Thursday, June 30, 2011

OWL-izing the Cognitive Atlas

Recently I have spent some time turning the Cognitive Atlas knowledge base into a full-blown ontology.  This effort came about as I was working on responding to reviews from a paper describing the project (submitted to Frontiers in Neuroinformatics).  We made the choice at the outset of the project to store it in a custom relational database, rather than using an ontology language as the basic storage format, because we wanted to retain flexibility to store things that are not necessarily ontology-friendly.  We always said that we would come up with a way to later translate the knowledge into a formal ontology, but I began to get a bit itchy about our ability to actually do this.  So, over the last few weeks I have created a pipeline for turning the database into an OWL ontology.  I have made the code and ontology available at https://github.com/poldrack/cogat in case anyone is interested in having a look.  I am a complete newbie when it comes to ontologies, so any comments on the structure of the ontology are very welcome. (We would also welcome comments on the content of the ontology, but if you don't like the content then you really should just go into the Cognitive Atlas site and change it yourself!)

I started with RDF dumps of the concepts and tasks, which are available from the SPARQL endpoint page.  Assertions about relations in the database are not currently available from the endpoint, so I got a custom dump of those as well.  I then wrote a python script to finesse all of this into an OWL ontology. I have to say that this is a great way to learn about the structure of OWL!  I used Protégé to help validate my OWL and examine the contents, which was really useful.  

Part of the work in setting up this ontology was deciding how to align it with other ontologies, particularly with CogPO. I had a long meeting at OHBM2011 with Jessica Turner and Angie Laird, during which we hashed out a set of classes and relations that will serve to structure the task representation in both of our ontologies.  For our representation of tasks, we are inheriting the BehavioralExperimentalParadigm class from CogPO. 

I have also registered the Cognitive Atlas with the NCBO BioPortal site, which I hope will give it increased visibility.  In the long run, I plan to create a pipeline by which the ontology will the automatically generated and updated directly from the database, but for now will do regular manual updates.

Saturday, April 9, 2011

Some updates on the Cognitive Atlas Project

It's been a while since I posted anything so I thought I would catch everyone up on what's been going on.  The project ended up having a number of very quiet months last year while we transferred the grant from UCLA to UT Austin.  Now that the grant is in place at UT, we have been cranking forward on the next release of the Cognitive Atlas, which we hope to release some time later this year.  Some new features will include:

  • a personal "dashboard" that will provide easy access to relevant infomation
  • improved interface for displaying relations, which will work better when there are large numbers of relations
  • an improved interface to PubMed
  • relations based on literature mining
  • many more improvements behind the scenes
We have also welcomed Jack Van Horn from UCLA to the Cognitive Atlas team; Jack will be working with the rest of the team to develop new ways to seed the database and visualize the results.  

I have also just recently made a thorough curation run through the database and will soon be cleaning out the database.  Discussions with a number of people (particularly Gwen Friskoff from Georgia State) highlighted that there were some terms in the database that were not really mental constructs.  For example, there were a number of linguistic concepts (such as "vowel" and "agglutinative language") which refer to things in the world rather than to mental constructs.  Because the concepts list in the Cognitive Atlas is meant to include only mental constructs, these are not appropriate for the knowledge base.  Instead, a concept like "vowel processing" would be appropriate because it would refer to a mental construct rather than to a thing in the world.  

Another common confusion is between tasks and concepts. For example, "trace conditioning" was previously listed as a concept in the database.  However, trace conditioning is an empirical phenomenon that is evoked using particular learning paradigm; it is, of course, supported by particular learning processes, and it is those processes that count as mental concepts, rather than the experimental paradigm, which should instead be listed as a task.  

Finally, we are in the process of making a thorough sweep through the task database, integrating with a number of other task lexica, and cleaning it up so that entries are more consistent.  

We look forward to your continued contributions and always welcome feedback about the project.

