International Council for Science : Committee on Data for Science and Technology

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C O D A T A

CODATA National Member:

India
Indian National Science Academy

Chair/Delegate: Dr. Baldev Raj, FNA

Dr.Baldev Raj, FNA
Distinguished Scientist & Director
Indira Gandhi Centre for Atomic Research
Kalpakkam – 603 102
Tel:044-27480420(O)
044-27481342 (R)
Fax:044-2748 0060
E.mail:dir@igcar.ernet.in

Members:

Dr.V.P.Dimri, FNA
Director
National Geophysical Research Institute
Uppal Road
Hyderabad- 500 007
Tel:040-2343 4600(O)
040-2343 4623 (R)
Fax:040-2343 4651
E.mail:dimrivp@rediffmail.com

Professor Alok Bhattacharya, FNA
School of Life Sciences
Jawaharlal Nehru University
New Delhi – 110 067
Tel:2670 4516(O)
2613 3295 (R)
9810881439(M)
E.mail:alok0200@mail.jnu.ac.in

Dr.K.Sekar
Principal Research Scientist
Bioinformatics Centre
Indian Institute of Science
Bangalore-560 012
Tel:080-23601409
Fax:080-23600683
E.mail:sekar@physics.iisc.ernet.in

Professor Jitendra Kumar
Professor & Head
Materials Science Programme
Indian Institute of Technology
Kanpur – 208 016. (U.P)
Tel:0512-2597107(O)
0512-2598227 (R)
09450938992 (M)
Fax:0512 2597664
E.mail:jk@iitk.ac.in

National Committee Activities

(a) Extracts of the Minutes of the first meeting of the reconstituted CODATA National Committee on June 3,2004 at INSA premises

The first meeting of the reconstituted CODATA National Committee was held on June 3,2004 at INSA. The following members were present:

1. Professor S.K. Sikka, FNA Chairman
2. Dr. K. Sekar Member
3. Dr. Baldev Raj Member
4. Dr. S. Kailas Member
5. Dr. Krishan Lal, FNA Member
6. Dr. Alok Moitra INSA Representative

Dr. F Roy could not attend the meeting due to some other commitments.

The Chairman, at the outset, welcomed the members of the CODATA National Committee and thereafter took up the agenda for discussion. Dr. Sikka expressed the opinion that except Dr. Krishan Lal all other members of the committee are new to CODATA and it will be a good idea to brief them about its broad activities.

CODATA is concerned with all types of quantitative data resulting from experimental measurements or observations in the physical, biological, geological and astronomical sciences. Particular emphasis is given to data management problems common to different scientific disciplines and to data used outside the field in which they were generated. The general objectives are the improvement of the quality and accessibility of data, as well as the methods by which data are acquired, managed and analyzed; the facilitation of international cooperation among those collecting, organizing, and using data; and the promotion of an increased awareness in the scientific and technical community of the importance of these activities.

The Chairman also stressed that databases in India, compared to other countries, are not fully accessible to the scientific community of the country. At times, there are restrictions in the use of databases or they are only partially accessible. The scientific community very strongly feels that all the data generated through scientific research should be freely available to the community.

Dr. Krishan Lal then made a detailed presentation about CODATA, its objectives, structure and its Task Groups and Working Groups. CODATA was born during the 11^th General Assembly of ICSU which was held in Mumbai in January, 1966. The Committee works on the general guidelines laid down by the Executive Committee headed by President of CODATA. The day to day activities are coordinated by the Executive Director of CODATA. There are 23 national delegates and 14 Union delegates of CODATA. He further discussed the Task Groups and Working Groups of CODATA. The Academy in recent past had hosted the meeting of the CODATA General Assembly and the associated International Conference, Task Group on Data Information and Visualization and Task Group on Data Sources in Asian Oceania (all in 1998). This year Academy hosted the meeting of the Task Group of Data on Natural Gas Hydrates (February, 2004). A summary of the proceedings of the Task Group meeting on Natural Gas Hydrates was circulated to the members.

In addition to the presentations by Dr. S.K. Sikka and Dr. Krishan Lal on CODATA activities, Dr. K. Sekar and Dr. Baldev Raj made specific presentation on the databases prepared and managed by them. Dr. Sekar discussed about Protein Data Bank (PDB), Genome Data Base (GDB), Structural Classification of Proteins (SCOP) and Cambridge Structural Database (CSD). Some databases have also been prepared by him and his group at Indian Institute of Science, Bangalore, sponsored by Department of Biotechnology and Jai Vigyan National Science Foundation of Government of India. Dr. Baldev Raj discussed the database of Indira Gandhi Centre for Atomic Research (IGCAR) for professional bodies such as Material Research Society of India (MRSI) and Indian Institute of Metals (IIM).

