©
1997 Oxford University Press
81-84
Footnote
The Radiation Hybrid Database
The Radiation Hybrid Database
Patricia
Rodriguez-Tomé*
and
Philip
Lijnzaad
EMBL Outstation, Hinxton-The European Bioinformatics Institute, The Wellcome
Trust Genome Campus, Hinxton,
Cambridge
CB10 1SD,
UK
Received September 3, 1996;
Accepted October 8, 1996
ABSTRACT
Since July 1995, the European Bioinformatics Institute (EBI ) has maintained
RHdb, a public database for radiation hybrid data. Radiation hybrid data are
used in the generation of alternative genetic maps as they can include non-polymorphic markers and are also powerful enough to order unresolved
genetic clusters of polymorphic STSs. The EBI is an Outstation of the European
Molecular Biology Laboratory (EMBL).
INTRODUCTION
The radiation hybrid mapping technique orders genetic loci along a chromosome
and estimates physical distances between adjacent loci. Radiation hybrids are
produced by fusing irradiated donor cells with recipient rodent cells. These
hybrid cells lines (grouped in `panels' of identical radiation doses) each
contain many large chromosome fragments produced by radiation breakage and are
then screened by PCR amplification (producing `scoring data') to identify those
hybrids that have retained a given locus. Nearby loci will tend to show similar
retention patterns thus allowing proximity to be inferred. This RH linkage
method is a statistical procedure that requires some measure of the relative
likelihood of the localization and order of the loci. This likelihood is
expressed as a LOD score (
1
,
2
).
Radiation hybrid methods exploit differences between species (donor and
recipient) and can be used to map both polymorphic markers such as sequence
tagged sites (STS) or expressed sequence tags (EST). These maps are
indispensable in the study of multifactorial diseases.
THE RADIATION HYBRID DATABASE
The Radiation Hybrid Database can be accessed on the World Wide Web at the URL http://www.ebi.ac.uk/RHdb (Fig.
1
). This page provides information about the database and access to reports and
query tools.
Figure 1
.
RHdb WWW home page: http://www.ebi.ac.uk/RHdb
The first release of RHdb in July 1995 contained 1115 scoring data, and release
6 in August 1996 contained 28516 scoring entries, which represent a 25-fold increase in 1 year.
The RH mapping project
The radiation hybrid mapping project is a collaboration of a consortium of
European and US Genome Centres that aims to build high resolution maps of the
human genome integrating human cDNA with meiotically ordered polymorphic
markers. In January 1995, this consortium asked the EBI to build a database for
collecting the raw scoring data on radiation hybrid panels and the resulting
maps (
3
,
4
). STSs belonging to one(or more) of the following categories are being used for
mapping.
(i)
Random genomic human clones.
(ii)
CpG islands.
(iii)
Expressed sequences: STS were developed from cDNA sequences taken from the
UniGene and UniEST collections (
5
), from Expressed Sequence Tags (
6
) in the dEST database (
7
) or the Genexpress index (
8
).
(iv)
Genetic markers from the Généthon genetic map (
9
) or developed at the Cooperative Human Linkage Center (
10
).
(v)
Chromosome specific libraries.
To avoid duplicating effort between mapping groups selecting the same ESTs
sequences from the above resources, a database has been created at the Sanger
Centre (UK). This database, RHalloc (
11
), can detect cases where different groups have selected the same EST sequence
for mapping and can notify those groups.
Figure 2
.
An example of an input file.
Figure 3
.
A flat-file output example.
While the data in RHdb comes mainly from this consortium, the database is built
to be species independent.
The Relational Database
RHdb is maintained in the relational database management system (RDBMS) ORACLE.
The schema of the database can be accessed at the URL http://www.ebi.ac.uk/RHdb/schema.html
The data
Each entry in the database is assigned an accession number which is a permanent
unique identifier.
The main type of entry in the database contains the scoring results of a
specific PCR hybridization on given PANELS using a specific STS (for which the
primers sequences are given). This type of entry is given an accession number
of the form RHn, which serves as a permanent unique identifier.
There are three other primary types of entries in the database, for which
accession number are widely used:
(i)
the hybrid cell lines grouped in PANELs (the name is used as accession number),
with information about the authors, distributors and the clones used
(ii)
the maps constructed using the RH linkage programs (having an accession number
of the form FWn) with the STSs order and LOD scores
(iii)
the PCR experimental conditions (accession number of the form EIn) in free text.
An RH entry also includes other types of information, each assigned a unique
identifier:
(i)
the author identification (of form CIn)
(ii)
the corresponding bibliographic information (of form PIn) if available
(iii)
a `flag' describing the type of STS used (EST, genetic marker, CpG island . . .
).
Cross-references to other databases are systematically added when they are given
by the submitter or can be inferred. To date, these databases include:
(i)
the nucleotide sequences databases (EMBL/GenBank/DDBJ) accession number is
mandatory (
12
)
(ii)
dbEST and dbSTS
(iii)
GDB (the Genome Database) (
13
)
(iv)
the submitting group's own unique identifiers
(v)
RHalloc (from the RH mapping consortium)
(vi)
Medline.
