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OBOFoundry / OBOFoundry.github.io

Metadata and website for the Open Bio Ontologies Foundry Ontology Registry
http://obofoundry.org
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Add clearer citation/publications metadata #1671

Open cmungall opened 2 years ago

cmungall commented 2 years ago

We have the ability to add publications as metadata:

publications:
  - id: http://www.ncbi.nlm.nih.gov/pubmed/22293552
    title: "Uberon, an integrative multi-species anatomy ontology"
  - id: http://www.ncbi.nlm.nih.gov/pubmed/25009735
    title: "Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon"

http://obofoundry.org/ontology/uberon

this shows up under "cite":

Cite Uberon, an integrative multi-species anatomy ontology Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

Is a citation link the same as a publication link? If someone has a zenodo DOI for their github repo can/should they put this under "publication"

I think we need more guidance here, especially for ontologies with no peer-reviewed publication

cthoyt commented 2 years ago

zenodo DOI points to an archive of the code/data/software while a publication DOI is about the academic record of the work. I think they're complementary and should both be included.

GitHub said that the citation.cff should be used to cite the code directly, but it's way more practical to include the citation for the academic work under which the repo was published so it's hard to give guidance here.

matentzn commented 2 years ago

I feel that we should not be to restrictive with this field - The owners of an ontology should be able to decide which digital objects they wish listed as publications, or whether to use zenodo or github to cite code (or ontologies). Its not really our concern as OBO, at least not formally.

I personally prefer citation.cff over zenodo because of its simplicity, but is there a way the latest release tag as well? Right now, you have to manually curate the version label of citation.cff which seems cumbersome. And adding yet another GH action for updating the version in a CFF file seems total overkill.

Matentzoglu, N., Mungall, C., & Goutte-Gattat, D. (2021). Ontology Development Kit (Version 1.2.29) [Computer software]. https://doi.org/10.5281/zenodo.4662066