Finding the Right Neuron: Introducing Protégé, OWL, and the Neuron Phenotype Ontology

Figure 1. Details of two layer 2 pyramidal neurons sitting side-by-side from a sample of around 50,000 neurons in a cubic millimeter of human cortex scanned at electron microscopic resolution and provided in a publicly available database.

It’s been three years since I last wrote to you here. I’ve been busy in theoretical and computational neuroscience after several years focused on the semantic web and artificial intelligence technologies company I founded in 2001. My big surprise is that neuroscientists continue to painstakingly search for and extract data from research papers by hand!

Of course there will always be a need to read and pull data and ideas straight from research papers but I thought that by now, 20 years later, easy-to-use web pages would provide globally aggregated brain research data. Not yet. There is exciting linked-data based work going on and a wide range of useful ontologies used by brain researchers with sophisticated working understandings of semantic web technologies but there appears to be a large gap in tools for those not steeped in this knowledge. Neuroscientists don’t have easy rapid access to data answering, for example, the question,  “what is the average spike rate of pyramidal neurons in layer 5B primary motor cortex?”

The infrastructure that enables expert searches through piles of data is everywhere. Google, Apple, and the Allen Institute for Brain Science are just a few of the institutions that use semantic web technologies (ontologies, reasoners, linked-data) but these technologies remain mostly hidden and unrecognized by the public. Indeed, most programmers are at best only vaguely aware of them.

Speed Date with Semantic Web Technologies

Let’s take a look at semantic web technologies in the brain sciences today by diving into the important new Neuron Phenotype Ontology. The Neuron Phenotype Ontology was created to help find and categorize neurons with particular sets of traits (phenotypes).

Figure 2. Protégé loaded with the Neuron Phenotype Ontology.

To follow along, download the latest Protégé version and set up the ELK Reasoner (see the Protégé Setup with ELK Reasoner box below). Then downloaded the Neuron Phenotype Ontology OWL file from the National Center for Biomedical Ontology BioPortal (see the Neuron Phenotype Ontology OWL File box below).

Protégé Setup with ELK Reasoner

1. To download the ELK Reasoner, select Check for plugins … from the Protégé File menu and the Automatic Update window will pop up.

2. Check the Install box next to ELK Reasoner and click on the window’s Install button.

3. Select the ELK Reasoner by opening the Protégé Reasoner menu and selecting ELK Reasoner.

4. Run the reasoner by opening the Protégé Reasoner menu and selecting Start Reasoner.

Ideally, an otology has access to a world of linked-data through the Internet. The Neuron Phenotype Ontology is in its infancy and so it’s available as an evaluation version with a relatively small set of data from three sources (Henry Markram’s Blue Brain Project, the Allen Institute for Brain Science, and Josh Huang’s laboratory). With limited links and data, just any search won’t do. For example, most of the linked-data are from visual and somatosensory cortices, there are a small number of neurons from auditory cortex, but there are no neurons from motor cortex. With this in mind, let’s take a look.

Neuron Phenotype Ontology OWL File

1. Look for the Submissions section on the Neuron Phenotype Ontology page in the BioPortal,  and find the latest version (top) and under Downloads click on the OWL link. The npo.ttl file will download to your computer.

2. In Protégé, open the File menu and select Open. Find and load the npo.ttl file.

A Brief Tour of Neuron Phenotype Ontology

We can do a simple query but first a very brief tour of our ontology so that you may start building your own queries. Select the Entities tab at top left and you see several tabs below. Open the Classes sub-tab. These are the things, in OWL known as classes, that you may work with in the Neuron Phenotype Ontology. You may only see the top thing owl:Thing. Select the > to the left of owl:Thing and a whole sub-tree of classes should appear. Labels for many of these may not make sense to the human reader but are important classes for machine reasoning.

Figure 3. Searching for morphological phenotype in the Protégé Search window.

Let’s find an important human readable class in this ontology using Protégé search. Click on the Search… button in the far upper right. The Search window pops up (see Figure 3 above). Type in morphological phenotype. At the top of the resulting list should be the class, represented by an orange circle at left, named ‘Morphological phenotype’. The blue rectangles represent properties. More on these in a minute. Double click on the ‘Morphological phenotype’ class. Move or close your Search window and you’ll see that a sub-tree opened up in your Classes sub-tab list and the class Morphological phenotype is highlighted. Searching is the best way to get around in an ontology.

Look at the list of sub-classes under the Morphological phenotype class (select the > at left to see them) . These are the pre-defined cell morphology phenotypes currently in the Neuron Phenotype Ontology. Also notice that there are a whole lot of other classes under the high-level Phenotype class that break out neuron phenotypes in different ways including axon, cell, dendrite, and electrophysiological. You can use these classes to find the data you want.

To carry out a query you’ll need properties in addition to classes. You can think of classes as things in the world. Physical or mental things. Properties are, well, properties of those things. A bicycle is a thing with a color property. A blue bicycle. Blue is a thing that is a property of the bicycle. Likewise, a morphological phenotype is a thing but it is also a property of cells, including neurons. Notice that listed under the ‘Morphological phenotype’ class (yellow circle) in Figure 3 above is the hasMorphologicalPhenotype property (blue rectangle). Now you’re ready to query the data for a particular neuron phenotype.

Query for Neurons with Dendritic Spines

Many of the most complex neurons in cortex have dendrites with a lot of spines on them like in the image of two human cortical neurons at top in Figure 1. Each spine has a synapse (yellow dot) with an incoming axon from another neuron. We will query for data about neurons with spiny dendrites. Select the DL Query tab in Protégé and type Neuron and hasMorphologicalPhenotype some ‘Spiny phenotype’ into the Query (class expression) text box.

Neuron is the class of cells you’re looking for with spiny morphology. That is, you’re looking for every neuron that has the morphological phenotype of dendrites with spines (‘Spiny phenotype’ is a sub-class of ‘Dendrite phenotype’).

You should get around 454 results. Most and perhaps all data for this query was collected at the Allen Institute. Normally what you want a query to return is linked-data from around the world. In this case we are using a proof-of-concept version of the ontology with a small local dataset. Also, the classes you see in your results represent the data. Typically end results provide links (URLs) to the actual data.


Why do neuroscientists continue to painstakingly search for and extract data from research papers by hand when technology is available to automate much of the process? The number one reason is most likely the complexity of neuroscience data. A lot of work went into creating the Neuron Phenotype Ontology … and there is much still to do. Another probable reason is the work and expense that goes into building and maintaining the necessary web-based user friendly tools. Finally, there is the question of how much linked-data is openly available to the neuroscience community. I believe that there is a large and growing collection of neuroscience linked-data now openly available. Check back soon and I’ll share with you what I find.