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 providing details on the people, policies, and issues being addressed in association with OBI. (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. (shrink)

Background: Food-borne outbreaks have been associated with sourcing unsafe food. Therefore, the first preventative strategy should be to source safe food. Even if the sourced food is safe, measures need to be put in place to ensure that it remains safe during the transfer, storage, preparation and serving activities that follow. An understanding of the ship food supply and transfer chain will help to illustrate the points at which the food can become contaminated en route to the point of consumption. (...) Objectives: The study was conducted in selected sea port in the core Niger Delta to assessed the microbiological quality of food served at different ship galley to crew and passengers and compared it to standard. Methods: Samples of food were taken from three (Port Harcourt Area one (PHSP), Warri (WSP) and Koko (KSP)) seaports within the South-South zone for laboratory analysis to uncover food spoilage microorganisms capable of causing disease outbreak among ship which could result to Transborder diseases. Eleven samples of different ready to eat food were collected from the locations, which included cooked rice; fried fish, irish potato porridge, vegetable soup, griki, pepper soup, fried irish potato, salad and bread were collected randomly. The samples were prepared and analyzed using standard procedures. Mean viable counts of aerobic and anaerobic bacteria were determined, ranging from (13×103cfu/g to 78×104 cfu/g) for ready to eat food. Results: Based on the finding KSP I, KSP J and KSP K food samples had the highest bacterial contamination on food while WSP F, WSP G and WSP H food samples had the least with the following isolates Salmonella spp, Nocardia spp, Shigella spp, Listeria spp, Bacillus cereus, Leuconostoc spp, Acinetobacter spp, Acetobacter spp, campylobacter spp, Clostridium spp and Vibrio spp which revealed that the isolates were susceptible to any of these antibiotics Septrin, Chloramphenicol, Gentamycin, Tarvid, Streptomycin, Reflacin, Augumetin, Ceporex, Nalidixic acid, Ampicillin, Ciproflox, Penicillin and Erythromycin. Conclusion: Thus, ships operators and regulatory body are expected to take all practicable measures to ensure that they do not receive unsafe or unsuitable food and maintain adequate food temperature at all time. (shrink)