Bioportal: Ontologies and integrated data resources at the click of the mouse

BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in OWL, RDF(S), OBO format, Protégé frames, and Rich Release Format. BioPortal functionality, driven by a service-oriented architecture, includes the ability to browse, search and visualize ontologies (Figure 1). The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content

Ontology Web Services for Semantic Applications

http://bioportal.bioontology.orgInternational audienceResearchers have turned to the Semantic Web to integrate, summarize, and interpret disparate knowledge. Ontologies provide the domain knowledge to drive such data integration and information retrieval, on the Semantic Web. The successful creation of semantic applications in the health and life sciences requires services that provide software applications with access to ontologies over the Web. The National Center for Biomedical Ontology (NCBO), one of seven National Centers for Biomedical Computing created under the NIH Roadmap, has developed BioPortal, which provides access to one of the largest repositories of biomedical ontologies both via Web browsers and Web services (via RESTful services). The BioPortal Ontology Web services allow programmatic access, download and traversal of ontologies in software applications, the NCBO Annotator Web service “tags” text automatically with terms from BioPortal ontologies, and the NCBO Resource Index provides an ontology based search of public data resources.The Ontology Web services provide access to ontologies, their characteristics, information about different versions, ontology downloads, navigation of the class hierarchy and details of each class. Developers can to embed this functionality in software applications, such as the Microsoft Word 2007’s Ontology Add-in, used to mark up a research article at the time of writing or ISAcreator, used to annotate experimental metadata. The NCBO Annotator Web service processes text to recognize relevant biomedical ontology terms. Users can customize the Web service to limit results to a particular ontology (e.g. SNOMED CT) or to a certain UMLS semantic type (e.g. T017 for ‘Anatomical Structure’). The concept recognition engine, MGREP, was developed by the National Center for Integrative Bioinformatics and is combined with BioPortal Ontology Web services to create the NCBO Annotator service to make the task of creating ontology-based annotations accessible for any biomedical researcher. BioPortal indexes several biomedical data repositories available online (e.g., GEO, ClinicalTrials.gov, PharmGKB) on the basis of their textual metadata, and links their records to ontology terms. These linkages take advantage of the semantic relationships in BioPortal, including subsumption relationships among ontology entities and mappings between entities in different ontologies. The NCBO Resource Index Web service allows biomedical investigators to use ontology terms to search programmatically the resulting index of online public repositories. For example, one can search for all experiments and clinical trials corresponding to ‘malignant melanoma’ from GEO and ClinicalTrials.gov.BioPortal offers researchers a one-stop shop on the Web for biomedical ontologies. The Web services provided by BioPortal are available at www.bioontology.org/wiki/index.php/NCBO_REST_services and the BioPortal technology is open-source and domain-independent

Culture conditions greatly impact the levels of vesicular and extravesicular Ago2 and RNA in extracellular vesicle preparations

Abstract Extracellular vesicle (EV)‐carried miRNAs can influence gene expression and functional phenotypes in recipient cells. Argonaute 2 (Ago2) is a key miRNA‐binding protein that has been identified in EVs and could influence RNA silencing. However, Ago2 is in a non‐vesicular form in serum and can be an EV contaminant. In addition, RNA‐binding proteins (RBPs), including Ago2, and RNAs are often minor EV components whose sorting into EVs may be regulated by cell signaling state. To determine the conditions that influence detection of RBPs and RNAs in EVs, we evaluated the effect of growth factors, oncogene signaling, serum, and cell density on the vesicular and nonvesicular content of Ago2, other RBPs, and RNA in small EV (SEV) preparations. Media components affected both the intravesicular and extravesicular levels of RBPs and miRNAs in EVs, with serum contributing strongly to extravesicular miRNA contamination. Furthermore, isolation of EVs from hollow fiber bioreactors revealed complex preparations, with multiple EV‐containing peaks and a large amount of extravesicular Ago2/RBPs. Finally, KRAS mutation impacts the detection of intra‐ and extra‐vesicular Ago2. These data indicate that multiple cell culture conditions and cell states impact the presence of RBPs in EV preparations, some of which can be attributed to serum contamination