sbmlsecretary
commented
5 years ago - labels: --> Level 3 Version 1 Core, Level 3 Version 2 Core
Original comment by: luciansmith
Closed sbmlsecretary closed 2 years ago
sbmlsecretary
commented
5 years ago Original comment by: luciansmith
sbmlsecretary
commented
5 years ago My inclination is to not change the biomodels.net/sbo URL since it's used in namespaces, to be consistent. Thanks for the list!
Original comment by: luciansmith
sbmlsecretary
commented
5 years ago Original comment by: luciansmith
sbmlsecretary
commented
5 years ago This is now fixed in SVN, including updating the bibliography to get some of the other URLs you found--thanks! Otherwise, my list matched yours--got new URLs for genome.jp examples.
I was not able to mark any updated URL in red except when it was not flagged as a URL (as in the examples in the 'annotation' section), but I don't think this is a huge problem.
Given that the editors already signed off on this change in the other issue tracker item (https://sourceforge.net/p/sbml/sbml-specifications/293/) for l2v5, I'm marking this as accepted/pending as well, though if any editor wants to chime in for any reason, feel free.
Also added to http://sbml.org/Documents/Specifications/SBML_Level_3/Version_2/Core/Confirmed_issues_in_the_Level_3_Version_2_Core_Specification .
Original comment by: luciansmith
sbmlsecretary
commented
5 years ago Original comment by: luciansmith
sbmlsecretary
commented
3 years ago Original comment by: luciansmith
sbmlsecretary
commented
3 years ago Released.
Original comment by: luciansmith
Various URLs in the spec can be updated to use https instead of http. From Matthias:
Hi Lucian, I just had a look at the spec. Yes, namespaces must stay, but many links can be updated. Here my impression:
Replace http://www.biopax.org/ -> https://www.biopax.org/ (url, https exists) http://www.uniprot.org/ -> https://www.uniprot.org/ http://identifiers.org/ -> https://identifiers.org/ http://www.ebi.ac.uk/ -> https://www.ebi.ac.uk/ http://www.genome.jp/dbget-bin/www_bget?ec:3.5.4.4 -> https://www.genome.jp/dbget-bin/www_bget?ec:3.5.4.4 http://www.cellml.org/specification -> https://www.cellml.org/specification http://tools.ietf.org/html/rfc6350 -> https://tools.ietf.org/html/rfc6350
Remove http://www.godatabase.org/cgi-bin/amigo/go.cgi?view=details&query=GO:0007268 (link is dead, resource probably does not exist any more) http://us.expasy.org/cgi-bin/nicezyme.pl?3.5.4.4 (link is dead, resource does not exist any more) http://www.math.uwaterloo.ca/bingalls/Pubs/conservation.pdf (link is dead, resource does not exist anymore) . Not sure about http://biomodels.net/sbo/ -> https://www.ebi.ac.uk/sbo/main/ (forwards, https exists, careful this is also part of namespaces, only replace when the website is mentioned)
Don't replace http://sbml.org/ (urls, no https yet) http://www.sbml.org/sbml/ (namespace) http://www.w3.org/ (namespace) http://www.mysim.org/ns (namespace) http://www.struct.org/ns (namespace) http://www.othersim.com/ (namespace) http://www.sbgn.org/ (url, no https yet) http://www.psidev.info/index.php?q=node/60 (url, no https yet) http://biomodels.net/ (used in definitionURL) http://co.mbine.org/ (no https yet, part of namespaces) http://purl.org/dc/ (namespace) http://www.informatics.jax.org/searches/GO.cgi?id=GO:0007268 (url, no https yet) http://dublincore.org/* (url, no https yet)
Reported by: luciansmith
Original Ticket: sbml/sbml-specifications//357