Intelligence Information System in Bio-Nano Informatics

Introduction:formatting and handling figure references and
In the field of biomedical engineering, the biomedicalcitations [5]. Other tools and utilities incorporated into
informatics research, a major goal is to translatethe system are LaTeX2rtf for creating an output
lab-based research to bed-side patient care. The Keyformat that is readable by Microsoft Word and
technologies include genomic and proteomic datasMArTH , which gives users a friendly interface for
mining, sequence analysis, biomarker discovery, andcreating complex equations without having to learn
molecular pathway modeling.LaTeX syntax. The flexibility of our system is built
In year 2005 national cancer institute (NCI) establishinto the data model used in the reporting database.
national centre of cancer nanotechnology excellenceIn addition to text integration, we also use
(CCNE).The objective of CCNE is to combine cancervisualization to represent progress for different
biology with nanotechnology and informatics toprojects. All project results are designed to have a
deliver novel molecular imaging probes,web-based SVG representation.
nanotherapeutics, and biocomputing tools to treat,Each tool window is implemented using HTML frames,
detect and diagnose cancer.which allows for resizing and reorganizing the
In this project more than seventy faculty memberswindows.
and clinicians from biology, engineering, and clinicalNew Prototyping User Interface:
oncology are involved in this large-scale center [1]. ItFor new prototyping user interface contains data
has found from research results from these individualcollection and quality control, data analysis and
groups are shared with each other and are reportedmodeling and results interpretation also validation.
to the NCI periodically. To manage this informationThe upper left frame is the starting point, where
flow, it is important to develop advanced laboratorydata sets are uploaded or identified. For biomarker
information management systems (LIMS). Recent andselection; these data sets are most likely
current intelligence information management systemsoligonucleotide microarrays, mass spectrometry data,
aim to achieve the following objectivesor protein chips [6]. In the analysis window (top
1. To reduce administrative costs and redundancy; 2.center), the user can run high performance codes on
To develop laboratory methods to facilitate theour computing cluster. The example in Figure 3 shows
usage of laboratory instruments and reagents; 3. Toa visualization of a genetic algorithm that uses
integrate different instruments into an automatedpattern recognition to find markers in microarray
workflow architecture; 4. To facilitate datadata.
production, storing, mining, visualization; 5. To ensureThe results interpretation window (top right) shows a
data quality and accessibility to other scientists forweb service built on top of the Gene Ontology that
information dissemination; and 6. To report researchwill be updated to use a new gene significance
status to funding agencies as required.indicator. This new indicator will replace the pvalue
Above aim of intelligence information system showstatistics, which has been found by our work with
that, however, are not amenable to extension tocollaborators to be somewhat misleading because of
large research centers with this propose project [2].the incomplete state of the Gene Ontology. P-value
Furthermore, the nature of multidisciplinary andis also ill-suited for comparative studies.
collaborative projects specifically requires systems toThe information behind these blocks can be
address data heterogeneity, diverse health careintegrated to support knowledge-based text
cultures and traceability at various organizationalprocessing and mining. The final frame along the
levels.bottom shows an assortment of validation methods
Content:for biomarker discovery: confocal microscopy, tissue
Intelligence Information Processing System:staining, and fluorescent nanoparticles [7].
In hospital- oncology unit, faced with the specificThese results can be quantified, stored using the
needs as described above, it have need to developgeneral storage format mentioned in a previous
an intelligence-based, readily scalable informationsection, and can further contribute to the knowledge
processing and management system. This system willbase available to the analysis (or modeling) package.
assist data screening and integration by comparingDiscussion Propose Project:
with existing patents and literature, and will provide aThe design and implementation of this fully integrated
prioritized list based on requirement from users.data interpretation and integration system has its
Intelligence information system has evaluated threeorigins in knowledge-based text mining and
factors in design: usability, interoperability, andSVG-based visualization.
extensibility.This system has proven an important
The primary approach to extensibility is to makeaccomplishment in cancer nanotechnology center.
each piece of the design modular and to useAlso developing an interface to allow the Editor to do
common standards to represent inputs and outputsmore high-level reorganization before the report
to each module.compile and generation step is executed.
