i202 Fall 2010 School of Information, UC Berkeley

 http://berkeley.worldcat.org/title/semantic-senselab-implementing-the-vision-of-the-semantic-web-in-neuroscience/oclc/506082546&referer=brief_results

What is being organized – things, information about things, information?

Neuroscience research data

Ontology design

What is the scope and scale of the domain?

Biomedical Semantic Web resources, including Subcellular Anatomy ontologies, Brain Architecture Management System, the Gene Ontology, BIRNLex, and UniProt.

Neuroscience domain

Neurological diseases – Alzheimer’s disease and Parkinson’s disease

Why it is being organized – what functions or capabilities are being enabled, and for whom? 

Neuroscience is in need of a new informatics framework that enables semantic integration of diverse data source.  Experimental data is collected across different scales, from cell to tissue to organ, using a wide variety of experimental procedures taken from diverse discipline.

Are the uses and users known or unknown?

These Semantic Web technologies can be used to integrate neuroscience knowledge and to make such integrated knowledge more easily accessible to researchers. 

Is the organization being done to achieve personal, social, or institutional goals?

The major goal is to accelerate the bidirectional communication between basic research and clinical practice, in order to speed up the development of new clinical guidelines, tests, and therapies.  The Semantic Web has the potential to facilitate the aggregation and integration of information from different institutes involved in neuroscience research. 

How much is it being organized – what is the extent or degree of description, classification, or relational structure being imposed?

SenseLab databases:

NeuronDB – anatomical structure of neurons

BrainPharm – research on drugs and neurological disorders

ModelDB – computational neuroscience models and simulations. 

These databases allow the researchers to query information and run simulations pertaining to the function of neurons in healthy and disease states.

What principles guide and are embodied in the organization?

The ontology is primarily organized around direct representations of physical objects and processes (e.g. neuronal cells, ionic currents) in reality, and not around their abstractions (e.g. concepts and database entries).  ~ Open Biomedical Ontologies Foundry (OBO Foundry [12])

When is it being organized – when it is created, at design time, or at runtime, just in case, just in time, all the time?

When it is created and at design time.

By whom (or by what computational processes) it is being organized – by individuals, by informal groups, by formal groups, by professionals, by automated methods?

By a small group of people with no dedicated software for collaborative ontology editing was used

Created by someone with expertise in both ontology engineering and neuroscicnee.