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I was writing some code scripts to analyze some plasmodium spp. using this database. However the names assigned to the various epitopes and other items on the list is very very very disorganized. In some places there are acronyms and other places the full name. Sometimes hyphens replace the spaces for the same epitope name. So I was trying to collect lists of all the different names that are actually synonyms of each other. However there were some words that were added on sometimes that I wasn't sure would count as synonyms:

  • "xxx" and "xxx, putative" synonyms?
  • "xxx" and "xxx like antigen" synonyms? (this one made little sense to me as both are epitopes
  • "xxx" and "xxx 1" synonyms?
  • "xxx" and "xxx partial" close enough to be synonyms for sake of grouping?

I'm rather new at analyzing these sorts of databases. I'm sure I'll find other such messy naming issues and was wondering how to approach such a problem and solve such discrepancies.

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closed as unclear what you're asking by kmm, another 'Homo sapien', James, canadianer, AliceD Jul 5 '17 at 21:46

Please clarify your specific problem or add additional details to highlight exactly what you need. As it's currently written, it’s hard to tell exactly what you're asking. See the How to Ask page for help clarifying this question. If this question can be reworded to fit the rules in the help center, please edit the question.

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The answer of David explains most of the common/general problems you encountered and how to tackle them. In case you don't have anyone more experienced to consult, I'll try to give suggestions for the specific cases you mentioned.

  • "xxx" and "xxx, putative"
    These might synonyms, but the 'putative' indicates that the authors of the entry weren't sure themselves. If you want robust results don't group these together (or exclude the putative ones). If you need more samples, group them but maybe test how much difference it makes.

  • "xxx" and "xxx like antigen"
    I think it's quite likely that many of these will not be synonyms. Many genes and proteins are named after similar known ones ('xxx' - known; 'xxx like' - new gene), but that doesn't mean they have related functions.

  • "xxx" and "xxx 1"
    These could be synonyms. I don't know any examples where two different genes/proteins named like this exist. To be save you should check this on a case by case basis and look up both versions on uniprot or NCBI.

  • "xxx" and "xxx partial"
    You can group these together. You're dealing with peptide antigens, so fragments of proteins. Therefore partial proteins are not a problem.

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  • $\begingroup$ Thanks! This answer helped a lot! Both of your answers did! :) $\endgroup$ – Clangorous Chimera Jul 1 '17 at 14:55
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It’s not the fault of the database, it’s the fault of the individual scientists that described the epitopes. O.K. in a perfect world the curators would have gone through the entries and tried to standardize the descriptions. But they probably lack the time or expertise. I sympathize with them.

So what can you do? You have to use your own expertise or that of experimental scientists you are working with and make your own decisions, some of which will be incorrect.

This is a general problem with databases compiled from papers or individual submissions, and is a headache for data mining: misspellings, spaces or no spaces, hyphenated or not, different names for the same entity. Unfortunately there’s no fairy with a magic wand to solve the problem for you.

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  • $\begingroup$ Thanks! I wish there were some kind of dictionary at least that kind of outlined some of the basic terminology(like when to use and when not to). I guess I've been spoiled by IUPAC in orgochem. $\endgroup$ – Clangorous Chimera Jul 1 '17 at 14:58

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