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How Do You Suggest To Enter Gene Mutations In Protege

I am creating an OWL file from Human Genome at run time so I can later open it in Protege. A first problem I saw is that I can't enter something like HIV-1.c.2752A>T" because of that ">" in it., protege says it is an illegal character. What do you suggest to do?

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updated by Pierre Lindenbaum Pierre Lindenbaum • written by aghili.babak • aghili.babak

how would it be used ? As a Resource or as a Literal ?

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, I don't really know that much the difference between resource or literal . In the "Code" I am passing them as Classes.. in Protege I am creating them as "Class" too, right click on "thing" and adding a class with a name like "HIV-1.c.2752A>T" to it....which gives error.

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written by aghili.babak • aghili.babak

1 answer

As far as I understand, you're trying to create a class having a URI containing "HIV-1.c.2752A>T". I don't use protege but I think it is a misunderstanding about protege and RDF/OWL.

  • You're not creating a class but an instance (individual) of class. "HIV-1.c.2752A>T" is an instance of a class "Variation"
  • you need to create to create an ontology describing what is a Variation, or you can use an existing ontology ( see http://bioportal.bioontology.org/ )
  • "HIV-1.c.2752A>T" would be part of a text, a label. Not a URI
  • The URI would be a unique identifier for this mutation. Something like http://my.database.org/variations/9808912 or nothing (anonymous URI).

A the end, you're expecting something like this:

(...)
<my:Variation rdf:about="&lt;a href=" http:="" my.database.org="" variations="" 9808912"="" rel="nofollow">http://my.database.org/variations/9808912">
  <my:label>HIV-1.c.2752A>T</my:label>
  <my:position>2752</my:position>
   <my:ref>A</my:ref>
   <my:alt>T</my:alt>
</my:Variation>
(...)
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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, so if I understand correetly that "HIV-1.c.2752A>T" should be an "Instance" or "individual " of the class that represents it... please correct me if I understood wrong..thanks.

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written by aghili.babak • aghili.babak

But you cannot use the sentence: "HIV-1.c.2752A>T" as the URI/identifier of the variation. It wouldn't be a valid URI.

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written by Pierre Lindenbaum Pierre Lindenbaum

Thanks Pier, Think of a TreeView in a Windows application, users can expand nodes and drill down to the child nodes, etc... I had the same thing in mind but with OWL and Protege, so they can expand hierarchy of a gene and drill down to the genes , mutations, .... so I guess my visual thought to begin with was wrong and some of these Gene info we should model them and show them in other places of Protege, like on Individuals section of a class, etc... How do you envision such a thing visually?

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written by aghili.babak • aghili.babak

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