caCORE: A common infrastructure for cancer informatics

Covitz, Peter A.; Hartel, Frank W.; Schaefer, Carl F.; Coronado, Sherri de; Fragoso, Gilberto; Sahni, Himanso; Gustafson, Scott F.; Buetow, Kenneth H.

doi:10.1093/bioinformatics/btg335

Cited by 123 publications

(81 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…9 This tool provides users with a web-based interface for data entry by using caBIG semantics that standardizes biospecimen vocabularies for quality assurance and query interfaces which allow scientists to search the collection of stored samples to request distribution of samples for scientific investigations. 11 One of the primary benefits of caTissue is the ability of multiple sites throughout Puerto Rico to enter biospecimens preliminary data before their shipment to Ponce for acquisition and storage, whereas the maintenance of the software and hardware are centralized at PSMHS. The final step of deployment will be connecting caTissue Suite to caGrid and establish the grid node to permit data sharing with the caBIG network and allow MCC to query and extract data from the PSMHS instance.…”

Section: Data Management Integration and Maintenancementioning

confidence: 99%

The Establishment of the First Cancer Tissue Biobank at a Hispanic-Serving Institution: A National Cancer Institute–Funded Initiative between Moffitt Cancer Center in Florida and the Ponce School of Medicine and Health Sciences in Puerto Rico

Flores

Muñoz-Antonia²,

Matta³

et al. 2011

Biopreservation and Biobanking

View full text Add to dashboard Cite

Section: Data Management Integration and Maintenancementioning

confidence: 99%

The Establishment of the First Cancer Tissue Biobank at a Hispanic-Serving Institution: A National Cancer Institute–Funded Initiative between Moffitt Cancer Center in Florida and the Ponce School of Medicine and Health Sciences in Puerto Rico

Flores

Muñoz-Antonia²,

Matta³

et al. 2011

Biopreservation and Biobanking

View full text Add to dashboard Cite

“…Purely technical means thus cannot solve it, but they may help. A number of projects have attempted to combat interoperability problems, among them BioMOBY, TAMBIS [47] and caBIO [48]. A newcomer is SADI (sadiframework.org, [46]), a framework based on the Semantic Web standards RDF and OWL to enable use of OWL reasoners and SPARQL.…”

Section: (I) Interoperabilitymentioning

confidence: 99%

e-BioFlow: Improving Practical Use of Workflow Systems in Bioinformatics

Wassink

Ooms

Neerincx

et al. 2010

Information Technology in Bio- And Medical Informatics, ITBAM 2010

View full text Add to dashboard Cite

Abstract. Workflow management systems (WfMSs) are useful tools for bioinformaticians. As experiences with using WfMSs accumulate, shortcomings of current systems become apparent. In this paper, we focus on practical issues that hinder WfMS users and that arise in the design and execution of workflows, and in access of web services. We present e-BioFlow, a workflow engine that demonstrates in which way a number of these problems can be solved. e-BioFlow offers an improved user interface, can deal with large data volumes, stores all provenance, and has a powerful provenance browser. e-BioFlow also offers the possibility to design and run workflows step by step, allowing its users an explorative research style.

show abstract

“…Previous projects, specifically in the bio/medical domain, that have attempted to achieve deep interoperability include caBIO (Covitz et al, 2003) and TAPIR (De Giovanni et al, 2010). The former created a rich SOAP-based API, enforcing a common interface over all repositories.…”

Section: Introductionmentioning

confidence: 99%

Interoperability and FAIRness through a novel combination of Web technologies

Wilkinson

Verborgh

Santos³

et al. 2017

PeerJ Computer Science

View full text Add to dashboard Cite

Data in the life sciences are extremely diverse and are stored in a broad spectrum of repositories ranging from those designed for particular data types (such as KEGG for pathway data or UniProt for protein data) to those that are general-purpose (such as FigShare, Zenodo, Dataverse or EUDAT). These data have widely different levels of sensitivity and security considerations. For example, clinical observations about genetic mutations in patients are highly sensitive, while observations of species diversity are generally not. The lack of uniformity in data models from one repository to another, and in the richness and availability of metadata descriptions, makes integration and analysis of these data a manual, time-consuming task with no scalability. Here we explore a set of resource-oriented Web design patterns for data discovery, accessibility, transformation, and integration that can be implemented by any general-or specialpurpose repository as a means to assist users in finding and reusing their data holdings. We show that by using off-the-shelf technologies, interoperability can be achieved atthe level of an individual spreadsheet cell. We note that the behaviours of this architecture compare favourably to the desiderata defined by the FAIR Data Principles, and can therefore represent an exemplar implementation of those principles. The proposed interoperability design patterns may be used to improve discovery and integration of both new and legacy data, maximizing the utility of all scholarly outputs.

show abstract

caCORE: A common infrastructure for cancer informatics

Cited by 123 publications

References 13 publications

The Establishment of the First Cancer Tissue Biobank at a Hispanic-Serving Institution: A National Cancer Institute–Funded Initiative between Moffitt Cancer Center in Florida and the Ponce School of Medicine and Health Sciences in Puerto Rico

The Establishment of the First Cancer Tissue Biobank at a Hispanic-Serving Institution: A National Cancer Institute–Funded Initiative between Moffitt Cancer Center in Florida and the Ponce School of Medicine and Health Sciences in Puerto Rico

e-BioFlow: Improving Practical Use of Workflow Systems in Bioinformatics

Interoperability and FAIRness through a novel combination of Web technologies

Contact Info

Product

Resources

About