Time to Organize the Bioinformatics Resourceome

The initial steps toward a bioinformatics resourceome are clear. First, an overall ontology with the high-level concepts (algorithms, databases, organizations, papers, people, etc.) must be created, with a set of standard attributes and a standard set of relations between these concepts (e.g., people publish papers, papers describe algorithms or databases, organizations house people, etc.). The initial ontology should be compact and built for distributed collaborative extension. Second, a mechanism for people to extend this ontology with subconcepts in order to describe their own resources should be designed. The precise location of a tool within a taxonomy is not critical—the author will place it somewhere based on the location of similar/competing resources or based on a best-informed guess. Others may create links to the resource from other appropriate locations in the taxonomy in order to ensure that competing interpretations of the appropriate conceptual location for the resource are accommodated. Third, the formats for the ontologies and the resource descriptions should be published so enterprising software engineers can create interfaces for surfing, searching, and viewing the resources. The resulting distributed system of resource descriptions would be extensible, robust, and useful to the entire biomedical research community

A Semantic Web for bioinformatics: goals, tools, systems, applications

The quantity of biological information is increasing at an impressive rate. An integrated access to this huge amount of information requires complex search and retrieval software and automation of analysis processes. Automation of integration procedures mainly concerns how to link data, how to select and extract information and how to pipe retrieval and analysis steps. This automated approach to data analysis requires the adoption of new technologies and tools in the bioinformatics domain

SaDA: From Sampling to Data Analysis—An Extensible Open Source Infrastructure for Rapid, Robust and Automated Management and Analysis of Modern Ecological High-Throughput Microarray Data

One of the most crucial characteristics of day-to-day laboratory information management is the collection, storage and retrieval of information about research subjects and environmental or biomedical samples. An efficient link between sample data and experimental results is absolutely important for the successful outcome of a collaborative project. Currently available software solutions are largely limited to large scale, expensive commercial Laboratory Information Management Systems (LIMS). Acquiring such LIMS indeed can bring laboratory information management to a higher level, but most of the times this requires a sufficient investment of money, time and technical efforts. There is a clear need for a light weighted open source system which can easily be managed on local servers and handled by individual researchers. Here we present a software named SaDA for storing, retrieving and analyzing data originated from microorganism monitoring experiments. SaDA is fully integrated in the management of environmental samples, oligonucleotide sequences, microarray data and the subsequent downstream analysis procedures. It is simple and generic software, and can be extended and customized for various environmental and biomedical studies

Combining ontologies and workflows to design formal protocols for biological laboratories

Background Laboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of laboratory protocols two levels of formalization are needed: one for the entities and individuals operations involved in protocols and another one for the procedures, which can be manually or automatically executed. This study aims to combine ontologies and workflows for protocol formalization. Results A laboratory domain specific ontology and the COW (Combining Ontologies with Workflows) software tool were developed to formalize workflows built on ontologies. A method was specifically set up to support the design of structured protocols for biological laboratory experiments. The workflows were enhanced with ontological concepts taken from the developed domain specific ontology. The experimental protocols represented as workflows are saved in two linked files using two standard interchange languages (i.e. XPDL for workflows and OWL for ontologies). A distribution package of COW including installation procedure, ontology and workflow examples, is freely available from http://www.bmr-genomics.it/farm/cow webcite. Conclusions Using COW, a laboratory protocol may be directly defined by wet-lab scientists without writing code, which will keep the resulting protocol's specifications clear and easy to read and maintain

TRAIT (TRAnscript Integrated Table): a knowledgebase of human skeletal muscle transcripts.

Abstract Summary: TRAIT is a knowledgebase integrating information on transcripts with related data from genome, proteins, ortholog genes and diseases. It was initially built as a system to manage an EST-based gene discovery project on human skeletal muscle, which yielded over 4500 independent sequence clusters. Transcripts are annotated using automatic as well as manual procedures, linking known transcripts to public databases and unknown transcripts to tables of predicted features. Data are stored in a MySQL database. Complex queries are automatically built by means of a user-friendly web interface that allows the concurrent selection of many fields such as ontology, expression level, map position and protein domains. The results are parsed by the system and returned in a ranked order, in respect to the number of satisfied criteria. Availability: http://muscle.cribi.unipd.it and http://muscle.cribi.unipd.it/features/querystrait.html Contact: [email protected]; [email protected] * To whom correspondence should be addressed

I mobility scooter: da ausili per la mobilità di disabili e anziani a nuovi veicoli per una mobilità sostenibile?

