The CAP cancer protocols – a case study of caCORE based data standards implementation to integrate with the Cancer Biomedical Informatics Grid

BACKGROUND: The Cancer Biomedical Informatics Grid (caBIG™) is a network of individuals and institutions, creating a world wide web of cancer research. An important aspect of this informatics effort is the development of consistent practices for data standards development, using a multi-tier approach that facilitates semantic interoperability of systems. The semantic tiers include (1) information models, (2) common data elements, and (3) controlled terminologies and ontologies. The College of American Pathologists (CAP) cancer protocols and checklists are an important reporting standard in pathology, for which no complete electronic data standard is currently available. METHODS: In this manuscript, we provide a case study of Cancer Common Ontologic Representation Environment (caCORE) data standard implementation of the CAP cancer protocols and checklists model – an existing and complex paper based standard. We illustrate the basic principles, goals and methodology for developing caBIG™ models. RESULTS: Using this example, we describe the process required to develop the model, the technologies and data standards on which the process and models are based, and the results of the modeling effort. We address difficulties we encountered and modifications to caCORE that will address these problems. In addition, we describe four ongoing development projects that will use the emerging CAP data standards to achieve integration of tissue banking and laboratory information systems. CONCLUSION: The CAP cancer checklists can be used as the basis for an electronic data standard in pathology using the caBIG™ semantic modeling methodology

Protégé: A Tool for Managing and Using Terminology in Radiology Applications

The development of standard terminologies such as RadLex is becoming important in radiology applications, such as structured reporting, teaching file authoring, report indexing, and text mining. The development and maintenance of these terminologies are challenging, however, because there are few specialized tools to help developers to browse, visualize, and edit large taxonomies. Protégé (http://protege.stanford.edu) is an open-source tool that allows developers to create and to manage terminologies and ontologies. It is more than a terminology-editing tool, as it also provides a platform for developers to use the terminologies in end-user applications. There are more than 70,000 registered users of Protégé who are using the system to manage terminologies and ontologies in many different domains. The RadLex project has recently adopted Protégé for managing its radiology terminology. Protégé provides several features particularly useful to managing radiology terminologies: an intuitive graphical user interface for navigating large taxonomies, visualization components for viewing complex term relationships, and a programming interface so developers can create terminology-driven radiology applications. In addition, Protégé has an extensible plug-in architecture, and its large user community has contributed a rich library of components and extensions that provide much additional useful functionalities. In this report, we describe Protégé’s features and its particular advantages in the radiology domain in the creation, maintenance, and use of radiology terminology

PubFocus: semantic MEDLINE/PubMed citations analytics through integration of controlled biomedical dictionaries and ranking algorithm

BACKGROUND: Understanding research activity within any given biomedical field is important. Search outputs generated by MEDLINE/PubMed are not well classified and require lengthy manual citation analysis. Automation of citation analytics can be very useful and timesaving for both novices and experts. RESULTS: PubFocus web server automates analysis of MEDLINE/PubMed search queries by enriching them with two widely used human factor-based bibliometric indicators of publication quality: journal impact factor and volume of forward references. In addition to providing basic volumetric statistics, PubFocus also prioritizes citations and evaluates authors' impact on the field of search. PubFocus also analyses presence and occurrence of biomedical key terms within citations by utilizing controlled vocabularies. CONCLUSION: We have developed citations' prioritisation algorithm based on journal impact factor, forward referencing volume, referencing dynamics, and author's contribution level. It can be applied either to the primary set of PubMed search results or to the subsets of these results identified through key terms from controlled biomedical vocabularies and ontologies. NCI (National Cancer Institute) thesaurus and MGD (Mouse Genome Database) mammalian gene orthology have been implemented for key terms analytics. PubFocus provides a scalable platform for the integration of multiple available ontology databases. PubFocus analytics can be adapted for input sources of biomedical citations other than PubMed

Swordfish bill injury involving abdomen and vertebral column: case report and review

<p>Abstract</p> <p>Background</p> <p>Penetrating injuries of the abdomen and spinal canal that involve organic material of animal origin are extremely rare and derive from domestic and wild animal attacks or fish attacks.</p> <p>Case presentation</p> <p>In this case report we present the unique, as far as the literature is concerned, unprovoked woman's injury to the abdomen by a swordfish. There are only four cases of swordfish attacks on humans in the literature - one resulted to thoracic trauma, two to head trauma and one to knee trauma, one of which was fatal - none of which were unprovoked. Three victims were professional or amateur fishermen whereas in the last reported case the victim was a bather as in our case. Our case is the only case where organic debris of animal's origin remained in the spinal canal after penetrating trauma.</p> <p>Conclusions</p> <p>Although much has been written about the management of penetrating abdominal and spinal cord trauma, controversy remains about the optimal management. Moreover, there is little experience in the management of patients with such spinal injuries, due to the fact that such cases are extremely rare. In this report we focus on the patient's treatment with regard to abdominal and spinal trauma and present a review of the literature.</p

OntoCAT -- simple ontology search and integration in Java, R and REST/JavaScript

<p>Abstract</p> <p>Background</p> <p>Ontologies have become an essential asset in the bioinformatics toolbox and a number of ontology access resources are now available, for example, the EBI Ontology Lookup Service (OLS) and the NCBO BioPortal. However, these resources differ substantially in mode, ease of access, and ontology content. This makes it relatively difficult to access each ontology source separately, map their contents to research data, and much of this effort is being replicated across different research groups.</p> <p>Results</p> <p>OntoCAT provides a seamless programming interface to query heterogeneous ontology resources including OLS and BioPortal, as well as user-specified local OWL and OBO files. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies. It is also available as a stand-alone MOLGENIS database and a Google App Engine application.</p> <p>Conclusions</p> <p>OntoCAT provides a robust, configurable solution for accessing ontology terms specified locally and from remote services, is available as a stand-alone tool and has been tested thoroughly in the ArrayExpress, MOLGENIS, EFO and Gen2Phen phenotype use cases.</p> <p>Availability</p> <p><url>http://www.ontocat.org</url></p

Subdural Effusions with Hydrocephalus after Severe Head Injury: Successful Treatment with Ventriculoperitoneal Shunt Placement: Report of 3 Adult Cases

Background. Subdural collections of cerebrospinal fluid (CSF) with associated hydrocephalus have been described by several different and sometimes inaccurate terms. It has been proposed that a subdural effusion with hydrocephalus (SDEH) can be treated effectively with a ventriculoperitoneal shunt (V-P shunt). In this study, we present our experience treating patients with SDEH without directly treating the subdural collection. Methods. We treated three patients with subdural effusions and hydrocephalus as a result of a head injury. All the patients were treated with a V-P shunt despite the fact that there was an extra-axial CSF collection with midline shift. Results. In all of the patients, the subdural effusions subsided and the ventricular dilatation improved in the postoperative period. The final clinical outcome remains difficult to predict and depends not only on the successful CSF diversion but also on the primary and secondary brain insult. Conclusion. Subdural effusions with hydrocephalus can be safely and effectively treated with V-P shunting, without directly treating the subdural effusion which subsides along with the treatment of hydrocephalus. However, it is extremely important to make an accurate diagnosis of an SDEH and differentiate this condition from other subdural collections which require different management