Semantic resources project/PRO/Tau Discussion 09-07-2010

Tau

 * the difference between canonical sequence and "wild type"
 * do we need to represent wild-type-ness?
 * Does a site like "Arg-406" really need to be described with "Arg?" Why not just "406"?
 * Globally replace 'E' with 'R'
 * Add placeholder terms for NFT and PHF?
 * PRO protein complex work is going to be relevant to understand the way that NFTs are made up of multiple phosphorylated versions of Tau.

Presenilin

 * shares a lot of common features with Tau and APP: mutations, causes early onset,
 * 9 transmembrane domains in the complex
 * 2 of the transmembrane proteins, TM-6 and TM-7, contain the enzymatic activity,
 * but these don't work on their own.
 * other parts have their own functions, which we'll need to enumerate.
 * but does it as a component of a multi-protein complex.
 * the other three major componets of gamma-secretase complex
 * plethora of regulatory proteins (post-translational protein transport through the ER trans-golgi network, both antero-grade and retro-grade; lots of protein trafficking).
 * lots of checkpoint proteins that ensure that proteins which have been properly translated and folded
 * will send a chapter from her Presenilin review.

B-list

 * NMDA receptors
 * Heat shock proteins
 * synuclein
 * Huntingtin
 * SOD-1
 * prion protein
 * "candidate proteins that have been classified as protein-opathies."

Gwen's Notes

 * we went through the flow chart, TWD explained all the parts and terms.
 * He will revise it slightly and clean up some minor typos (E3 and E4 should be R3 and R4, referring to microtubule-binding repeats) and then he will go back to Alan and Paolo to decide what to send to Darren. They will hopefully send something to Darren soon.
 * No protein complex term (ie NFT or PHF) are represented on the obo file or flowchart, but we both agree that these are important, and want to ask PRO to consider the possible ways to represent these protein complexes, such as:
 * NFT "has_part" tau N2R4 or something like that.
 * This would also be applicable to more difficult protein complexes that we tackle in the future such as gamma secretase.
 * While we wait for PRO to respond to the tau use case, we are going to go ahead and start working on Presenilin, as a component of gamma secretase, but also having early onset mutations, splice variants, etc.
 * Towards that goal, I will send TWD some background reading and I will start putting together a Powerpoint file that describes specific pro issues affecting presenilin proteins.