Research Article |
Open Access |
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BIOUROLOGY.COM |
Uría González-Tova Juan *, Mora Durban Miguel,
Saladié Roig Jose María |
Hospital Universitario Germans Trias I Pujol Carretera de
Caney s/n. 08915 Badalona Barcelona. Spainy |
| *Corresponding author: |
Dr. Uría González-Tova Juan, Hospital Universitario Germans
Trias I Pujol Carretera de
Caney s/n. 08915 Badalona Barcelona, Spain,
E-mail : 30859jug@comb.es |
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| Received December 29, 2008; Accepted January 15, 2009; Published January 15, 2009 |
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Citation:
Uría GTJ, Mora DM, Saladié RJM (2009) BIOUROLOGY.COM. J Proteomics Bioinform 2: 064-066. doi:10.4172/jpb.1000062 |
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Copyright: © 2009 Uría GTJ, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution
License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and
source are credited. |
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Objectives |
In order to be updated with the latest improvements in the field of molecular biology and because of the huge
amount of available information and the multiple sources, we have tried to develop a tool with the objective of
joining and organizing the published knowledge about basic research on Urology, mainly in regards to bladder,
prostate, kidney and testicular tumors. |
Material and Methods |
|
We have developed a search engine, with automated daily updates. This engine show the obtained results organized into genomics, proteomics, metabolic pathways, pharmacogenomics, drugs developments, clinical trialsand pubmed references. |
This idea is one of the final projects for the 2º MS con Bioinformatics for Health Sciences, organized by Pompeu
i Fabra University (UPF) and Barcelona University (UB). |
Our main reference has been the OMIM database (NCBI) where are published the relationships between
genes and human diseases. Using its public web services in a programmatic way, it is possible to get the reference
identifications and to use these to look for further information in multiple related databases. |
These results are saved into a local database and the information is showed in a structured and navigable way,
related to the original sources. |
We also offer the possibility of subscribing to an Alerts Newsgroup in order to receive and automated email
with each new entry. |
All these information is also available through a set of public web services. |
Results |
|
We think, we have been able to join in a web site, and in an easy using way, the main information about molecular
mechanisms involved in the oncogenesis of urinary bladder, prostate, kidney and testis. |
We also offer an alerts newsgroup and a complete set of public web services. |
Conclusions
|
|
We try to offer a tool to help and make easy to general urologists keep an up-to-date state of the art about the
mechanisms of molecular biology in oncological Urology, because we are sure that these are going to be the
definitive therapeutic targets of these tumors. |
Objectives |
|
Thinking about the huge amount of available information,
the multiple sources and the necessary skills needed to be
informed about developments in the field of molecular biology,
we have tried to design a tool with the objective of
facilitate to general urologist, joining and organizing the published
knowledge about basic research on Urology, mainly
in regards to bladder, prostate, kidney and testicular tumors. |
This idea has been one of the final projects for the 2º MS
con Bioinformatics for Health Sciences, organized by
Pompeu i Fabra University (UPF) and Barcelona University
(UB). |
The tool is free accessible in Internet under this url:
www.biourology.com. The novelty of this article is to explain
why and how we have developed this tool and to spread
it with the intention of making it accessible for as many
users as possible. |
We don’t know about the existence of similar tools for
specific specialties in the medical fields. This tool is searchengine
oriented to inexperienced users and it will allow every
physician to get a lot of information from basic to clinical
and translational research, just by navigating through
the links in the web site. |
A very interesting tool is the DISEASE CARD
(www.diseasecard.org) developed by Institute of Health
Carlos III. With this other tool you can look for a specific
disease and get in a structured way a lot of information
about basic research, more oriented to trained professionals. |
Material and Methods |
|
We have developed a web search engine, based on automated daily updates. This engine show the obtained results organized into genomics, proteomics, metabolic pathways, pharmacogenomics, drugs developments, clinical trials and pubmed references. |
