The Neuroinformatics Portal of the International Neuroinformatics Coordinating Facility

Chapter 115 The Neuroinformatics Portal of the International Neuroinformatics Coordinating Facility

Jan G. Bjaalie

There is a clear need in the neuroscience community for databases extending from genes to cognition and disease mechanisms, for data sharing, and for modeling and use of computational tools at different levels [1, 2]. For this reason, the Global Science Forum (GSF) of the OECD (Organization of Economic Coopera- tion and Development) has initiated an International Neuroinformatics Coordinating Facility (INCF), to facilitate the development of Neuroinformatics. Each member nation contributes in relation to Research and Development expenditure in the par- ticular nation [3], (see also INCF platform documents at http://www.incf.org/med/ INCF Understanding.pdf and http://www.incf.org/med/INCF BusinessPlan.pdf). The current member nations are Belgium, the Czech Republic, Finland, France, Germany, Italy, Japan, the Netherlands, Norway, Poland, Sweden, Switzerland, the United Kingdom, and the United States. INCF also receives support from the Eu- ropean Commission. The central Secretariat of the INCF is located in Stockholm. Each member has established, or is about to establish, a National node. The nodes will contribute with infrastructure developments and neuroinformatics research in the context of the global network of member nations. The mission of the INCF Secretariat and the global network of National nodes is to: r r coordinate and foster international activities in neuroinformatics in general contribute to the development of scalable, portable, and extensible applications that can be used to further knowledge of the human brain and its development, r function and disease contribute to the development and maintenance of speciﬁc database and other r computational infrastructures and support mechanisms focus on developing mechanisms for the seamless ﬂow of data, information, and knowledge among government agencies, academics and libraries, the publication industry and private enterprises.

J.G. Bjaalie International Neuroinformatics Coordinating Facility, Secretariat, Karolinska Institutet, SE - 171 77 Stockholm, Sweden email: [email protected]

R. Wang et al. (eds.), Advances in Cognitive Neurodynamics, 667 C Springer Science+Business Media B.V. 2008 668 J.G. Bjaalie

The INCF will establish a strong external operative representation. Directed to the world-wide, open and diverse neuroscientiﬁc community, such a basic representation will be based on a unifying web portal, the INCF Neuroinformatics Portal. This new portal will serve as a platform for providing research oriented services to the neuroscience community world-wide, in agreement with the INCF work plan (http://www.incf.org/med/INCF BusinessPlan.pdf). The present report provides a brief outline of the current plans for the INCF portal.

State-of-the-Art and International Coordination

A large number of neuroinformatics resources are currently available, including data repositories, advanced database applications, software tools for data visualization, analysis, and modeling of brain function at multiple levels. Also biophysically spec- iﬁed computational models are to some extent shared. Several neuroscience portal services, general or focused, have been initiated around the world over the last few years, such as: r BIRN portal / Biomedical Informatics Research Network portal (https://portal. r nbirn.net/) r Neurocommons (http://sciencecommons.org/projects/data) r NDG / Neuroscience Database Gateway (http://www.sfn.org/ndg) r NIF / Neuroscience Information Framework (http://neurogateway.org) Japan Node/The Portal system for Neuroinformatics in Japan (http://www. neuroinf.jp)

Creating synergies and collaborations among the existing portals will be a key strategy in INCF operations.

INCF Portal: Goals and Basic Approach

A major component of the new INCF portal will be services for navigation and integration of distributed resources, across continents, within specific domains of neurosciences. The portal effort will act on two levels: (1) It will help shepherd diverse protocols of interoperability across the world. This will facilitate the development of consensus positions on standards and “best practice”. Specifically, it will provide a final international vetting body for neuroscience-specific ontologies and related ontologies in other fields. (2) It will then implement these consensus international interoperability standards and provide example and exemplar resources and data sets and test suites. To facilitate the process of establishing such services, the status of different portal initiatives as well as the collaborative dividing of maintenance and development tasks will be dealt with in the INCF workshop series, with major stakeholders 115 The Neuroinformatics Portal of the INCF 669 present. A sound basis for a collaborative effort exists, since the INCF portal initia- tive and several of the existing portal developments have emerged from a relatively similar background.

INCF Portal: Domain Oriented Services

The rationale for providing domain oriented services, allowing navigation and integration of distributed resources, is that the gathering of comprehensive sets of available resources on the internet and through other available channels requires a substantial effort in the form of manual searching and coordination. A large number of different and isolated systems are used for access, referencing, technical standards, user interface principles, and quality standards. This poses problems at several levels when using distributed resources in cutting-edge research. INCF will use its technical and coordinating capabilities as well as its domain authority established via the INCF Workshops series and INCF Expert panels, to address these issues. At a general level, examples of approaches to be taken by the domain oriented services include database mediation, data fusion and mining, data driven navigation, specialized multi-level categorization, and search engines. Among the values to be reached by establishing domain oriented services are r a general information efficiency boost due to less administrative and coordinative r overhead on the part of the end user scientific information gain by facilitating data fusion and new levels of integrated r information refinement strategic resource persistence and standardization advantages with regards to r quality, referencing and availability the establishment of an international community derived authority in the given domains, in connection with INCF Workshops and Expert panels funded by other r INCF resources general organizational development with regards to cooperation and communi- r cation between neuroscientific and technological institutes around the world increased opportunities for improved IT-infrastructures in the neuroinformatics community of developers, as a result of a new focus on their deliverables and r increased use of these r the establishment of standards and common principles technological spin-offs within fields such as data fusion, database mediation, sensemaking, distributed information services, usability and platform indepen- dence

