R & D Area > Bioinformatics Home || Contact Us
 
 
 
Bioinformatics
 

Plant Based Bioinformatics || ICT Developments

 
 
R&D PROGRAMMES AND ACHIEVEMENTS

South Asia Legume Database developed in collaboration with University of Reading, UK under the aegis of International Legume Database Information Service (ILDIS)
 
NBRI-BC is the first in South Asia, which has joined the International network programme on plant based Bioinformatics – International Legume Database and Information Service (ILDIS) by establishing the regional center for ILDIS for South Asia. NBRI-BC pursued the work in international ILDIS project as per proposed targets and following national/ international workshops were organized:
  1. International Workshop at NBRI, Lucknow, INDIA (7-13 March, 1994). (1&2)
  2. International Workshop at NBRI, Lucknow, INDIA (26-30 April, 1995) and Tribhuwan University, NEPAL (1-3 May, 1995). (3&4)
  3. International Workshop in INDIA, MALDIVES and SRI LANKA (3-11 March, 1997). (5)
  4. UNESCO sponsored International training course in MAURITIUS (26-30 January, 1998).
  5. UNESCO sponsored International training course in SRI LANKA & MALDIVES (30 May to 2 June, 1998).
  6. Session on plant diversity databases and on-line demonstration in a two-day lecture–discussion-demonstration workshop directed by Dr. P. Pushpangadan, on Procedures for Establishment of Gene Bank, Demonstration of Biodiversity database during the International Symposium on the “Utilization of Natural Products in developing Countries: Trends and Needs” organized by the UNIVERSITY OF WEST INDIES, KINGSTON, JAMAICA (10-20 July 2000). (6)
  7. Session on South Asia Legume Database and an on-line demonstration in ILDIS workshop: New Directions on 4th July 2001 at the Fourth International Legume Conference (ILC-4) at AUSTRALIAN NATIONAL UNIVERSITY, CANBERRA, AUSTRALIA. (7 & 8)
NBRI coordinated the development of this database of Legumes of eight South Asian countries viz. India, Pakistan, Nepal, Bangladesh, Bhutan, Myanmar, Sri Lanka and Maldives in collaboration with the University of Reading, UK and the Royal Botanic Gardens, Kew, UK by simultaneously developing two databases – ILDIS database using Alice software and NBRI database that, in addition to the data categories defined by ILDIS also contained geography details up-to the district level and all published Vernacular Names in all regional languages.

Score sheets containing all the available information for each tribe were printed from the NBRI database, which were further edited. The NBRI database was accordingly modified and once again the score sheets were printed in two formats – one for the NBRI database and other for ILDIS database. The score sheets were randomly checked with the original editing, to ensure the correctness of data entry.

A South Asian slice of 620 taxa was received from ILDIS Directorate at NBRI. Using this as a start-up database, the data from the score sheets in ILDIS format was transferred into the ILDIS database using the ALICE software ver. 2.0.

The ILDIS Phase I database on South Asian legumes contains 1968 taxa (1573 species and 395 infraspecific taxa) and occupies about 26 MB of disk space. The bibliography in the printed checklist lists various references including floras, monographs, checklists, general reference works, miscellaneous articles, and even a few references to individual specimens. The printed volume and the database are the result of over four years’ work on the part of the authors with much consultation with specialists on various legume groups, ILDIS Directorate, University of Reading (F. A. Bisby, Sue Hollis and Judith Heald) and the members of the Herbarium at Royal Botanic Gardens, Kew (R. M. Polhill, B. Schrire, J. M. Lock & L. Rico, etc.).

The Phase I database was subjected to a careful scrutiny to improve the quality of the database at the Royal Botanical Gardens, Kew, UK. The entire dataset was studied to ascertain the taxonomic status of 20 such taxa that were not recorded in South Asian literature but recorded by other botanists/ monographers outside South Asia. The references for the place of occurrence for such taxa were noted from the World Database of Legumes. These references were then checked for the herbarium specimens cited in the reference for the occurrence in South Asia. After examining the source reference these taxa were treated as out-of-area records and it was decided to retain them in the database and add relevant notes. e.g. Acacia polyacantha Willd. subsp. polyacantha was recorded as Native to Sri Lanka by Ross, 1979. However, this species could not be traced in any South Asian literature. Hence, “Recorded once for Sri Lanka but not recorded in literature from that region” was added as note in the note field.

