Sunday, 22 September 2013

Indian Institute of Science to Launch 'Online Digital Database' on Flora of Karnataka

Sankara K. Rao
Herbarium JCB, Center for Ecological Sciences
Indian Institute of Science (IISc)
Bangalore 560012, Karnataka, India
E-mail: bharadwaj@ces.iisc.ernet.in 

Introduction
    A conventional herbarium database maximizes the usefulness of the collection by providing authentic and lasting information. This information can effectively be used for the preservation of species and spaces (hábitats). Presently several herbaria, world over are actively engaged in developing digital databases for their collections. Herbarium at Centre for Ecological Sciences of Indian Institute of Science, Bangalore which houses the specimen mainly from Karnataka is likely to be digitized and will be available online very soon.
Panormic view of one geographical region of Karnatka
   
State of Karnataka is gifted with immeasurable plant diversity confined to different forest types and unique niches and functions in a critical manner in the ecology and climate. Management measures including conservation of this invaluable natural resource are possible only through dissemination of knowledge about it, using the latest technologies. Herbaria have the necessary authentic data and botanists have a responsibility in developing knowledge bases and make them freely available on the internet. Building a database encompassing the entire flora of Karnataka was my important first step in my efforts to modernize the Herbarium JCB (the name, listed in global index of herbarium) and its services.

 BackGround
 JCB Herbarium indexed on the website of 'The New York Botanical Garden
    I have a sentimental attachment to this herbarium. Dr. Saldanha and I began botanical explorations together in 1964 at St. Joseph’s college, Bangalore that resulted in the founding of this herbarium. Herbarium JCB at the Centre for Ecological Sciences (CES), Indian Institute of Science, Bangalore is a collection of several decades and lifetime work of Dr. C.J. Saldanha (Saldanha, 1984, 1995). It is the only holding in the region that has specimens collected from all over Karnataka state, correctly identified and the determinations authenticated by specialists, and with duplicates deposited with herbaria of Royal Botanic Gardens at KEW, England and the Smithsonian Institution, Washington DC, USA. The herbarium is indexed in the global directory 'The Index Herbariorum (IH)' of 'The New York Botanical Garden'. The collection is richest in species from the forests of Western Ghats, an area not well represented in most South Indian Herbaria. The present virtual herbarium initiative is an endeavor in taking Dr. Saldanha’s work forward and developing a knowledge system for the flora of Karnataka state to make it available across the world.
Seven years of tenacious work of my dedicated team (Arun Singh R, Dr. Sringeshwara A, Deepak Kumar, Imran Baig, Ravali RMV and Sasidhara Kaimal) has resulted in a herbarium-based plant information system for the state. To be presented shortly on the ‘Herbarium JCB’ website, this database is designed to be user-friendly, interactive, and complete with respect to species information and encompasses more than 4,500 angiosperms and ferns. The major objective of the initiative is to generate a readily accessible information system to help evolve strategies of effective conservation and sustainable utilization of plant resources in the state (for details, please see Current Science 102- 9, 2012.)

Components of Database
The information content of the plant database is largely built on the voucher specimens in the herbarium. The taxonomic data portrayed on each species include all information presented on the herbarium specimen label, namely, species name, author citation, sub-species if any, variety if any, family, subfamily, collection number, locations, date of collection, habitat and the collector’s name. The database further features detailed species description, citation of the ‘Flora’ in which it is described, nomenclature updates as per ‘The Plant List’(http://www.theplantlist.org/), phenology, species distribution, threat status and comments on any special features of the taxa. The arrangement of angiosperms followed in the database is on the lines proposed by Dr. A. Cronquist in The Evolution and classification of flowering Plants-1968 and that of ferns is as proposed by Dr. C.R. Fraser-Jenkins (Taxonomic revision of Indian subcontinental Pteridophytes, 2008).
  
Specimen Details
Digitized at a minimum resolution of 300 dpi, the herbarium specimens are displayed for almost every species. The digital images of live specimens of most species provided in the database form an important information synergy. Accurately drawn, true-to-the specimen line drawings depicting such features as the shape of the corolla, number of locules and ovules in a locule, their disposition are also portrayed in the database for a good many species.
    A gallery of photographs of live specimens is displayed that allows species to be identified by browsing images. Each image is hyperlinked to the corresponding species web page. Alphabetically-sorted species names, both botanical and vernacular and family lists allow users to browse by species name and family, respectively. The website provides basic and advanced search capabilities. Text entered in basic search is searched in all fields of the herbarium database whereas the advanced search allows text to be searched in one or more fields (for example, genus, threat status, or common name). A comment widget allows users to report corrections or provide feedback.  
Construction of Database and Websites
    Plant taxonomic data presented on the ‘Herbarium JCB’ was first entered on Microsoft Excel spreadsheets by herbarium staff and volunteers. The data were subjected to scrutiny for accuracy and formatting consistency and subsequently imported into MySQL database tables.
Home page of proposed website of JCB Herbarium
    The website was developed using standard open-source software on the Linux operating system including Apache, a web server (http://www.apache.org/), MySQL, a database system (http://www.mysql.com/), and PHP, a scripting language (http://www.php.net/). Plant taxonomic data were stored in the database which allows rapid indexed searches to be carried out and the content to be generated dynamically. Binary (non-text) content such as high-quality digital image files and documents requiring considerable storage are stored on the file system instead of inside the database for greater efficiency.

