Dupe ids and URI issue #10
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Thanks Jane - lovely to hear from you! I've added this to the current milestone for our imminent next release, so this is perfect timing. There are some big changes coming up, mostly in how we import EDAM and the general tidiness of the ontology. Now, at a very quick count there are 712 classes that have the "http://www.ebi.ac.uk/efo/swo" prefix and 554 that have the standard "http://www.ebi.ac.uk/swo" prefix. I'm not sure why the efo prefix came in... @jamesmalone do you remember anything reason from SWO history for these? I'm happy to reconcile and remove the http://www.ebi.ac.uk/efo/swo prefix and replace with http://www.ebi.ac.uk/swo but as you've pointed out Jane, this will require checking for duplicates and therefore needs to be done carefully. If James also agrees that we should clean these IRIs, I'll try to do it this week one evening as I'd like to get the 1.7 release out very soon. Jane - if you or your pharma customers would like a peak at the new SWO, your thoughts would be appreciated. It isn't published as a release, but the current working copy of the pre-release file can always be found at https://github.com/allysonlister/swo/blob/master/dev/ontology/swo-merged.owl Thanks! Ally :) |
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Hi Ally, indeed, the URIs http://www.ebi.ac.uk/efo/swo/SWO_nnnnnnn don't resolve. It's frustrating because some of the software URIs are fine (http://www.ebi.ac.uk/swo/SWO_0000015 for Excel 2002), but most of dead. Happy to shoot over a list of URI I've tested and their status codes, if that's helpful. Many thanks, Mark. |
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I've created a list of efo URIs from SWO (see attached). Happy to have your list, and compare them if that helps? Please note I'm working from the upcoming release file, which is currently available at https://github.com/allysonlister/swo/blob/master/dev/ontology/swo-merged.owl Here's the list of 661 URIs that begin with http://www.ebi.ac.uk/efo/swo: For each of these I'd need to:
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Thanks! Here's the results of my testing this morning. |
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SWOtest2_20191001.zip |
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That's OK - it makes sense that they're 404 - I expect there was a batch creation of SWO classes some time ago, and the "efo" URI was used instead of the standard one. I'd just like confirmation from James before I make any such large changes to the IRIs. Thanks! |
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oo, since you're working on SWO, could you add some new terms? URIs for BCBio and ShinyNGS would be good. |
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@drmarkreuter thanks for the suggestion - you'll find I've asked you to provide some basic info on each at #11 and #12 :-) |
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I've spoken with @TheOntologist @jamesmalone and Helen Parkinson. James' thought is that, because SWO was created under the auspices of EFO, some of the IRIs have that structure. However, as they don't resolve, I'm going to go ahead and make the changes. This will be a multi-step process, and the code used to generate the changes together with mappings will be stored in its own directory in the dev/ folder. Broadly, here's what will happen:
The file for step 1 is ready, and I'm just working on step 2 now. I'll let you know when I've made the change. |
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After Step 1 above, there remained 14 clashes in the SWO namespace:
In all cases, the updated IRI as suggested above was manually added to https://github.com/allysonlister/swo/blob/master/dev/IriRefactor/refactor-efo-swo-mappings.csv and the mappings were re-run. Equally, we sorted out #18 #16 and #17 in this mapping file. |
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This is closed now, but I would really appreciate @janelomax and @drmarkreuter checking the resulting SWO pre-release file. As you requested the IRI change, please can you download https://github.com/allysonlister/swo/blob/master/dev/ontology/swo-merged.owl and see if you are happy with these changes? Many IRIs were modified. If you notice any issues, please reopen this ticket. Please note that, as this is still a pre-release, the new IRIs will not be resolvable in OLS etc, as they won't be loaded/indexed by those sites until the actual release happens. Thanks very much! |
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I loaded it into Protege and checked a few of the ids we have been discussing and all looks good to me! |
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checking now. I'm no ontology expert, but I'm spend some time on this this morning. Thanks for adding those terms! |
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Thanks guys I appreciate it. It's important to have a few people look at such a big change, I don't want to miss anything. :-) |
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Potential issue with SWO0000199 (GenePix Pro 4.0). robot couldn't convert from owl to obo... |
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I don't see any issues...?? |
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Thanks @drmarkreuter - I'm not familiar with OBO conversions, but the error message seems to indicate that there is more than one "name" in a class. If "name" in OBO corresponds to rdfs:labels, then I do think that there may be a few cases in SWO where more than one label has crept in over time. However, http://www.ebi.ac.uk/swo/SWO_0000199 is not one of these; it has a single label. Could it be that the obo converter is seeing the old obsolete IRI http://www.ebi.ac.uk/efo/swo/SWO_0000199 as "the same class"? In any case, the output you're looking at after a ttl conversion looks correct. If you can figure out exactly what the robot converter is upset about in that class, I can look into changing things, but the OWL itself is sound as far as I can tell. Thanks - I think we're good with the refactoring! |
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I agree, it all looks fine to me. I've manually checked some of the previous clashes, and happy to see that they have shiny new URIs.
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Hi Allyson - hope you are well, long time no see!
One of our pharma customers is using SWO and spotted a dupe id: SWO_0000075
In OLS they have slightly different URIs:
http://www.ebi.ac.uk/efo/swo/SWO_0000075
http://www.ebi.ac.uk/swo/SWO_0000075
(the http://www.ebi.ac.uk/efo/swo/ URIs don't resolve anywhere)
thanks
Jane
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