A set of ontologies to drive tools for the control of vector-borne diseases

We are developing a set of ontologies that deal with vector-borne diseases and the arthropod vectors that transmit them. For practical reasons (application priorities), we initiated this project with an ontology of insecticide resistance followed by a series of ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease transmission. These will be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide the community with a set of ontological tools that can be used both in the development of specific databases and, most importantly, in the construction of decision support systems to control these diseases

MIRO and IRbase: IT Tools for the Epidemiological Monitoring of Insecticide Resistance in Mosquito Disease Vectors

It is a historical fact that a successful campaign against vector populations is one of the prerequisites for effectively fighting and eventually eradicating arthropod-borne diseases, be that in an epidemic or, even more so, in endemic cases. Based mostly on the use of insecticides and environmental management, vector control is now increasingly hampered by the occurrence of insecticide resistance that manifests itself, and spreads rapidly, briefly after the introduction of a (novel) chemical substance. We make use here of a specially built ontology, MIRO, to drive a new database, IRbase, dedicated to storing data on the occurrence of insecticide resistance in mosquito populations worldwide. The ontological approach to the design of databases offers the great advantage that these can be searched in an efficient way. Moreover, it also provides for an increased interoperability of present and future epidemiological tools. IRbase is now being populated by both older data from the literature and data recently collected from field

IDOMAL: an ontology for malaria

<p>Abstract</p> <p>Background</p> <p>Ontologies are rapidly becoming a necessity for the design of efficient information technology tools, especially databases, because they permit the organization of stored data using logical rules and defined terms that are understood by both humans and machines. This has as consequence both an enhanced usage and interoperability of databases and related resources. It is hoped that IDOMAL, the ontology of malaria will prove a valuable instrument when implemented in both malaria research and control measures.</p> <p>Methods</p> <p>The OBOEdit2 software was used for the construction of the ontology. IDOMAL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium.</p> <p>Results</p> <p>The first version of the malaria ontology covers both clinical and epidemiological aspects of the disease, as well as disease and vector biology. IDOMAL is meant to later become the nucleation site for a much larger ontology of vector borne diseases, which will itself be an extension of a large ontology of infectious diseases (IDO). The latter is currently being developed in the frame of a large international collaborative effort.</p> <p>Conclusions</p> <p>IDOMAL, already freely available in its first version, will form part of a suite of ontologies that will be used to drive IT tools and databases specifically constructed to help control malaria and, later, other vector-borne diseases. This suite already consists of the ontology described here as well as the one on insecticide resistance that has been available for some time. Additional components are being developed and introduced into IDOMAL.</p

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics.

VectorBase (http://www.vectorbase.org) is a NIAID-supported bioinformatics resource for invertebrate vectors of human pathogens. It hosts data for nine genomes: mosquitoes (three Anopheles gambiae genomes, Aedes aegypti and Culex quinquefasciatus), tick (Ixodes scapularis), body louse (Pediculus humanus), kissing bug (Rhodnius prolixus) and tsetse fly (Glossina morsitans). Hosted data range from genomic features and expression data to population genetics and ontologies. We describe improvements and integration of new data that expand our taxonomic coverage. Releases are bi-monthly and include the delivery of preliminary data for emerging genomes. Frequent updates of the genome browser provide VectorBase users with increasing options for visualizing their own high-throughput data. One major development is a new population biology resource for storing genomic variations, insecticide resistance data and their associated metadata. It takes advantage of improved ontologies and controlled vocabularies. Combined, these new features ensure timely release of multiple types of data in the public domain while helping overcome the bottlenecks of bioinformatics and annotation by engaging with our user community

Establishment of computational biology in Greece and Cyprus: Past, present, and future.

We review the establishment of computational biology in Greece and Cyprus from its inception to date and issue recommendations for future development. We compare output to other countries of similar geography, economy, and size—based on publication counts recorded in the literature—and predict future growth based on those counts as well as national priority areas. Our analysis may be pertinent to wider national or regional communities with challenges and opportunities emerging from the rapid expansion of the field and related industries. Our recommendations suggest a 2-fold growth margin for the 2 countries, as a realistic expectation for further expansion of the field and the development of a credible roadmap of national priorities, both in terms of research and infrastructure funding

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms.

BACKGROUND: Genome sequencing of many eukaryotic pathogens and the volume of data available on public resources have created a clear requirement for a consistent vocabulary to describe the range of developmental forms of parasites. Consistent labeling of experimental data and external data, in databases and the literature, is essential for integration, cross database comparison, and knowledge discovery. The primary objective of this work was to develop a dynamic and controlled vocabulary that can be used for various parasites. The paper describes the Ontology for Parasite Lifecycle (OPL) and discusses its application in parasite research. RESULTS: The OPL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. The first version of the OPL models complex life cycle stage details of a range of parasites, such as Trypanosoma sp., Leishmaniasp., Plasmodium sp., and Shicstosoma sp. In addition, the ontology also models necessary contextual details, such as host information, vector information, and anatomical locations. OPL is primarily designed to serve as a reference ontology for parasite life cycle stages that can be used for database annotation purposes and in the lab for data integration or information retrieval as exemplified in the application section below. CONCLUSION: OPL is freely available at http://purl.obolibrary.org/obo/opl.owl and has been submitted to the BioPortal site of NCBO and to the OBO Foundry. We believe that database and phenotype annotations using OPL will help run fundamental queries on databases to know more about gene functions and to find intervention targets for various parasites. The OPL is under continuous development and new parasites and/or terms are being added.RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are

