4 Reasons Why Semantics Help Make Biobanks Better

My first blog post at 5AM is up:

The Semantic Web provides a means to link information on the web to each other and to things in real life in an interoperable way. Internationalized Resource Identifiers, of which URLs are a type, are used to identify nearly everything, and linked data makes it possible to visit those URLs to get more information about the things they represent. This has some very useful applications, especially in biobanking. Semantics was literally made for biomedical research, and here are 4 ways in which that relationship can help make biobanks better information resources…

Read more at http://info.5amsolutions.com/blog/bid/152921/4-Reasons-Why-Semantics-Help-Make-Biobanks-Better.

Validating RDF

I spent the day listening in on the RDF Validation Workshop, which kind of spilled over into the Cambridge Semantic Web Meetup. Here are my general musings and notes from the day. They may be completely wrong for many reasons, including possible misunderstandings of what the speaker said and information that is now out of date.

Google Says They’re Triplifying the Web

The Google Knowledge Graph is including a need to support users in how they can provide rich snippets in Google search results. They are building a validator for these formats against the RDF representations of their microdata. Most of their constraints are property paths, and they use SPARQL for the rest. They are also mostly concerned with suitability to their purpose, which is based on rich snippets and knowledge graph. They are using SPARQL-based constraints and are using RDFlib for prototyping, but will be moving to their own parser, which is used by the Structured Data Testing Tool. Here is an example path constraint, with the resulting SPARQL queries that are generated from it:

schema:reservationFor/schema:flightNumber
SELECT ?context WHERE {?context schema:flightNumber ?constraint.}
ASK WHERE {?context schema:flightNumber ?constraint.}

Currently, they are only validating things that are necessary, they won't check for things that are optional.

Semantic Web Meetup

The general idea seems to be that the RDF community needs to provide a means to say the following things about RDF graphs:

  • The graph must at least contain X.
  • The graph must contain at most Y.
  • The graph can never contain Z.

The general idea seems to be to provisionally close any given RDF graph before validation in order to produce the report. That closure can include some fixed set of other graphs (such as vocabularies used), but ultimately, for the purposes of validation, the Unique Name Assumption and the Closed World Assumption need to be used to validate the graph as given. Eric Prud'hommeaux presented an interesting framework based on YACC-style grammars by providing "shapes" of objects to validate. This is similar to OSLC's (Open Services for Lifecycle Collaboration) Resource Shape vocabulary, but with additional capabilities around disjunction and non-declarative validation processes.

Citing Your Sources on the Web

I was involved in the World Wide Web Consortium (W3C) Provenance Working Group, which was an amazing experience, even though I couldn’t put as much time into it as I would have liked. My friend and collaborator, Tim Lebo, edited the Provenance Ontology (PROV-O). PROV-O is, in my narrow perspective of the world, a fantastic foundation for talking about how stuff happens and, most importantly to this post, how to cite people and resources on the web.

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Getting Up Early in the Morning

Well, sort of. I have some exciting news: in August I will be starting at 5AM Solutions as a data scientist. I’ll be finishing my time at Yale University with Michael Krauthammer, and will soon be wrapping up my computer science Ph.D. at Rensselaer Polytechnic Institute in the Tetherless World Constellation. Continue reading

Thanksgiving Science!

I’ve got a little formula that predicts how long it will take for our Thanksgiving turkey to cook. It works really well for our temperatures and preparation, but I’d like to make it a little more general so everyone else can use it, regardless of temperature. As a wise man once said, if it’s worth doing, it’s worth overdoing, unless you’re overcooking turkey.

Towards that end, and because this is a science blog, I would like to perform a hypothesis-generating experiment. If you’re willing to further science, please share some details about how you prepared your turkey, and how it turned out. Humanity will thank you. Turkeys will not. I will post the results when I can, and maybe we can try again next year for a full prediction.

Click here to share your turkey data.

How to fix the economy

  1. I’m not an economist, so this probably has errors in it.
  2. None of these ideas are mine. I’ll hunt down where I got them from as soon as I can. See citations where I put them in.

Businesses aren’t investing in jobs because they have no reason to. They sit on huge piles of cash and continue to make acceptable profits without adding any jobs. Astonishingly, we manage to be in a period when inflation is nil, but prices are still going up. You know what gets people investing in new things? Inflation. Mild-to-moderate inflation drives capital into investments because otherwise the value of that money decreases over time.[1]

How would someone in charge of, say, the Fed, manage to increase inflation? They start by buying debt from banks, which frees up cash in existing banks to make other loans. Home mortgages would be a great start. The Fed can easily start buying up underwater mortgages and forgive the principal above and beyond the current market value. This puts a floor on the housing market and stops the glut of foreclosures, which gives the construction industry something to do again.

