Figure 1 . Report of the oligonucleotide detailed description (ERG136F).

Table 1 Present basic data set and MPDB data structure

Field name	Main item values	Data type	Multi record a
Name		free text
Tipology	PM	encoded
	PB
	AS
	PNA
Length		integer b
Nucleotide sequence		char string c
Bibliography		free text	yes
Gene		encoded	yes
Organism	HU	encoded
	VIR
	BA
Chromosome localization		char string c
Polymorphic		encoded
Notes on polymorphism		free text
Localization of the oligo within the gene		free text
Recognized specificities		encoded	yes
Applications		encoded	yes
Methods		encoded	yes
Laboratory		encoded
Notes		free text

^a More than one item of information can be inserted for each oligonucleotide. ^b Data automatically determined by the system on the basis of the nucleotide sequence. ^c International code.

Table 2 A list of methods related to oligo number present in MPDB

Method code	Complete description	Oligo number
PCR	polymerase chain reactions	3004
RT-PCR	reversal transcriptase polymerase chain reactions	122
DGGE	denaturant gradient gel electrophoresis	69
PCRSE	polymerase chain reactions direct sequencing	44
PCREL	ELISA polymerase chain reactions	38
PCRN	nested polymerase chain reactions	26
PHOS	phosphorotioate oligonucleotides	18
RACE	rapid amplification 3' c-DNA end	5
PCRC	competitive polymerase chain reactions	3
DEIA	DNA enzime immunoassay	1

The tipology field is devoted to the description of the function for which each oligonucleotide is normally used. In this context, the only allowed values were PM, corresponding to oligos employed as PCR primers, and PB, used for probes. In addition to these, the following values have now been added: AS, antisense oligonucleotides ( 4 ), and PNA, peptide nucleic acid ( 5 ) that are used mostly in the gene therapy.

Recently, new methodologies have been implemented: some methods are PCR-derived, other are of a new generation. In order to take these extensions into account, a new field related to used methods has been added to the database (Table 2 ). Users can, therefore, immediately single out if oligo information inherent to determinate laboratory techniques is present.

Table 3 Comparison between MPDB contents at the end of July 1995 and of September 1996

		July 1995	September 1996	Increase (%)
Oligonucleotides
	Total	3600	4300	19.44
	Human Gene Specific	3070	3536	15.18
	Viral Gene Specific	512	670	30.86
	Others	18	94	422.0
Genes
	Total	748	793	6.0
	Human Target Genes	618	663	7.28
	Viral Target Genes	112	112	-
	Others	18	18	-
Main applications
	Genetic Polymorphism	1849	1944	5.14
	Molecular Diagnosis of Hereditary Diseases	765	834	9.02
	Molecular Diagnosis of Infectious Diseases	600	713	18.83
	Cancer Diagnosis	280	517	84.64
	Hormone Receptor Studies	77	77	-
	Molecular Diagnosis of Neurologic Diseases	40	72	80.0
	Allelic Imbalance	-	54	-
	Anti Oncogenes	-	44	-
	Molecular Diagnosis of Autoimmune Diseases	40	40	-
	RNA Studies	-	25	-
	Apoptosis	-	12	-
	Loss of Heterozygosity	-	10	-

MPDB CURRENT DATA CONTENTS

At present, information regarding ~4300 oligonucleotides is recorded in the MPDB. In particular, during the last year, 700 oligonucleotides have been added. Among them, 237 oligos relate to cancer diagnosis (30 for breast and ovary cancer, 54 for retinoblastoma, 68 for prostate cancer, etc.), 75 to leukemia diagnosis (39 for AML1, 22 APL, etc.) and 113 to viral diagnosis (50 for HCV, 50 for HIV, etc.), while 37 oligos are specific for hemoglobinopathies, 111 for genetic studies and 127 for the molecular biology studies. Our database contains 3520 primers, 698 probes and 32 antisense oligonucleotides.

