#171 Change ChEBI mapping errors

closed
8
2008-05-28
2008-05-14
Kristian Axelsen
No

Hi,

I just tried to change the mapping of chebi:17214 to chebi:1467. I did not succeed and in the process I noticed several oddities.

1. For Rhea:13365 I got the message: The resulting reaction already exists in the database.

This is not true. When I search for 4-methyl-2-oxopentanoic acid I only find Rhea:13365

2. Rhea:24647 was included in the list. This I think is an error as 24647 is a complex reaction consisting of Rhea:13365 and Rhea:11201.

Complex reactions should not be included in such a change mapping scheme since they will automatically change when the underlying simple reactions are changed. Furthermore, it should not be possible to change them directly since they depend on the underlying simple reactions, so updating them may lead to unexpected behaviour (see below).

I tried to perform the update in the development tool, and I could see no difference when I looked at 24647 again. I also tried to repeat the update, and saw both reactions again. But now 24647 (also) gives the message: The resulting reaction already exists in the database.

/Kristian

Discussion

    • labels: 584831 --> Rhea curator tool
    • priority: 5 --> 8
     
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    I think this error substantiates the need to be able to merge identical reactions. This could most probably have avoided this situation as 24647 is obsolete because it is identical to 25082.

    That it is obsolete is impossible to see in the change chebi mapping window. If I had known this I would probably not have tried to perform the update.

    /Kristian

     
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    Kristian,

    1. The reaction does exist (RHEA:25078, as you mention). I found it by searching for the other two participants: the query string 'chebi:48430 chebi:16526' gives me 5 results, one of them being the conflicting reaction.
    I don't know why you only get RHEA:13365. When I searched for '4-methyl-2-oxopentanoic_acid' I got 7 results, RHEA:13365 and RHEA:25078 among them.

    2. Replacing a compound must update also related complex reactions, as their fingerprint changes as a result. I understand that their update should not be optional: if you accept the replacement for RHEA:13365, RHEA:24647 should automatically update; if you don't, it shouldn't. Right.

    3. Yes, merging reactions is a pending issue. A merged reaction should get an 'obsolete' status, I think.

    Regards,

    Rafa

     
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    1. OK, today I get the same set as you, so no error here
    3. I don't mind what status they get as long as they disappear from searches, mappings, etc. If not you will continue to find them again and again and that would be confusing i.e. , if Rhea:1 is merged into Rhea:2, 1 should disappear and 2 should continue to be there without any apparent differences (of course x-refs and other differences in data from 1 should be integrated in 2).

    /Kristian

     
    • status: open --> closed