THE PIG GENETIC DIVERSITY DATABASE AND THE WWW (LA BASE DE DATOS SOBRE DIVERSIDAD GENÉTICA PORCINA Y LA WWW)

Russell G.A.

Description

Abstract
The pig genetic diversity database (PigDBase) and its associated web site (http://www. projects.roslin.ac.uk/pigbiodiv/) provide secure storage of data from studies of genetic diversity in pigs including microsatellite and AFLP genotypes. The design of the database is such that it could be applied to any species and, with appropriate standardisation protocols, could extend to any laboratory wishing to contribute data. Access to PigDBase is effected via the World Wide Web using the diversity browser. The information stored includes details of microsatellite markers, breeds, sample and contact details. Full information on unprocessed data, as well as summary information on genetic measurements and export formats are also available.
Resumen
La base de datos sobre la diversidad genética porcina (PigDbase) y su sitio Web asociado (http://www.projects.roslin.ac.uk/pigbiodiv/) provee de un almacén de datos seguro para los estudios sobre la diversidad genética de los cerdos incluyendo los genotipos de microsatélites y AFLPs. El diseño de la base de datos es tal que podría ser aplicado a cualquier especie y, con adecuados protocolos de estandarización, podría extenderse a cualquier laboratorio que deseara aportar datos. El acceso a PigDbase se efectúa vía WWW utilizando el browser diversidad. La información almacenada incluye detalles de los marcadores microsatélites, muestra y detalles de contacto. La información completa sobre datos no procesados, así como información resumida sobre medidas genéticas y formatos de exportación también están disponibles.

Sujets

• World Wide Web
• Bioinformatics
• AFLP
• Microsatellite
• WWW
• Bioinformática
• Microsatélite

Informations

• Publié par: erevistas
• Publié le: 01 janvier 2003
• Nombre de lectures: 44
• Langue: English

