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2.  An Information System for European culture collections: the way forward 
SpringerPlus  2016;5(1):772.
Culture collections contain indispensable information about the microorganisms preserved in their repositories, such as taxonomical descriptions, origins, physiological and biochemical characteristics, bibliographic references, etc. However, information currently accessible in databases rarely adheres to common standard protocols. The resultant heterogeneity between culture collections, in terms of both content and format, notably hampers microorganism-based research and development (R&D). The optimized exploitation of these resources thus requires standardized, and simplified, access to the associated information. To this end, and in the interest of supporting R&D in the fields of agriculture, health and biotechnology, a pan-European distributed research infrastructure, MIRRI, including over 40 public culture collections and research institutes from 19 European countries, was established. A prime objective of MIRRI is to unite and provide universal access to the fragmented, and untapped, resources, information and expertise available in European public collections of microorganisms; a key component of which is to develop a dynamic Information System. For the first time, both culture collection curators as well as their users have been consulted and their feedback, concerning the needs and requirements for collection databases and data accessibility, utilised. Users primarily noted that databases were not interoperable, thus rendering a global search of multiple databases impossible. Unreliable or out-of-date and, in particular, non-homogenous, taxonomic information was also considered to be a major obstacle to searching microbial data efficiently. Moreover, complex searches are rarely possible in online databases thus limiting the extent of search queries. Curators also consider that overall harmonization—including Standard Operating Procedures, data structure, and software tools—is necessary to facilitate their work and to make high-quality data easily accessible to their users. Clearly, the needs of culture collection curators coincide with those of users on the crucial point of database interoperability. In this regard, and in order to design an appropriate Information System, important aspects on which the culture collection community should focus include: the interoperability of data sets with the ontologies to be used; setting best practice in data management, and the definition of an appropriate data standard.
doi:10.1186/s40064-016-2450-8
PMCID: PMC4912550  PMID: 27386258
Culture collection; Microorganism; Information Technology; Microbial domain Biological Resource Centre
3.  Geena 2, improved automated analysis of MALDI/TOF mass spectra 
BMC Bioinformatics  2016;17(Suppl 4):61.
Background
Mass spectrometry (MS) is producing high volumes of data supporting oncological sciences, especially for translational research. Most of related elaborations can be carried out by combining existing tools at different levels, but little is currently available for the automation of the fundamental steps.
For the analysis of MALDI/TOF spectra, a number of pre-processing steps are required, including joining of isotopic abundances for a given molecular species, normalization of signals against an internal standard, background noise removal, averaging multiple spectra from the same sample, and aligning spectra from different samples.
In this paper, we present Geena 2, a public software tool for the automated execution of these pre-processing steps for MALDI/TOF spectra.
Results
Geena 2 has been developed in a Linux-Apache-MySQL-PHP web development environment, with scripts in PHP and Perl. Input and output are managed as simple formats that can be consumed by any database system and spreadsheet software. Input data may also be stored in a MySQL database. Processing methods are based on original heuristic algorithms which are introduced in the paper.
Three simple and intuitive web interfaces are available: the Standard Search Interface, which allows a complete control over all parameters, the Bright Search Interface, which leaves to the user the possibility to tune parameters for alignment of spectra, and the Quick Search Interface, which limits the number of parameters to a minimum by using default values for the majority of parameters.
Geena 2 has been utilized, in conjunction with a statistical analysis tool, in three published experimental works: a proteomic study on the effects of long-term cryopreservation on the low molecular weight fraction of serum proteome, and two retrospective serum proteomic studies, one on the risk of developing breat cancer in patients affected by gross cystic disease of the breast (GCDB) and the other for the identification of a predictor of breast cancer mortality following breast cancer surgery, whose results were validated by ELISA, a completely alternative method.
Conclusions
Geena 2 is a public tool for the automated pre-processing of MS data originated by MALDI/TOF instruments, with a simple and intuitive web interface. It is now under active development for the inclusion of further filtering options and for the adoption of standard formats for MS spectra.
