1. Mission Statement

The Task Force on Bioinformatics has been established to facilitate the generation, exchange and use of biological information. It will act in order to promote the access of all countries to biological information, with a special emphasis on the acute needs of developing countries.

The aims of the task Force are:

• To advise IUPAB council of significant problems and developments in the field of bioinformatics
• To accumulate and serve as a source of specialist information in this field
• To support progress in this field by encouraging workshops, conferences and schools, especially in developing countries
• To attract young scientists to bioinformatics
• To provide an interface between IUPAB and other specialist organizations active in bioinformatics, especially the Inter-Union Bioinformatics Group
• To assist in the development of international programmes to support the provision of equipment and software to meet the needs of colleagues in the developing countries.

2. Composition

The Task Force is composed of H. Berendsen, C. Cantor, J. Garnier (Convenor) and M. Vijayan.

The Task Force has an Advisory Committee of nineteen members.

Report of Activity, 2001

Jean Garnier, Convenor.

The Task Force has been involved in the organization of two meetings in 2001, one being the continuation of the Bioinformatics Industrialization Workshop held in United States in June 2000 and the other corresponding to the final meeting of the Inter-Union Bioinformatics Group (IUBG).

1-Bioinformatics Industialization Workshop II, Hinxton, UK, October 20 and 21, 2001. Initially this workshop was set up to last from October 18 till October 21 and was devoted to Bioinformatics and Medicine, see the web site: http://www.wellcome.ac.uk/hinxton/bioinformatics2001 . The Task Force on Bioinformatics of IUPAB was one of the sponsors with IBM, the Department of Energy (USA), the European Bioinformatics Institute and the Wellcome Trust. The financial support of the Task Force was limited to some fellowships for young scientists from underdeveloped countries up to a total of US$ 3,038.89. This was possible because two fellowships, one for a Chinese student, another for a Nigerian student had not being used for the first workshop last year due to difficulties to obtain a visa to United States.

However, many speakers, mainly from United States but some from Europe, cancelled their participation to the meeting late September and the organizers of the meeting, Michael Ashburner, Barry Robson and myself, decided to postpone the meeting to April 4-7 2002 at the same place. It was also decided to hold instead a small interim meeting in Hinxton during the weekend of October 20-21, in part as a prelude to the Inter-Unions Bioinformatics Group meeting on Monday, 22 October. About twenty people, including the participants to the IUBG meeting, attended the interim meeting, hosted by Wellcome Trust in the Hinxton Hall Conference Center at the Genome Center. Although limited in number, interesting talks were given on the IBM project SHAMAN by B. Robson, the Genome Ontology programme of EBI by M. Ashburner, XML as a web standard by P. v.d. Eijk… and a round table on protein structure prediction mediated by myself.

2 Inter-Unions Bioinformatics Group meeting on October 22, 2001.

An informal meeting on September 15 at ICSU headquarter in Paris between Herman Berendsen and myself has preceded this meeting. Its purpose was to compile the proposals made after the IUBG meeting in June 2000 and to make a synthesis to be discussed at the IUBG meeting in Hinxton, UK on October 22, 2001. From this synthesis, Herman Berendsen wrote a draft report that was put on the web site (http://md.chem.rug.nl/~berends/berends.html) mid October for analysis by the IUBG members.

The meeting itself suffered from the present reluctance of people for travelling, however each union of the group was represented: P. Bourne for IUCr and the PDB, R. Cammack for IUBMB, A. McNaught, for IUPAC, A. Lesk, for CODATA and myself for IUPAB, other attendees were P. Murray-Rust and B. Robson. We heard D. Hartley, Executive Director of the Cambridge Crystallographic Data Center. We came to a proposal of statements and recommendations, which are presently submitted, to each Union for their comments and approval. The text is added as an Appendix and should be examined during the IUPAB executive council meeting. Finally it will be later submitted to ICSU, early next year.

Appendix

Statements

Statement 1 on the safeguarding of biological data

It is the obligation of nations to archive primary (i.e., fundamental experimental) scientific data, including, but not exclusive to, nucleotide sequences of biological organisms, amino-acid sequences of proteins, and three-dimensional structures of biological molecules, expression data from microarrays, yeast2hybrid data and mass spectrometry measurements. These data must be validated, stored, made publicly accessible, and safeguarded for future availability and access. Access must be public and unrestricted and no single organization should have a monopoly on these data. These primary scientific data are crucial for the development of science; they belong to the cultural assets and should be preserved as part of the human heritage.

Statement 2 on the obligations of data generators

It is the obligation of scientists who generate primary biological data in the course of publicly funded research to preserve these data for present and future reference and unrestricted access. Regardless of whether publication in journals is appropriate, such data must be deposited into the archival databases to guarantee their present and future availability. Primary data producers in the private sector are also obligated to deposit primary data when it is deemed to be no longer of commercial value.

Statement 3 on intellectual property rights

Scientific advances rely on full and open access to data. Primary data that are accessible through the archival databases cannot be subject to intellectual property rights, and no national or supranational legislation may limit the fair use of such data. The form in which data are made available, and the subsequent processing of such data may be appropriately protected by copyright laws, but the fair usage of the primary data itself must never be subject to restrictions. Fair use includes the use for educational purposes.

Statement 4 on standardization issues

There are four different aspects associated with primary data for which standardization should be considered: content, nomenclature, data format, and data exchange protocol. All require high-level agreement among scientists of various fields in order to insure understanding and knowledge exchange across borders of scientific disciplines. It is recognized that the technologies to support standardization change and this should be considered where possible.

Recommendations

It is recommended that International Unions and other scientific societies actively encourage their membership to deposit primary biological data to recognized data repositories which provide unrestricted access to these data. Journals of these Unions and societies should not accept publications in their journals that do not meet these requirements. This should be made clear to new members of these organizations and those renewing their membership.

It is recommended that funding agencies insist that all primary data produced by grants that they fund be deposited in recognized data repositories which provide unrestricted access to these data. International Unions and scientific societies should lobby government agencies until this recommendation is met.

It is recommended that funding agencies actively encourage existing and newly funded primary data repositories to provide the mechanism to preserve in perpetuity the data deposited therein and to preserve it in a form which is fully recoverable by future generations of researchers.

It is recommended that for-profit organizations be actively encouraged by primary data resources to deposit their data when it no longer has commercial value. This should be done by lobbying members of International Unions and scientific societies who are employed by such organizations.

It is recommended that publishers who accept primary data as part of a publication make these data freely and publicly available under the same conditions as they make the printed article available. Authors are encouraged not to publish in journals that do not conform to these rules. It is recommended that CODATA, in conjunction with IUPAB, IUBMB, IUCr and IUPAC, and after consultation of editors-in-chief of major journals, draws up an editorial code describing the conditions under which scientific articles are acceptable, as far as these are related to the deposit of primary data.

Following the recommendations of the ICSU/CODATA Ad Hoc Group on Data and Information, it is recommended that legislators take the impact of intellectual property laws on research and education into account, in order to allow fair use for scientific and educational purposes.

It is recommended that International Unions and scientific societies play an active role in the definition of standards in the fields they represent. This should be done through existing Nomenclature Committees (NC) and new committees converse in the technologies needed for a full definition of the field (ontology) and the means of exchanging data without loss of information.