Dr. S. Kailas made a brief presentation about the database of scientific and technical personnel of BARC. He mentioned that the BARC database needs a lot of updation. Dr. Sikka mentioned that Department of Atomic Energy should take the lead in the compilation of nuclear data and human resource database.

The members also felt the need for a extensive data base on scientific and technical personnel in India. There are many organizations who have their own databases for the scientific and technical person employed with them or working in the areas of interest to those organizations. Many professional bodies in India have developed and maintained excellent databases. Mention was made of DSIR database and the databases of MRSI and IIM. Chairman was requested to contact such professional bodies and request them to follow the pattern of CODATA databases. In order to increase the visibility of Indian databases, it was suggested that INSA News should carry information about such databases. Similarly, the newsletters of professional bodies may also publish information about databases of relevance to their subject area. Most of the professional bodies have their annual / biannual meeting where the scientific community should be made aware of such data bases by making presentation. Dr. K. Sekar was requested by Dr. Krishan Lal to make presentation about his databases created at Indian Institute of Science, Bangalore at the next meeting of the Indian Crystallography Association to be held in Guwahati later this year.

(b) Report on Regional Workshop on CODATA Task Group On Natural Gas Hydrates at Indian National Science Academy, New Delhi on 19 – 20 February, 2004

As a part of the ICSU sponsored project on gas hydrates, a series of regional workshops are being held at different places. One such regional workshop was held at Indian National Science Academy, New Delhi on 19-20 February, 2004. The purpose of this meeting was to involve experts from different organizations and institutes to put forward their views and perspectives.

Participants from the following Indian Organizations attended workshop:

i. Department of Ocean Development (DOD), Government of India, New Delhi,
ii. K.D. Malviya, Institute of Petroleum Exploration (KDMIPE), Dehradun,
iii. Directorate of Hydro Carbons (DTHC), Government of India, New Delhi,
iv. National Centre for Antarctica and Ocean Research (NCAOR), Goa,
v. National Geophysical Research Institute (NGRI), Hyderabad,
vi. National Institute of Oceanography (NIO), Goa; and
vii. National Physical Laboratory (NPL), New Delhi.

Acad. F.A. Kuznetsov, Director, Institute of Inorganic Chemistry, Novosibirsk, Russia and Chairman of the CODATA Task Group and Prof. Yuri F. Makogon, Texas A&M University, Houston, USA, also participated in the Workshop.

The Workshop comprised of the following four sessions:

i. Inaugural Session;

ii. Presentations from participant Institutes and Organizations– Part-I

iii. Presentations from participant Institutes and Organizations – Part-II

iv. Consolidation Session

Dr. Harsh K. Gupta, Secretary, DOD inaugurated the Workshop. He gave an overview on the activities of DOD in this field and the various initiatives that the country is taking to exploit the gas hydrates. R&D work is being pursued in laboratories of DOD, CSIR, ONGC among others. Dr. Harsh K. Gupta mentioned about the opening of an Indo-Russian Centre on Gas Hydrates in National of Ocean Technology, Chennai. This Centre will help in enhancing cooperation between Indian and Russian scientists in this important field.

Acad. Kuznetsov gave a background of the workshop, which is one in a series of regional meetings being held under the ICSU sponsored project. He mentioned that workshops have already been held in Russia, Europe, USA and Japan. He stressed that he is aware of the good work being done in India in this field. Already, an Indo-Russian Centre has been established in Chennai (in NIOT), which had just been opened on 12^th February, 2004. Indeed, Acad. Kuznetsov has led the Russian delegation in the formal opening of the Centre.

Dr. Krishan Lal welcomed all the participants and explained in his opening remarks the genesis of this workshop and what is expected from its deliberations.

In the two sessions of presentations, three general presentations and seven institutional presentations were made. Dr. Krishan Lal gave a broad overview on CODATA and its various activities at present. Acad. Kuznetsov gave details of the ICSU project on gas hydrates. Professor Makogon spoke on the overall area of gas hydrates and expressed great hopes that India may become the first country to exploit this wonderful natural resource. Professor Makogon was one of the discoverers of gas hydrates on land in 1960s. He discussed the results obtained by a variety of geo-physical techniques for locating gas hydrates at the ocean beds.