Electronic supplementary material
The online version of this article (doi:10.1186/s12859-016-0911-2) contains supplementary material, which is available to authorized users.
doi:10.1186/s12859-016-0911-2
PMCID: PMC4896264  PMID: 26961516
Computational Proteomics; Computational Mass Spectrometry; MALDI/TOF mass spectrometry; MS spectra comparison/alignment; Automation of data analysis; Web application; LAMP
4.  NETTAB 2014: From high-throughput structural bioinformatics to integrative systems biology 
BMC Bioinformatics  2016;17(Suppl 4):62.
The fourteenth NETTAB workshop, NETTAB 2014, was devoted to a range of disciplines going from structural bioinformatics, to proteomics and to integrative systems biology. The topics of the workshop were centred around bioinformatics methods, tools, applications, and perspectives for models, standards and management of high-throughput biological data, structural bioinformatics, functional proteomics, mass spectrometry, drug discovery, and systems biology.
43 scientific contributions were presented at NETTAB 2014, including keynote, special guest and tutorial talks, oral communications, and posters. Full papers from some of the best contributions presented at the workshop were later submitted to a special Call for this Supplement.
Here, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement.
doi:10.1186/s12859-016-0907-y
PMCID: PMC4896255  PMID: 26960985
5.  Tools and data services registry: a community effort to document bioinformatics resources 
Nucleic Acids Research  2015;44(Database issue):D38-D47.
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is that scientists must often struggle to find, understand, compare and use the best resources for the task at hand.
Here we present a community-driven curation effort, supported by ELIXIR—the European infrastructure for biological information—that aspires to a comprehensive and consistent registry of information about bioinformatics resources. The sustainable upkeep of this Tools and Data Services Registry is assured by a curation effort driven by and tailored to local needs, and shared amongst a network of engaged partners.
As of November 2015, the registry includes 1785 resources, with depositions from 126 individual registrations including 52 institutional providers and 74 individuals. With community support, the registry can become a standard for dissemination of information about bioinformatics resources: we welcome everyone to join us in this common endeavour. The registry is freely available at https://bio.tools.
doi:10.1093/nar/gkv1116
PMCID: PMC4702812  PMID: 26538599
6.  Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics 
BMC Bioinformatics  2015;16(Suppl 9):S1.
This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014.
doi:10.1186/1471-2105-16-S9-S1
PMCID: PMC4464032  PMID: 26050789
7.  NETTAB 2013: Semantic, social, and mobile applications for bioinformatics and biomedical laboratories 
BMC Bioinformatics  2014;15(Suppl 14):S1.
The thirteenth NETTAB workshop, NETTAB 2013, was devoted to semantic, social, and mobile applications for bioinformatics and biomedical laboratories.
Topics included issues, methods, algorithms, and technologies for the design and development of tools and platforms able to provide semantic, social, and mobile applications supporting bioinformatics and the activities carried out in a biomedical laboratory.
About 30 scientific contributions were presentedat NETTAB 2013, including keynote and tutorial talks, oral communications, and posters. Best contributions presented at the workshop were later submitted to a special Call for this Supplement.
Here, we provide an overview of the workshop and introduce manuscripts that have been accepted for publication in this Supplement.
doi:10.1186/1471-2105-15-S14-S1
PMCID: PMC4255736  PMID: 25471662
8.  NETTAB 2012 on "Integrated Bio-Search" 
BMC Bioinformatics  2014;15(Suppl 1):S1.
The NETTAB 2012 workshop, held in Como on November 14-16, 2012, was devoted to "Integrated Bio-Search", that is to technologies, methods, architectures, systems and applications for searching, retrieving, integrating and analyzing data, information, and knowledge with the aim of answering complex bio-medical-molecular questions, i.e. some of the most challenging issues in bioinformatics today. It brought together about 80 researchers working in the field of Bioinformatics, Computational Biology, Biology, Computer Science and Engineering. More than 50 scientific contributions, including keynote and tutorial talks, oral communications, posters and software demonstrations, were presented at the workshop. This preface provides a brief overview of the workshop and shortly introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement.
doi:10.1186/1471-2105-15-S1-S1
PMCID: PMC4015131  PMID: 24564635
9.  Integrated Bio-Search: challenges and trends for the integration, search and comprehensive processing of biological information 
BMC Bioinformatics  2014;15(Suppl 1):S2.
