scicrunch.org/page/Curation%20Guidelines
U.S. Department of Energy: Office of Scientific and Technical Information. (n.d.-a). DOE CODE: Software Policy. https://www.osti.gov/doecode/policy
U.S. Department of Energy: Office of Scientific and Technical Information. (n.d.-b). FAQs. OSTI.GOV. https://www.osti.gov/faqs

Policy examples: Authorship

CASRAI. (n.d.). CRediT - Contributor Roles Taxonomy. CASRAI. https://casrai.org/credit/
Committee on Publication Ethics: COPE. (2020a). Authorship and contributorship. https://publicationethics.org/authorship
Committee on Publication Ethics: COPE. (2020b). Core practices. https://publicationethics.org/core-practices
Dagstuhl EAS Specification Draft. (2016). The Software Credit Ontology. https://dagstuhleas.github.io/SoftwareCreditRoles/doc/index-en.html
Journal of Open Source Software. (n.d.). Ethics Guidelines. https://joss.theoj.org/about/#ethics
ORNL DAAC (n.d) Authorship Policy. https://daac.ornl.gov/submit/
PeerJ Journals. (n.d.-a). Author Policies. https://peerj.com/about/policies-and-procedures/#author-policies
PeerJ Journals. (n.d.-b). Publication Ethics. https://peerj.com/about/policies-and-procedures/#publication-ethics
PLOS ONE. (n.d.). Authorship. https://journals.plos.org/plosone/s/authorship
National Center for Data to Health. (2019). The Contributor Role Ontology. https://github.com/data2health/contributor-role-ontology

Policy examples: Metadata Schema

ANDS: Australian National Data Service. (n.d.). Metadata. ANDS. https://www.ands.org.au/working-with-data/metadata
ANDS: Australian National Data Service. (2016). ANDS Guide: Metadata. https://www.ands.org.au/__data/assets/pdf_file/0004/728041/Metadata-Workinglevel.pdf
Bernal, I. (2019). Metadata for Data Repositories. https://doi.org/10.5281/zenodo.3233486
bio.tools. (2020). Bio-tools/biotoolsSchema. https://github.com/bio-tools/biotoolsSchema
bio.tools. (2019). BiotoolsSchema documentation. https://biotoolsschema.readthedocs.io/en/latest/
The CodeMeta crosswalks. (n.d.) https://codemeta.github.io/crosswalk/
Citation File Format (CFF). (n.d.) https://doi.org/10.5281/zenodo.1003149
The DataVerse Project. (2020). DataVerse 4.0+ Metadata Crosswalk. https://docs.google.com/spreadsheets/d/10Luzti7svVTVKTA-px27oq3RxCUM-QbiTkm8iMd5C54
OntoSoft. (2015). OntoSoft Ontology. https://ontosoft.org/ontology/software/
OpenAPI Specification. (2020). http://spec.openapis.org/oas/v3.0.3
Zenodo. (n.d.-a). Schema for Depositing. https://zenodo.org/schemas/records/record-v1.0.0.json
Zenodo. (n.d.-b). Schema for Published Record. https://zenodo.org/schemas/deposits/records/legacyrecord.json

Policy examples: Conditions of use policy

Allen Institute. (n.d.). Terms of Use. https://alleninstitute.org/legal/terms-use/
Europeana. (n.d.). Usage Guidelines for Metadata. Europeana Collections. https://www.europeana.eu/portal/en/rights/metadata.html
U.S. Department of Energy: Office of Scientific and Technical Information. (n.d.). DOE CODE FAQ: Are there restrictions on the use of the material in DOE CODE? https://www.osti.gov/doecode/faq/#are-there-restrictions
Zenodo. (n.d.). Terms of Use. https://about.zenodo.org/terms/

Policy examples: Privacy policy

Allen Institute. (n.d.). Privacy Policy. https://alleninstitute.org/legal/privacy-policy/
CoMSES Net. (n.d.). Data Privacy Policy. https://www.comses.net/about/data-privacy/
Nature. (2020). Privacy Policy. https://www.nature.com/info/privacy
Research Data Australia. (n.d.). Privacy Policy. Research Data Australia. https://researchdata.ands.org.au/page/privacy
SciCrunch. (2018). Privacy Policy. SciCrunch. https://scicrunch.org/page/privacy
Science Repository. (n.d.). Privacy Policies. https://www.sciencerepository.org/privacy
Zenodo. (n.d.). Privacy policy. https://about.zenodo.org/privacy-policy/

