Mapping the Gene Ontology Into the Unified Medical Language System

We have recently mapped the Gene Ontology (GO), developed by the Gene Ontology Consortium, into the National Library of Medicine's Unified Medical Language System (UMLS). GO has been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for integrating large numbers of disparate terminologies, primarily for the purpose of providing better access to biomedical information sources. The mapping of GO to UMLS highlighted issues in both terminology systems. After some initial explorations and discussions between the UMLS and GO teams, the GO was integrated with the UMLS. Overall, a total of 23% of the GO terms either matched directly (3%) or linked (20%) to existing UMLS concepts. All GO terms now have a corresponding, official UMLS concept, and the entire vocabulary is available through the web-based UMLS Knowledge Source Server. The mapping of the Gene Ontology, with its focus on structures, processes and functions at the molecular level, to the existing broad coverage UMLS should contribute to linking the language and practices of clinical medicine to the language and practices of genomics

Hvordan opplever erfarne lærere digitaliseringen av skolehverdagen?

Mastergradsoppgave i språk, kultur og digital kommunikasjon, Avdeling for lærerutdanning og naturvitenskap, Høgskolen i Hedmark, 2011.Norsk: Denne studien handler om hvordan fem erfarne lærere opplever digitaliseringen av hverdagen i den videregående skolen. Det er den avsluttende masteroppgaven i studiet ‟Språk, kultur og digital kommunikasjon‟ ved Høgskolen i Hedmark, og er forankret i en humanistisk tradisjon med fokuset på meningsskaping i det digitale samfunnet. I løpet av den tiden de fem lærere i undersøkelsen har vært yrkesaktive har samfunnet gjennomgått store forandringer og betingelsene for å utføre jobben som lærer har forandret seg. Etter Kunnskapsløftet i 2006 er digital kompetanse en av de grunnleggende ferdighetene som skolen i Norge skal jobbe med. De som jobber med ungdommer er i kontakt med brukere av de nyeste trendene og samfunnsmessige tendenser på kommunikasjonsfronten. Sosiale medier, "Web 2.0", 'digital natives – digital immigrants' og 'nettgenerasjonen' er en del av bakteppet til denne undersøkelsen. Studien er foretatt som en kasusstudie med semi-strukturerte personlige intervjuer med de fem lærerne både før og etter ulike digitale kompetansehevingskurs. Den kvalitative tilnærmingen er valgt for å komme så tett som mulig inn på hvordan disse fem forskjellige menneskene opplever forandringer i premissene for læreryrket. Målet med studien er å få et innblikk i en omstillingsprosess og få belyst utfordringene som den enkelte læreren opplever i det daglige arbeidet med ungdommer på videregående skole. På teorifronten dras det nytte av blant annet Michael Fullans arbeid med endringsprosesser i utdanningsinstitusjoner (Fullan, 2007), identitetskonsepter av Pierre Bourdieu og diskursbegrepet som utarbeidet av Michel Foucault. Resultatene av denne studien viser at erfarne lærere har forskjellige opplevelser når det gjelder utfordringene med å tilegne seg nye digitale kompetanser, men har til felles stor frustrasjon og bekymring over hvordan elevene bruker pc-en i klasserommet til andre aktiviteter enn læring. Alle opplever at kommunikasjonsmønstre i skolen og maktposisjoner i klasserommet er under forandring, og dette har innvirkning på hvordan de ser på læreridentiteten.English: This study looks at how five experienced teachers experience the process of digitalisation of the Norwegian school system. They all qualified as teachers in a pre-digital age, and have several years of teaching experience before the introduction of pc's into the classroom. The study is the final part of the Master of Language, Culture and Digital communication at the University College of Hedmark in Norway, a course of study which is based in a humanistic tradition concerned with investigating meaning-making in a digital environment. In the course of the working experience of these five teachers, society has undergone many changes. The Norwegian national educational reform of 2006 “Kunnskapsløftet” introduced digital skills as one of the core areas of the national curriculum and this has lead to changes in the teaching profession. Social media, “Web 2.0”, 'digital natives – digital immigrants', the 'net generation', are all part of the backdrop to this study, which has been undertaken as a case study using semi structured personal interviews as the method of data collection. The qualitative method was chosen in order to gain as close an understanding as possible of the personal experiences of the five participants. The aim of the study is to get as close an understanding as possible of how these teachers experience the changes in the teaching profession in their daily work in the upper secondary school. The theoretical background includes the work of Michael Fullan (2007) on the process of educational change, Peirre Bourdieu's work on identity and Michel Foucault on power structures in society. The results of this study show that although the participating teachers had varying experiences with their own personal learning experience with digital skills, they were all in agreement when it came to their concern for how their pupils use their computers on activities other than their school subjects during lesson time. They all experience that there are changes in modes of communication and power structures facing schools and society in the digital age that have an effect on how they view their own personal identity and that of the teaching profession

Cross-Product Extensions of the Gene Ontology

The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries

Survey-based naming conventions for use in OBO Foundry ontology development

A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data

How the gene ontology evolves.

BACKGROUND: Maintaining a bio-ontology in the long term requires improving and updating its contents so that it adequately captures what is known about biological phenomena. This paper illustrates how these processes are carried out, by studying the ways in which curators at the Gene Ontology have hitherto incorporated new knowledge into their resource. RESULTS: Five types of circumstances are singled out as warranting changes in the ontology: (1) the emergence of anomalies within GO; (2) the extension of the scope of GO; (3) divergence in how terminology is used across user communities; (4) new discoveries that change the meaning of the terms used and their relations to each other; and (5) the extension of the range of relations used to link entities or processes described by GO terms. CONCLUSION: This study illustrates the difficulties involved in applying general standards to the development of a specific ontology. Ontology curation aims to produce a faithful representation of knowledge domains as they keep developing, which requires the translation of general guidelines into specific representations of reality and an understanding of how scientific knowledge is produced and constantly updated. In this context, it is important that trained curators with technical expertise in the scientific field(s) in question are involved in supervising ontology shifts and identifying inaccuracies

Relations in biomedical ontologies

To enhance the treatment of relations in biomedical ontologies we advance a methodology for providing consistent and unambiguous formal definitions of the relational expressions used in such ontologies in a way designed to assist developers and users in avoiding errors in coding and annotation. The resulting Relation Ontology can promote interoperability of ontologies and support new types of automated reasoning about the spatial and temporal dimensions of biological and medical phenomena