Extrait

THE PIG GENETIC DIVERSITY DATABASE AND THE WWW
LA BASE DE DATOS SOBRE DIVERSIDAD GENÉTICA PORCINA Y LA WWW
Russell, G.A., A.L. Archibald, C.S. Haley and A.S. Law
Roslin Institute. Roslin. EH25 9PS. UK.
Contact adress: [e-mail]
ADDITIONAL KEYWORDS PALABRAS CLAVE ADICIONALES
Genetic diversity database. World Wide Web. Base de datos de diversidad genética. WWW.
Bioinformatics. AFLP. Microsatellite. Bioinformática. AFLP. Microsatélite.
SUMMARY
tes y AFLPs. El diseño de la base de datos es talThe pig genetic diversity database (PigDBase)
and its associated web site (http://www. que podría ser aplicado a cualquier especie y,
projects.roslin.ac.uk/pigbiodiv/) provide secure con adecuados protocolos de estandarización,
storage of data from studies of genetic diversity podría extenderse a cualquier laboratorio que
deseara aportar datos. El acceso a PigDbase sein pigs including microsatellite and AFLP
genotypes. The design of the database is such efectúa vía WWW utilizando el browser diversi
dad. La información almacenada incluye detallesthat it could be applied to any species and, with
appropriate standardisation protocols, could de los marcadores microsatélites, muestra y
extend to any laboratory wishing to contribute detalles de contacto. La información completa
data. Access to PigDBase is effected via the sobre datos no procesados, así como informa
ción resumida sobre medidas genéticas y formatosWorld Wide Web using the diversity browser.
The information stored includes details of de exportación también están disponibles.
microsatellite markers, breeds, sample and
contact details. Full information on unprocessed
data, as well as summary information on genetic INTRODUCTION
measurements and export formats are also
Directed selection of economicallyavailable.
desirable traits can lead to genetic
erosion of individual breeds of pigs and
affect the whole pig population. ThisRESUMEN
reduced genetic base could limit
opportunities to select productionLa base de datos sobre la diversidad gené
characteristics that may be vital in thetica porcina (PigDbase) y su sitio Web asociado
(http://www.projects.roslin.ac.uk/pigbiodiv/) future. It is therefore important that
genetic diversity in any species isprovee de un almacén de datos seguro para los
estudios sobre la diversidad genética de los maintained to provide a base from which
new characteristics can be selected.cerdos incluyendo los genotipos de microsatéli
Arch. Zootec. 52: 165 172. 2003.RUSSELL, ARCHIBALD, HALEY AND LAW
Polymorphic molecular genetic allow ready access to information by
markers provide a means to assess those interested in the maintenance of
within and between breed genetic genetic diversity in pigs. This information
diversity. In particular, microsatellite could be used in selection programmes
markers have been used to charac aimed at improving the quality of pig
terise a wide variety of breeds and products, welfare and health through
species of farm animals (e.g. Cañon et the extensification of farming systems.
al., 2000; Hanslik et al ., 2000; Laval et To address this need, a database
al., 2000; Ritz et al., 2000; Wimmers (PigDBase) has been designed and
et al., 2000) and are currently built to hold data generated by the EC
recommended as the marker of choice funded Pig Diversity Project. The
for studies of domestic animal diversitydatabase stores details of sample
(FAO, 1998; http://dad.fao.org/en/ information and genotyping data as
Home.htm). Amplified fragment length well as information on the genetic
polymorphisms (AFLPs) have also markers used. Full information on
been used in studies of genetic diversity,unprocessed data, as well as summary
including the EC pig genetic diversity information on genetic measurements
project. However, it is likely that singlehas been made available to the wider
nucleotide polymorphisms (SNPs) will community through a World Wide Web
eventually replace microsatellites as interface. This provides immediate
the marker of choice for studies of access to the stored data and allows
genetic diversity as the number of analyses to be performed on exported
characterised SNPs for farm animal data.
species increases and the cost of their
typing decreases.
Regardless of the type of molecular EC PIG DIVERSITY PROJECT WEB
genetic markers used to evaluate SITE
genetic diversity, the sharing of data is
As part of the EC funded projectessential. As it is necessary to consider
entitled Characterisation of geneticgenetic diversity on a global scale,
variation in the European pig toresearch groups that study their local
facilitate the maintenance andpopulations can make a valuable
exploitation of biodiversity (Pig contribution either acting alone or
BioDiv), a web site (http://www.preferably as part of wider collaborative
projects.roslin.ac.uk/pigbiodiv/) hasnetwork. The value of small studies of
indigenous breeds is greatly enhanced been established to act as a focal point
if the data can be combined across for communication. Project progress
studies. Indeed, it is arguable that if is disseminated via meeting reports
the data from small studies cannot be and other documents published on the
integrated into global analyses now or site. It also includes general information
at some future date then the studies on the project background and
are of minimal value. approach, details of project participants,
The establishment of a database breeds used in the project and the
that holds such diversity data would microsatellite markers chosen. The
Archivos de zootecnia vol. 52, núm. 198, p. 166.PIG GENETIC DIVERSITY DATABASE
web site provides a public interface tobe restored relatively simply to any
the project and a source of informationgiven state should the need arise. In
on genetic diversity studies in pigs and addition, standard operating procedures
links to other resources. have been implemented to fully
Thus, the Web site acts as a portaldocument changes made to the
to information on pig diversity gene database system.
rated within the project and to other The requirement to make the data
sources of information including the accessible to a geographically scattered
Food and Agriculture Organisation network of collaborators and users has
(FAO) (http://www.fao.org/dad is/) been addressed by mounting the
and the European Association for Ani database on the World Wide Web.
mal Production (EAAP) animal genetic The WWW interfaces use CGI scripts
bank (http://www.tiho hannover.de/ implemented in Webintool – a PHP
einricht/zucht/eaap/index.htm). The like scripting language that was
web site also provides access to the pig developed at Roslin (Hu et al ., 1996) –
diversity database. and Perl.
Although a Web forms interface to
the database has been provided, access
DATABASE OVERVIEW to those forms and the data within the
system (including genotypes, export
Data sharing is essential in order toand analysis applications) is currently
maximise the value of genetic diversitypassword protected and restricted to
data. A genetic diversity database is collaborators within the EC pig diversity
critical to effective data sharing. The project. However, details of contact
requirements for a genetic diversity information, microsatellite markers,
database include the maintaining of theand data from the PiGMaP pilot
integrity of the data, making the data diversity project (Laval et al., 2000)
accessible, enabling different views of are accessible to the general public.
the data and providing tools to export
the data in the formats for a range of
analysis programs. DATABASE CONTENTS
Based on our experience of
developing resource and genome Information in the database is held
databases to support genome research in forty six linked tables. The database
in farm animals (Law and Archibald, contains breed and line information for
2000; Hu et al., 2001) we elected to animals sampled from 60 distinct
use a robust and established relational populations as well as sex, date of
database management system (RDBMS) birth, sire name and dam name (where
CA INGRES as the data store. This available). Sample information also
is primarily to ensure data integrity. includes details of the amount and
1The database is automatically check concentration of DNA held in two
pointed on a regular basis and all
changes are tracked using the built in 1Protocols for access to these DNA samples are
journaling tools. Thus the system can currently being developed.
Archivos de zootecnia vol. 52, núm. 198, p. 167.RUSSELL, ARCHIBALD, HALEY AND LAW
secure long term repositories at Roslin location of the marker and citations of
Institute (Edinburgh) and INRA the papers describing the markers.
Laboratoire de Génétique Cellulaire, There are 467536 individual genoty
Toulouse. Breed information is linked pings recorded – 118188 are from
to the EAAP animal genetic databank, microsatellite markers while 349348
which contains phenotype information represent AFLPs. The database also
for the majority of European breeds contains a subset of data generated
(http://www.tiho hannover.de/einricht/ during the PiGMaP project (http://
zucht/eaap/index.htm). www.projects.rosli