I would also start buying up and forgiving student loans of unemployed college grads. This would put them in a position to take greater risks with their careers, either taking jobs that aren’t directly in their fields or giving them room to start up businesses of their own.

This would be hugely controversial, of course, but the Fed chairman is appointed so that he can make these calls. We need something decisive either way, so someone needs to bite the bullet.

But what about everyday prices? Increasing inflation means, in the short term, increases in prices of stuff in general. True, but with the hardest hit people getting loan forgiveness, their overall costs will decrease. Also, investment in new technologies generally decreases real prices even as apparent prices go up. Finally, inflation doesn’t actually impact the poor significantly because they have little savings. In an economy with inflation, wages tend to increase with inflation.

On the fiscal side, there needs to be a resolution to the structural deficit spending. Most of this comes from the Bush tax cuts. Letting them expire takes care of 1/3 of the problem. Another portion of the problem comes from health care costs in medicare and medicaid. These costs can be amortized over a larger population by combining medicare and medicaid into one pool and opening up that pool to everyone. Medicare and Medicaid take care of the most expensive patients in the country, so opening it up to the rest of us would only decrease the overall risk. [2]

Finally, social security can easily be addressed by increasing the witholding limit above 90k. This will put it on sound footing for the next 100 years, based on figures I’ve heard. [2]

  1. Krugman, Paul. Why Is Deflation Bad? http://krugman.blogs.nytimes.com/2010/08/02/why-is-deflation-bad/
  2. Reich, Robert. What If Everyone Saw This Clip Of Robert Reich Exposing 7 GOP Lies? http://front.moveon.org/what-if-everyone-saw-this-clip-of-robert-reich-exposing-7-gop-lies

Obama is for Science, We’re for Obama

[Edited to add Obama's positions on NASA and Space Exploration]

Those of you who know me already know that I support Barack Obama for president. I’ve hesitated to post this here, due to the non-political nature of this blog. However, it is long past time for me to make the case for Obama and his policies on science and research. More after the cut on his key positions and why they are important.

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Zen Neuroscience: Observing Mindfulness

There are specific neural processes that take place when people meditate, which is demonstrated in the PLoS ONE paper “Thinking about Not-Thinking”: Neural Correlates of Conceptual Processing during Zen Meditation:

Recent neuroimaging studies have identified a set of brain regions that are metabolically active during wakeful rest and consistently deactivate in a variety the performance of demanding tasks. This “default network” has been functionally linked to the stream of thoughts occurring automatically in the absence of goal-directed activity and which constitutes an aspect of mental behavior specifically addressed by many meditative practices. Zen meditation, in particular, is traditionally associated with a mental state of full awareness but reduced conceptual content, to be attained via a disciplined regulation of attention and bodily posture. Using fMRI and a simplified meditative condition interspersed with a lexical decision task, we investigated the neural correlates of conceptual processing during meditation in regular Zen practitioners and matched control subjects. While behavioral performance did not differ between groups, Zen practitioners displayed a reduced duration of the neural response linked to conceptual processing in regions of the default network, suggesting that meditative training may foster the ability to control the automatic cascade of semantic associations triggered by a stimulus and, by extension, to voluntarily regulate the flow of spontaneous mentation.

Cross-Reference Visualizations

The bar graph that runs along the bottom represents all of the chapters in the Bible. Books alternate in color between white and light gray. The length of each bar denotes the number of verses in the chapter. Each of the 63,779 cross references found in the Bible is depicted by a single arc - the color corresponds to the distance between the two chapters, creating a rainbow-like effect.

Bible Cross-References: The bar graph that runs along the bottom represents all of the chapters in the Bible. Books alternate in color between white and light gray. The length of each bar denotes the number of verses in the chapter. Each of the 63,779 cross references found in the Bible is depicted by a single arc - the color corresponds to the distance between the two chapters, creating a rainbow-like effect.

This is a pretty cool visualization of bible cross-references that was developed by Chris Harrison to show bible cross references throughout the length of the bible. I can’t help but think of how interesting this could be for genome visualization: the cross references could be based on genes that are transcription factors for other genes. (activate or deactivate those genes). Chris has lots of other fascinating visualization projects to look at, and is very stimulating to browse it.