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Introduction to the PC-NPGRIS

Data Management System of Chinese Taipei

Shu Chen and Ming-Jen Fan

Taiwan Agricultural Research Institute-NPGRC

Wufeng, Taichung, Taiwan 41301

npgris@hgp40.npgrc.tari.gov.tw

Abstract

The PC-NPGRIS Data Management System was designed for breeders and their allied workers within our Economy to input, verify, and transfer their data to the NPGRIS main database server easily. The information also can be managed as a mini-database owned by the agricultural workers themselves. Now, we offer this idea to APEC Economy Members. The PC-NPGRIS have been modified to include an English version in order to provide a simple and useful tools for other Members to establish a mini-database on germplasm owned by themselves. The hardware and database architecture will be described in detail.

Introduction

Plant germplasm is the main source of developing new crop cultivars and the basis of crop improvement. It is well recognized that an efficient data management system of germplasm can help breeders and related scientists to search for needed germplasm information and select appropriate materials to be utilized in crop improvement.

Our National Plant Genetic Resources Information System (NPGRIS) was established in 1993. There are three main activities of the NPGRIS.

(1) to set up a database for all crop cultivars in the country, including related germplasm information for breeders and allied researchers to search for needed information.

(2) to develop a genetic resources information network within our country and hopefully around the world to strengthen the communication of information on germplasm.

(3) to handle the processing and storage activities of germplasm at the National Plant Genetic Resources Center (NPGRC).

In order to accelerate the exchange of plant germplasm information among breeders and related scientists all over the world, the NPGRIS has also upgraded its hardware and entered the World Wide Web since 1997. There are multi-functions in our web including the introduction to NPGRC, database query, plant germplasm catalogs, plant genetic resources newsletter, etc. (http://www.npgrc.tari.gov.tw or http://192.192.196.1)

Currently, there are about 30,000 records of passport data, 20,000 records of characterization data and 1,000 records of image data had been built in the NPGRIS database (Table 1). These accessions represent more than 119 families, 367 genera and 500 species of plant germplasm. Most of the data were provided by the breeders and related evaluators. To ensure the accuracy of the data, we designed the end-user application program for the scientists to input, verify, transfer their data to NPGRIS easily, and manage the mini-database by the workers themselves. This end-user application program was called “PC-NPGRIS Data Management System”.

The main objective of this paper is to introduce the PC-NPGRIS Data Management System. The hardware and database architecture regarding how PC-NPGRIS Data Management System was linked to the NPGRIS main database server are also described in this paper.

Now, we wish to extend this PC-NPGRIS idea to APEC Economy Member. We have modified the programs and translated the language into an English version in order to provide a simple and useful tool so that other Members may establish an mini-database on germplasm owned by themselves.

Hardware Architecture

The frame of hardware architecture of NPGRIS is illustrated in Figure 1. The ORACLE database management system and UNIX operation system are built in the HP9000 800/G40 database server. To modernize and computerize the operations of the NPGRC, all the personal computers of NPGRC-related laboratories are capable of being linked to the database server with a client-server local network architecture. For information exchange, the NPGRIS has been linked to other genetic resources centers around the world through the World Wide Web.

In order to strengthen the communication of germplasm information within our Economy, the NPGRIS provides telephone dial-up system for agricultural scientists of other 29 research institutions within our Economy to access information. Besides, interested researchers can also enter into the NPGRIS database through network within our Economy such as TANET, Hinet or SeedNet. Thus, they can not only search for needed germplasm information, but also send data from PC-NPGRIS Data Management System to NPGRIS database server.

Database Architecture

The NPGRIS employs ORACLE as a relational database management system. The NPGRIS database has stored the related data of plant germplasm, including passport data, characterization data and image data. The passport data and characterization data are both usually provided by the breeders or collectors. To ensure the accuracy of the data, the “PC-NPGRIS Data Management System” was developed for the breeders to input, verify, transfer their data to NPGRIS, and manage as a mini-database owned by the breeders themselves.

Because the PC-NPGRIS Data Management System was based on the Microsoft Window operation system, its operation is very easy and user-friendly. In addition, all of the coded files used in NPGRIS database server must be import to PC-NPGRIS Data Management System in order to ensure the consistent data format (Figure 2). These coded files including accession type, country code, organization code, sample status, collection status, collection source, sample type, usage code and taxonomy files were entered in the PC-NPGRIS passport data subsystem. The plant characteristic code and its description files were used in PC-NPGRIS characteristic data subsystem. In such a way, the users just need to pop-down the code list, select and fill data in PC-NPGRIS directly. The key-in operation will be reduced¾, this is the another benefit of PC-NPGRIS.

The passport data record the background information of germplasm, such as scientific name, pedigree, donor, collector, location of collection, criteria of distribution, etc. In our PC-NPGRIS passport data subsystem, these data fields were divided into 6 display pages such as basic information, scientific name, pedigree, cultural practice, collection data and other notes. The users can click the menu bar on the top of the passport data subsystem to choose the display page he want to fill in (Figure 3A). We also design the option buttons on the right side of the passport data subsystem for the users to add, update, delete, save, query and find data records with a “previous-next” options conveniently. The option buttons can also help the users to export data files to NPGRIS main database server or print these data on printed document. The program flow of PC-NPGRIS passport data subsystem is shown in Figure 4.

