One of the most important use cases of ontologies is the calculation of similarity scores between a query and items annotated with classes of an ontology. The hierarchical structure of an ontology does not necessarily reflect all relevant aspects of the domain it is modelling, and this can reduce the performance of ontology-based search algorithms. For instance, the classes of phenotype ontologies may be arranged according to anatomical criteria, but individual phenotypic features may affect anatomic entities in opposite ways. Thus, "opposite" classes may be located in close proximity in an ontology; for example enlarged liver and small liver are grouped under abnormal liver size. Using standard similarity measures, these would be scored as being similar, despite in fact being opposites. In this paper, we use information about opposite ontology classes to extend two large phenotype ontologies, the human and the mammalian phenotype ontology. We also show that this information can be used to improve rankings based on similarity measures that incorporate this information. In particular, cosine similarity based measures show large improvements. We hypothesize this is due to the natural embedding of opposite phenotypes in vector space. We support the idea that the expressivity of semantic web technologies should be explored more extensively in biomedical ontologies and that similarity measures should be extended to incorporate more than the pure graph structure defined by the subclass or part-of relationships of the underlying ontologies.
📖 On page 143of 425 of A Riddle in Ruby by Kent Davis
The story is starting to move along now. We’ve discovered where the father has been taken, but we’re still completely in the dark about why things are happening. The color and description of the world is coming more firmly into place.
This is "Sawyer on the elasticity of the liberal arts education" by Williams College on Vimeo, the home for high quality videos and the people who love them.
One of them is creating a simple mobile workflow to take headlines from Twitter and get them into my reading queue. Previously I had used an IFTTT.com recipe to take things I “liked” in my Twitter stream to strip off URLs and put them into Pocket for reading later. In fact, very few of my thousands of likes in Twitter are traditional “likes” because I’m really using that functionality to indicate “I’d like to read the article linked to in this Tweet at a later date”. Somewhere in the past couple of months I’ve mused to at least one person on the PressForward team that it would be nice to have a simple indicator to send articles from Twitter to PressForward like this, but even if I were building it all by hand, this would be a bit further down the list of priorities. What to do in the erstwhile?
RSS has long been going out of fashion, particularly among the major social silos who want to keep you in their clutches, but it dawned on me to check to see if Pocket or Instapaper provide RSS feeds. Sure and gloriously enough, they do! In fact, Pocket has an unread feed, an archive feed, an all items feed (that includes both of the other two), and as a lovely additional touch, they’ve even got the ability to make feeds private. Instapaper has RSS feeds too, though they were a bit more hidden and took a right click/view source along with a manual completion of their base URL. The nice part is that one can take these RSS feeds and plug them straight into one’s PressForward RSS feedet voilà there they are on my own site! (From the viewpoint of PressForward, this is also very close to being able to nominate items directly from Twitter.) While this is more of a PESOS feed, the result is a no-brainer and provides a near real-time experience that’s more than adequate for my needs (at least until yet another silo goes down).
And as added bonuses, if I feel like using Pocket or Instapaper from time to time, I can do so without loss of data along the stream and the small handful of people with whom I interact on Pocket won’t notice the fact that I’ve disappeared.
For the millionth time, G-d bless RSS, a wonderful tool I use every single day.