Table 3 reports a comparison between MPDB ( 2 ) main contents at the end of July 1995 and of September 1996.

Oligonucleotides described in MPDB are specific for 793 different genes (663 human, 112 viral and 18 from various other species). In particular, 3536 are related to human genes, 670 to viral genes and 94 to other species. There has been a substantial increase in the number of oligonucleotides specific to other species, and the number of oligonucleotides related to viral gene has also increased.

With reference to applications, there has been an increase of oligonucleotides used for the identifications of tumoral diseases (Cancer Diagnosis) and for neurologic disease diagnosis; moreover, we reported on oligos used for some new applications: Allelic Imbalance; Anti Oncogenes; RNA Studies; Apoptosis and Loss of Heterozygosity.

The quality of information on oligonucleotides is assured by the use of controlled vocabularies.

MPDB DATA DISTRIBUTION

MPDB is currently archived by using WAIS, distributed by means of a Gopher server and can therefore be accessed and searched through the Internet simply having either a Gopher, WAIS or WWW client (see contacts section for relevant addresses). MPDB was also included in the SRSWWW system (in this context it is called MOLPROBE) and can thus be searched at some of the SRSWWW sites (see contacts section). Objectives and search strategies for MOLPROBE have already been published ( 2 ).

Some statistics relative to access to MPDB during 1996 were computed deriving information from the `log files' of the WAIS server. These files include the most important data both on each search and information retrieving performed through the server and, among those, the name of the host from which the request was originated, searched terms and results. Attention has been put on the total number of searches and on the country of origin (results are reported in Figs 2 and 3 ). Statistics on accesses to MOLBROBE through SRSWWW are not available.

Figure 2 . Distribution of WAIS searches carried out on MPDB (January 1996-September 1996). (Data for July are missing due to technical problems.)

Figure 3 . Percentages of connections by geographic area (January 1996-September 1996).

With reference to Figure 2 , it can be pointed out that during the first 9 months of 1996 MPDB has been searched 91.5 times per month, with a minimum of 68 times in August and a maximum of 124 times in May. Although the distribution does not show a clear decrease of searches from January to September, the average is significantly lower than in 1995.

As to the origin of the searches (Fig. 3 ), it can be pointed out that the majority of connections were made from European countries. This is in contrast with 1995 data, that showed a clear prevalence of North American connections over European ones. Percentages of accesses originated from Italy and the Rest of the World remained substantially equal to 1995. These data suggest that the reduced number of searches is due mainly to the lowering of requests from US and Canada, due, perhaps, to the concurrent setting up of a US database on oligonucleotides.

CONTACTS

Further information can be obtained by contacting: Dr M. Giuseppina CAMPI, Telematics Applications in Biotechnology Group, 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}ist.unige.it.

The relevant URLs are the following:

BIOTECH Department WWW server URL: http://www.biotech.ist.unige.it

MPDB WWW home page URL: http://www.biotech.ist.unige.it/interlab/mpdb.html

MPDB Gopher directory URL: gopher://gopher.ist.unige.it/11/interlab/mpdb

SRSWWW in Heidelberg: http://www.embl-heidelberg.de/srs/srsc

SRSWWW at New York University: http://mcbi-34.med.nyu.edu/srs/srsc

REFERENCES

1 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.

2 Campi,M.G., Romano,P., Thüroff,E., Visconti,P., Manniello,M.A., Iannotta,B., Rondanina,G., Molina,F., Ruzzon,T. and Santi,L. (1996) Nucleic Acids Res., 24, 64-67.

3 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.

4 Pierga,J.Y. and Magdelenat,H. (1994) Cell. Mol. Biol., 40, 237-261.

5 Nielsen,P.E. (1995) Annu. Rev. Biophys. Struct., 24, 167-183.

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^* To whom correspondence should be addressed. Tel: +39 10 573 7292; Fax: +39 10 573 7295; Email: giusy{at}ist.unige.it
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