I mobility scooter, in particolare quelli cabinati, sono potenzialmente un ausilio formidabile per la mobilità a breve e medio raggio delle persone sia abili che disabili, con innegabili benefici anche per il traffico urbano e l’ambiente, ma a condizione di una drastica revisione normativa. La modifica all’art. 46 del Codice della Strada intervenuta nel 2010, che ha demandato genericamente la definizione delle “macchine per uso di invalidi” (non considerate veicoli) a “vigenti disposizioni comunitarie” (che invece equiparano i mobility scooter ad autoveicoli), sembra aver sortito un risultato opposto al suo intento chiarificatore, con implicazioni finanche inquietanti per quanto riguarda la possibilità che i mobility scooter siano effettivamente ammessi a circolare in aree aperte al pubblico. Il recente decreto per la sperimentazione su strada dei dispositivi per la micromobilità elettrica, che ha ignorato il dispositivo obiettivamente più versatile, sicuro e “serio”, ha perso una grande occasione, ma si può ancora rimediare. La loro classificazione come “veicoli” adatti sia agli abili che ai disabili – anche ai sensi dell’orientamento comunitario – ed una specifica regolamentazione della loro circolazione nelle aree pubbliche attraverso una serie di modifiche al Codice della Strada, al suo Regolamento di attuazione ed al decreto per la sperimentazione su strada dei dispositivi di micromobilità elettrica, nonché l’individuazione di un organismo di controllo e informazione, porrebbero facilmente fine ad un pericoloso vuoto normativo ed alla confusione e disinformazione che ne sono derivate, favorendo finalmente la meritata diffusione dei mobility scooter: ciò contribuirebbe anche ad abbattere i costi d’acquisto dei moderni e versatili scooter cabinati, ancora relativamente elevati seppur inferiori a quelli di un’autovettura elettrica, a tutto vantaggio delle categorie spesso non abbienti per cui questi dispositivi sono stati originariamente concepiti

Agents in bioinformatics, computational and systems biology

The adoption of agent technologies and multi-agent systems constitutes an emerging area in bioinformatics. In this article, we report on the activity of the Working Group on Agents in Bioinformatics (BIOAGENTS) founded during the first AgentLink III Technical Forum meeting on the 2nd of July, 2004, in Rome. The meeting provided an opportunity for seeding collaborations between the agent and bioinformatics communities to develop a different (agent-based) approach of computational frameworks both for data analysis and management in bioinformatics and for systems modelling and simulation in computational and systems biology.The collaborations gave rise to applica- tions and integrated tools that we summarize and discuss in context of the state of the art in this area. We investigate on future challenges and argue that the field should still be explored from many perspectives ranging from bio-conceptual languages for agent-based simulation, to the definition of bio-ontology-based declarative languages to be used by information agents, and to the adoption of agents for computational grid

Use of Telemedicine Healthcare Systems in Pediatric Assistance at Territorial Level: Consensus Document of the Italian Society of Telemedicine (SIT), of the Italian Society of Preventive and Social Pediatrics (SIPPS), of the Italian Society of Pediatric Primary Care (SICuPP), of the Italian Federation of Pediatric Doctors (FIMP) and of the Syndicate of Family Pediatrician Doctors (SIMPeF)

Technological innovation can contribute to a reorganization of healthcare, particularly by supporting the shift in the focus of care from the hospital to the territory, through innovative citizen-centered models, and facilitating access to services in the territory. Health and social care delivery modalities, enabled by telemedicine, are crucial in this regard. The objective of this Consensus document, written by the main Italian Scientific Societies involved in the use of telemedicine in pediatrics, is to define a standard for its use at the territorial level in various declinations in the pediatric field; this paper also identifies priority areas for its application and the types of services that most require intervention and investment. The changes that are underway in digital transformation in all sectors are unstoppable, and for the digital transformation to take place in a productive sense, the contribution of not only all health professionals, but also of patients, is necessary. From this perspective, authors from different backgrounds were involved in the drafting of this Consensus and, in the future, other figures, primarily patients, are expected to be involved. In fact, this belongs to the vision of connected care, in which the citizen/patient actively participates in the treatment path so that they are assisted in a personalized, predictive and preventive way. The future scenario must be able to provide for the involvement of patients from the initial stages of planning any treatment path, even in the pediatric age, and increasing, where possible, the proximity of the health service to the families