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avoid raw github URLs for ontologies in the spec #205

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cmungall opened this issue May 3, 2022 · 1 comment
Open

avoid raw github URLs for ontologies in the spec #205

cmungall opened this issue May 3, 2022 · 1 comment

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@cmungall
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cmungall commented May 3, 2022

Under https://hupo-psi.github.io/mzTab/2_0-metabolomics-release/mzTab_format_specification_2_0-M_release.html#the-psi-mass-spectrometry-controlled-vocabulary-cv

You have rows like this:

Cell Type ontology (https://raw.githubusercontent.com/obophenotype/cell-ontology/master/cl-basic.obo).

For OBO ontologies, always use an OBO PURL for the content. These are guaranteed stable, whereas the above URL will break if we reorganize our repo structure or move away from github

For a web page describing an ontology, every OBO has a URL of form https://obofoundry.org/ontology/cl

nilshoffmann added a commit that referenced this issue May 4, 2022
Addressing issue #205 to provide stable URL for recommended ontologies.
@nilshoffmann nilshoffmann self-assigned this May 4, 2022
@nilshoffmann nilshoffmann added this to the mzTab-M 2.0.1 milestone Apr 12, 2024
@nilshoffmann
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@cmungall Thank you for the pointer, we will update the spec doc for the next minor version release.

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