Following these three principles, Findings and results[8]For future work specific to CCNE, the plan is to
show that a designed and developed a newintegrate this reporting system with GForge, an
information system:open-source software bug tracking system that will
(a) That is simple, flexible, and adaptable to neworganize problems reported by users of our software
discoveries and (b)That has a multi-scale informationand report on the progress of our developers in
reporting hierarchy ranging from detailed technicalresolving those problems.
data to high-level executive summaries.Conclusion:
Although, also it is a web-based system that collectsAll in all, currently, the usability study metric is being
research progress updates from each researcher anddeveloped to quantitatively analyze the system
allows research leaders, directors, and managers toaccessibility to non-computer savy users. This
customize and generate status reports based onproposes project accomplish through Intelligence
predefined templates, reporting hierarchies, andInformation System for data management,
intelligent text mining and scoring methods [3]. Thisinterpretation, and for translation of new results to
system can be configured to deal with a variety ofclinical application.
dynamic collaborative efforts and yet is simpleReferences:
enough to be used by project teams with little[1] M. Steinlechner, W. Parson, “Automation and
computational expertise.high through-put for a DNA database laboratory:
This intelligence information system saves time anddevelopment of a laboratory information
allows researchers to focus more on their research.management system,” Croat Med J, vol. 42, no.
At the same time, the quality of their reports should3, pp. 252-255, 2001.
be improved because updates are submitted at the[2] H. Sanchez-Villeda, S. Schroeder, M. Polacco, M.
moment when researchers are focused on thatMcMullen, S. Havermann, G. Davis et al,
project rather than recalling and organizing them from“Development of an integrated laboratory
memory later.information management system for the maize
In this system, content cleaning, expansion ormapping project,” Bioinformatics, vol. 19, no. 16,
focusing will often take place on the side of thepp. 2022-2030, May 2003.
Editor, and this is to ensure that they have plenty of[3] M-M. Cordonnier-Pratt, C. Liang, H. Wang, D.S.
high-quality contents to work with. For example,Kolychev, F. Sun, R. Freeman, R. Sullican, L.H. Pratt,
figures may be required for certain update types on“MAGIC database and interfaces: an integrated
a per-member basis. The information will be scoredpackage for gene discovery and expression, ”
based on human knowledge such as scientificComp Funct Genom, vol. 5, pp. 268- 275, 2004.
importance, level of detail, urgency, etc. These[4] K. Thurow, B. Gode, U. Dingerdissen, N. Stoll,
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The key step for data integration is developed in the[5] Chang F. Quo, B. Wu, May D. Wang. Development
LAMP (Linux Apache mySQL PHP) web platform.of a Laboratory Information System for Cancer
Cascading Style Sheets (CSS) are used so that theCollaboration Projects. Proceedings of the 2005 IEEE
look and feel of the system can be easily modified toEngineering in Medicine and Biology 27th Annual
integrate within existing LIMS [4]. The email reminderConference. Shanghai,China. Sept. 2005.
system is dependent on being hosted on the Linux[6] P. A. Pevzner, Educating biologists in the 21st
Unix operation system as cron and sendmail are used.century: bioinformatics scientists versus bioinformatics
The LaTeX formatting standard is used to enhancetechnicians, Bioinformatics, 20 (2004), pp. 2159-2161.
the readability of reports.[7] P. Shafer, T. Isganitis and G. Yona, Hubs of
This formatting language has long been used in theknowledge: using the functional link structure in Biozon
scientific community to format papers for submissionto mine for biologically significant entities, Bmc
to conferences and journals and is thus a de factoBioinformatics, 7 (2006)
standard for this type of system. It has evaluated[8] Landau, R. H., D. Vediner, et al. (2002). "Future
the HTML standard, but found that it did not providescientific digital documents with MathML, XML, and
important features such as automated equationSVG." Computing in Science & Engineering 4(2): 77-85.