Many efforts exist to design and implement approaches and tools for data capture, integration and analysis in the life sciences. Challenges are not only the heterogeneity, size and distribution of information sources, but also the danger of producing too many solutions for the same problem. Methodological, technological, infrastructural and social aspects appear to be essential for the development of a new generation of best practices and tools. In this paper, we analyse and discuss these aspects from different perspectives, by extending some of the ideas that arose during the NETTAB 2012 Workshop, making reference especially to the European context.
First, relevance of using data and software models for the management and analysis of biological data is stressed. Second, some of the most relevant community achievements of the recent years, which should be taken as a starting point for future efforts in this research domain, are presented. Third, some of the main outstanding issues, challenges and trends are analysed. The challenges related to the tendency to fund and create large scale international research infrastructures and public-private partnerships in order to address the complex challenges of data intensive science are especially discussed. The needs and opportunities of Genomic Computing (the integration, search and display of genomic information at a very specific level, e.g. at the level of a single DNA region) are then considered.
In the current data and network-driven era, social aspects can become crucial bottlenecks. How these may best be tackled to unleash the technical abilities for effective data integration and validation efforts is then discussed. Especially the apparent lack of incentives for already overwhelmed researchers appears to be a limitation for sharing information and knowledge with other scientists. We point out as well how the bioinformatics market is growing at an unprecedented speed due to the impact that new powerful in silico analysis promises to have on better diagnosis, prognosis, drug discovery and treatment, towards personalized medicine. An open business model for bioinformatics, which appears to be able to reduce undue duplication of efforts and support the increased reuse of valuable data sets, tools and platforms, is finally discussed.
doi:10.1186/1471-2105-15-S1-S2
PMCID: PMC4015876  PMID: 24564249
10.  Bioinformatics in Italy: BITS 2012, the ninth annual meeting of the Italian Society of Bioinformatics 
BMC Bioinformatics  2013;14(Suppl 7):S1.
The BITS2012 meeting, held in Catania on May 2-4, 2012, brought together almost 100 Italian researchers working in the field of Bioinformatics, as well as students in the same or related disciplines. About 90 original research works were presented either as oral communication or as posters, representing a landscape of Italian current research in bioinformatics.
This preface provides a brief overview of the meeting and introduces the manuscripts that were accepted for publication in this supplement, after a strict and careful peer-review by an International board of referees.
doi:10.1186/1471-2105-14-S7-S1
PMCID: PMC3633006  PMID: 23815154
11.  Clinical Bioinformatics: challenges and opportunities 
BMC Bioinformatics  2012;13(Suppl 14):S1.
Background
Network Tools and Applications in Biology (NETTAB) Workshops are a series of meetings focused on the most promising and innovative ICT tools and to their usefulness in Bioinformatics. The NETTAB 2011 workshop, held in Pavia, Italy, in October 2011 was aimed at presenting some of the most relevant methods, tools and infrastructures that are nowadays available for Clinical Bioinformatics (CBI), the research field that deals with clinical applications of bioinformatics.
Methods
In this editorial, the viewpoints and opinions of three world CBI leaders, who have been invited to participate in a panel discussion of the NETTAB workshop on the next challenges and future opportunities of this field, are reported. These include the development of data warehouses and ICT infrastructures for data sharing, the definition of standards for sharing phenotypic data and the implementation of novel tools to implement efficient search computing solutions.
Results
Some of the most important design features of a CBI-ICT infrastructure are presented, including data warehousing, modularity and flexibility, open-source development, semantic interoperability, integrated search and retrieval of -omics information.
