Molecular probe data base (MPDB)
Maria Giuseppina
Campi
1,
*
,
Paolo
Romano
1
,
Edward
Thüroff
3
,
Paola
Visconti
1
,
M. Assunta
Manniello
1
,
Beatrice
Iannotta
1
,
Gabriella
Rondanina
1
,
Francesco
Molina
1
,
Tiziana
Ruzzon
1
and
Leonardo
Santi
1,2
1
National Institute for Cancer Research,
2
Institute of Clinical and Experimental Oncology of the University of Genoa and
3
TIB MOLBIOL c/o Advanced Biotechnology Center, Largo R. Benzi 10, I-16132
Genoa
,
Italy
Received October 2, 1995
;
Accepted October 4, 1995
ABSTRACT
The molecular probe data base (MPDB) contains detailed information on synthetic
oligonucleotides, including their identification, target genes, applications
and bibliographic references. It is available on-line through Internet and can be searched by using Network Information
Retrieval tools. In this article the most recent enhancements of MPDB, both in
terms of data contents and new ways of access, are described. These include a
recently established collaboration with EMBL Data Library, in the sphere of
SRSWWW network browser, in view of a better integration of MPDB with other
molecular biology databases.
INTRODUCTION
Molecular biology laboratories synthetize a high number of oligonucleotides,
which are frequently used in basic research and in diagnostics. MPDB focuses on
data related to human oligonucleotides useful in the study of genetic
polymorphisms and in the diagnosis of genetic and infectious diseases (
1
-
3
).
It is managed by an interdisciplinary group, the Telematics Applications in
Biotechnology (TAB) group, whose experience derives from the carrying out of
the Interlab Project (
4
). MPDB and the other services that are managed by the TAB group, including the
Cell Line Data Base (CLDB) (
5
), are hosted at the Advanced Biotechnology Center (ABC) in Genoa.
During the last year, the main efforts have been devoted to insertion of new
data, update and quality control of previously recorded data, and to the
enhancement of data distribution methods.
MPDB CURRENT CONTENTS
A comparison between MPDB contents respectively at the end of July 1994 and of
July 1995 is shown in Table
1
. This table reports the total number of oligonucleotides and of target genes
and the distribution of oligonucleotides with reference to main applications.
Synthetic oligonucleotides described in MPDB are now ~3600. They are specific for 748 different genes (618 human, 112 viral and
the remaining 18 from various other species). In detail, about 3070
oligonucleotides are specific to human genes, while 512 are related to viral
genes. As to their specific utilization, data included in MPDB refers to
oligonucleotides used as PCR primers (~2930) and as probe (~670).
1725 oligonucleotides are used to reveal different pathologies (their
distribution is shown in Fig.
1
). Of these, about one half (45%) reveal hereditary diseases and about one third
(34%) are specific for infectious agents. The remaining oligonucleotides are
used for the diagnosis of cancer (16%), autoimmune diseases (2%) and
neurological disorders (2%).
MPDB DATA DISTRIBUTION
As described in articles that previously appeared in this journal (
1
-
3
), MPDB was created and is managed through the Oracle relational data base
management system. External access to MPDB can be carried out by means of the
most widely used Network Information Retrieval (NIR) clients through a textual
version that is periodically created and indexed by means of the public domain
WAIS software.
Starting from the beginning of 1995, basic information about MPDB, including its
current contents and an overview of main applications and target genes, can
also be retrieved with WWW software clients, such as Mosaic, Netscape and Lynx,
at the Advanced Biotechnology Centre (ABC) WWW server, at the following URL:
http://www.ist.unige.it/interlab/mpdb.html (see corresponding home page in Fig.
2
).
This page gives access to currently available MPDB searching ways: (i) link to
IST gopher server for accessing WAIS indexed database, and (ii) search through
the SRSWWW network browser for databanks in molecular biology (
6
,
7
). Corresponding URLs are reported at the end of this paper.
Integration of MPDB, that is called MOLPROBE in this context, with other
molecular biology databanks is made possible through existing references to
EMBL Data Library accession numbers that are reported with each oligonucleotide
target gene.
CONTACTS
Further information can be obtained by contacting:
Dr M. Giuseppina CAMPI
Telematics Applications in Biotechnology
Advanced Biotechnology Centre
Largo Rosanna Benzi, 10
I-16132 Genoa
Italy
Tel: +39 10 5737 292
Fax: +39 10 5737 295
E-mail: giusy{at}istge.ist.unige.it
The relevant URLs are the following:
BIOTECH Department WWW server URL: http://www.
biotech.ist.unige.it
1 Aresu, O., Parodi,P., Romano, P., Romani, M., Angelini, G., Manniello, A., Iannotta, B., Rondanina, G., Ruzzon, T. and Santi L. (1992) Nucleic Acids Res., 20, suppl., 2009-2011.
2 Romano, P., Aresu, O., Parodi, B., Manniello, A., Campi, G., Angelini, G., Romani, M., Iannotta, B., Rondanina, G., Ruzzon, T. and Santi, L. (1993) Nucleic Acids Res., 21, 3007-3009.MEDLINE Abstract
3 Aresu, O., Campi, M.G., Romano, P., Parodi, B., Manniello, A., Thuroff, E., Molina, F., Saguato, F., Iannotta, B., Rondanina, G., Ruzzon, T. and Santi, L. (1994) Nucleic Acids Res., 22, 3474-3480.MEDLINE Abstract
4 Romano, P., Aresu, O., Iannotta, B., Manniello, A., Parodi, B., Rondanina, G., Ruzzon, T. (1993), Binary, 5, 62-72.
5 Romano, P., Manniello, A., Campi, G., Parodi, B., Aresu, O., Visconti, P., Iannotta, B., Rondanina, G. and Ruzzon, T. (1995) J. Exp. Clin. Cancer Res., 14, suppl., 6-7.
6 Pfeffer, U., Fecarotta, E., and Vidali, G. (1995) BioTechniques, 17, in press.
7 Etzold, T. and Argos, P., (1993) Computer Appl. Biosci., 9, 49-57.
8 Etzold, T. (1994) Proc. of the Meeting on `Interconnection of Molecular Biology Databases', Stanford University, San Francisco Bay Area, August 9-12, 1994.