Thursday, July 15, 2010

NIMH Research Domain Criteria Meeting

I spent the last two days in Bethesda at the first workshop of the NIMH RDoC project, which was one of the most interesting scientific meetings I've been to in quite a while.  This project is meant to address two major problems in psychiatry.  First, there is widespread dissatisfaction with the current categorical approaches to psychiatric diagnoses, and a growing realization that better understanding of these disorders requires a dimensional (rather than categorical) perspective (e.g., Kraemer, 2007).  Second, there is  an increasing realization of the need to ground psychiatric diagnoses in neuroscience (Miller, 2010). The goal of the RDoC project is to help determine what the best candidates are for neuroscientifically validated dimensions that are most likely to be relevant to mental disorders.


This workshop was the first of several, each of which will focus on a particular construct or domain.  This first meeting was focused on the concept of "working memory."  The group was quite broad, from researchers who study working memory in mental disorders to neurobiologists who study the molecular basis of sustained activity in rodents.  The first charge of the group was to come up with a definition of working memory.  Given how prevalent this concept is in the literature (more than 11,000 hits in PubMed), it might seem that a definition would be obvious, but it took the better part of an hour for each of the two  working groups to come up with a definition that most of us could agree on.  Remarkably, the definitions generated independently by each group were very similar!  A summary of the consensus definition (generated through additional discussion of the whole group) has been entered as the new definition of the "working memory" concept in the Cognitive Atlas and can be found here. 


Much of the remainder of the workshop focused on characterizing the tasks, neural systems, molecules, and genes that are relevant to working memory.  Although each group came up with lists of tasks that were thought to best capture the construct of working memory, there was some trepidation about publishing this list, lest it become a blessing for the uncritical use of these tasks as "working memory tasks".  Rather, the group focused more on discussing what task features are most important for ensuring construct validity of tasks meant to measure working memory.  These will be published soon as part of the output from the workshop.


Another interesting point of discussion centered around how to relate the different levels of analysis, from molecules to neuropsychological tests.  The challenge comes in thinking about how construct mechanistically realistic links between molecular constructs (such as allelic variation in the COMT gene) and behavior (such as performance on the N-back task).  Drawing from the approach that has been developed within the UCLA Consortium for Neuropsychiatric Phenomics, Bob Bilder and I argued that this should be thought of in terms of links between successive levels of structure. For example, we can establish links between cognitive processes and neural systems, between neural systems and cellular systems, and so on down to genes and environmental influences. These different levels can then be traversed to provide a sophisticated mechanistic understanding of how we can get from genes to cognitive function.


Finally, there was a good bit of interesting discussion about the need for measures of working memory that are better validated, both conceptually and psychometrically. There was a clear undercurrent of dissatisfaction with the degree to which the imaging literature has relied on tasks that are not well validated in either of these senses (the N-back task being the poster child for this).  There seems to be great interest in developing a battery of validated tests, and maybe even greater interest in the potential of using these for online testing of large groups across studies.  For example, this seems to be the only realistic way to get sample sizes large enough to make well-powered genome-wide association analyses feasible for cognitive phenotypes.


The RDoC meeting was particularly exciting because of how well it dovetails with the Cognitive Atlas Project.  Getting researchers involved in clarifying their concepts and specifying how they relate to tasks and other levels of analysis is exactly what this project was designed to do.  I have already entered a good bit of the knowledge that was generated in this first RDoC workshop into the system, and I hope that we can make the Cognitive Atlas a repository for all of the knowledge that is generated in the subsequent RDoC workshops as well.  It was heartening to see that the framework that we have developed for representing this kind of knowledge is so well aligned to the kinds of knowledge building that NIMH clearly sees as essential for progress.



Tuesday, July 13, 2010

Hello!

This is the first post to our new Cognitive Atlas blog.  This blog will focus on topics related to the role of informatics in cognitive neuroscience, as well as providing updates and highlights regarding the Cognitive Atlas project.  Keep your eyes peeled for more content soon!