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[BUG] BioFSharp.IO.Obo.parseOboTerms parsing error with ':' #111

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Freymaurer opened this issue Feb 11, 2021 · 0 comments
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[BUG] BioFSharp.IO.Obo.parseOboTerms parsing error with ':' #111

Freymaurer opened this issue Feb 11, 2021 · 0 comments
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@Freymaurer
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Describe the bug
I used the function mentioned in the issue header to parse obo files for SwateDB and noticed that i have some duplicate entries:

Example:
image

Now i checked into it and found out that most are created due to parsing errors as can be seen here:
image

If you check the accession numbers, e.g.:

http://purl.obolibrary.org/obo/MS_1001151
http://purl.obolibrary.org/obo/MS_1001261

the problem seems to involve ':' as part of the ontology term name.

To Reproduce
Steps to reproduce the behavior:

  1. .fsx with biofsharp referenced.
  2. use code snippet below to read in ms.obo.
  3. search for shown accession values (id's).

codesnippet:

let msOntologyTerms = 
   __SOURCE_DIRECTORY__ + @"/../../ms.obo"
   |> Seq.fromFile
   |> parseOboTerms
   |> Array.ofSeq

Expected behavior
Should parse term name correctly or throw error.

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