Conclusions
Clinical Bioinformatics goals are ambitious. Many factors, including the availability of high-throughput "-omics" technologies and equipment, the widespread availability of clinical data warehouses and the noteworthy increase in data storage and computational power of the most recent ICT systems, justify research and efforts in this domain, which promises to be a crucial leveraging factor for biomedical research.
doi:10.1186/1471-2105-13-S14-S1
PMCID: PMC3439676  PMID: 23095472
12.  Gender and Age-Dependent Etiology of Community-Acquired Urinary Tract Infections 
The Scientific World Journal  2012;2012:349597.
Urinary tract infections (UTIs) are among the most frequent community-acquired infections worldwide. Escherichia coli is the most common UTI pathogen although underlying host factors such as patients' age and gender may influence prevalence of causative agents. In this study, 61 273 consecutive urine samples received over a 22-month period from outpatients clinics of an urban area of north Italy underwent microbiological culture with subsequent bacterial identification and antimicrobial susceptibility testing of positive samples. A total of 13 820 uropathogens were isolated and their prevalence analyzed according to patient's gender and age group. Overall Escherichia coli accounted for 67.6% of all isolates, followed by Klebsiella pneumoniae (8.8%), Enterococcus faecalis (6.3%), Proteus mirabilis (5.2%), and Pseudomonas aeruginosa (2.5%). Data stratification according to both age and gender showed E. coli isolation rates to be lower in both males aged ≥60 years (52.2%), E. faecalis and P. aeruginosa being more prevalent in this group (11.6% and 7.8%, resp.), as well as in those aged ≤14 years (51.3%) in whom P. mirabilis prevalence was found to be as high as 21.2%. Streptococcus agalactiae overall prevalence was found to be 2.3% although it was shown to occur most frequently in women aged between 15 and 59 years (4.1%). Susceptibility of E. coli to oral antimicrobial agents was demonstrated to be as follows: fosfomycin (72.9%), trimethoprim/sulfamethoxazole (72.9%), ciprofloxacin (76.8%), ampicillin (48.0%), and amoxicillin/clavulanate (77.5%). In conclusion, both patients' age and gender are significant factors in determining UTIs etiology; they can increase accuracy in defining the causative uropathogen as well as providing useful guidance to empiric treatment.
doi:10.1100/2012/349597
PMCID: PMC3351074  PMID: 22629135
13.  Towards linked open gene mutations data 
BMC Bioinformatics  2012;13(Suppl 4):S7.
Background
With the advent of high-throughput technologies, a great wealth of variation data is being produced. Such information may constitute the basis for correlation analyses between genotypes and phenotypes and, in the future, for personalized medicine. Several databases on gene variation exist, but this kind of information is still scarce in the Semantic Web framework.
In this paper, we discuss issues related to the integration of mutation data in the Linked Open Data infrastructure, part of the Semantic Web framework. We present the development of a mapping from the IARC TP53 Mutation database to RDF and the implementation of servers publishing this data.
Methods
A version of the IARC TP53 Mutation database implemented in a relational database was used as first test set. Automatic mappings to RDF were first created by using D2RQ and later manually refined by introducing concepts and properties from domain vocabularies and ontologies, as well as links to Linked Open Data implementations of various systems of biomedical interest.
Since D2RQ query performances are lower than those that can be achieved by using an RDF archive, generated data was also loaded into a dedicated system based on tools from the Jena software suite.
Results
We have implemented a D2RQ Server for TP53 mutation data, providing data on a subset of the IARC database, including gene variations, somatic mutations, and bibliographic references. The server allows to browse the RDF graph by using links both between classes and to external systems. An alternative interface offers improved performances for SPARQL queries. The resulting data can be explored by using any Semantic Web browser or application.
Conclusions
This has been the first case of a mutation database exposed as Linked Data. A revised version of our prototype, including further concepts and IARC TP53 Mutation database data sets, is under development.
