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geneontology / paint

This curation tool allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions.
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Speed up of loading is essential #2

Closed selewis closed 9 years ago

selewis commented 9 years ago

As an example PTHR23315 (1443 nodes) takes over an hour and still is stuck sorting terms out. Possibly it's crashed quietly, but I'm guessing it is traffic back-and-forth to GoLR. Need to work with Seth and Heiko on this

hdietze commented 9 years ago

One optimization is to replace the OWLGraphWrapper.getAncestors method. This method is known to be slow and has very high memory requirements. The stop gap is to use a similar approach to the amigo loader (ExpressionMaterializingReasoner) until a full switch to Scigraph for such queries can be made.

hdietze commented 9 years ago

See example snippet: https://gist.github.com/hdietze/af03c672a1d18817b1b8