Motivation: The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME ...specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. Results: Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. Availability: The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at . Release notes and annotation examples are provided. The MO is also provided via the NCICB's Enterprise Vocabulary System (). Contact:Stoeckrt@pcbi.upenn.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Motivation:Sites with substantive bioinformatics operations are challenged to build data processing and delivery infrastructure that provides reliable access and enables data integration. Locally ...generated data must be processed and stored such that relationships to external data sources can be presented. Consistency and comparability across data sets requires annotation with controlled vocabularies and, further, metadata standards for data representation. Programmatic access to the processed data should be supported to ensure the maximum possible value is extracted. Confronted with these challenges at the National Cancer Institute Center for Bioinformatics, we decided to develop a robust infrastructure for data management and integration that supports advanced biomedical applications. Results: We have developed an interconnected set of software and services called caCORE. Enterprise Vocabulary Services (EVS) provide controlled vocabulary, dictionary and thesaurus services. The Cancer Data Standards Repository (caDSR) provides a metadata registry for common data elements. Cancer Bioinformatics Infrastructure Objects (caBIO) implements an object-oriented model of the biomedical domain and provides Java, Simple Object Access Protocol and HTTP–XML application programming interfaces. caCORE has been used to develop scientific applications that bring together data from distinct genomic and clinical science sources. Availability: caCORE downloads and web interfaces can be accessed from links on the caCORE web site (http://ncicb.nci.nih.gov/core). caBIO software is distributed under an open source license that permits unrestricted academic and commercial use. Vocabulary and metadata content in the EVS and caDSR, respectively, is similarly unrestricted, and is available through web applications and FTP downloads. Supplementary information: http://ncicb.nci.nih.gov/core/publications contains links to the caBIO 1.0 class diagram and the caCORE 1.0 Technical Guide, which provide detailed information on the present caCORE architecture, data sources and APIs. Updated information appears on a regular basis on the caCORE web site (http://ncicb.nci.nih.gov/core).
Resumo O artigo trata de uma pesquisa exploratória com o objetivo de analisar o discurso da logomarca da Estratégia Saúde da Família (ESF) à luz do conceito de família contemporânea. A análise se deu ...pela teoria Semiolinguística de Patrick Charaudeau da Escola Francesa do Discurso. O resultado mostrou um quadro discursivo com importantes restrições quanto ao ato de linguagem como o aspecto monologal do processo e um sujeito de fala não institucional constituído pelo agente publicitário contratado pelo Ministério da Saúde. Na análise evidenciou-se uma discrepância entre o conteúdo verbal que mostra a expressão “Saúde da Família” tendendo à abrangência da política implementada pela ESF quando comparado à parte imagética cujos elementos demonstraram o predomínio da família tradicional. Trabalhou-se a relevância de múltiplos contextos como o cultural, o social e o de gênero que influenciam na interpretação de textos mistos. Apontou-se a necessidade de reformulação da marca para torná-la mais abrangente e condizente com os novos formatos de família na contemporaneidade. Sugere-se estudos futuros que explorem, de maneira mais crítica e incisiva, o caráter limitante implícito na visão da logomarca.
Abstract This article deals with exploratory research with the objective of analyzing the discourse of the Family Health Strategy (ESF) logo in the light of the concept of the contemporary family. The analysis was made using the “Semiolinguistic” theory of Patrick Charaudeau of the French School of Discourse. The result revealed a discursive framework with important restrictions regarding the act of language as the monologue aspect of the process and a subject of non-institutional speech constituted by the advertising agent hired by the Ministry of Health. In the analysis, a discrepancy was found between the verbal content that shows the expression “Family Health” tending to the comprehensiveness of the policy implemented by the ESF, when compared with the image aspect, the elements of which demonstrated the predominance of the traditional family. The relevance of multiple contexts, such as cultural, social and gender aspects, which influenced the interpretation of mixed texts, was studied. The need to reformulate the brand was pointed out to make it more comprehensive and consistent with the new contemporary family formats. Future studies are suggested that address the limiting character implicit in the concept behind the logo in a more critical and incisive manner.
Resumo O artigo trata de uma pesquisa exploratória com o objetivo de analisar o discurso da logomarca da Estratégia Saúde da Família (ESF) à luz do conceito de família contemporânea. A análise se deu ...pela teoria Semiolinguística de Patrick Charaudeau da Escola Francesa do Discurso. O resultado mostrou um quadro discursivo com importantes restrições quanto ao ato de linguagem como o aspecto monologal do processo e um sujeito de fala não institucional constituído pelo agente publicitário contratado pelo Ministério da Saúde. Na análise evidenciou-se uma discrepância entre o conteúdo verbal que mostra a expressão “Saúde da Família” tendendo à abrangência da política implementada pela ESF quando comparado à parte imagética cujos elementos demonstraram o predomínio da família tradicional. Trabalhou-se a relevância de múltiplos contextos como o cultural, o social e o de gênero que influenciam na interpretação de textos mistos. Apontou-se a necessidade de reformulação da marca para torná-la mais abrangente e condizente com os novos formatos de família na contemporaneidade. Sugere-se estudos futuros que explorem, de maneira mais crítica e incisiva, o caráter limitante implícito na visão da logomarca.
The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains ...are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed in association with OBI. The current release of OBI is available at http://purl.obolibrary.org/obo/obi.owl.
Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the ...adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems.
The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG.
The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development.
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