The publication of variation information as Linked Data opens new perspectives: the exploitation of SPARQL searches on mutation data and other biological databases may support data retrieval which is presently not possible. Moreover, reasoning on integrated variation data may support discoveries towards personalized medicine.
doi:10.1186/1471-2105-13-S4-S7
PMCID: PMC3303732  PMID: 22536974
14.  Bioinformatics in Italy: BITS2011, the Eighth Annual Meeting of the Italian Society of Bioinformatics 
BMC Bioinformatics  2012;13(Suppl 4):I1.
The BITS2011 meeting, held in Pisa on June 20-22, 2011, brought together more than 120 Italian researchers working in the field of Bioinformatics, as well as students in Bioinformatics, Computational Biology, Biology, Computer Sciences, and Engineering, representing a landscape of Italian bioinformatics research.
This preface provides a brief overview of the meeting and introduces the peer-reviewed manuscripts that were accepted for publication in this Supplement.
doi:10.1186/1471-2105-13-S4-I1
PMCID: PMC3314567  PMID: 22536954
15.  Semantic Web Applications and Tools for the Life Sciences: SWAT4LS 2010 
BMC Bioinformatics  2012;13(Suppl 1):S1.
As Semantic Web technologies mature and new releases of key elements, such as SPARQL 1.1 and OWL 2.0, become available, the Life Sciences continue to push the boundaries of these technologies with ever more sophisticated tools and applications. Unsurprisingly, therefore, interest in the SWAT4LS (Semantic Web Applications and Tools for the Life Sciences) activities have remained high, as was evident during the third international SWAT4LS workshop held in Berlin in December 2010. Contributors to this workshop were invited to submit extended versions of their papers, the best of which are now made available in the special supplement of BMC Bioinformatics. The papers reflect the wide range of work in this area, covering the storage and querying of Life Sciences data in RDF triple stores, tools for the development of biomedical ontologies and the semantics-based integration of Life Sciences as well as clinicial data.
doi:10.1186/1471-2105-13-S1-S1
PMCID: PMC3471345  PMID: 22373274
16.  MetaBase—the wiki-database of biological databases 
Nucleic Acids Research  2011;40(Database issue):D1250-D1254.
Biology is generating more data than ever. As a result, there is an ever increasing number of publicly available databases that analyse, integrate and summarize the available data, providing an invaluable resource for the biological community. As this trend continues, there is a pressing need to organize, catalogue and rate these resources, so that the information they contain can be most effectively exploited. MetaBase (MB) (http://MetaDatabase.Org) is a community-curated database containing more than 2000 commonly used biological databases. Each entry is structured using templates and can carry various user comments and annotations. Entries can be searched, listed, browsed or queried. The database was created using the same MediaWiki technology that powers Wikipedia, allowing users to contribute on many different levels. The initial release of MB was derived from the content of the 2007 Nucleic Acids Research (NAR) Database Issue. Since then, approximately 100 databases have been manually collected from the literature, and users have added information for over 240 databases. MB is synchronized annually with the static Molecular Biology Database Collection provided by NAR. To date, there have been 19 significant contributors to the project; each one is listed as an author here to highlight the community aspect of the project.
doi:10.1093/nar/gkr1099
PMCID: PMC3245051  PMID: 22139927
17.  Tools and collaborative environments for bioinformatics research 
Briefings in Bioinformatics  2011;12(6):549-561.
Advanced research requires intensive interaction among a multitude of actors, often possessing different expertise and usually working at a distance from each other. The field of collaborative research aims to establish suitable models and technologies to properly support these interactions. In this article, we first present the reasons for an interest of Bioinformatics in this context by also suggesting some research domains that could benefit from collaborative research. We then review the principles and some of the most relevant applications of social networking, with a special attention to networks supporting scientific collaboration, by also highlighting some critical issues, such as identification of users and standardization of formats. We then introduce some systems for collaborative document creation, including wiki systems and tools for ontology development, and review some of the most interesting biological wikis. We also review the principles of Collaborative Development Environments for software and show some examples in Bioinformatics. Finally, we present the principles and some examples of Learning Management Systems. In conclusion, we try to devise some of the goals to be achieved in the short term for the exploitation of these technologies.
doi:10.1093/bib/bbr055
PMCID: PMC3220874  PMID: 21984743
social networks; open source; collaborative research; collaborative development; collaborative learning
18.  Biomedical semantics in the Semantic Web 
Journal of Biomedical Semantics  2011;2(Suppl 1):S1.