A wide variety of aspects of gas hydrates in India were covered in the seven presentations as indicated by the titles given below:

i. Exploration and Exploitation Scenario of Gas Hydrates in India – D. Choudhuri, KDMIPE;

ii. Application of Marine Geophysical data for Delineating The Indian Legal Continental Shelf and Hydrocarbon Resources – U.K. Singh, NCAOR;

iii. Strategies for Geophysical Data Collection in Relevance to Gas Hydrate Exploration – B. Ashalatha, NGRI;

iv. Estimation & Modelling of Gas Hydrate Resources – Kalachand Sain, NGRI;

v. Database Management System for Gas Hydrates – T. Ramprasad, NIO;

vi. Marine Data & Information Regional Network in the Indian Ocean – J.S. Sarupria, NIO;

vii. Indo-Russian Collaboration in Gas Hydrate Research – S.K. Das, DOD; and

viii. Presentation on National Gas Hydrate Programme – N.K. Sethi, Dte. Of Hydro Carbons.

In the Consolidation Session, each participant was to give his specific views on the aims and objectives of the ICSU sponsored project on gas hydrates. Practically all of the participants expressed concern that there is no general policy in India on the extent to which scientific data on gas hydrates can be shared. There are commercial and strategic angles, which needs to be considered. It was clarified that all countries have data, which is sensitive from defense as well as economic angles. No country shares such data. However, there is a lot of data in the open, which can be shared, exchanged and consolidated. It was suggested that perhaps DOD or other relevant organizations can look into these issues. Therefore, it was necessary that all scientists present in this Work will have discussions in their respective organization and then make decisions about participation in this effort. Later, a lot of discussion took place on the following points:

i. Attitude of the participants in relation to the CODATA Task Group project to create a globally distributed information system, covering all major aspects of gas hydrates;

ii. Do the participants wish to be recognized as one of the database groups on gas hydrates?

iii. What model can the participants accept for in-country and international collaboration? Their views were sought on format for collection, storage and exchange of data and modes of access to data bases;

iv. How the work in India can be organized for data on gas hydrates?

v. Would the participants support organization of

– A national CODATA task group on gas hydrates.

– A web site on gas hydrates; and

vi. Where Indian database should be situated? Should it be at one place or mirror sites can be established?

vii. Major Challenges – Commercial and Strategic.

It was strongly suggested that a website highlighting CODATA activities in India particularly on gas hydrates may be prepared and launched expeditiously. The funds of the Regional Workshop may be used, if necessary.

(c) Some Biology and Bio-Crystallography Related Databases

(i) CADB: Conformation Angles DataBase of Proteins

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user-interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL:http://144.16.71.148/cadb/ .

(ii) THGS: a web-based database of Transmembrane Helices in Genome Sequences

Transmembrane Helices in Genome Sequences (THGS) in an interactive web-based database, developed to search the transmembrance helices in the user-interested gene sequence available in the Genome Database (GDB). The proposed database has provision to search sequence motifs in transmembrane and globular proteins. In addition, the motif can be searched in the other sequence databases (Swiss-Prot and PIR) or in the macro-molecular structure database, Protein Data Bank (PDB). Further, the 3D structure of the corresponding queried motif, if it is available in the solved protein structures deposited in the Protein Data Bank, can also be visualized using the widely used graphics package RASMOL. All the sequence databases used in the present work are updated frequently and hence the results produced are up to date. The database THGS is freely available via the world wide web and can be accessed at http://pranag.physics.iisc.ernet.in/thgs or http://144.16.71.10/thgs/ .

(iii) LySDB – Lysozyme Structural DataBase

LySDB (Lysozyme Structural DataBase) is an integrated database containing 740 three-dimensional structures of Iysozyme available in the Protein Data Bank. The database can be used to visualize the three-dimensional structure of the entire protein model or the substructures in which the user is interested (for example, insertions and deletions of animo acids) using the three-dimensional atomic coordinates. The database is provided with a search engine with several useful built-in facilities. The public domain graphics program RASMOL has been deployed for visualization. The three-dimensional structures used to create the database are updated at regular intervals and hence the users are provided with the current information available in the literature. The database LySDB is available over the World Wide Web and can be accessed at the URL http://iris.physics.iisc.ernet.in/lysdb/ or http://144.16.71.2/lysdb/ .

