'''Date''': October 23-24, 2019 '''Venue''': :Protein Information Resource :Georgetown University Medical Center :Suite 1300 :3300 Whitehaven Street NW (Milton Harris Building), :Washington, DC 20007, USA For '''logistic questions''' please call BS at (716) 361-5100 '''Parking''' is available [https://buffalo.app.box.com/v/PRO-parking-map here] ($11 per day) '''Zoom''': https://georgetown.zoom.us/j/3531468363 ==Goals== The goals of this meeting are: *1. To describe the future of PRO in light of the aims of the upcoming grant proposal: ::(a) represent proteoforms of clinical interest ::(b) connect sequence variations with molecular mechanisms using semantic web technologies ::(c) link disease biomarker, antibody, and drug target information to appropriate proteoforms ::(d) connect proteoform expression profiles to cell types ::(e) enhance PRO quality control and distribution mechanisms. *2. To describe PRO's collaborating projects and how they fit into PRO. *3. To discuss implementation plans, especially with respect to collaborations. ==Schedule: Wednesday, October 23, 2019== :8:15 Breakfast '''Advancing disease understanding with site information: PRO and UniProtKB''' ''Chair: Darren Natale'' :8:45 Logistics and introductions (Barry Smith) :9:00 [https://buffalo.box.com/s/9k3mnsy2ddodun7wje10ud9fe1dzuepg Meeting objectives] (Darren Natale) :9:20 [https://buffalo.box.com/s/2ge3p0ae5x6dd8oidks6vh4xgms9ichu General introduction to PRO] (Darren Natale) :9:35 [https://buffalo.box.com/v/Ruttenberg-PRO-Sites PRO sites] (Alan Ruttenberg) :9:45 [https://buffalo.box.com/s/og1tusat1l4ucbbhm51wd6zh539dxfyk PRO Sites] (Darren Natale) :10:15-10:30 Break '''Uncovering disease mechanisms: connecting site annotations to ontologies''' ''Chair: Judith Blake'' :10:30 [https://buffalo.box.com/s/d93kobo8dh0alyb5ykkina6e1nw81s5p UniProtKB Feature Viewer] (Alexander Bateman) :11:00 [https://buffalo.box.com/s/ylbpwqz19y7cvxuwhg2eqg40yzxq7mr5 UniProtKB's molecular impact information] (Harold Drabkin) - connecting feature line information to ontologies :11:30 [https://buffalo.box.com/s/42fky2o87di08dk4q943t52l4ktpovi0 Disease Ontology] (Melody Swen) - introduction to DO and how it can be used to go from UniProtKB variants to disease identifiers :12:00 [https://buffalo.box.com/v/PRO-meeting-BFO-OGMS Basic Formal Ontology and Ontology for General Medical Science] (Barry Smith) - introduction to OGMS and to the new ISO/IEC 21838 top-level ontology standard :12:30-13:30 Lunch '''Uncovering disease mechanisms: connecting variants to diseases''' ''Chair: Judith Blake'' :13:30 [https://buffalo.box.com/s/p640nyu246h7736k7xt8sbkak6twffoz Mouse models of human disease] (Li Ni) :14:00 [https://buffalo.box.com/s/jo07sdssyn52fj89j3stn63aucx6a5yv Extracting variant / disease associations from text] (Cecilia Arighi) :14:30 [https://buffalo.box.com/s/d1qbf10l14lv31bnnpg2i17oi1re49r6 Discovering molecular mechanisms underlying disease] (Karen Ross, Natarajan Kannan) - the PRO/ProKinO/NeXtProt work as a model for what's to come :15:00-15:30 Break :15:30 [https://buffalo.box.com/s/6kdes4lhv1s0rz89fn6tm943jxb3ajca Leveraging PRO in EuPathDB, OrthoMCL, and NIAGADS Genomics] (Chris Stoeckert) :16:00 [https://buffalo.box.com/s/ygac6ictkvsfqvx79snsl8jxgejewyiz Protein aggregates] (Lauren Wishnie) :16:30 Close of Day 1 :18:00 Working dinner ==Schedule: Thursday, October 24, 2019== [https://docs.google.com/document/d/1PiVxUQcEjsMlbudSGbxkVKwg3ib7KFnRyvHgv-CpUa4/edit?ts=5db0bc19 Googledocs discussion page from Day 1] :8:15 Breakfast '''Clinical discovery: connecting clinically-relevant information to proteoforms and complexes''' ''Chair: Peter d'Eustachio'' :8:45 Introduction to Day 2 theme (Darren Natale) / Logistics (Barry Smith) :9:00 [https://buffalo.box.com/s/x66k2vdtw0cjnqvl2npklofj92pi08bm Reactome's disease pathways] (Peter d'Eustachio) - how they can be used with PRO to make new proteoform/disease associations :9:30 [https://buffalo.box.com/s/pptezlimqnxqd7maxamw2aa9ke33nla3 Using DTO and PRO for Drug target discovery] (Stephan Schürer) :10:00 [https://buffalo.box.com/s/xvaekv096s5pmwhium9c73jwmc2xn45x Connecting diseases to epitopes and proteins] (Randi Vita) :10:30-10:45 Break '''Cell type discovery: proteoform expression and clinically-relevant cell types''' ''Chair: Alexander Diehl'' :10:45 [https://buffalo.box.com/s/0sexse2ofjo7nl96d0dy4qahtvkgbhic Cell Ontology and its use of PRO] (Alexander Diehl) :11:05 Proteoform-based cell type dictionary (Alexander Diehl) :11:30 [https://buffalo.box.com/s/q5qpc7v0dsfi0kiksc6id4r5k89yysdz ImmPort and its use of PRO] (Patrick Dunn) :12:00 [https://buffalo.box.com/s/y2lcjgvha37ls6xmxx829qah4x6enbwy Communicating and cataloging proteoforms within the Blood Proteoform Atlas] (Paul Martin Thomas and Richard Dann LeDuc) :12:30-13:00 Lunch :13:00 [https://buffalo.box.com/s/gvmwx3nzb24p30kz1xrqaqvot8wlnm00 Sequences beyond the Central Dogma: describing, quality controlling, exchanging, and visualizing proteoforms with concrete chemical semantics using BpForms/BcForms] (Jonathan Karr) :13:30 TBD :13:45 PRO grant working session :15:00 Close of meeting ---- == '''Participants''' == :Cecilia Arighi (Delaware / PRO) :Alexander Bateman (EBI)* :Judith Blake (JAX) :Peter d'Eustachio (NYU) :Alexander Diehl (Buffalo) :Harold Drabkin (JAX) :Patrick Dunn (ImmPort) :Natarajan Kannan (Georgia) :Jonathan Karr (MSSM) :Richard LeDuc (Northwestern) :Yu Lin (FDA) :Birgit Meldal (EBI)* :Darren Natale (Georgetown/PRO) :Li Ni (JAX) :Karen Ross (Georgetown/PRO) :Alan Ruttenberg (Buffalo) :Stephan Schürer (Miami) :Henry Schaefer (ImmPort) :Barry Smith (Buffalo) :Christian Stoeckert (Penn) :Melody Swen (Baltimore) :Paul Martin Thomas (Northwestern) :Randi Vita (San Diego) :Lauren Wishnie (Buffalo) :Cathy Wu (Delaware / PRO) :Sara Yang (NIST) *=online Please contact [mailto:phismith@buffalo.edu Barry Smith] for further information. == '''Sponsors''' == :[http://pir.georgetown.edu/pro/ The Protein Ontology Consortium] :[http://ncor.buffalo.edu National Center for Ontological Research]