The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability

Abstract Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an “eXtensible Ontology Development” (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).https://deepblue.lib.umich.edu/bitstream/2027.42/140740/1/13326_2017_Article_169.pd

The cellular microscopy phenotype ontology

BACKGROUND: Phenotypic data derived from high content screening is currently annotated using free-text, thus preventing the integration of independent datasets, including those generated in different biological domains, such as cell lines, mouse and human tissues. DESCRIPTION: We present the Cellular Microscopy Phenotype Ontology (CMPO), a species neutral ontology for describing phenotypic observations relating to the whole cell, cellular components, cellular processes and cell populations. CMPO is compatible with related ontology efforts, allowing for future cross-species integration of phenotypic data. CMPO was developed following a curator-driven approach where phenotype data were annotated by expert biologists following the Entity-Quality (EQ) pattern. These EQs were subsequently transformed into new CMPO terms following an established post composition process. CONCLUSION: CMPO is currently being utilized to annotate phenotypes associated with high content screening datasets stored in several image repositories including the Image Data Repository (IDR), MitoSys project database and the Cellular Phenotype Database to facilitate data browsing and discoverability

Thematic issue of the Second combined Bio-ontologies and Phenotypes Workshop.

This special issue covers selected papers from the 18th Bio-Ontologies Special Interest Group meeting and Phenotype Day, which took place at the Intelligent Systems for Molecular Biology (ISMB) conference in Dublin in 2015. The papers presented in this collection range from descriptions of software tools supporting ontology development and annotation of objects with ontology terms, to applications of text mining for structured relation extraction involving diseases and phenotypes, to detailed proposals for new ontologies and mapping of existing ontologies. Together, the papers consider a range of representational issues in bio-ontology development, and demonstrate the applicability of bio-ontologies to support biological and clinical knowledge-based decision making and analysis.The full set of papers in the Thematic Issue is available at http://www.biomedcentral.com/collections/sig

Combinación de clustering, selección de atributos y métodos ontológicos para la clasificación semántica de texto

Con el aumento exponencial en la cantidad de datos textuales disponibles en Internet desde fuentes diversas como redes sociales, blogs/foros, sitios web, correos electrónicos, bibliotecas en línea, etc., se ha hecho necesaria la utilización de la Inteligencia Artificial en plataformas digitales, como la aplicación de métodos de aprendizaje profundo y de reconocimiento de patrones, para que esta información pueda ser aprovechada por todo tipo de modelos de negocios, estudios de mercado, planes de marketing, campañas políticas o toma de decisiones estratégicas entre otros, con la finalidad de hacer frente a la competencia y dar respuesta de manera eficiente. El objetivo de esta tesis doctoral fue desarrollar un modelo que combina clustering, selección de atributos y métodos ontológicos para la clasificación semántica de texto, que permita estructurar una metodología aplicable en conjuntos de datos textuales y así mejorar la clasificación automática de texto. El modelo propuesto en esta tesis doctoral se realizó siguiendo los siguientes objetivos específicos: redactar el estado del arte relacionado con la temática estudiada; conformación de un conjunto de datos textuales lo suficientemente extenso para la aplicación de las diferentes técnicas de análisis de datos; desarrollo de una metodología para la clasificación semántica de datos textuales y evaluación de los resultados obtenidos. La metodología consistió de 9 etapas, las 5 primeras (preprocesamiento, clustering, se- lección de atributos, clasificación y test estadístico. Posteriormente 4 etapas adicionales correspondientes análisis ontológico (validación del clúster, análisis semántico, interpretación y representación de relaciones). Se pudo determinar que haciendo SToWVector junto con selección de atributos mediante el wrapper MOES (estrategia de búsqueda) y NaiveBayesMultinomial (evaluador) con ACC (métrica), se obtienen mejores resultados con el clasificador NaiveBayesMultinomial que con otros métodos de clasificación evaluados. Además el método de búsqueda ENORA ha sido utilizado y evaluado demostrando ser un método eficaz para la selección de atributos en datos textuales. De igual manera se pudo dar significado a los dos clústeres obtenidos, logrando identificar un concepto para cada clúster. Clúster 1: UE-G20-G77-MEC y clúster 2: Resto del mundo. Ello permitió establecer una relación directa entre los clústers.With the exponential increase in the amount of textual data available on the Internet from various sources such as: social networks, blogs/forums, websites, emails, online libraries, etc. It has made necessary the use of artificial intelligence in digital platforms, the application of parallel processing, deep learning and pattern recognition so that this information can be used by all kinds of models business, market research, marketing plans, political campaigns or making strategic decisions among others, in order to deal with competition and respond efficiently. This doctoral thesis is focused on developing a model that allows combine clustering, attribute selection and ontological methods for the semantic classification of text, which allows tructuring an applicable methodology in textual data sets to improve the automatic classification of text. The model proposed in this doctoral thesis is carried out following the following specific objectives: draft the status of the art related to the theme studied, conformation of a set of textual data extensive enough for the application of different data analysis techniques, development of a methodology for the semantic classification of textual data and evaluation of the results obtained. The methodology consisted of 9 stages, the first 5 (preprocessing, clustering, attribute selection, classification, and statistical test. Finally, 4 additional stages corresponding to ontological analysis (cluster validation, semantic analysis, interpretation, and relationship representation). Could determine that by doing SToWVector together with feature selection using the MOES wrapper (search strategy) and NaiveBayesMultinomial (evaluator) with ACC (metric), better results are obtained with the NaiveBayesMultinomial classifier than with other classification methods evaluated, in addition, the ENORA search method has been used and evaluated, proving to be an effective method for the selection of attributes in text data. In the same way, it was possible to give meaning to the two clusters obtained, managing to identify a concept for each cluster. Cluster 1: EU−G20−G77−MEC and cluster 2: Rest of the world. This allowed us to establish a direct relationship between the clusters

EU US Roadmap Nanoinformatics 2030

The Nanoinformatics Roadmap 2030 is a compilation of state-of-the-art commentaries from multiple interconnecting scientific fields, combined with issues involving nanomaterial (NM) risk assessment and governance. In bringing these issues together into a coherent set of milestones, the authors address three recognised challenges facing nanoinformatics: (1) limited data sets; (2) limited data access; and (3) regulatory requirements for validating and accepting computational models. It is also recognised that data generation will progress unequally and unstructured if not captured within a nanoinformatics framework based on harmonised, interconnected databases and standards. The implicit coordination efforts within such a framework ensure early use of the data for regulatory purposes, e.g., for the read-across method of filling data gaps

Webulous and the Webulous Google Add-On - a web service and application for ontology building from templates

Background: Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such experts. As requests for new terms are made, the need for expert ontologists represents a bottleneck in the development process. Furthermore, the ability to rigorously enforce ontology design patterns in large, collaboratively developed ontologies is difficult with existing ontology authoring software.Description: We present Webulous, an application suite for supporting ontology creation by design patterns. Webulous provides infrastructure to specify templates for populating ontology design patterns that get transformed into OWL assertions in a target ontology. Webulous provides programmatic access to the template server and a client application has been developed for Google Sheets that allows templates to be loaded, populated and resubmitted to the Webulous server for processing.Conclusions: The development and delivery of ontologies to the community requires software support that goes beyond the ontology editor. Building ontologies by design patterns and providing simple mechanisms for the addition of new content helps reduce the overall cost and effort required to develop an ontology. The Webulous system provides support for this process and is used as part of the development of several ontologies at the European Bioinformatics Institute