'''Where:''' Paul Berg Hall A #230, [https://maps.google.com/maps?q=Li+Ka+Shing+Center+for+Learning+and+Knowledge&ie=UTF-8&ei=R2MWUreRB5DK9QTUloGoBg&ved=0CAoQ_AUoAg Li Ka Shing Center for Learning and Knowledge], 291 Campus Drive West, Stanford School of Medicine, Stanford, CA 94305. '''When:''' September 4-5, 2013 '''Audience''' *Day 1 is intended for all those engaged in information-driven immunology research who have an interest in the work of ImmPort and/or in ontology and data standardization *Day 2 (by invitation only) is intended primarily for those interested in CyTOF and related issues of data management in immunological science. '''Background resources''' *An overview of ontologies proposed by ImmPort for use across the immunology research community is provided [http://ncorwiki.buffalo.edu/index.php/Immunology_Ontologies here] If you are interested in attending please contact [mailto:phismith@buffalo.edu Barry Smith] as soon as possible. == Wednesday, September 4, 2013 == '''Schedule''' :8:30 Registration and Continental Breakfast :9:00 Barry Smith (Buffalo): Overview of ImmPort Ontologies [http://ncor.buffalo.edu/2013/Immunology/Smith.pptx Slides] :9:15 Jeff Wiser (Northrop Grumman): Discussion on the Role of Ontologies in ImmPort :9:45 Atul Butte (Stanford / ImmPort): The Future of ImmPort [http://ncor.buffalo.edu/2013/Immunology/Butte.pdf Slides] :10:00 Garry Nolan (Stanford): Goals for CyTOF :11:00 Break :11:15 Alex Diehl (Buffalo): PRO and CL [http://ncor.buffalo.edu/2013/Immunology/Diehl.pptx Slides] :11:45 Alan Ruttenberg (Buffalo): The Ontology for Biomedical Investigations (OBI) [http://ncor.buffalo.edu/2013/Immunology/Ruttenberg.pdf Slides] :12:15 Lunch :13:00 Holden Maecker (Stanford):Flow Cytometry Standardization and the Problem of Cell Typing [http://ncor.buffalo.edu/2013/Immunology/Maecker.pdf Slides] :14:00 Ryan Brinkman (Vancouver): [http://ontology.buffalo.edu/pro/CytometryOntologyFramework.pdf The Cytometry-Ontology Framework] [http://ncor.buffalo.edu/2013/Immunology/Lyoplate_CL%20mapping_29AUG2013%20(1).xlsx Supplementary data] :14:45 Melanie Courtot (Vancouver): Enabling Faster and More Accurate Analysis of Vaccine Adverse Event Reports with Ontology Support :15:15 Break :15:30 Lindsay Cowell (Southwestern Medical Center): VDJ Repertoire and Ontology-Based Data Sharing [http://ncor.buffalo.edu/2013/Immunology/Cowell.pdf Slides] [http://ncor.buffalo.edu/2013/Immunology/Cowell1.pdf Slides 1] [http://ncor.buffalo.edu/2013/Immunology/Cowell2.pdf Slides 2] == Thursday, September 5, 2013 == '''Schedule''' :8:30 Continental Breakfast :9:00 Nikesh Kotecha (Stanford / Cytobank): Software Challenges for Cytometry [http://ncor.buffalo.edu/2013/Immunology/Kotecha.pdf Slides] :9:30 Yannick Pouliot, Alex Diehl, Chris Mungall: Symposium on the Cell Ontology (CL) ::Cell types, cell stages, cell populations and CL terms and definitions. :10:30 Break :11:00 Alan Ruttenberg, Barry Smith: A Debate on Strategies for Use of Ontologies in ImmPort :12:00 Lunch :13:00 Open Discussion: Consequences for the Future of Immunological Science ::Topics to be addressed ::*The Cell Ontology as Canonical Ontology: The Case of OncoCL [http://ncor.buffalo.edu/2013/Immunology/Dolan.pdf Slides] ::*How do we create a Cell Stage / Cell State Ontology? ::*Do we need a Cell System (Immune Cell System, Cancer Cell System, (Intercellular, Stroma ...) :15:00 Shai Shen-Orr (Tel Aviv): Ontology, NLP and the Semantic Enhancement of Immunology Research Literature :16:30 '''Major Questions for Discussion''' 1. Evaluation of the cell type definitions proposed in [http://www.ncbi.nlm.nih.gov/pubmed/22343568 Maecker et al.] (if possible do this prior to the meeting) 2. What should be the framework by which we can represent cell populations identified through given sorts of assays in such a way that we can later promote them to cell types recognized in the CL? 3. How do we determine what is really a new cell type rather than either a refinement of an existing cell type generated by additional markers, or (2) a transient activation state of some known cell type? *Subtasks: :'''Ontological Background''' ::a. explain the difference between continuant and occurrent ::b. summarize how this difference is handled in other ontologies (especially GO) ::c. list a set of properties that distinguish a cell type (continuant) from a transient state type (occurrent) :'''Metadata''' :What metadata need to be captured in order to enable the downstream determination that a cell population identified by some assay is in fact either (a) a bona fide cell type that should be included in CL, or (b) a bona fide cell state type? *Proposed: :a. composition of the antigen panel :b. antibodies used to probe each antigen (expressed as ImmPort Antibody Registry ID) :c. the type of flow experiment: traditional, phosphoflow, CyTOF :d. unique experiment ID :e. species of the cells being probed (NCBI Taxonomy ID) :f. type of sample (whole blood, PBCs) :g. combination of markers that define a cell type according to the experimenter :h. clinical status of subjects (affected, unaffected; vaccinated/unvaccinated) :i. interventions (e.g., which arm of a trial the subject belongs to) (At least in the short-run, it is anticipated that these data will be obtained from ImmPort's store of flow data.) More ambitious questions for discussion if time allows: 3. Can we leverage CyTOF to develop a true step-by-step picture of hematopoiesis? This is a question for both ontology and the experimental approach. 4. What surface markers or internal proteins have reliable associations with biological processes, such that when we see a novel cell type or a variant of a known cell type we can predict the cell's function or (in other words the GO:Biological Processes it is capable of carrying out or participating in)? This question can obviously leverage existing GO annotations for particular proteins, some of which already have co-annotation with CL terms. But it can also lead to new terms for GO:Biological Processes and for CL cell types. == '''Participants''' == * Sanchita Bhattacharya (ImmPort / Stanford) * Ryan Brinkman (Vancouver, BC) * Atul Butte (ImmPort / Stanford) * Quan Chen (NIH / NIAID) * Lindsay Cowell (UT Southwestern, Dallas) * Melanie Courtot (Vancouver, BC) * Alexander Diehl (ImmPort / Buffalo) * Nikesh Kotecha (Stanford) * Suzanna Lewis (Berkeley) * Holden Maecker (Stanford) * Chris Mungall (Berkeley) * Garry Nolan (Stanford) * Yannick Pouliot (ImmPort / Stanford) * Alan Ruttenberg (ImmPort / Buffalo) * Nikolay Samusik (Stanford) * Ravi Shankar (ImmPort / Stanford) * Shai Shen-Orr (ImmPort / Technion Institute) * Barry Smith (ImmPort / Buffalo) * Nicole Vassilesky (OHSU, Oregon) * Jeff Wiser (ImmPort / Northrop Grumman) * Ashley Xia (NIH / NIAID) Plus further participants from Stanford area.