Policy examples: Retention Policy

Caltech Library. (n.d.). CaltechDATA FAQ. https://www.library.caltech.edu/caltechdata/faq
CoMSES Net Computational Model Library. (n.d.). How long will models be stored in the Computational Model Library? https://www.comses.net/about/faq/
Dryad. (2020). Dryad FAQ - Publish and Preserve your Data. https://datadryad.org/stash/faq/#preserved
Software Heritage. (n.d.). Content policy. https://www.softwareheritage.org/legal/content-policy/
Zenodo. (n.d.). General Policies v1.0. https://about.zenodo.org/policies/

Policy examples: End-of-life policy

Bioconductor. (2020). Package End of Life Policy. https://bioconductor.org/developers/package-end-of-life/
Figshare. (n.d.). Preservation and Continuity of Access Policy. https://knowledge.figshare.com/articles/item/preservation-and-continuity-of-access-policy
Open Science Framework. (2019). FAQs. OSF Guides. http://help.osf.io/hc/en-us/articles/360019737894-FAQs
NASA Earth Science Data Preservation Content Specification (n.d.) https://earthdata.nasa.gov/esdis/eso/standards-and-references/preservation-content-spec
Zenodo. (n.d.). Frequently Asked Questions. https://help.zenodo.org/

Authors

The guidelines were authored by:

Alain Monteil, INRIA: HAL/Software Heritage, https://orcid.org/0000-0003-3150-4837
Alastair Kelly, NLM
Alejandra Gonzalez-Beltran, Science and Technology Facilities Council, UK Research and Innovation, https://orcid.org/0000-0003-3499-8262
Alexandros Ioannidis, CERN: Zenodo, https://orcid.org/0000-0002-5082-6404
Alice Allen, ASCL, https://orcid.org/0000-0003-3477-2845
Allen Lee, ASU, CoMSES Net, https://orcid.org/0000-0002-6523-6079
Andre Jackson, DDMoRe Model Repository
Anita Bandrowski, SciCrunch, UCSD, https://orcid.org/0000-0002-5497-0243
Bruce E. Wilson, ORNL DAAC, https://orcid.org/0000-0002-1421-1728
Bryce Mecum, NCEAS, UC Santa Barbara: CodeMeta, https://orcid.org/0000-0002-0381-3766
Cai Fan Du, iSchool, University of Texas at Austin: CiteAs, https://orcid.org/0000-0003-2538-607X
Carly Robinson, DOE-OSTI, https://orcid.org/0000-0002-8523-1478
Daniel S. Katz, University of Illinois at Urbana-Champaign, Associate EiC for JOSS, FORCE11 Software Citation Implementation Working Group co-chair, https://orcid.org/0000-0001-5934-7525
Daniel Garijo, Information Sciences Institute, University of Southern California (Representing Ontosoft), http://orcid.org/0000-0003-0454-7145
David Long, EiC for RSCL, https://orcid.org/0000-0002-1852-3972
Genevieve Milliken, New York University: IASGE, https://orcid.org/0000-0002-3057-0659
Hervé Ménager, Institut Pasteur: ELIXIR bio.tools, https://orcid.org/0000-0002-7552-1009
Jessica Hausman, JPL PO.DAAC, https://orcid.org/0000-0002-1861-1526
Jurriaan Spaaks, Netherlands eScience Center: Research Software Directory, https://orcid.org/0000-0002-7064-4069
Katrina Fenlon, University of Maryland: iSchool, https://orcid.org/0000-0003-1483-5335
Kristin Vanderbilt, IMCR, https://orcid.org/0000-0003-1439-2204
Lorraine Hwang, Computational Infrastructure for Geodynamics, UC Davis, http://orcid.org/0000-0002-1021-3101
Lynn Davis, DOE-OSTI
Martin Fenner, DataCite, FORCE11 Software Citation Implementation Working Group co-chair, https://orcid.org/0000-0003-1419-2405
Michael R. Crusoe, CWL; Debian-Med, https://orcid.org/0000-0002-2961-9670
Mike Hucka, Caltech, Caltech, SBML, COMBINE, https://orcid.org/0000-0001-9105-5960
Ming Fang Wu, RDA, https://orcid.org/0000-0003-1206-3431
Neil Chue Hong, SSI, FORCE11 Software Citation Implementation Working Group co-chair, https://orcid.org/0000-0002-8876-7606
Peter Teuben, UMD, https://orcid.org/0000-0003-1774-3436
Shelley Stall, AGU, https://orcid.org/0000-0003-2926-8353
Stephan Druskat, German Aerospace Center (DLR)/University Jena/Humboldt-Universität zu Berlin: Citation File Format, https://orcid.org/0000-0003-4925-7248
Ted Carnevale, Neuroscience Department, Yale: ModelDB
Tom Morrell, Caltech, https://orcid.org/0000-0001-9266-5146