Friday, November 6, 2009

That's (not) highly illogical Jim

Our next update to the HAO has been posted to the OBO foundry. While our existing versions passed the OBO edit verifications we were still generating logical redundancies. For example if we know that A is_a B and B part_of C then we can deduce A part_of C. In around 70 cases we were additionally adding this A part_of C statement, these are all now removed. Whether or not these are actually "harmful" is still somewhat unclear, for instance the other arthropod ontologies all have logical redundancies (Spider: 6 , Tick: 2 Mosquito: 1, and Drosophila: 464), and some non-arthropod ontologies have even higher numbers (ZFIN has 2543).

The code to generate the Newick trees seen in the previous post is now live as well. We've made a simple form (see below) that allows users to customize and output trees. Several different node and "clade" highlighting options are available and we plan to expand these as well.

Below is the result of the tree generated above. It shows a categorical summary (increasing number with color darkness) of the number of immediate part_of children.

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