Fish Karyome: A karyological information network database of Indian Fishes

‘Fish Karyome’, a database on karyological information of Indian fishes have been developed that serves as central source for karyotype data about Indian fishes compiled from the published literature. Fish Karyome has been intended to serve as a liaison tool for the researchers and contains karyological information about 171 out of 2438 finfish species reported in India and is publically available via World Wide Web. The database provides information on chromosome number, morphology, sex chromosomes, karyotype formula and cytogenetic markers etc. Additionally, it also provides the phenotypic information that includes species name, its classification, and locality of sample collection, common name, local name, sex, geographical distribution, and IUCN Red list status. Besides, fish and karyotype images, references for 171 finfish species have been included in the database. Fish Karyome has been developed using SQL Server 2008, a relational database management system, Microsoft's ASP.NET-2008 and Macromedia's FLASH Technology under Windows 7 operating environment. The system also enables users to input new information and images into the database, search and view the information and images of interest using various search options. Fish Karyome has wide range of applications in species characterization and identification, sex determination, chromosomal mapping, karyo-evolution and systematics of fishes.


Background:
Fishes are the most diverse group of vertebrates, with ca. 32200 species (http://www.fishbase.org) characterized by great diversity of their morphology, physiology, ecology, life history and behaviour. The classical methodology for identification of fish species is based on morphometric and meristic characteristics that cannot precisely identify and characterize closely related fish species and subspecies leading to problems of fisheries management [1]. Cytogenetic markers are authentic tools for characterization of fish species as well as to screen putative hybrids [1,2]. These markers were found useful for detection of intraspecific stocks and populations within species [3] and in resolving taxonomic ambiguities between some species [4]. Cytogenetic (Figure 2) shows the structure of the database.

Web interface
The web interface for the database was developed using ASP.NET's Integrated Development Environment. We incorporated user friendly tools in the interface integrated with database to provide convenience to work with the database. The web interface utilizes HTML (Hyper Text Markup Language), CSS (Cascading Style Sheets) and ASP Scripts (Active Server pages) to provide the static and dynamic content to the user. We included all the database management functions in the web interface for security reasons. The web interface along with database was implemented on Windows Sever running Internet Information Server. (Figure 1) shows the architecture of the web database and sample screen view of the web interface integrated with database.

Results:
Accessing the Fish Karyome database content At present, our database provides karyological and phenotypic information about 171 fish species of India to the public on web page at URL: http://www.nbfgr.res.in/fishkaryome/ When the home page is accessed, a user web interface with six hyperlinks entitled "About us", "Family search", "Keyword search", "Specific search", "Acknowledgement", "Contact" and Feedback" is displayed. The user can get relevant information and work with the database through these hyperlinks. To access and update the database content, we integrated various search, browsing, and data submission tools through user login section only for authenticated users in our database through the web interface.

Querying the database
The web interface of the database provides a rich set of functions for searching the database. These search functions are 'Family Search', 'Specific Search' and 'Keyword Search'. These search function allows the user to make query with the database in the interactive way.

Keyword Search
This is a simple text based search that allows the user to perform the search on all fields of the database based on the keyword using all, any one and exactly tools, either of the search criteria. This provides freedom to the user to query with the database and view the information based on the keyword of interest.

Data Management
To work with data, we integrated the database management functions in the web interface for security reasons. These functions are only available to the authenticated users and here the user can not only submit and upload the data but also modify the submitted data through query with the database. The review of literature on database related to fish cytogenetics indicated that no such database is available in India and globally that provides the comprehensive karyotype information in addition to phenotypic information on fishes.
Researchers can use our database to access images of chromosomal complements of a particular species and to make a comparative study of karyotypes of closely related fishes. The database has wide range of applications in species characterization and identification, chromosomal mapping, searching sex determination, karyo-evolution and systematics of fishes.

Conclusions and future directions
To the best of our knowledge this is the first endeavour to construct an integrated database of karyotype images and information on Indian fishes. Our database system contains classical karyotype images of fish chromosomes as well as phenotypic information and is a powerful research tool for researchers working on fish chromosomes. The database has been kept open through World Wide Web for everyone to view the records of karyological information. We have also provided a submission panel that allows the users to upload their data voluntarily from the panel. It is planned to make further modifications to improve the usability of the database by including the chromosome images of more fish species and by linking our database to other genomic resource databases. We also intend to rearrange all the karyotype images stored in our database according to the taxonomic trees. It is expected that Fish Karyome will become a more useful tool for researchers working in the field of fish cytogenetics and genomics.
Supplementary material: Table 1: List of selected parameters to collect the karyotype and phenotypic Information about the fish species   TYPE OF INFORMATION PARAMETRS  SUB PARAMETERS  DATA TYPE   PHENOTYPIC  TAXONOMY  ORDER  TEXT  SUBORDER  TEXT  FAMILY  TEXT  SPECIES NAME  TEXT  COMMON NAME  TEXT  LOCAL NAME  TEXT  SEX  TEXT  NUMBER OF SPECIMENS  NUMBER  TISSUE TYPE  TEXT