Neuroinformatics


Neuroinformatics is a scientific study of information flow and processing in nervous system. Neuroinformatics is devoted to the development of neuroscience data and knowledge bases together with computational models and analytical tools for sharing, integration, and analysis of experimental data and advancement of theories about the nervous system function. In the INCF context, neuroinformatics refers to scientific information about primary experimental data, ontology, metadata, analytical tools, and computational models of the nervous system. The primary data includes experiments and experimental conditions concerning the genomic, molecular, structural, cellular, networks, systems and behavioural level, in all species and preparations in both the normal and disordered states.
Neuroinformatics stands at the intersection of neuroscience and information science. Other fields, like genomics, have demonstrated the effectiveness of freely distributed databases and the application of theoretical and computational models for solving complex problems. In Neuroinformatics, such facilities allow researchers to more easily quantitatively confirm their working theories by computational modeling. Additionally, neuroinformatics fosters collaborative research—an important fact that facilitates the field's interest in studying the multi-level complexity of the brain.
There are three main directions where neuroinformatics has to be applied:
  1. the development of tools and databases for management and sharing of neuroscience data at all levels of analysis,
  2. the development of tools for analyzing and modeling neuroscience data,
  3. the development of computational models of the nervous system and neural processes.
In the recent decade, as vast amounts of diverse data about the brain were gathered by many research groups, the problem was raised of how to integrate the data from thousands of publications in order to enable efficient tools for further research. The biological and neuroscience data are highly interconnected and complex, and by itself, integration represents a great challenge for scientists.
Combining informatics research and brain research provides benefits for both fields of science. On one hand, informatics facilitates brain data processing and data handling, by providing new electronic and software technologies for arranging databases, modeling and communication in brain research. On the other hand, enhanced discoveries in the field of neuroscience will invoke the development of new methods in information technologies.

History

Starting in 1989, the United States National Institute of Mental Health, the National Institute of Drug Abuse and the National Science Foundation provided the National Academy of Sciences Institute of Medicine with funds to undertake a careful analysis and study of the need to create databases, share neuroscientific data and to examine how the field of information technology could create the tools needed for the increasing volume and modalities of neuroscientific data. The positive recommendations were reported in 1991. This positive report enabled NIMH, now directed by Allan Leshner, to create the "Human Brain Project", with the first grants awarded in 1993. The HBP was led by Koslow along with cooperative efforts of other NIH Institutes, the NSF, the National Aeronautics and Space Administration and the Department of Energy. The HPG and grant-funding initiative in this area slightly preceded the explosive expansion of the World Wide Web. From 1993 through 2004 this program grew to over 100 million dollars in funded grants.
Next, Koslow pursued the globalization of the HPG and neuroinformatics through the European Union and the Office for Economic Co-operation and Development, Paris, France. Two particular opportunities occurred in 1996.
The two related initiatives were combined to form the United States proposal on "Biological Informatics". This initiative was supported by the White House Office of Science and Technology Policy and presented at the OECD MSF by Edwards and Koslow. An MSF committee was established on Biological Informatics with two subcommittees: 1. Biodiversity, and 2. Neuroinformatics. At the end of two years the Neuroinformatics subcommittee of the Biological Working Group issued a report supporting a global neuroinformatics effort. Koslow, working with the NIH and the White House Office of Science and Technology Policy to establishing a new Neuroinformatics working group to develop specific recommendation to support the more general recommendations of the first report. The Global Science Forum of the OECD supported this recommendation.

The International Neuroinformatics Coordinating Facility

This committee presented 3 recommendations to the member governments of GSF. These recommendations were:
  1. National neuroinformatics programs should be continued or initiated in each country should have a national node to both provide research resources nationally and to serve as the contact for national and international coordination.
  2. An International Neuroinformatics Coordinating Facility should be established. The INCF will coordinate the implementation of a global neuroinformatics network through integration of national neuroinformatics nodes.
  3. A new international funding scheme should be established. This scheme should eliminate national and disciplinary barriers and provide a most efficient approach to global collaborative research and data sharing. In this new scheme, each country will be expected to fund the participating researchers from their country.
The GSF neuroinformatics committee then developed a business plan for the operation, support and establishment of the INCF which was supported and approved by the GSF Science Ministers at its 2004 meeting. In 2006 the INCF was created and its central office established and set into operation at the Karolinska Institute, Stockholm, Sweden under the leadership of Sten Grillner. Sixteen countries, and the EU Commission established the legal basis for the INCF and Programme in International Neuroinformatics. To date, eighteen countries are members of the INCF. Membership is pending for several other countries.
The goal of the INCF is to coordinate and promote international activities in neuroinformatics. The INCF contributes to the development and maintenance of database and computational infrastructure and support mechanisms for neuroscience applications. The system is expected to provide access to all freely accessible human brain data and resources to the international research community. The more general task of INCF is to provide conditions for developing convenient and flexible applications for neuroscience laboratories in order to improve our knowledge about the human brain and its disorders.