Introduction to Website  
Thumbnails of specimen

 The homepage includes a write-up on Herbarium JCB, Herbarium Usage Policy, Frequently Asked Questions (FAQs), Mission statement, Members, Important Visitors to this Herbarium, News and Contact details. The browsing menu includes Index A-Z, ‘About us’, Habitats, Image Gallery and Comments. 'Index A-Z' displays drop-down lists of botanical, common and vernacular names of species and list of plant Families.The species page further features thumbnails of detailed Description, Digitized herbarium specimen(s), Line drawing(s) and Field Image(s). By clicking on ‘Description’, a pop-up screen appears. A menu provided at the top allows forward, backward, toggle size (zoom option) and slide show of the thumbnails. To return to the species page, 'close' button needs to be clicked. The browsing menu 'Habitats' displays a film strip of various habitats. To be able to avail Advance Search capabilities, the 'Advance Search' option provided at the top of the homepage has to be clicked. A new page is displayed listing various search fields. Texts entered in one or more fields filters navigation to the relevant information [for eg. Endemism, Threat Status, Phenology etc.] For certain search fields on this page, a drop-down menu is provided to further narrow down search capabilities. 

 Conclusion
    The database provides a comprehensive high quality information system on plant resource in the state. We have designed it to cater to professional botanists as well as lay people equally. We are sure that it will have tremendous impact on research and education in taxonomy, field botany, ecology, plant communities study, environmental sciences, agriculture, and forestry. Furthermore, the digital preservation of archives as this will be engaged in advancing knowledge innovation, facilitating value-added creation and sustaining national competitiveness (Ramesh Singh and Kush Sharma, 2009. Jl.Dig.Assets. Management 5: 55-74)
    To be launched on the ‘Herbarium JCB’ website, the database will be maintained by Indian Institute of Science, Bangalore. It is hoped that every student of botany, ecology and conservation will find the database useful.

References
1. Cronquist. A. 1988. The evolution and classification of Flowering Plants (Second Edition). New York Botanical Garden, New York.
2. http://www.apache.org/
3. http://www.php.net/
4. http://www.currentscience.ac.in/Volumes/102/09/1240.pdf
5. http://www.mysql.com/
6. K. Sankara Rao - Flowering Plants of Indian Institute of Science: A Field Guide- IISc Press, 2010
7. K. Sankara Rao, A.N. Sringeswara, Deepak Kumar, Sandeep Pulla and R. Sukumar. 2012. A digital herbarium for the flora of Karnataka. Curr. Sci. 102 (9) 1268-71
8. K.Sankara Rao, H.R. Bhat and Y.N.Seetharam. 2012. Chamaecrista rotundifolia (Leguminosae-Caesalpinioideae) – A new record for India. Rheedea. 22(1) 66-67
9. K. Sankara Rao et al. - Indian Institute of Science Campus: A Botanist’s Delight- IISc Press, 2009
10. Ramesh Singh and Kush Sharma, 2009. J.Dig.Assets. Management 5: 55-74
11. Saldhanha CJ, 1984. Flora of Karnataka, Vol 1, (Oxford & IBH Publishers, New Delhi),.
12. Saldanha, C. J., 1996. Flora of Karnataka. Vol. 2. Oxford & IBH Publishing Co. PVT. LTD, New Delhi.
13. Varsha A. Kulkarni, Y.N. Seetharam and K. Sankara Rao. 2011 Alstonia venenata R.Br. (Apocynaceae): A note on distribution pattern of an endemic species. Nelumbo. 53:2011-2012

8 comments:

  1. When we have various online database available world-wide, digitizing the Indian herbarium is a good move.
    Botanical Survey of India (BSI) should co-ordinate and lead in integrating and making it available online, all the herbaria of India.

    ReplyDelete
  2. This a good attempt; similarly KFRI, peechi have done digitization of flora of kerala

    ReplyDelete
    Replies
    1. Can you share the detail with us. We will be delighted to publish the information. Our e-mail indianbotanists@gmail.com

      Delete
  3. Good work!
    Kerala Forest Research Institute, Peechi have done similar work
    Its address is www.kfriherbarium.org

    ReplyDelete
  4. Similar attempts should be made to compile the flora of Jharkhand through a Harbarium repository under Guidance of Plant taxonomists from Universities in collaboration with NGPGR centre Ranchi

    ReplyDelete
  5. Best herbarium database useful to all Botanist Thankful to IISc Bangaluru.

    ReplyDelete
  6. Best herbarium database useful to all Botanist Thankful to IISc Bangaluru.

    ReplyDelete

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