NeuroCommons FAQ

Q: What is the Semantic Web and what does it have to do with Neurocommons?
A: The Neurocommons builds on URIs and RDF, and that make it part of the Semantic Web.


Q: What is the difference between the RDF distribution and the triple store?
A: The Neurocommons RDF distribution is a set of files containing RDF that may be used by any application that uses RDF, such as a triple store. The Neurocommons Triple store is a particular instantiation of the RDF distribution running on a server maintained by our project.


Q: How is SPARQL different from SQL?
A: SPARQL is the query language for RDF, which is a knowledge representation language of simple logical assertions. RDF is oriented to knowledge sharing and data interoperation. SQL is a query language for relational databases, which hold data organized into tables.


Q: What is an ontology, and what's the difference between an ontology and a schema?
A: Ontologies organize what we know about the world. A schema organizes information in a database.


Q: BFO and Realism look like a lot of work. Why are they worth doing?
A: There are too many different approaches to representing knowledge. Settling on one provides the discipline needed to have a chance at achieving consistency between independently developed ontologies.


Q: What does data integration mean? What is a "data mashup"?
A: Data (or knowledge) integration is the combination of independently developed information sources to permit queries that span them. A data mashup is an application of a data integration.


Q: How do I write a query for the Neurocommons?
A: You will need to learn SPARQL and use it with our SPARQL endpoint (or another one that loads the RDF distribution).


Q: What's in the triple store?
A: The RDF distribution.


Q: Why are you limiting the project to neuroscience?
A: Neuroscience is not a limit but a starting point. In order to demonstrate utility we need to begin with one field. Neuroscience is a rich source of data and of integration challenges.


Q: Why isn't there a user interface?
A: We are working first to build the knowledge base and develop technologies that enhance its value.


Q: How is the Neurocommons related to the linked data/dbpedia/triplify projects?
A: These projects have a very similar philosophy and like Neurocommons all contribute to the Semantic Web. The Neurocommons is designed with scholarly research, and science in particular, in mind, and is therefore executed in a somewhat different way.


Q: How is the Neurocommons related to the W3C Health Care and Life Sciences Interest Group?
A: Science Commons participated in HCLS from the group's conception, in particular by developing best practice recommendations for URIs and by preparing many of the RDF sources used in its 2007 Banff demo.


Q: What are the technical specifications and capacity of the Neurocommons triple store server?
A:


Q: Can I rely on the infrastructure? Is the content stable? Can I build applications that depend on it?
A: For now the RDF distribution and triple store should be considered prototypes. Please work with us if you are interested in building on either.


Q: I would like to help. Who can I talk to?
A: We encourage you to join our Google group and send a message to the list.


Q: How can I add my data to the Neurocommons?
A: Take a look at the URI requirements. If you'd like to move forward, please join our Google group. We're happy to talk with you about it.


Q: Is the Neurocommons open access?
A: Yes, to the extent permitted by the sources we import. See their terms of use.


Q: Why do you use OWL?
A: OWL lets us express how elements in our representations relate to one another, and how they do not. With the aid of an automated reasoner, this kind of information can help detect errors in what we and others do. Such information also lets us express facts concisely and lets a reasoner fill in implied details. As such OWL simplifies data conversion and enriches search.


Q: How come my query is returning no results?
A: It could be many things. Join our Google group -- we may be able to help you out.


Q: Do you have debugging tools?
A: Currently the development effort focuses on developing methods and content. The tools will come later, or will be created by others in the Semantic Web community.


Q: How do I apply a CC license to my database?
A: We encourage you to follow the Science Commons Protocol for Implementing Open Access Data.


Q: What is the Gene Ontology?
A: See their introduction. The GO is a workhorse of bioinformatics, and is available in RDF form in our RDF distribution.


Q: Can you point me to other open resources for the life sciences?
A: You can find one list of resources here, but it is certain to be incomplete. We have not checked the terms of use of each resource listed.


Q: Can I import your data? Do you have a MySQL dump?
A: We represent information as RDF, not as relational tables. You can load the RDF distribution into any capable triple store.