Society for Neuroscience Brain Information Group

On the foundation of all of these activities, Huda Akil, the 2003 President of the Society for Neuroscience established the Brain Information Group to evaluate the importance of neuroinformatics to neuroscience and specifically to the SfN. Following the report from BIG, SfN also established a neuroinformatics committee.
In 2004, SfN announced the Neuroscience Database Gateway as a universal resource for neuroscientists through which almost any neuroscience databases and tools may be reached. The NDG was established with funding from NIDA, NINDS and NIMH. The Neuroscience Database Gateway has transitioned to a new enhanced platform, the Neuroscience Information Framework. Funded by the NIH Neuroscience BLueprint, the NIF is a dynamic portal providing access to neuroscience-relevant resources from a single search interface. The NIF builds upon the foundation of the NDG, but provides a unique set of tools tailored especially for neuroscientists: a more expansive catalog, the ability to search multiple databases directly from the NIF home page, a custom web index of neuroscience resources, and a neuroscience-focused literature search function.

Collaboration with other disciplines

Neuroinformatics is formed at the intersections of the following fields:
neuroscience,
computer science,
biology,
experimental psychology,
medicine,
engineering,
physical sciences,
mathematics, and
chemistry.
Biology is concerned with molecular data ; medicine and anatomy with the structure of synapses and systems level anatomy; engineering – electrophysiology, brain imaging; computer science – databases, software tools, mathematical sciences – models, chemistry – neurotransmitters, etc. Neuroscience uses all aforementioned experimental and theoretical studies to learn about the brain through its various levels. Medical and biological specialists help to identify the unique cell types, and their elements and anatomical connections. Functions of complex organic molecules and structures, including a myriad of biochemical, molecular, and genetic mechanisms which regulate and control brain function, are determined by specialists in chemistry and cell biology. Brain imaging determines structural and functional information during mental and behavioral activity. Specialists in biophysics and physiology study physical processes within neural cells neuronal networks. The data from these fields of research is analyzed and arranged in databases and neural models in order to integrate various elements into a sophisticated system; this is the point where neuroinformatics meets other disciplines.
Neuroscience provides the following types of data and information on which neuroinformatics operates:
Neuroinformatics uses databases, the Internet, and visualization in the storage and analysis of the mentioned neuroscience data.

Research programs and groups

Australia

; Neuroimaging & Neuroinformatics, Howard Florey Institute, University of Melbourne

Canada

; , Montreal Neurological Institute, McGill University

Denmark

; The THOR Center for Neuroinformatics

Germany

; The Neuroinformatics Portal Pilot
; Computational Neuroscience, ITB, Humboldt-University Berlin
; The Neuroinformatics Group in Bielefeld

Italy

; Laboratory of Computational Embodied Neuroscience

Japan

; Japan national neuroinformatics resource
; Laboratory for Mathematical Neuroscience, RIKEN Brain Science Institute

The Netherlands

; Netherlands state program in neuroinformatics

Pakistan

; NUST-SEECS Neuroinformatics Research Lab

Switzerland

; The Blue Brain Project
; The Institute of Neuroinformatics

United Kingdom

; Genes to Cognition Project
; The CARMEN project
; EBI Computational Neurobiology, EMBL-EBI

United States

; Neuroscience Information Framework
; Neurogenetics GeneNetwork
; The Neuronal Time Series Analysis
; The Cognitive Atlas
; Brain Big Data research group at the Allen Institute for Brain Science

Technologies and developments

The main technological tendencies in neuroinformatics are:
  1. Application of computer science for building databases, tools, and networks in neuroscience;
  2. Analysis and modeling of neuronal systems.
In order to organize and operate with neural data scientists need to use the standard terminology and atlases that precisely describe the brain structures and their relationships.
Another approach in the area of the brain mappings is the probabilistic atlases obtained from the real data from different group of people, formed by specific factors, like age, gender, diseased etc. Provides more flexible tools for brain research and allow obtaining more reliable and precise results, which cannot be achieved with the help of traditional brain atlases.

Citations

Books