Biomedical Engineering Reference
In-Depth Information
high-throughput data. Rawflow cytometry data (in the formof listmode data files) can
be used to cluster data automatically (without any researcher effort or intervention).
These methods are very similar to those used to analyze microarray data. Information
standards have been used for microarray data [159] and recently for flow cytometry
data, the latter providing the Minimum Information about a Flow Cytometry
Experiment (MIFlowCyt) [160] developed by a cross-disciplinary international group
comprising bioinformaticians to basic research scientists. Establishing the flow
cytometry minimal standard was based on understanding the fundamental concepts
of data acquisition workflows, including best practice in flow cytometry. The
MIFlowCyt standard includes recommendations for describing the specimens and
reagents included in the flow experiment, instrument configuration, and the data
processing protocols used to interpret the primary output data. MIFlowCyt has been
adopted as a standard by the International Society for Advancement of Cytometry
(ISAC).
To meet the immediate vision for a global exchange of flow cytometry data and
including the need to develop data repositories ensuring open access and data sharing
for the healthcare and research community, collaborative efforts are being taken to
build suitable data models with common ontologies and vocabulary [161]. The
Functional Genomics Experiment (FuGE) formalizes common aspects of compre-
hensive and high-throughput experiments across different biological technolo-
gies [162]. This has been extended to map MIFlowCyt terms into a FuGE object
model to accommodate flow cytometry data and metadata. These aspirations are
likely to develop alongside other major projects such as The Ontology for Biomedical
Investigations (OBI; http://purl.obolibrary.org/obo/obi) project that offers an inte-
grated ontology for the description of biological and clinical investigations. This
is a typical endeavor where the ontology supports the consistent annotation of
biomedical investigations. It is likely that as approaches such as FuGE roll out to
include microscopy and high-throughput imaging technologies, the community
meets an ideology for cytometry platform integration.
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