The characterization data record the characteristics of a germplasm accession, such as agronomic traits, resistance and tolerances to stress, chemical composition, etc. As the NPGRC preserves numerous plant germplasm accessions and the characteristic items of each species are different, we organized crop committees to define the uniform list of items and related descriptor states according to different crops. This uniform format of characteristic descriptors of plant can also enable our researchers to follow. Currently, there are formats of 72 descriptors in NPGRIS (Table 2). In the PC-NPGRIS characterization data subsystem, users can pop-down the list of characteristic items to choose the described ones. Once the item is selected, the description and its related code will be pop-down. The users can input data directly. These characterization data will be integrated with passport data by accession number. We also design the option buttons on the top of the characterization data subsystem for users to add, update, delete, save, query and find data records with “previous-next” option, as well as to export data files or print on paper (Figure 3B). The program flow of PC-NPGRIS characterization data subsystem is shown in Figure 5.

Table 1. Statistics on the NPGRIS

^Crop	^{Scientific Name}	^{No. of} ^{Passport data}	^{No. of} ^{Characterization data}
^Soybean	^{Glycine max}	¹²⁹²²	⁵⁹⁸⁶
^Tomato	^{Lycopersicon esculentum}	⁴³³⁹	⁰
^Mungbean	^{Vigna radiata}	⁴¹⁸⁴	⁸³³⁰
^Rice	^{Oryza sativa}	⁴¹⁵⁰	⁸⁶⁵⁹
^Pepper	^{Capsicum annuum}	²⁵²²	²³
^{Common Flax}	^{Linum vsitatissimum}	¹⁸¹¹	⁰
^Sugarcane	^{Saccharum officinarum}	¹³⁹⁷	⁵⁶⁸
^Peanut	^{Arachis hypogaea}	¹³⁸¹	¹³⁴⁹
^{Asparagus Bean}	^{Vigna nguiculata}	¹⁰²⁰	²¹⁹
^Corn	^{Zea mays}	⁷⁴⁶	¹⁹³
^{Sweet Potato}	^{Ipomoea batatas}	⁴⁸³	⁰
^{Chinese Cabbage}	^{Brassica campestris Pekinensis group}	⁴⁷⁰	⁰
^Eggplant	^{Solanum melongena}	³⁷⁴	¹⁸¹
^Sorghum	^{Sorghum bicolor}	³⁷⁰	⁰
^{Medicinal Crops}	^{Medicinal Crops}	²⁵⁶	⁰
^Peach	^{Prunus persica}	²³⁰	¹⁵⁷
^Araceae	^Araceae	²⁰³	⁰
^{Snap Bean}	^{Phaseolus vulgaris}	²⁰¹	¹¹⁶
^Jute	^{Corchours capsularis}	¹⁸⁸	⁰
^Mango	^{Mangifera indica}	¹⁷⁴	²²
^{Snow Pea}	^{Pisum sativum}	¹⁶²	⁴⁵
^{Adzuki Bean}	^{Phaseolus angularis}	¹⁵⁵	¹⁵⁰
^Muskmelon	^{Cucumis melo}	¹⁵³	¹⁰²
^{Edible Amaranth}	^{Amaranthus tricolor}	¹⁴⁹	⁰
^Morus	^Morus^sp.	²⁰⁹	⁰
^Sunflower	^{Helianthus annuus}	¹²⁵	⁰
^Taro	^{Colocasia esculenta}	¹²⁵	³⁵
^{Bottle Gourd}	^{Lagenaria siceraria}	¹²¹	⁵²
^Watermelon	^{Citrullus lanatus}	¹¹³	⁴³
^Asparagus	^{Asparagus officinalis}	¹⁰⁹	⁰
^Cucumber	^{Cucumis sativus}	¹⁰⁴	⁴⁸
^{Fruit Trees}	^{Fruit Trees}	¹⁰¹	⁰
^Tea	^{Camellia sinensis}	¹⁰¹	⁸⁴
^Banana	^Musa^spp.	¹⁰⁰	⁶³
^{Other < 100 accession}		²⁶⁹⁶	¹³⁶
^Total		³⁰⁹²⁷	²⁰⁶¹⁹

Figure 1. The hardware architecture of NPGRIS

Figure 3. The English version of data management system is developed in Microsoft window operation system.

(A) The windows of the passport data subsystem on the screen

(B) The windows of the characterization data subsystem on the screen

Table 2. Crops in the NPGRC with characteristic descriptors format

Crops	Number
Food Crops：	7
RICE、SOYBEAN、PEANUT、CORN、MUNGBEAN、ADZUKI BEAN、SWEET POTATO
Vegetable：	37
CABBAGE、MUSTARD、CHINESE CABBAGE、CAULIFLOWER、VEGETABLE SOYBEAN、SNOW PEA、KOHLRABI、CHINESE KALE、RAPE、BROCCOLI、BITTER MELON、CHINESE MUSTARD、RADISH、ASPARAGUS BEAN、LIMA BEAN、SNAP BEAN、WAXGOURD、WATERMELON、SQUASH、BOTTLE GOURD、POTATO、PEPPER、ORIENTAL PICKLING MELON、MUSKMELON、EGGPLANT、LUFFA、WATER CONVOLVULUS、CELERY、TOMATO、CUCUMBER、GARLIC、LETTUCE、EDIBLE AMARANTH、TARO、STRAWBERRY、ALLIUM SPP. 、ASPARAGUS
Fruit Crop：	18
LITCHI、LOGAN、BANANA、PAPAYA、GRAPE、MANGO、PERSINMMON、LOQUAT、PLUM、PEAR、PINEAPPLE、PEACH、APPLE、INDIAN JUJUBE、CITRUS、GUAVA、CARAMBOLA、WAX APPLE
Special Crops：	6
SUGARCANE、MULBERRY、TEA、HSIAN-TSAO、YAM、ANUECTOCHILUS
Forage：	2
GRAMINEAE FORAGE、LEGUMINOSAE FORAGE
Other：	2
CYMNOSPERMAE、ANGIOSPERMAE
TOTAL	72

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Solanum melongena

^{Solanum melongena}