Some species were not out-of-area records and for them only relevant notes had to added e.g. Vicia faba var. minor Beck. was recorded as Introduced in India, Nepal and Pakistan by Bond, 1976, but was not traceable in any of the South Asian literature. Dr. F. A. Bisby, Tribe Coordinator for Vicieae, suggested the inclusion of the following notes in the database:

 
  1. South Asian stocks of this crop are of two varieties [Bond, 1976].
  2. The infra-specific names are widely used in South Asia.
 
Ambiguity in author strings such as occurrence of several similar author abbreviations, use of wrong abbreviations for author names, etc. was standardized following standards of Brummitt & Powell, 1992.

Relevant notes were included for a few taxa where the formation of new combination was required. e.g. Moghania praecox var. angusta (Craib)Mukerjee exists as Provisionally Accepted Name in the database. A note has been added for this taxon stating, “This species transferred to Flemingia, but a new combination is needed for its variety”.

Authors or a group of authors were removed after ‘emend’ and the relevant notes were added in the note field.

The various checklists of South Asian region were lacking the life form details in as many as 80 taxa. These were incorporated after a thorough research using CD-ROM of Index Kewensis, protologue, recent literature including monographs and regional floras and consulting Herbarium specimens, etc. at RBG, Kew.

Attempts were made to include the infraspecific taxa details, nomenclatural details and any other disputed information, etc. in the notes, as far as possible, in a uniform pattern so as to enable the researchers to advance work further on various aspects of legumes of this region.

The complete list of bibliography was checked for the author names, year of publications, etc. and the details of the references were standardized as specified by S. Hollis, 1990. Any duplicity was removed from the bibliography ‘dictionary’ by making the record blank or adding pointers in the reference for the original reference number.

In the South Asia checklist to reduce the volume of publication, the number of references cited for each data category has been reduced as per the criteria decided upon by the ILDIS Coordinator. i.e. Just one reference may be attached to the accepted name and synonym, which may be a major South Asian Flora or a monographic treatment. Only one reference has been retained for each country/ area, which is either a major national flora or a monograph. Only South Asian references were retained for literature pointers and vernacular names. The prioritization of references was done on the bibliography list in order to identify the references that must be retained in the checklist before the actual reduction was done.

After incorporating these changes, country checklists were generated using Awrite utility in the Alice software package for India, Nepal, Pakistan and Sri Lanka and sent to the respective regional specialists for their comments.

The hard copy and electronic outputs for each tribe were further sent to world experts (Tribe Coordinators) to obtain their final opinion on the taxonomy of each tribe. (9)

South Asia Legume database is thus, the first authentic and up-to date dataset on 2030 legumes of eight South Asian countries.

 
 
The database contains information on most recent nomenclature (accepted name, and synonyms) and the latest information on geographical distribution in South Asian countries - India (1561 species (77%)), Pakistan (691 species (34%)), Myanmar (607 species (30%)), Sri Lanka (512 species (25%)), Nepal (469 species (23%)), Bhutan (324 species (15%)), Bangladesh (255 species (12%)) and Maldives (45 species (2%)). Besides nomenclature and geography, the database contains information on life form details, conservation status, common names, description, economic uses and bibliography etc. Thus this database with recent legume taxonomy, distribution and descriptive data for legumes of South Asia, is unique in a level of detail and authenticity that cannot be found in any of the previously published sources from the South Asia region (Fig. 1).
 
 
 
 
 
 
The first output “A checklist of Legumes of South Asia” has been published from RBG, Kew in April 2003 and this formally launched on 6th June 2003 by the-then Hon’ble Minister of State, Science & Technology (9).
 
 
 

Legumes of South Asia –A checklist

Release of the Legumes of South Asia publication by Shri Bachhi Singh Rawat, MOS for S&T.

 
 
 
NBRI BC holds the World Database of 19,554 Legumes and is connected online on Web with over 40 renowned specialists worldwide (http://www.ildis.org) (10).
 
 
 
ILDIS Legumes of the World CD