The Semantic Web offers an ideal platform for representing and linking biomedical information, which is a prerequisite for the development and application of analytical tools to address problems in data-intensive areas such as systems biology and translational medicine. As for any new paradigm, the adoption of the Semantic Web offers opportunities and poses questions and challenges to the life sciences scientific community: which technologies in the Semantic Web stack will be more beneficial for the life sciences? Is biomedical information too complex to benefit from simple interlinked representations? What are the implications of adopting a new paradigm for knowledge representation? What are the incentives for the adoption of the Semantic Web, and who are the facilitators? Is there going to be a Semantic Web revolution in the life sciences?
We report here a few reflections on these questions, following discussions at the SWAT4LS (Semantic Web Applications and Tools for Life Sciences) workshop series, of which this Journal of Biomedical Semantics special issue presents selected papers from the 2009 edition, held in Amsterdam on November 20th.
doi:10.1186/2041-1480-2-S1-S1
PMCID: PMC3105493  PMID: 21388570
19.  IBWS: IST Bioinformatics Web Services 
Nucleic Acids Research  2010;38(Web Server issue):W712-W718.
The Bioinformatics group at the National Cancer Research Institute (IST) of Genoa has been involved since many years in the development and maintenance of biomedical information systems. Among them, the Common Access to Biological Resources and Information network services offer access to more than 130 000 biological resources, like strains of micro-organisms and human and animal cell lines, included in 29 collections from some of the most known European Biological Resource Centers. An Sequence Retrieval System (SRS) implementation of the TP53 Mutation Database of the International Agency for Research on Cancer (Lyon) was made available in order to improve interoperability of this data with other molecular biology databases. ‘SRS by WS (SWS)’, a system for retrieving information on public SRS sites and for directly querying them, was also implemented. In order to make this information available through application programming interfaces, we implemented a suite of free web services (WS), called the ‘IST Bioinformatics Web Services (IBWS)’. A support web site, including a description of the system, a list of available WS together with help pages, links to corresponding WSDLs and forms for testing services, is available at http://bioinformatics.istge.it/ibws/. WSDL definitions can also be retrieved directly at http://bioinformatics.istge.it:8080/axis/services.
doi:10.1093/nar/gkq416
PMCID: PMC2896171  PMID: 20484374
20.  Survival Online: a web-based service for the analysis of correlations between gene expression and clinical and follow-up data 
BMC Bioinformatics  2009;10(Suppl 12):S10.
Background
Complex microarray gene expression datasets can be used for many independent analyses and are particularly interesting for the validation of potential biomarkers and multi-gene classifiers. This article presents a novel method to perform correlations between microarray gene expression data and clinico-pathological data through a combination of available and newly developed processing tools.
Results
We developed Survival Online (available at ), a Web-based system that allows for the analysis of Affymetrix GeneChip microarrays by using a parallel version of dChip. The user is first enabled to select pre-loaded datasets or single samples thereof, as well as single genes or lists of genes. Expression values of selected genes are then correlated with sample annotation data by uni- or multi-variate Cox regression and survival analyses. The system was tested using publicly available breast cancer datasets and GO (Gene Ontology) derived gene lists or single genes for survival analyses.
Conclusion
The system can be used by bio-medical researchers without specific computation skills to validate potential biomarkers or multi-gene classifiers. The design of the service, the parallelization of pre-processing tasks and the implementation on an HPC (High Performance Computing) environment make this system a useful tool for validation on several independent datasets.
doi:10.1186/1471-2105-10-S12-S10
PMCID: PMC2762059  PMID: 19828070
21.  Trends in modeling Biomedical Complex Systems 
BMC Bioinformatics  2009;10(Suppl 12):I1.
