IUBG Report

Last modified: May 5, 2010

IUBG

INTER-UNION BIOINFORMATICS GROUP

REPORT

Editor: Herman J.C. Berendsen
Biophysical Chemistry, University of Groningen
Nijenborgh 4, 9747 AG GRONINGEN, the Netherlands

Tel.: +31-503634323
tel. secr.: +31-50.3634378

fax: +31.50.3634800
home: +31-594-502629
email: H.J.C.Berendsen@rug.nl

internet:
http://www.hjcb.nl

Date: May 14, 2002

This report is available at the editor’s website:
href=”http://www.hjcb.nl/personal/IUBG-FinalReport.html

Acknowledgment The work of the IUBG and the production of
this report have been funded by the ICSU Grants Programme



Contents:



Introduction

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The IUBG was established on initiative of the IUPAB in 1998 as an Inter-Union
activity addressing issues concerning the availability, maintenance, and
free access of biological and biophysical scientific data. The availability
of sequence data on the human genome and on gene sequences of other organisms,
and of structural data on proteins and other bio-macromolecules, is growing
rapidly. Combined with the growing impact of these data on applied sciences
and medicine with their concomitant commercial interests, concerns have
been raised about the proper archiving of such data, its quality control,
the guaranteed unrestricted access, and the safeguarding of archival data
for future generations. Such primary scientific data as sequences and structures
must be considered as cultural assets that should be made accessible and
kept available for future generations as part of the human heritage. In a
way they are comparable to basic scientific data such as the physical properties
of the elements, or to taxonomic data of biological organisms, which are
well-documented and readily available to the worldwide community of pure
and applied scientists.

A difference with the ‘classical’ data is that the latter are archived
and available in the open literature, which is kept accessible by scientific
libraries of universities and institutes. National libraries have the specialized
task, recognized and supported by the governments of several countries, to
safeguard the access of relevant documents for future generations. On the
contrary, bio-data are presently not published in detail in scientific journals,
but rather deposited in databases. These databases are maintained by institutions
that do not have the support status of national libraries. It is not yet
generally recognized at the government level that the archiving of such
data needs protection similar to the archiving of literature, and that governments
and supranational bodies bear a responsibility to maintain the collections
and safeguard their integrity and access into the far future.

As the quantity of primary information grows at an exponential rate, its
proper archiving and maintenance become more and more a matter of concern.
Organisations that maintain archival databases are confronted with an ever-growing
work load. Without adequate public funding they may be forced to make selections
based on non-scientific considerations, relax the strict requirements of
quality control, or impose restrictions to access that are detrimental to
public availability in a worldwide community. There is also a need for international
cooperation of the institutions concerned, and for the definition of standards
for data treatment and data exchange.

Another matter of concern is the national and international legislation
on intellectual property rights, which is at present actively discussed.
While there is no doubt that the author of a creative process possesses intellectual
property rights on the product of his creative process, and that such rights
need protection by law, there is also no doubt that primary biological data
per se can never become the subject of intellectual property rights,
and their ‘fair use’ for scientific and educational purposes must not be
impeded by regulations. Careful distinction must be made between the data
themselves and the added value of the form in which they are presented,
or the processes to which they are subjected.

The rate of growth of the biological primary data and of the various techniques
that are being developed to make use of these data, present challenges to
scientists as well as to current university curricula. Not only are the
changes fast and the applications novel, but the combination of skills required
for managing these data is far from traditional. One must combine aspects
of biological or medical sciences with mathematics and informatics in an unprecedented
way. Apart from a selected group of specialists, the majority of scientists
will be left behind if educational curricula do not quickly adjust to these
changes. The IUBG feels that much can be gained by international cooperation
in aspects of education, and addresses this topic as well in this report.


The IUBG and its mission

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The IUBG is a Joint Initiative of the International Union for Pure and
Applied Biophysics (IUPAB), the International Union of Biochemistry and Molecular
Biology (IUBMB), the International Union of Crystallography (IUCr), the
International Union of Pure and Applied Chemistry (IUPAC) and the Committee
on Data for Science and Technology (CODATA). The IUBG seeks overlap with
the nomenclature committees of IUCr, IUBMB, IUPAC, and CODATA. The IUBG has
received support from the ICSU (International Council for Science) Grants
Programme and UNESCO (United Nations Educational, Scientific and Cultural
Organisation). [See the Appendix
for a list of acronyms]. Its mission statement is:

  • To monitor worldwide developments in Bioinformatics
  • To take measures as required to ensure and facilitate inter-process
    communication, such as standardization of data formats
  • To act when the continuity or reliability of key informatics providers
    is endangered
  • To act when the free access to data in the public domain is endangered
  • To catalyse actions by the appropriate authorities in areas of the
    world where Internet access to servers and data providers is technically
    inadequate
  • To organize relevant educational activities.