The domain areas to be included in the portal will be decided on by the Governing board of the INCF. Each domain area is critically analyzed by a workshop, with rep- resentatives of the main stakeholders in a given area. The INCF workshops deliver penetrating reports that includes recommendations for actions. One report example is provided by the 1st INCF workshop on Large-scale modeling of the nervous 670 J.G. Bjaalie system, available via the INCF web site and via Nature Proceedings [4]. Follow-up of the workshop recommendations are in turn overseen by expert panels, derived with each panel linked to a program ofﬁcer at the INCF Secretariat. Examples of domain areas that are currently considered for inclusion are: r r Large-scale modeling of the nervous system r Digital brain atlasing systems r Integration of fMRI and other neuroimaging data resources Neuroanatomical nomenclature and taxonomy

Future domain areas to be considered include also biologically problem-oriented domains, such as Action, Learning and Memory, Vision, and Cellular neurobiology. Building on the workshop and expert panel mechanism, the INCF has at hand the necessary international authority, connected to the community of lead scientists.

INCF Portal: Basic Services

The basic services that will be included in the portal are software provision and general community building support. A broad use of these services is expected. A primary concern is to support the domain oriented services of the portal.

Software Provision

The development, distribution and use of specialized software tools will be facilitated and supported by the portal. This is quite challenging since many of the developers represent small research groups, many specialized approaches are used, few standards are applied, and tracking of the use of tools as well as feedback and reward to the developers are limited. From the perspective of the end users, the concerns that will be targeted include the overhead work involved in ﬁnding and getting access to software tools, the problems of quality assurance relative to purpose of use, platform dependency problems, and updating and support. From the perspective of the tools developers, the concerns that will be targeted include tools Lifecycle Management, coordination of user feedback and usage statistics, release management and redistribution, and the interface and buffer between the tools developer community and the user community (by which individuals are often members of both). In the context of the portal developments, the INCF will aim to identify high quality tools from all relevant resources (helped by its workshops and expert panels) and facilitate access to such tools via the portal services. Further, structural support systems in the form of code repositories, version control and issue tracking mechanism will be provided. Such systems, essential in the context of development of high quality software and associated with a resource overhead often beyond the ca- pacity of individual scientists or small research groups, will be provided. Therefore, state-of-the-art software development support services, tailored for the needs of the 115 The Neuroinformatics Portal of the INCF 671 neuroinformatics community, will be developed. Substantial weight will be placed on platform-independency and continuing availability of key software applications through new versions of operating systems and hardware, i.e. forward-porting. A possible solution for some types of software may also be the use of managed servers holding relevant and frequently used software and removing the need to download software.

Community Building Support

General community building support services relates directly to the coordination objectives of the INCF. These services will include functions such as online meeting forums, blogs with emphasis on news and commentaries for the different divisions of the portal, and calendars of neuroscience and neuroinformatics events. Given the focus on domain oriented services, the above functionalities will address the different domains speciﬁcally, but also offer integration of communication across domains.

Concluding Remark

A key element in the INCF operation is to work closely with the scientiﬁc community in adjusting and translating the INCF work plan to practical action. To the extent possible, actions of the INCF will always seek to build on a careful map- ping of existing resources and, when possible, to prepare for the full use of these in combination with new developments. The INCF portal will be one of several instruments that will play a role in establishing a future neuroinformatics capability, the aim of which will be to have the same role in basic and clinical neuroscience as bioinformatics has for genomics and proteomics.

Acknowledgements and Information J.G.B. is the Executive Director of the INCF. R. Ritz and M. Naeslund at the INCF Secretariat have contributed to the development of the portal plan, with valuable input also received from from R.W. Williams and S. Grillner. This article describes principles only. INCF strategies and actions are subject to continuous monitoring and approval by the INCF Governing Board.

References

1. Amari S-I, Beltrame F, Bjaalie JG, Dalkara T, De Schutter E, Egan GF, Goddard NH, Gonzalez C, Grillner S, Herz A, Hoffmann K-P, Jaaskelainen I, Koslow SH, Lee S-Y, Matthiessen L, Miller PL, Silva FMD, Novak M, Ravindranath V, Ritz R, Ruotsalainen U, Sebestra V, Subramaniam S, Tang Y, Toga AW, Usui S, Pelt JV, Verschure P, Willshaw D, Wrobel A (2002) Neuroinformatics: The integration of shared databases and tools towards integrative neuroscience. J Integrative Neurosci. 1:117–128. 2. Gardner D, Toga AW, Ascoli GA, Beatty JT, Brinkley JF, Dale AM, Fox PT, Gardner EP, George JS, Goddard N, Harris KM, Herskovits EH, Hines ML, Jacobs GA, Jacobs RE, Jones EG, Kennedy DN, Kimberg DY, Mazziotta JC, Miller PL, Mori S, Mountain DC, 672 J.G. Bjaalie

Reiss AL, Rosen GD, Rottenberg DA, Shepherd GM, Smalheiser NR, Smith KP, Strachan T, Van Essen DC, Williams RW, Wong ST (2003) Towards effective and rewarding data sharing. Neuroinformatics. 1:289–295. 3. Bjaalie JG, Grillner S (2007) Global neuroinformatics: the international neuroinformatics coordinating facility. J Neurosci. 27:3613–3615. 4. Djurfeldt M, Lansner A (2007) Workshop report: 1st INCF Workshop on Large-scale Mod- eling of the Nervous System. Available from Nature Precedings http://dx.doi.org/10.1038/ npre.2007.262.1.