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#145 Obsolete links to BioModels.net Qualifiers
closed
5
2014-05-27
2009-05-11
No
The link to BioModels.net Qualifiers provided on the SBML specification Level 2 Version 4 Release 1, is obsolete.
This link is in the section 6.2 "XML namespaces in the standard annotation" (page 92 of the PDF version).
This obsolete link is also mentioned in the section 6.5 "Relation elements" (page 95 of the PDF version).
The obsolete link is: http://www.ebi.ac.uk/compneur-srv/miriam-main/mdb?section=qualifiers
Several valid options exists:
- http://www.biomodels.net/qualifiers/ (redirection)
- http://www.biomodels.org/qualifiers/ (redirection)
- http://www.ebi.ac.uk/miriam/qualifiers.html (direct link)
I would suggest one of the two first options.
I am accepting this issue as valid.
I am accepting this issue as valid.
You're absolutely right. Thank you for reporting it.
To the editors: I suggest we replace the link text with Camille's first suggested option.
I am accepting this issue as valid.
I would also choose Camille´s first suggestion.
Yes the first.
I agree with the proposed change and that it should be done.
I am accepting this issue as valid.
Definitely none of the first 2. Miriam according to tracker item 2790011(https://sourceforge.net/tracker/index.php?func=detail&aid=2790011&group_id=71971&atid=894711) is at http://www.ebi.ac.uk/miriam/ thus it makes absolutely no sense go through biomodels. We should be consistent.
I am accepting this issue as valid.
I prefer the first option, and then of course go in 2790011 with http://www.biomodels.net/miriam/
I agree with the proposed change and that it should be done.
I am accepting this issue as valid.
Stefan is right that it should be consistent. I agree with Frank that it should be www.biomodels.net/miriam in both cases, even more if this is what the MIRIAM people suggest.
After further discussions with various parties, we are gravitating towards using the following:
http://sbml.org/miriam/qualifiers
This would be a redirection set up on sbml.org to point to http://biomodels.net/qualifiers/
It appears a majority of the editors accept this issue and the latest proposed solution. I'm going ahead and changing the Group attribute to "Accepted: changes without conformance implications".
As per Editor protocol, this issue will be listed on the errata page for
SBML L2v4r1 and this issue will stay with status "Pending" until such time
as it is fixed in a future L2v4r2 specification.
This Tracker item was closed automatically by the system. It was
previously set to a Pending status, and the original submitter
did not respond within 730 days (the time period specified by
the administrator of this Tracker).
Changed to 'pending' again. Just an l2v4 issue; not an l2v5-only issue.
This has performance implications. Performance implications means it affects software behavior, and this certainly does, because it changes what software writes into annotations.
I agree with Mike (beside the fact that I still don't understand Lucian's will to issue a L2V4-r2 in addition to an L2V5).
Regarding the URI, the official one is definitively:
http://biomodels.net/qualifiers/
This is what we should redirect to if a redirection is put in place. We are thinking about a way to build a more serious infrastructure for those, in particular describing the qualifiers in OWL, to make the transition towards semanticWeb easier. That would also provide identifiers.org capabilities.
But even then the redirection will be towards biomodels.net/qualifiers
I was assuming that l2v4 would continue to be a viable specification, with models exchanged in it, etc. If there are non-conformance clarifications that can be added to the l2v4 spec, I believe we should put them in, for the people that read the l2v4 spec directly. They will, after all, be applicable to l2v4 models.
I do not, however, have strong opinions about which edits those should be. If something has or even might have a conformance implication, I'm fine with that being an l2v5-only change.