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

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

Disease Ontology: improving and unifying disease annotations across species.

Model organisms are vital to uncovering the mechanisms of human disease and developing new therapeutic tools. Researchers collecting and integrating relevant model organism and/or human data often apply disparate terminologies (vocabularies and ontologies), making comparisons and inferences difficult. A unified disease ontology is required that connects data annotated using diverse disease terminologies, and in which the terminology relationships are continuously maintained. The Mouse Genome Database (MGD, http://www.informatics.jax.org), Rat Genome Database (RGD, http://rgd.mcw.edu) and Disease Ontology (DO, http://www.disease-ontology.org) projects are collaborating to augment DO, aligning and incorporating disease terms used by MGD and RGD, and improving DO as a tool for unifying disease annotations across species. Coordinated assessment of MGD\u27s and RGD\u27s disease term annotations identified new terms that enhance DO\u27s representation of human diseases. Expansion of DO term content and cross-references to clinical vocabularies (e.g. OMIM, ORDO, MeSH) has enriched the DO\u27s domain coverage and utility for annotating many types of data generated from experimental and clinical investigations. The extension of anatomy-based DO classification structure of disease improves accessibility of terms and facilitates application of DO for computational research. A consistent representation of disease associations across data types from cellular to whole organism, generated from clinical and model organism studies, will promote the integration, mining and comparative analysis of these data. The coordinated enrichment of the DO and adoption of DO by MGD and RGD demonstrates DO\u27s usability across human data, MGD, RGD and the rest of the model organism database community. Dis Model Mech 2018 Mar 12;11(3):dmm032839

Wikidata and biomedical information.pdf

Wikidata and biomedical information presentation for Wikimania 2017, in Montreal, Canada

Paratransgenesis and ontology driven informatic tools: two different approaches to fight mosquito-borne diseases

The mosquito is one of the most dangerous organisms for the human, due to its ability to act as a vector to a multitude of diseases, e.g. malaria and dengue fever. There have been many attempts at combating those diseases in many decades, either looking at the problem from the side of the vector or from the side of the pathogen. Until recently, the main mode of defense against the vector was the use of insecticides, but we have reached a crucial point in the phenomenon of insecticide resistance. Thus, the scientific community is also starting to look into new avenues, one which is the method of paratransgenesis. Here, the suitability of Asaia sp. to act as an agent in this method was examined.In the last few decades the field of bioinformatics has come to aid in this field, through the development of a slew of IT tools and data bases, wherein the huge amounts of information that are constantly produced, can be stored. It is imperative that those tools can not only communicate with each other, but also with the data available right now, and in the future. The solution to this matter are ontologies. Having in mind all those facts, we decided to develop the ontology of dengue fever, so that it can act as a linchpin between all those tools.Το κουνούπι είναι ένας από τους πιο επικίνδυνους οργανισμούς για τον άνθρωπο, λόγω της ικανότητάς του να δρα ως φορέας σε διάφορες ασθένειες, όπως είναι η ελονοσία και ο δάγκειος πυρετός. Για δεκαετίες γίνονται προσπάθειες αντιμετώπισης των νόσων, είτε από πλευράς του φορέα, είτε από πλευράς του παθογόνου. Μέχρι πρόσφατα, ο κύριος τρόπος αντιμετώπισης του φορέα ήταν τα εντομοκτόνα. Έχουμε φτάσει όμως σε ένα κομβικό σημείο της ανθεκτικότητας και για αυτόν τον λόγο η επιστημονική κοινότητα έχει στραφεί και σε άλλες μεθόδους, όπως αυτή της παραδιαγένεσης. Στην παρούσα διατριβή εξετάστηκε η καταλληλότητα του Asaia sp. να δράσει ως παράγοντας σε αυτή τη μέθοδο.Τις τελευταίες δεκαετίες, στην προσπάθεια αντιμετώπισης του προβλήματος ήρθε να συμβάλει και η βιοπληροφορική, μέσω ανάπτυξης ενός πλήθους εργαλείων και της δημιουργίας βάσεων δεδομένων, όπου αποθηκεύεται ο τεράστιος όγκος πληροφοριών που παράγονται. Καθίσταται αναγκαίο τα εργαλεία αυτά να μπορούν να επικοινωνούν αφενός μεταξύ τους και αφετέρου με τα δεδομένα που υπάρχουν και που θα υπάρξουν μελλοντικά. Η λύση για αυτό το ζήτημα είναι οι οντολογίες. Με αυτό το σκεπτικό και στα πλαίσια αυτή της διατριβής αναπτύχθηκε η οντολογία του δάγκειου πυρετού, για να δράσει ως ο συνδετικός κρίκος ανάμεσα σε όλα αυτά τα εργαλεία

GSC and MIxS - Standards for genomic, metagenomic and marker gene sequence data

<p>An introduction to GSC (Genomic Standards Consortium) and MIxS (Minimal Information for any=x sequence) from the ICBO 2015 conference.</p

Describing the breakbone fever: IDODEN, an ontology for dengue fever.

BACKGROUND:Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate, among other things, the construction of optimized search engines. To address the need to expand the toolbox available for the control and prevention of vector-borne diseases we embarked on the construction of specific ontologies. We present here IDODEN, an ontology that describes dengue fever, one of the globally most important diseases that are transmitted by mosquitoes. METHODOLOGY/PRINCIPAL FINDINGS:We constructed IDODEN using open source software, and modeled it on IDOMAL, the malaria ontology developed previously. IDODEN covers all aspects of dengue fever, such as disease biology, epidemiology and clinical features. Moreover, it covers all facets of dengue entomology. IDODEN, which is freely available, can now be used for the annotation of dengue-related data and, in addition to its use for modeling, it can be utilized for the construction of other dedicated IT tools such as decision support systems. CONCLUSIONS/SIGNIFICANCE:The availability of the dengue ontology will enable databases hosting dengue-associated data and decision-support systems for that disease to perform most efficiently and to link their own data to those stored in other independent repositories, in an architecture- and software-independent manner

Wikidata: A platform for data integration and dissemination for the life sciences and beyond

An introduction into how Wikidata can be used as a semantic platform for the life sciences and beyond