In this paper we provide an introduction to the techniques for multi-scale complex biological systems, from the single bio-molecule to the cell, combining theoretical modeling, experiments, informatics tools and technologies suitable for biological and biomedical research, which are becoming increasingly multidisciplinary, multidimensional and information-driven. The most important concepts on mathematical modeling methodologies and statistical inference, bioinformatics and standards tools to investigate complex biomedical systems are discussed and the prominent literature useful to both the practitioner and the theoretician are presented.
doi:10.1186/1471-2105-10-S12-I1
PMCID: PMC2762057  PMID: 19828068
22.  Semantic Web Applications and Tools for Life Sciences, 2008 – Introduction 
BMC Bioinformatics  2009;10(Suppl 10):S1.
doi:10.1186/1471-2105-10-S10-S1
PMCID: PMC2755817  PMID: 19796393
23.  Cell Line Data Base: structure and recent improvements towards molecular authentication of human cell lines 
Nucleic Acids Research  2008;37(Database issue):D925-D932.
The Cell Line Data Base (CLDB) is a well-known reference information source on human and animal cell lines including information on more than 6000 cell lines. Main biological features are coded according to controlled vocabularies derived from international lists and taxonomies. HyperCLDB (http://bioinformatics.istge.it/hypercldb/) is a hypertext version of CLDB that improves data accessibility by also allowing information retrieval through web spiders. Access to HyperCLDB is provided through indexes of biological characteristics and navigation in the hypertext is granted by many internal links. HyperCLDB also includes links to external resources. Recently, an interest was raised for a reference nomenclature for cell lines and CLDB was seen as an authoritative system. Furthermore, to overcome the cell line misidentification problem, molecular authentication methods, such as fingerprinting, single-locus short tandem repeat (STR) profile and single nucleotide polymorphisms validation, were proposed. Since this data is distributed, a reference portal on authentication of human cell lines is needed. We present here the architecture and contents of CLDB, its recent enhancements and perspectives. We also present a new related database, the Cell Line Integrated Molecular Authentication (CLIMA) database (http://bioinformatics.istge.it/clima/), that allows to link authentication data to actual cell lines.
doi:10.1093/nar/gkn730
PMCID: PMC2686526  PMID: 18927105
24.  A Semantic Web for bioinformatics: goals, tools, systems, applications 
BMC Bioinformatics  2008;9(Suppl 4):S1.
doi:10.1186/1471-2105-9-S4-S1
PMCID: PMC2367628  PMID: 18460170
25.  SWS: accessing SRS sites contents through Web Services 
BMC Bioinformatics  2008;9(Suppl 2):S15.
Background
Web Services and Workflow Management Systems can support creation and deployment of network systems, able to automate data analysis and retrieval processes in biomedical research. Web Services have been implemented at bioinformatics centres and workflow systems have been proposed for biological data analysis.
New databanks are often developed by taking into account these technologies, but many existing databases do not allow a programmatic access. Only a fraction of available databanks can thus be queried through programmatic interfaces. SRS is a well know indexing and search engine for biomedical databanks offering public access to many databanks and analysis tools. Unfortunately, these data are not easily and efficiently accessible through Web Services.
Results
We have developed ‘SRS by WS’ (SWS), a tool that makes information available in SRS sites accessible through Web Services. Information on known sites is maintained in a database, srsdb. SWS consists in a suite of WS that can query both srsdb, for information on sites and databases, and SRS sites. SWS returns results in a text-only format and can be accessed through a WSDL compliant client. SWS enables interoperability between workflow systems and SRS implementations, by also managing access to alternative sites, in order to cope with network and maintenance problems, and selecting the most up-to-date among available systems.
Conclusions
Development and implementation of Web Services, allowing to make a programmatic access to an exhaustive set of biomedical databases can significantly improve automation of in-silico analysis. SWS supports this activity by making biological databanks that are managed in public SRS sites available through a programmatic interface.
doi:10.1186/1471-2105-9-S2-S15
PMCID: PMC2323664  PMID: 18387203

Results 1-25 (30)