The steering committee consists of

  • Herman J.C. Berendsen (former president IUPAB), Secretary
  • Helen M. Berman (IUCr)
  • Richard Cammack (IUBMB)
  • Charles Cantor (former IUPAB Council)
  • Jean Garnier (President IUPAB), Chairman
  • Arthur Lesk (representing CODATA)
  • Alan McNaught (IUPAC)
  • Richard Roberts (ICSU)
  • M. Vijayan (IUPAB, IUCr)

In addition to the members of the steering committee, as mentioned
above, the following advisors were present on invitation at one or more
of the IUBG meetings, and have contributed to this report:

  • Rolf Apweiler (Swissprot/EBI)
  • Michael Ashburner (EBI)
  • Philip Bourne (PDB)
  • Nobuhiro Go (Kyoto)
  • Marianne Minkowski (ESF: European Science Foundation)
  • Carlos Martinez-Riera (EC: European Commission)
  • Peter Murray-Rust (Cambridge University)
  • Barry Robson (IBM)
  • Patricia Rodriguez-Tome (EBI/EMBL)
  • John Rumble (President CODATA)
  • Jay Russell Snoddy (ORNL)
  • Hideaki Sugawara (DDBJ)

The following meetings were held:

  • 28-29 June, 2000: Whitehead Institute, Cambridge, Mass, USA
  • 17 October, 2000: Baveno, Italy
  • 22 October 2001: EBI, Hinxton, Cambridgeshire, UK
  • 14 May 2002: ICSU, Paris, France


Primary scientific data: care and responsibility

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Classification of data

There are two basically different types of databases: archival databases
and derived databases. The former carry the primary public data; the latter
use or recombine these data to derive new properties and relations. One can
also distinguish databases by their content: there are structural databases
and protein and nucleic acid sequence databases. There are databases on
taxonomy, on metabolic pathways, on phenotypes, on biodiversity, and many
more, as well as organism-specific databases. Finally, one may distinguish
databases by their ownership: public and private.

The IUBG concerns itself primarily with the archival databases, in the
fields of biophysics/biochemistry/molecular biology. The archival databases
are those to which the researchers submit their data (or which collect data
actively from primary sources); the proper archiving of primary biological
structure and sequence data for the future is put into their hands by the
scientific community. This imposes a great responsibility on the database
managing authorities and their sponsors. Not only must they provide lasting
storage; they must – as much as possible – provide for validation and annotation
of the data, and cooperate to avoid duplication and ensure completeness.
These responsibilities should be made explicit.

Obligations for journals and funding agencies

Since journal publications do not include all of the primary data described
in research reports, it must become mandatory to deposit data in a public
archival database, and journal editors must require such deposition before
accepting a manuscript for publication. In the case of structural data of
biological macromolecules, IUCr plays a vigorous role in providing guidelines
for deposition and release of data. Its publications carry much weight and
have resulted in the practice that such structural data are indeed deposited
into the Protein Data Bank (PDB). Unfortunately such a requirement has not
become common practice for structural data of small molecules. Neither does
a requirement exist for public deposition of thermodynamic, kinetic, and
spectroscopic data. For nucleic acid sequence data the situation has become
unclear and the scientific journals do not at present follow a common policy.
Although it would follow a long tradition that scientific publications are
only acceptable if they include the data on which the publication is based,
there are recent examples that publications have been accepted when the
relevant data were only promised to be made available by the author or
his (commercial) sponsor on a private site; this limits free access and
lacks the guarantee of a permanent archive of the data. One restriction is
that public archival databases are not allowed to copy such data into their
database. These examples include the publications in Science about the human
genome [Science 291 (2001) 1304-1351] and the rice genome [Science
296 (2002) 79; 92], in which cases the data are available from
commercial databases. The acceptability of such publications is at least
questionable, and the International Scientific Unions are urged to consider
the principles and set out guidelines for data deposition related to scientific
publications. There should be a balance between the commercial interest of
the data producer and the requirement of accessibility of data which accompany
scientific publications. The commercial interest could be protected by a
well-defined limited period of denial of public access, and the requirement
of public access could be met by the deposition of the data in a public
archival database under a suitable embargo. There should be a wide acceptance
of requirements of this type, and articles from authors who do not follow
the agreed requirements should simply be rejected by scientific journal editors.

