owlcollab / owlcollab/owltools

Ensure imports closure is used in all OGW methods

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Description

From cmung...@gmail.com on October 29, 2013 08:51:50

Test case from Tony S:

Here, for example, is the definition of GO:0003330 that we get from
parsing go.owl:

TERM|GO:0003330|regulation of extracellular matrix constituent secretion|P|N DEFI|GO:0003330|Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. DEFX|GO:0003330|GOC|tb DEFX|GO:0003330|GOC|dph EDGE|GO:0003330|GO:0051128|I EDGE|GO:0003330|GO:0070278|R EDGE|GO:0003330|GO:0051046|I EDGE|GO:0003330|GO:0060341|I

and here is what we get from go-plus.owl:

TERM|GO:0003330|regulation of extracellular matrix constituent secretion|P|N DEFI|GO:0003330|Any process that modulates the rate, frequency, or extent of the controlled release of molecules that form the extracellular matrix, including carbohydrates and glycoproteins by a cell or a group of cells. EDGE|GO:0003330|GO:0060341|I EDGE|GO:0003330|GO:0051046|I EDGE|GO:0003330|GO:0051128|I

Original issue: http://code.google.com/p/owltools/issues/detail?id=82

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating the OGW methods responsible for producing the shown go.owl and go-plus.owl definitions, then trace how each method loads imports. Use the GO:0003330 examples as a comparison point; done means all OGW methods consistently use the imports closure and produce the expected imported edges.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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