Internet, Taxonomic Database

  

Internet, Taxonomic Database

You can refer website for understanding no. of plant species  in the world through a database:

1.      IPNI-International Plant Name Index: www.ipni.org

2.      Index Kewensis

3.      Flora of China

4.      Any database which deals with the taxonomic literature like plant name, family, authors name, publication, etc.

The Applications of computer to taxonomy. By Sneath, P.H. (1957). I. Gen. Microbial. 17:201-226.

An updated Classification of class Angiospermae in http://www.inform.umd.edu/PBIO/fam/thorneangiosp99.html.

Angiosperm Phylogeny Website: http://www.mobot.org/MOBOT/research

The Families of Flowering Plants-Description and Illustrations: http://biodiversity.uno.edu/delta

http://www.apache.org/
http://www.php.net/ 
http://www.currentscience.ac.in/Volumes/102/09/1240.pdf
http://www.mysql.com/ 

Taxonomic Database:

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 (habitats). 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 so

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.

  Back Ground

JCB Herbarium indexed on the website of 'The New York Botanical Garden

Dr. Saldanha started 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 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.