Adherence to the principles outlined above should be demanded by the
research supporting agencies
which are publicly funded, as an imposed
condition on the recipient of the funding. To be precise, the sponsor should
require that data generated during the course of a funded project, be deposited
in public archival data bases, and allow submission of publications only
to journals that adhere to the principle of public deposition. The funding
agencies are – as many do in practice – urged to follow the recommendations
of international bodies representing the scientific community, such as the
International Unions. Such a policy of the major funding agencies will be
an effective tool to enforce implementation of these principles in the scientific
and publishing world. It will counteract any tendencies that may otherwise
arise to exploit data generated by public funding to the benefit of local
rather than public interests.

The general opinion is that archival databases should be public. Public
means unrestricted access in the sense that no moral judgments may be
made who should get the data,
but “public” is not the same as “free”.
The costs of maintaining the archival databases must be recovered somehow.
The ideal is that data are both public and free, but this requires a worldwide
commitment of national and international funding agencies.

International obligations

The maintenance of archival databases is in essence a supranational activity.
The obligation to deposit data must be followed worldwide. There must be
a single archive even if distributed over more than one site. Data
must remain uniform. Therefore, ideally an international agreement should
be reached for funding international archival databases. At present, there
is an asymmetry in funding: there are different funding models for the sequence
databases and the structural databases and there are different funding models
in Europe, the USA, and Japan. The funding models change with time. The PDB
is funded under a ‘memorandum of understanding’ by a consortium of US government
agencies (NSF, DOE, NIH); GenBank is funded by a special allocation by the
US Government. The deposition sites in Japan, the DDBJ for sequence data and
the Institute of Protein Research at Osaka University for structural data,
are financed by MEXT, the Japanese Ministry of Education, Culture, Sports,
Science and Technology. The European deposition site at the European Bioinformatics
Institute (EBI) functions as an outstation of the European Molecular Biology
Laboratory (EMBL) with limited basic funding, extended with funding by the
EU and the Wellcome Trust. Other national institutions do not have a recognized
role in the international safeguarding of archival data. The ideal would
be a wide international agreement at the government level that can stabilize
the situation and guarantee cooperation, consistency, and funding.

While several instances exist of international organizations with funding
at the government level, directly or jointly through a United Nations organization,
the establishment of such an organization is not at all trivial and is considered
premature for the present purpose. The subject is likely to be considered
too specialized for agreements at the government level, and referred to existing
international bodies as EMBL and EMBO and to the national and supranational
research funding agencies . It is in fact in the direct interest of
fundamental and applied research worldwide, and thus of the research funding
agencies, that scientific data are properly archived, validated and made
accessible. Therefore the research funding agencies, both public and private,
and both national and supranational, are in fact responsible for safeguarding
scientific data. Although this applies to such organisations worldwide, the
primary responsibility lies with the major funding agencies in the USA,
Europe and Japan, who have the means to fulfil this task. It is important
that they will also show their resolve to fulfil this task, which requires
long-term commitments to support the archival databases.

Support by the funding agencies involves more than the support of short-term
projects related to the archival data bases. It is mandatory that the funding
agencies commit themselves to long-term support of the archival databases.
This may involve long-term support of the data-archiving activities, but
in the interest of flexibility and proper quality control the support should
be made dependent on a periodic review of the performance. The exact terms
are of course a matter of the funding agencies themselves; the essential
ingredient is that the major funding agencies consider data archiving activities
as their permanent responsibility. The responsibility extends – under strict
quality control – beyond existing and recognized archival data bases to new
archiving activities if the need arises.


The public databases

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In this section we give a survey of the archival data bases as they presently
function, followed by requirements related to the validation and quality
of the data.

