In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl. (shrink)

In recent years, sequencing technologies have enabled the identification of a wide range of non-coding RNAs (ncRNAs). Unfortunately, annotation and integration of ncRNA data has lagged behind their identification. Given the large quantity of information being obtained in this area, there emerges an urgent need to integrate what is being discovered by a broad range of relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a systematically structured and precisely defined controlled vocabulary for the (...) domain of ncRNAs, thereby facilitating the discovery, curation, analysis, exchange, and reasoning of data about structures of ncRNAs, their molecular and cellular functions, and their impacts upon phenotypes. The goal of NCRO is to serve as a common resource for annotations of diverse research in a way that will significantly enhance integrative and comparative analysis of the myriad resources currently housed in disparate sources. It is our belief that the NCRO ontology can perform an important role in the comprehensive unification of ncRNA biology and, indeed, fill a critical gap in both the Open Biological and Biomedical Ontologies (OBO) Library and the National Center for Biomedical Ontology (NCBO) BioPortal. Our initial focus is on the ontological representation of small regulatory ncRNAs, which we see as the first step in providing a resource for the annotation of data about all forms of ncRNAs. The NCRO ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/ncro.owl. (shrink)

Research has indicated that microRNAs (miRNAs), a special class of non-coding RNAs (ncRNAs), can perform important roles in different biological and pathological processes. miRNAs’ functions are realized by regulating their respective target genes (targets). It is thus critical to identify and analyze miRNA-target interactions for a better understanding and delineation of miRNAs’ functions. However, conventional knowledge discovery and acquisition methods have many limitations. Fortunately, semantic technologies that are based on domain ontologies can render great assistance in this regard. In our (...) previous investigations, we developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), to provide the community with common data elements and data exchange standards in the miRNA research. This paper describes (1) our continuing efforts in the OMIT ontology development and (2) the application of the OMIT to enable a semantic approach for knowledge capture of miRNA-target interactions. (shrink)

Identification of non-coding RNAs (ncRNAs) has been significantly enhanced due to the rapid advancement in sequencing technologies. On the other hand, semantic annotation of ncRNA data lag behind their identification, and there is a great need to effectively integrate discovery from relevant communities. To this end, the Non-Coding RNA Ontology (NCRO) is being developed to provide a precisely defined ncRNA controlled vocabulary, which can fill a specific and highly needed niche in unification of ncRNA biology.

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of (...) large amounts of ncRNA biological and clinical data. (shrink)

Recenze: Jean-Henri FABRE, Život pavouka. Praha: Volvox Globator 2011, 196 s..

Formal semantic analyses often take words to be minimal building blocks for the purposes of compositionality. But various recent theories of morphology and syntax have converged on the view that there is no demarcation line corresponding to the word level. The same conclusion has emerged from the compositional semantics of superlatives. In the spirit of extending compositionality below the word level, this paper explores how a small set of particles (Japanese KA and MO, Chinese DOU, and Hungarian VALA/VAGY, MIND, and (...) IS) form quantifier words and serve as connectives, additive and scalar particles, question markers, and existential verbs. The main question is whether the meanings of these particles across the varied environments are highly regular, or they are lexicalized with a variety of different meanings that bear a family resemblance. This paper does not reach definitive conclusions, but it raises analytical possibilities using Boolean semantics and the semantics of alternatives. It also draws attention to systematic similarities and some differences between MO and DOU that have not been studied in the literature. (shrink)

Text představuje aktivní role-playing jako výzkumnou experimentální metodu v sociálních vědách. Zasazuje role-playing do rámce simulačních výzkumných metod, rozkrývá jeho epistemo- logii a dosavadní metodologická uchopení zejména v sociální psychologii. Hlavní linií textu je obhajoba epistemologických kvalit metody a experimentu v sociálních vědách obecně. Inspiračním zdrojem je zde na jedné straně Latourova kvalitativní sociologie asociací, tázající se po původu sociality a problematizující samotný před- mět sociálních věd, tj. sociálno. A na druhé straně přístupy naturalizující sociálně- vědné výzkumy propojením s kognitivní (...) vědou. V tomto ohledu je naším klíčovým předpokladem pro smysluplné uchopení sociální reality v její simulované podobě shodnost kognitivních mechanismů skutečného i simulovaného jednání. V pojetí textu jsou oba zdroje spojeny jejich akcentem na tematizaci sociálna jako inter-psychologického fenoménu mezi tradiční mikro a makro úrovní. Analogií s Petriho miskou text promýšlí posunutí původní metody situační sociální psycho- logie směrem k využití konstruovaných diegetických liminálních situací jako svého druhu laboratoří sociálna. (shrink)