Phylogenetic comparative analysis of integrated anatomical traits
A Short Course
When and Where?
- Date: June 26, 2019 (Wednesday)
- Time: 9:00 am-12:00 pm
- Location: South County Room, Omni Providence Hotel (adjacent to RICC)
- 9:00am Welcome and intros, goals
- 9:15 Background concepts: anatomy ontologies, phenotype annotations and character dependencies
- Using Phenoscape Knowledgebase and RPhenoscape
- 9:55 Obtaining presence/absence supermatrices
- Using OntoTrace with RPhenoscape
- 10:30 Break
- 10:45 Constructing stochastic character maps on a phylogeny
- Using the PARAMO pipeline with RevBayes
- 11:30 How to manage your own data
- Demo of Phenex and Phenoscape annotation guidelines
- 11:45 How to learn more
- Semantic similarity (optional demo), other applications
- How to retrieve candidate genes for anatomical traits
- Related efforts
Call for participation
Ontologies encode information about a domain of knowledge, such as how anatomical structures are related, which is crucial information for modeling character evolution. Phenoscape, in its current Semantic Comparative Analyses for Trait Evolution (SCATE) project, is developing tools that use the computable knowledge in ontologies to improve phenotypic character modeling and inform analyses of trait evolution. To train evolutionary biologists and developers of comparative analysis tools to adopt these new capabilities, the SCATE team will be holding a short course on using ontologies in comparative analyses of integrated anatomical traits, in conjunction with the 2019 iEvoBio and Evolution Meetings, on June 26, 2019 in Providence, Rhode Island.
Attendees will learn how to use R packages such as RPhenoscape to access a knowledgebase of ontology-linked phenotypes, build character matrices that take anatomical dependencies into account, and use these to construct stochastic character maps on a phylogeny. The course will also include a practical introduction to community ontologies for biodiversity domain knowledge (anatomy, taxonomy, phenotypic quality).
Graduate students, postdocs, faculty, and software developers with interests in comparative analyses, morphology, and phylogenetics are encouraged to apply.
Free registration: Applications accepted until May 15th or capacity is reached. Register by filling out the form at https://goo.gl/forms/802KN6cd6cQOI01Q2
- Jim Balhoff Renaissance Computing Institute
- Wasila Dahdul, U South Dakota
- Hilmar Lapp, Duke U
- Paula Mabee, U South Dakota
- Josef Uyeda, Virginia Tech
- Todd Vision, UNC Chapel Hill
- Dececchi et al. Toward Synthesizing Our Knowledge of Morphology: Using Ontologies and Machine Reasoning to Extract Presence/Absence Evolutionary Phenotypes across Studies. Systematic Biology 64, 936. 2015. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604830/
- Tarasov et al. PARAMO pipeline: reconstructing ancestral anatomies using ontologies and stochastic mapping. bioRxiv 2019 https://doi.org/10.1101/553370
SCATE is funded by the US National Science Foundation (NSF) as collaborative awards 1661456 (Duke University), 1661529 (Virginia Tech), 1661516 (University of South Dakota), and 1661356 (UNC Chapel Hill and RENCI) within the Advances in Biological Informatics (ABI) program.