Major archival databases for biological molecules:

  1. Nucleic acid sequences: DDBJ/EMBL/GenBank International Nucleotide
    Sequence Database (INSD)
    : NCBI (Natl Center for Biotechnology Information
    at NLM/NIH; “GenBank Database”)/ EBI (European Bioinformatics Institute,
    Outstation of EMBL; “EMBL Nucleotide Database”)/ DDBJ (DNA Data Bank of Japan,
    Natl Institute of Genetics; “DDBJ Database”). Data can be submitted to any
    of these and their contents are daily synchronized. EBI and DDBJ each receive
    10 to 15% of the entries, and GenBank receives 70 to 80%, but the three databases
    provide the same entries. Aim of the INSD is to record every publicly known
    nucleic acid sequence. Data are freely available.
  2. Protein sequences (including post-translational modifications):
    PIR-International
    (Protein Information Resource) is a collaboration
    between NBRF (Natl Biomedical Research Foundation, Georgetown)/ MIPS (Munich
    Information Center for Protein Sequences at the Max Planck Inst. for Protein
    Research, Munich)/ JIPID (Japan International Protein Information Database).
    Data are freely available. SWISS-PROT is an annotated protein sequence
    database maintained collaboratively by the Swiss Institute of Bioinformatics
    (Geneva) and the EBI. Data from SWISS-PROT are freely available for non-profit
    institutions only. Commercial users pay a yearly license fee. SWISS-PROT
    is not strictly an archival database, but it is unique in its annotation,
    accuracy and links to other databases. TrEMBL is a supplement to SWISS-PROT
    providing computer-annotated entries derived from the translation of all
    coding sequences in the EMBL Nucleotide Sequence database. SPTR (SWISS-PROT/SP-TrEMBL)
    is a weekly updated combination of both databases and checks on additional
    data in PIR and PDB.

    Biomolecular structure: The Protein Data Bank (PDB) of protein
    structures based on x-ray or NMR data is operated by the RCSB (Research
    Collaboratory for Structural Bioinformatics), funded jointly by the US Natl
    Science Foundation, Department of Energy, and two units of the Natl Institutes
    of Health. Partners are SDSC (San Diego Supercomputer Center at La Jolla,
    CA), Rutgers University (Piscataway, NJ), and NIST (Natl Inst. of Standards
    and Technology, Rockville, MD). Data can be submitted to the US site at
    Rutgers, the Institute of Protein Research at Osaka University in Osaka,
    Japan, or the MSD site at the EBI. The BMRB ( BioMagResBank
    at the University of Wisconsin, Madison) collects primary NMR data. PDB
    and BMRB data are freely available. The NDB (Nucleic Acid
    Database
    ) distributes data about nucleic acid structures and is managed
    by Rutgers University. It is funded by the National Science Foundation
    and the Department of Energy. The CSD (Cambridge Structure Database)
    is managed by the CCDC (Cambridge Crystallographic Data Centre),
    contains small molecules, and is available for a fee.

  3. Other databases: There are many databases of biological interest that
    are not mentioned here (bibliographic data, taxonomic data, data on specific
    organisms, data on lipids, carbohydrates, protein ligands, vitamins, etc.,
    metabolic data, etc.). If they are archival, they serve in principle the
    same public interest as the major archival databases, and such databases may
    encounter similar problems related to free access and funding as those discussed
    by the IUBG.

Requirements for validation and quality of public databases. Problems
of redundancy.

There are two aspects: quality control and annotation. Quality
control is an essential process before data can be entered into an archival
database. It involves error and redundancy checking, correspondence with
authors, etc. Corrections are difficult and require skill and experience.
A good partnership is needed between the curator and the depositor, and also
between the curator and the programmer. Although error-free data can never
be guaranteed, the usefulness of a database depends on its accuracy and
reliability. Annotation, such as the addition of literature references, the
comparison of gene sequences with other organisms, the relation of nucleotide
sequences to proteins, the comparison with other sequences or proteins, and
the reference to possible protein function, involves cross-referencing with
literature and other data and, again, requires skill and experience. Archival
databases need validation and annotation to be useful; however, the possibilities
and requirements are subject to change and the standards to be applied to
validation and annotation should be set by periodic peer review.

With the increasing rate at which data are deposited, curation and annotation
will become a quantitative and financial problem. Some two hundred new genes
(or rather genetic loci) come in each day: how can one keep pace with annotation?
It is required to hire, train and retain skilled curators and annotators.
There are good opportunities to involve countries around the world in distributed
annotation activities and in database-related work; countries like India
have a large reservoir of well-trained people. Much of the work can be done
in a distributed fashion while maintaining the integrity of the annotation
standards and methods. A program of visits by experts to these countries and
visits of scientists from these countries to the data centres could enhance
the cooperation with and involvement of countries outside US, EU, and Japan.