The splicing factor XAB2 interacts with ERCC1-XPF and XPG for R-loop processing

RNA splicing, transcription and the DNA damage response are intriguingly linked in mammals but the underlying mechanisms remain poorly understood. Using an in vivo biotinylation tagging approach in mice, we show that the splicing factor XAB2 interacts with the core spliceosome and that it binds to spliceosomal U4 and U6 snRNAs and pre-mRNAs in developing livers. XAB2 depletion leads to aberrant intron retention, R-loop formation and DNA damage in cells. Studies in illudin S-treated cells and Csb(m/m) developing livers reveal that transcription-blocking DNA lesions trigger the release of XAB2 from all RNA targets tested. Immunoprecipitation studies reveal that XAB2 interacts with ERCC1-XPF and XPG endonucleases outside nucleotide excision repair and that the trimeric protein complex binds RNA:DNA hybrids under conditions that favor the formation of R-loops. Thus, XAB2 functionally links the spliceosomal response to DNA damage with R-loop processing with important ramifications for transcription-coupled DNA repair disorders

VectorBase: a home for invertebrate vectors of human pathogens

VectorBase () is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes providing an integrated resource for the research community. Currently, VectorBase contains genome information for two organisms: Anopheles gambiae, a vector for the Plasmodium protozoan agent causing malaria, and Aedes aegypti, a vector for the flaviviral agents causing Yellow fever and Dengue fever

Ontology development to study tropical diseases

Ten years after the publication of the human genome, the functional analysis of human genes is still at an embryonic stage. The use of computers to analyze the increasing volume of the available data accelerated the process and underlined the necessity of bioinformatics into the modern research in the field of molecular biology. At the same time the need for new tools and new ways to semantically organize the available data it became obvious. The use of ontologies is a major step forward towards this direction. Within the frame of this work new ontologies have been created to describe the gross anatomy of mosquitoes, to facilitate detection and monitoring of insecticide resistance often observed in mosquito populations especially in the areas where spraying is the main measure for vector control and finally to describe malaria. Based on these ontologies new tools have been developed to facilitate gene annotation with anatomical terms. Moreover a new database to detect and monitor resistance in an area has been established based on our ontology and it has been adopted as a standard from various international efforts. Finally the malaria ontology created at IMBB resides at the heart of the malaria decision support system created by the innovative vector control consortium.Δέκα χρόνια μετά την αλληλούχιση του ανθρώπινου γονιδιώματος, παραμένει ζητούμενο ο ακριβής αριθμός και η λειτουργική ανάλυση των ανθρώπινων γονιδίων. Η ανάλυση του ολοένα και μεγαλύτερου όγκου διαθέσιμων δεδομένων με την βοήθεια ηλεκτρονικών υπολογιστών επιτάχυνε την διαδικασία και υπογράμμισε την αναγκαιότητα της βιοπληροφορική στην σύγχρονη βιολογική έρευνα. Ταυτόχρονα ανέδειξε την ανάγκη νέων εργαλείων και τρόπων οργάνωσης των βιολογικών δεδομένων. Η χρήση οντολογιών είναι κομβικό σημείο στην προσπάθεια αυτή. Στο πλαίσιο της παρούσας διατριβής δημιουργήθηκαν οντολογίες για: την περιγραφή της ανατομίας του κουνουπιού, την περιγραφή και τον έλεγχο της ανθεκτικότητας σε εντομοκτόνα που εμφανίζουν πληθυσμοί κουνουπιών και τέλος, για την ελονοσία. Με βάση αυτές τις οντολογίες αναπτύχθηκαν εργαλεία που δίνουν την δυνατότητα προσθήκης επισημειώσεων στις υπάρχουσες βάσεις δεδομένων για τον ιστό στον οποίο εκφράζονται συγκεκριμένα γονίδια, εμπλουτίζοντάς τες. Παράλληλα, καθιστούν δυνατή την παρακολούθηση και την ταυτοποίηση της εμφάνισης ανθεκτικότητας απέναντι στα εντομοκτόνα στους πληθυσμούς κουνουπιών κάποιας περιοχής. Τέλος αποτελούν την βάση γενικότερων πληροφοριακών συστημάτων που προσπαθούν να συνδυάσουν ετερογενείς πληροφορίες μεταξύ τους και είναι γνωστότερα σαν συστήματα υποστήριξης αποφάσεων. Η οντολογία της ελονοσίας που δημιουργήθηκε στο ΙΜΒΒ ήδη αποτελεί την βάση του αντίστοιχου συστήματος, ενώ η οντολογία και η βάση δεδομένων για την ανθεκτικότητα σε εντομοκτόνα έχει υιοθετηθεί σαν πρότυπο και από διεθνή προγράμματα και οργανισμού