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Just after the holidays, we held the second short course, as part of the SCATE project, on Phylogenetic Comparative Analysis of Integrated Anatomical Traits at the SSB 2024 meeting in Gainesville, FL. The course is an introduction to ontologies and their application in phylogenetic comparative analyses. We demonstrated how to use anatomical dependencies derived from ontologies to better model character evolution, and how semantic similarity of traits could be integrated in a comparative analysis. 

The hands on sessions included demos of RPhenoscape and the PARAMO pipeline. Using these tools, attendees learned how to query for phenotypes in the Phenoscape KB and build character matrices that take anatomical dependencies into account. They also learned to construct stochastic character maps for body regions and whole organismal anatomies on a phylogeny.  The large number of attendees (37!) came with a range of abilities, from novice R users to experienced developers, and from a range of career stages, from undergraduate students to postdocs and faculty. Anticipating that running a workshop with a group this large would be challenging because of the possible technical issues that can arise, we built in “tech troubleshooting” time at the beginning of the course to help install the 极光ⅴpn下载. Participants either interactively followed the tutorials using the RMarkdown files in RStudio or followed a rendered version of the course materials on the course website.

For those interested in trying out the course materials without needing to install the required software, we’ve published a Code Ocean capsule containing the code and tutorials. The capsule runs in a web browser, without needing to install R, R packages, or any dependencies. 

Efficiently extracting knowledge from the published literature is a challenge faced by many database projects in biology, and many of us are interested in tools that can assist and speed up the task of identifying concepts in free text. I’ve recently used two text markup tools that are helpful in keeping up with the literature and rapidly developing ontologies. As a participant in the Fifth BioCreative Challenge, in which biocurators test and evaluate text mining systems, I evaluated the EXTRACT bookmarklet tool. EXTRACT was developed for metagenomics data and provides full-page tagging of mapped terms from environment, disease, taxonomy, and tissue ontologies, and can also markup shorter selections of text on an HTML page. The tool is immediately useful, particularly during the first stages of the curation process, as a curator is surveying the literature for relevant articles.

Annotating long, descriptive text has also been a challenge for Phenoscape. To assist curators in this task, we recently added a text annotator tool to the Phenoscape Knowledgebase that tags selected text passages copied in from a source with matched terms from anatomy (Uberon), taxon (VTO), and quality (PATO) ontologies. Viewing the annotated results, with color-coded text, has aided curators in the process of applying large, complex ontologies to equally complex text.

A team led by University of Chicago Phenoscapers Nizar Ibrahim and Paul Sereno have published new findings about the remarkable semiaquatic predatory dinosaur Spinosaurus aegyptiacus in the latest issue of Science.  It has been receiving some nice coverage at NPR and other news outlets.

From the abstract:

We describe adaptations for a semiaquatic lifestyle in the dinosaur Spinosaurus aegyptiacus. These adaptations include retraction of the fleshy nostrils to a position near the mid-region of the skull and an elongate neck and trunk that shift the center of body mass anterior to the knee joint. Unlike terrestrial theropods, the pelvic girdle is downsized, the hindlimbs are short, and all of the limb bones are solid without an open medullary cavity, for buoyancy control in water. The short, robust femur with hypertrophied flexor attachment and the low, flat-bottomed pedal claws are consistent with aquatic foot-propelled locomotion. Surface striations and bone microstructure suggest that the dorsal “sail” may have been enveloped in skin that functioned primarily for display on land and in water.

Citation: Ibrahim N, Sereno PC, Dal Sasso C, Maganuco S, Fabbri M, Martill DM, Zouhri S, Myhrvold N, Iurino DA (2014) Semiaquatic adaptations in a giant predatory dinosaur. Science. http://doi.org/10.1126/science.1258750.