Threats to continuity and availability of publicly funded biological
databases

As mentioned above, there are several different funding mechanisms for
the archival databases. They all operate on a short-term basis, and lack
the long-term commitment needed for the guaranteed and continued functionality
and maintenance. What is particularly lacking is an international agreement
between sponsoring organisations and a commitment of such organisations in
other countries than the USA, the EU and Japan. The international cooperation
is now based on the goodwill of the people involved and not on agreed international
cooperation, backed up by the commitment of sponsoring organisations. In
such a chaotic situation, the integrity of the archival databases
is threatened.

The IUBG recognizes the need to convince government bodies and publicly
funded research organisations of their responsibilities to maintain infrastructure
for archival databases in order to guarantee continuous archiving and international
access to the archived data. The archived data are our heritage!


Intellectual Property Rights (IPR)

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The concern of the IUBG over free access to primary data bears on the Intellectual
Property Rights (IPR) issue that is widely debated at present. In 1996 the
UN organization WIPO (World Intellectual Property Organization) published
a draft “Treaty on Intellectual Property in Respect to Non Original Databases”,
extending existing copyright agreements to databases and supporting an overly
protectionist property rights regime. This draft was not adopted, however.
Its far-stretching consequences were immediately attacked by the US National
Committee for CODATA in a 1997 report “Bits of Power. Issues in Global Access
to Scientific Data”. The European Union has adopted a Directive on the Legal
Protection of Databases in 1996 (supposed to be implemented in national laws
by Jan 1, 1998) which extends copyrights to material contained in databases
without making appropriate explicit exceptions for fair use for personal,
scientific, and other non-commercial purposes. This Directive has raised
much concern, because – if such exceptions are not specified – the resulting
laws could impair the free scientific development by making original data
not freely available. The matter has been taken up by ICSU/CODATA (see

http://www.codata.org/codata/data_access/summary.html
) and a meeting on the subject was held in Baveno, Italy, on Oct. 14,
2000. It is also a subject of debate in connection with the proposed Global
Biodiversity Information Facility (GBIF, still in planning stage).

The IUBG is much concerned with overprotective measures that would limit
the worldwide free sharing of primary biodata. The primary biological data,
including all sequence and structure data derived from natural organisms,
should be freely accessible and their fair use for scientific purposes should
not be limited. The IUBG supports the activities undertaken by ICSU/CODATA.

A related topic is the patentability of nucleotide sequences. Measured
sequences are facts and not inventions, and should not be possible objects
for patents or copyrights.


Worldwide access to public data and inadequacies of the Internet

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Bioinformatics and biotechnology services take the shape of ‘interactive
only’ sessions in the vast majority of sites involved in the service provision
of genomic and gene-related data. The network infrastructure that makes this
possible is improving all the time and expands beyond European and North
American borders. However, the pace at which this growth happens is directly
related to the robustness in the relationships between network partners
in various continental regions, and to the flow of funds required to establish,
maintain and upgrade the networks. As a result, there are varying service
levels for the biotechnology user community in respect to these resources
over the Internet: some enjoy good connectivity and can submit jobs to interactive
services, while others are limited to accessing these resources through email
(this includes many parts of South and Central America, the Caribbean, Africa,
Indo-Asian subcontinent, many countries in the Pacific rim, and sometimes
even in the USA and Europe).

In the present situation the data-providing centers must make sure that
the tools for information retrieval and analysis are available to the biotech
community regardless of how well connected one is to the Internet. These
services must have both interactive and email based interfaces, while availability
on CD-ROM provides an additional service. While the interactive forms are
self-explanatory due to their visual nature, the email interface is not,
and the degree of experience that is required to become aquainted with all
options is very high. Therefore users with insufficient Internet functionality
do not in fact obtain a quality of service equal to that of the more fortunate.
It is in the interest of the high-level participation in international science
that internet facilities grow to high quality on a worldwide basis.

The general internet situation in third world countries is a subject that
goes far beyond the possible interventions of IUBG. The problems are common
to most scientific fields, although in the Bioinformatics field the insufficiencies
are most apparent. The IUBG will support any action of ICSU bodies (like
CODATA) to address this issue. Also in Europe, as in other non-US countries,
academic networks should improve. Dedicated research networks are not a solution.
The global message is: good access is required.