Data submission
The first purpose of this database is to collect large amounts of data to allow
the construction of high resolution maps. Thus there is a need for effective
acquisition methods. A data submission format of the form `
tag: text'
(Fig.
2
) has been developed to allow fast formatting of the data by the submitter and
fast input on the RHdb maintainer side. Each entry in the form ends with `//'.
A full description of the format for each type of entry can be found at URL http://www.ebi.ac.uk/RHdb/rh_formats.html . A syntax verification program for this format is provided on the EBI
anonymous FTP server at the URL ftp://ftp.ebi.ac.uk/pub/databases/RHdb/softs/rh_submit.tar.gz
Entries should be submitted by e-mail to
rhdb{at}ebi.ac.uk
with `
datasub
' as subject. Customised procedures are implemented for groups submitting very
large amounts of data.
Once received, the data are processed through verification and checking
programs:
(i)
the syntax of the taxonomy provided is verified
(ii)
the coherence of this taxonomy with the nucleotide sequence from which the
primers have been constructed (as stated above, this sequence accession number
is mandatory)
(iii)
the primers should be in the sequence, if not, the correct commentary is added
(iv)
cross-references between RHdb entries are added.
Well formatted submissions are processed within a day, and entries are
immediately created. Accession numbers are returned to the author by e-mail.
For small amounts of data, a WWW submission form is being developed in
collaboration with the HGMP resource centre (Hinxton, UK) that will allow
automatic data verification during the submission process, with respect to the
data already in the database.
Data access
Each type of entry (RH, experimental conditions, panels and maps) is represented
externally as an ASCII `flat-file'. The flat-file (Fig.
3
) is composed of lines beginning with a two character tag and followed by an
associated text. The entry ends with `//'. These files are available on the EBI
anonymous FTP server at URL ftp://ftp.ebi.ac.uk/pub/databases/RHdb with the filenames:
rh.dat
for the RH entries
(ii)
panel.dat
for the panel information
(iii)
exp.dat
for the experimental conditions
(iv)
map.dat
for the maps.
A full release of the database is made every two months, and new files replace
the previous ones in the FTP directory. Between consecutive releases, files
containing updates or new entries are also made available in the same
directory.
Data query/retrieval
The EBI provides a query/retrieval system using SRS, the Sequence Retrieval
System (
14
). This system allows entries to be retrieved based on a number of keywords.
Specific query forms are accessible at the URL: http://www.ebi.ac.uk/srs/srsc . RHdb flat-files are indexed using SRS and can be queried that way (Fig.
4
).
Figure 4
.
An example of a query form.
World Wide Web
Reports are automatically generated every night from the relational database.
Written in HTML format, they can be accessed through the EBI WWW server at URL http://www. ebi.ac.uk/RHdb/rh_reports.html and give the most up to date view of the data. We are developing query forms
that will provide answers to more specific questions (Fig.
4
).
Mapping software
RHdb also provides the scoring data in the format used by the most common RH
linkage programs: RHMAP (
15
,
16
), RHMAPPER [Kruglyak,L., Slonim,D.K., Stein,L.D. and Lander,E.S. unpublished]
and MULTIMAP (
17
). At each release, files are provided per chromosome, panel and program. A mail
service with a WWW form front-end allows the user to specify entries to be formatted (Fig.
5
). The result is sent back to the user by e-mail.
Figure 5
.
Getting the score data form.
Future developments
Once a map is built, the data in RHdb is used by researchers to place an STS of
interest on the map. For that purpose, access to large amounts of data is
necessary. SRS is a powerful query tool that allows retrieving the information
from inter-linked databases but does not provide such facilities needed for mapping.
To directly query the relational database, an external user needs on-site access to an ORACLE RDBMS and its network tools or to database
gateways. This user will also need a good knowledge of the relation schema of
the database. Any modification in that schema requires a modification of the
query programs.
The EBI is in the process of rationalising its internal infrastructure using the
Common Object Broker Architecture (CORBA) (
18
). RHdb will be part of this rationalisation and we will develop the necessary
tools and make them available to external users. The use of this standard will
also facilitate third party developments.
How to contact the RHdb at the European Bioinformatics Institute
http://www.ebi.ac.uk/RHdb (World Wide Web)
ftp://ftp.ebi.ac.uk/pub/databases/RHdb
(anonymous FTP server)
datalib@ebi.ac.uk (for general enquiries,
with RHdb in the subject)
RHdb@ebi.ac.uk (for data submission to
RHdb, with `datasub' in the subject)
Postal address:
RHdb
EMBL Outstation-the EBI,
The Wellcome Trust Genome Campus,
Hinxton,
Cambridge CB10 1SD,
UK
Telephone:
+44 (1223) 494401
Fax:
+44 (1223) 494468
ACKNOWLEDGEMENTS
We would like to thank C. Rice and P. Deloukas (Sanger Centre) for their advice
and suggestions during the creation of the database, and G. Cameron for
critical reading of this manuscript.
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Return
*To whom correspondence should be addressed. Tel: +44 1223 494409; Fax: +44 1223
494468; Email: tome@ebi.ac.uk