Our main reference has been the OMIM database (NCBI)
where are published the relationships between genes and
human diseases. Using its public web services in a programmatic way, it is possible to get the reference identifications
and to use these to look for further information in multiple
related databases. |
All these results are saved into a local database and the
information is showed in a structured and navigable way,
related to the original sources. |
We also offer the possibility of subscribing to an Alerts
Newsgroup in order to receive and automated email with
each new entry. The user only needs to write once the
name and email and this information is store to send emails
after each daily update with new entries to all subscribed
users. |
All these information is too available through a set of public
web services, in order to be accessible by other
informatics applications. |
We have developed a .NET application that takes information
daily from public sources and register the links in a
local MySql database. The steps that we have followed are: |
1. |
|
2. |
We check for matches in the OMIM database for 4
diseases “Bladder cancer”, ”Prostate Cancer”, ”Kidney
cancer” and ”Testis Cancer”. |
3. |
We register the OmimNumber, title and symbol of each
gene matching the search. |
4. |
Through these data we get the gene_id from the genes
database, as well as the chromosome, locus and position of
each gene. |
5. |
We get the associated nucleotides and proteins through
the gene_id and the genbank_id. |
6. |
We get the associated registers in the PDB database. |
7. |
Through the gene_id we also get the records in the
Reactome and KEGG pathways databases. |
8. |
We get the pharmacoresearch database link
(www.pharmgkb.org). |
9. |
Finally we get the pubmed publications matching the
symbol of the gene and the disease. We also perform a
generic “genomics and “ plus organ plus “cancer”. |
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We present the links to the original sources of all this information
in an easy and structured way. |
Results |
We describe each item of showed information. |
Genomics |
| Under this tab you can see the published genes in OMIM
related to each kind of tumor. The available information is
divided into Gene name Omim reference
(www.ncbi.nlm.nih.gov) , Entrez reference
(www.ncbi.nlm.nih.gov) , Genercard link
(www.genecards.org) , SNP (www.ncbi.nlm.nih.gov) and
loci MapView (www.ncbi.nlm.nih.gov) , with direct links to
original sources. |
Proteomics |
Using the gene_id obtained from OMIM we showed all
the protein sequences (www.ncbi.nlm.nih.gov) and PDB
structures (www.expasy.org) related to each gene. |
Metabolic Pathways |
We show the Reactome (www.reactome.org) and
KEGG (www.genome.jp) described pathways in relation
to the prior genes. |
Pharmaco Research |
| Information and links to the pharmagkb site (http://www.pharmgkb.org) for each gene. |
Drugs |
We offer a direct link to DrugBank (www.drugbank.ca)
and to Therapeutic Target Database (http://xin.cz3.nus.edu.sg/group/cjttd/TTD_ns.asp) in relation to each gene. |
Pubmed |
|
We show the title, Journal, Publication date and direct link
to pubmed (www.ncbi.nlm.nih.gov/pubmed) entry of all the
articles about each gene and the relation with one particular
tumor. |
We also offer a direct link to all articles about “genomics”
and each tumor, according to MeSH terms.
(http://www.ncbi.nlm.nih.gov) |
Clinical Trials |
| Direct link to the National Cancer Institute Clinical trials
search results. (http://www.cancer.gov) |
| We also offer an alerts newsgroup and a complete set of
public web services. |
Conclusions |
|
With this project, we would like to be able to join in a web
site, and in an easy using way, the main information about
molecular mechanisms involved in the oncogenesis of urinary
bladder, prostate, kidney and testis. We offer quick
links to the information of about 15 different public databases. |
We tried to offer a tool to help and make easy to general
urologists keep an up-to-date state of the art about the
mechanisms of molecular biology in oncological Urology,
because we are sure that these are going to be the definitive
therapeutic targets of these tumors. |
This working schema could be also useful for any kind of
tumor or disease. |
This tool could be easily integrated in any type of supporting
decision-making systems, through a external link to the
site or programmatically using the available web services.
It allows checking in an easy and quick way , specially what
clinical trials are being performed and review the newest
literature about the disease. |