Access in the present context could mean not only access to information
in the databases, but also access to the process of creating and maintaining
databases
. At present, the number of people involved in the process are
few and originate from a few countries. Highly competent manpower exists
in some reasonably developed, but comparatively poor countries in Asia and
Latin America. Involvement of well-trained scientists and technicians from
such countries in the development and maintenance of major databases could
be mutually beneficial. On the one hand, these scientists and technicians
would get an opportunity to participate in bioinformatics operations at the
international level. On the other hand, the organizers of the databases would
have access to trained manpower. In fact, it is possible that much of the
work could be carried out by the scientists and technicians in their home
laboratories in the course of cooperative projects, with occasional visits
to the main sites of the databases.


Standardization issues

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Standardization of data definitions and nomenclature.

Standardization of data definitions and nomenclature is important to prevent
confusion and to facilitate data exchange. There are two reasons to enforce
a controlled vocabulary: uniqueness and equivalency on various
levels. Requirements for classifications are: they should be unique, concise,
informative, and easy for searching. At present naming and classification
is missing for large classes of biomolecules. A systematic definition of
the ontology, describing the hierarchy of terms in which the knowledge
in a field can be expressed, is needed for the fields of genetics, molecular
biology and bioinformatics. Compatibility in data definitions is just one
step ensuring that the data are expressed in machine-readable form and that
data can be unequivocally interpreted.

Standardization of nomenclature is not a matter for a committee like the
IUBG. Experts are needed to establish standardization and classification.
The Unions should take responsibility on behalf of the scientific community
and establish working groups for the creation of a controlled vocabulary

for archival bioinformatics resources. They should also help secure
funds to finance such activities.

As example of existing standards is the EC number classification for enzymes.
Some enzymes have more than 50 names, but a functional classification, based
on reaction catalysed, had been found to be the most useful and robust system.
It is restricted to enzymes that catalyse a distinct and well-defined reaction,
and not every property of the enzyme is considered. The classification is
given by a number like EC 1.1.99.238, plus a common name, plus
a systematic name, plus a comment section with cross references
to sequence, structure, cofactors, substrates, metabolism. The number is
composed of

EC: defines the database

1 (first number): defines the enzyme type
1 (second number), and 99 (third number): define the reaction
238 (fourth number): is a catalogue number.

The databases should use standard nomenclatures for their contents if these
nomenclatures have been defined.

Standardization of data formats and data exchange

Considering data formats, the most important requirement is that the
format should be specified completely and in detail
. For each type of
data there must be an agreed format such that the data are machine-readable
and their meaning is unequivocal.


Education

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There is a demand for education in bioinformatics for students of life
sciences and chemistry, at levels from undergraduate to specialist postgraduate,
and for conversion courses for teachers. This can be through degree programmes
or summer schools. Bioinformatics should be integrated into the life sciences
curricula.

Training in diverse disciplines is required for those constructing databases.
Biologists, computer scientists and software engineers will be involved in
teams for creation of databases. Biologists need training in programming
and scripting languages, while computer scientists need appropriate training
in biology and chemistry.



Conclusion

Following the analysis presented above, the IUBG has formulated a series
of Statements and Recommendations as an independent document (see below).
These summarize the report and provide the necessary guidelines for further
actions.



Statements and Recommendations from the Inter-Union Bioinformatics Group
(IUBG)

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Statements

Statement 1 on the safeguarding of biological
data

It is the obligation
of the scientists and legislators of all nations to archive and support primary
(i.e., fundamental experimental) scientific data, including, but not exclusive
to, nucleotide sequences of biological organisms, amino-acid sequences of
proteins, three-dimensional structures of biological molecules, as well
as other primary data produced by genomics and proteomics studies. These
data must be validated, stored, made publicly accessible, and safeguarded
for future availability and access. Access must be public and unrestricted
and no organization should have a monopoly on these data. These primary scientific
data are crucial for the development of science and its applications.

Statement 2 on the obligations of data generators

It has always been
the practice that those who claim scientific advances by publication of their
work should support their claim by making openly available the objective
data on which their claim is based. Thus 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 urged to conserve and eventually deposit their primary data.