(iv) SSEP: SECONDARY STRUCTURAL ELEMENTS OF PROTEINS

SSEP is a comprehensive derived database related to the secondary structural elements present in the 25% and 90% non-redundant protein chains. The current version provides information about the alpha-helical segments, beta-strand fragments, 310-helices, beta-and gamma-turns and hairpin loops of varying lengths. The free graphics program RASMOL has been interfaced with the search engine to visualize the three-dimensional structures of the user queried secondary structural fragment. Several other useful information are also incorporated in the revised version. In addition, the package can be used to extract the three-dimensional atomic coordinates of the defined secondary structural elements. The database is updated regularly and is available through Bioinformatics web server at http://cluster.physics . iisc.ernet.in/ssep/or http://144.16.71.148/ssep/ .

(d) INDIAN EFFORT IN SCIENTIFIC DATA COMPILATION ON A FEW AREAS OF MATERIALS SCIENCE AND ENGINEERING

India has experience in maintaining databases for some of the areas in materials Science and engineering areas through professional bodies such as Indian Institute of Metals and Materials Research Society of India. The websites maintained by these professional bodies provide information on its members and various scientific activities. A need for compilation of important scientific information in the materials science and engineering areas in India was felt as early as in 1977 and a first brochure on chemical metallurgy was brought out by the Indian Institute of Metals during the year. It contained all the relevant information about the scientists, their specialization, equipment capability and range of research and development programme in the various institutes in India. Such data bank was highly appreciated among the materials scientists and technologists. Since then the brochure is being periodically updated with a broader field and the latest version includes the various activities related to the metal sciences in India.

To generate vital data on alloy phase diagrams, a programme with the support from Govt. of India was taken up with international efforts in 1982 by the Indian Institute of Metals. Today the data generated under this programme is acclaimed as most important one and a far-reaching effort in the International Commission of Alloy Phase Diagrams (APDIC). In India, the work is carried out under 12 different categories in a coordinated manner by different scientific groups all over the country. The systematic effort has resulted in the publications of monographs in several volumes containing phase diagrams of various alloy systems. Efforts have been made by the Materials Research Society of India and the Indian Institute of Metals for developing a date base for non-ferrous materials. Presently the data bank consists of large number of technology records on the non-ferrous materials. Value added reports and source book in this area have been published.

Another effort has been made on the sensor science and technology. Varieties of sensors for specific use such as chemical analysis, NDT evaluations, process control in sodium systems have been developed. The details of these sensors have been made available in a form of published booklets and information website.

The scientific data on alloy phase diagrams, information on metal sciences activities in India, data bank on non-ferrous materials and the details of the sensors are available as a source of information either on website or in the form of books which can be retrieved freely or on payment basis depending on the type of the data. Besides these data banks, experts list is also maintained by the Indian Institute of Metals for providing services to various industries. If these data bases are to be made of great value, more information and a better organization of it are required. For example, it should be possible to retrieve information on scientific data, research programs, materials being investigated, instruments available etc from a single source. It is planned to transfer these information in the CODATA format so that it could be integrated with the international database. (R. K. Dayal and Baldev Raj, Indira Gandhi Center for Atomic Research, Kalpakkam-603 102 (India)

Publications :

(i) CADB: Conformation Angles DataBase of Proteins
S.S. Sheik, P. Ananthalakshmi, G. Ramya Bhargavi and K. Sekar)
Nucl. Acids. Res. 31 (2003) 448-451.

(ii) THGS: a web-based database of Transmembrane Helices in Genome Sequences
S.A. Fernando P.Selvarani, Soma Das, Ch. Kiran Kumar, Sukanta Mondal, S. Ramakumar and K. Sekar
Nucl. Acids. Res. 32 (2004) D125-D128.

(iii) LySDB – Lysozyme Structural DataBase
(K.Samaya Mohan, C. Chockalingam, V.Shanthi and K. Sekar
Acta Cryst.D 60 (2004) 597-600

(iv) SSEP: SECONDARY STRUCTURAL ELEMENTS OF PROTEINS
V. Shanthi, P. Selvarani, Ch. Kiran Kumar, C.S. Mohire and K. Sekar
Nucl. Acids. Res. 31 (2003) 448-451.