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Incorrect UCUM mapping

Open kaiiam opened this issue 3 years ago • 6 comments

Hey @HajoRijgersberg @dr-shorthair, while working on https://github.com/kaiiam/UO_revamp/issues/2 I noticed in the https://github.com/HajoRijgersberg/OM/blob/master/om-2-ucum.ttl file the following issue:

image

Note that the second UCUM mapping is wrong: m not m^2

image

I'll let you know if I end up finding more of these.

Also unrelated I was having issues when sparql querying the om-2-ucum.ttl file (that @dr-shorthair recently added to) when using Robot query Same routine worked to query the QUDT VOCAB_QUDT-UNITS-ALL-v2.1.ttl file. The error message is the following. I think concerning imports or html tags.

The element type "p" must be terminated by the matching end-tag "</p>".

kaiiam avatar Mar 02 '21 16:03 kaiiam

Thanx, Kai! I wasn't able until now to look at this. I saw Simon has corrected the turtle file, but I'm having problems accepting it in Github. I'm not too familiar unfortunately in Github, and I'm missing the merge or commit buttons in that thread. Don't know why. I just also asked Simon. Maybe it is because he closed the thread, I don't know. As to the latter issue, @dr-shorthair could you have a look at that? Many thanks in advance! :)

HajoRijgersberg avatar Apr 21 '21 10:04 HajoRijgersberg

No worries @HajoRijgersberg

I'm having problems accepting it in Github

Looking at @dr-shorthair's PR in OM: https://github.com/HajoRijgersberg/OM/pull/49 it appears you've got some merge conflicts sometimes these are big deal sometimes not, sometimes github is just being overly cautious and flags things as conflicts where they aren't too bad. Hopefully something like this helps https://docs.github.com/en/github/collaborating-with-issues-and-pull-requests/resolving-a-merge-conflict-using-the-command-line.

Regarding this issue, later once the new system has more/all we can find of UCUM, I'll run @dr-shorthair's mappings through the new system to generate their UCUM codes and I'll check them against the labels in OM to look for mistakes in the mappings such as here.

kaiiam avatar Apr 21 '21 10:04 kaiiam

Hi Kai, Sorry for my late response; I must have overlooked your message. Thanx for it and your intentions of course! :) I hope to quickly come back to this issue. I have to dive into it again. Which of course I am very willing to do, appreciating the help of you, Simon, and others so much!

HajoRijgersberg avatar Jun 11 '22 11:06 HajoRijgersberg

Sorry again it took a (too long) while... Some while ago I have corrected W sr-1 m-1 Hz-1 manually. In the mean time I have become familiar with Git.

@dr-shorthair , have you been able to look at Kai's message:

Also unrelated I was having issues when sparql querying the om-2-ucum.ttl file (that @dr-shorthair recently added to) when using Robot query Same routine worked to query the QUDT VOCAB_QUDT-UNITS-ALL-v2.1.ttl file. The error message is the following. I think concerning imports or html tags.

The element type "p" must be terminated by the matching end-tag "</p>".

I have looked for:

<p>

but couldn't find it.

HajoRijgersberg avatar Mar 18 '23 18:03 HajoRijgersberg

I think it probably has something to do with the way it's being serialized into rdfxml or similar. I know this might be a bit much but I highly recommend the http://robot.obolibrary.org/ command line module from James Overton and co. It can do things like convert between serializations

image

Best of luck with your OM dev!

kaiiam avatar Mar 21 '23 07:03 kaiiam

Thanx Kai, that's (again) a very valuable hint! :) I'll definitely consider this option when I may have to standardize different formats used with/in OM. Cool work (again) of James's!

HajoRijgersberg avatar Mar 24 '23 15:03 HajoRijgersberg