Statement 3 on right to fair use of data

Scientific advances
rely on full and open access to data. Primary data that are accessible through
the archival databases should not be subjected to any restrictions that would
limit fair use of those data. Fair use includes the use for teaching and
research 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.
Standardization is an ongoing activity requiring high-level
agreement among scientists of various fields in order to ensure understanding
and knowledge exchange across borders of scientific disciplines.

Statement 5 on education

Considering the skills
required for archiving, validation and dissemination of data, educational
institutions should recognize the need for specific education in (bio)molecular
informatics

Recommendations

Recommendation 1 to International Unions and
scientific societies

(a) It is recommended
that each Union, on a regular and ongoing basis, identifies and publicizes
a list of key archival data bases.

(b) It is recommended
that International Unions and other scientific societies actively encourage
their membership to deposit primary data in recognized data repositories
which provide unrestricted access to these data.

(c) It is recommended
that journals of these Unions and societies ensure that these requirements
are met before accepting publications in their journals.

(d) It is recommended
that International Unions, specifically IUPAB, address the general issue
of education in the field of (bio)molecular informatics.

Recommendation 2 to funding agencies

(a) 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
work with funding agencies to create guidelines for this purpose.

(b) It is recommended
that funding agencies actively encourage and adequately support existing
and newly funded primary data repositories, including their updating and annotation,
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.

Recommendation 3 to for-profit organizations

It is recommended
that for-profit organizations deposit their data as early as possible in
public archival databases.

Recommendation 4 to publishers and authors

It is recommended
that journal publishers make the primary data on which a publication is based
available under the same conditions as they make the printed article available,
and – if applicable – require that such data are deposited in a recognized
key archival database. Authors are encouraged not to publish in journals
that do not conform to these rules.

Recommendation 5 to legislators

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

Recommendation 6 to scientific committees
for nomenclature and standardization

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 nomenclature and data standardization committees. They should
be conversant with both the content and the technologies needed for a full
definition of the field, in order to ensure the exchange of data without loss
of information.

Recommendation 7 to educational institutions

It is recommended
that bioinformatics curricula should include specific education in the creation
and curation of databases, as well as in their use. Life sciences curricula
should include courses and training in bioinformatics.


The steering Committee of IUBG:

Herman J.C. Berendsen
(IUPAB)
Helen M. Berman (IUCr)
Richard Cammack (IUBMB)
Charles Cantor (IUPAB)
Jean Garnier, (IUPAB), chairman

Arthur Lesk, (CODATA)
Alan McNaught, (IUPAC)
Richard Roberts, (ICSU)
M. Vijayan (IUPAB, IUCr)




APPENDIX

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Some institutions

ACRONYM TITLE OFFICER INTERNET
CODATA Committee on Data for Science and Technology J.Rumble, NIST (pres.) http://www.codata.org
GBIF Global Biodiversity Information Facility J.L. Edwards (Exec. Secr.),

Univ. of Copenhagen, Denmark

http://www.gbif.org
ICSU Int.Council for Science T. Rosswall (ex. dir.) http://www.icsu.org
ISCB Int. Society for Computational Biology P.E. Bourne (pres.) http://www.iscb.org
IUBG Inter-Union Bioinformatics Group J. Garnier, Paris; NIH (chair) http://md.chem.rug.nl/
~berends/IUBG/
IUBMB Int. Union of Biochemistry and Molecular Biology B.F.C. Clark (pres.)
J.H. Weil (secr.gen.)
http://www.iubmb.org
IUCr Int. Union of Crystallography W. Duax (pres.)
M.H. Dacombe (ex.secr.)
http://www.iucr.org
IUPAB Int. Union for Pure and Applied Biophysics J. Garnier (pres.)
F. Parak (secr.gen.)
http://www.iupab.org
IUPAC Int. Union of Pure and Applied Chemistry P. Steyn (pres.)

J.W. Jost (ex.dir.)

http://www.iupac.org
IUPAP Int. Union of Pure and Applied Physics B. Richter (pres.)
R. Turlay (secr.gen.)
http://www.iupap.org
JCBN (with NC-IUBMB) Joint Com. on Biological Nomenclature (with Nomenclature Committee
of IUBMB)
R.Cammack (chair)
S. Boyce (secr.)
http://www.iubmb.org/
nomenclature
UNESCO United Nations Educational, Scientific and Cultural Organisation Matsuura (dir. gen.) http://www.unesco.org
WIPO World Intellectual Property Organization K. Idris (dir. gen.) http://www.wipo.int
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