National Center for Integrative Biomedical Informatics
{{Use dmy dates|date=April 2016}}
{{Primary sources|article|date=November 2010}}The National Center for Integrative Biomedical Informatics (NCIBI) is one of seven National Centers for Biomedical Computing funded by the National Institutes of Health's (NIH) Roadmap for Medical Research.[http://nihroadmap.nih.gov/bioinformatics/ The NIH Common Fund, Bioinformatics and Computational Biology][http://www.ncbcs.org/summary.html National Centers for Biomedical Computing, Summary] The center is based at the University of Michigan and is part of the Center for Computational Medicine and Bioinformatics. NCIBI's mission is to create targeted knowledge environments for molecular biomedical research to help guide experiments and enable new insights from the analysis of complex diseases. It was established in October 2005.
The Center develops computational methods to effectively access and integrate biological data. Driving Biological Projects (DBPs) provide a starting point from which tool development is informed, launched, and tested. Current DBPs include gene fusion in cancers, major organ-specific complications of diabetes, nutrition and obesity, and co-morbid disease associations of bipolar disorder. In addition to testing tools for function, a separate team is dedicated to testing usability and user interaction.
Once tools are developed and validated, the Center disseminates data and software throughout the University and the broader biomedical research community. Various mechanisms such as training videos,[https://www.youtube.com/user/NCIBI9 NCIBI YouTube Channel] tutorials,[http://portal.ncibi.org/gateway/virtual-workshop.html NCIBI Virtual Workshops] and demonstrations and presentations at prominent scientific conferences are used to share NCIBI data and software nationally and internationally.[http://portal.ncibi.org/gateway/presentations.html NCIBI Presentations]
Available tools
In addition to the tools listed below, the enriched data contained in many NCIBI databases is available from the Databases tab on the Try Our Tools page.[http://portal.ncibi.org/gateway/tryourtools.html NCIBI Try Our Tools page]
=Exploratory analysis=
=Conceptual literature searching=
class="wikitable" |
Name
! Description |
---|
BioSearch-2D
| A tool that renders the contents of large biomedical document collections into a single, dynamic map |
Gene2Mesh
| An automated annotation tool that associates Medical Subject Heading (MeSH) terms with genes using the National Library of Medicine's PubMed literature database |
Metab2MeSH
| A tool that uses a statistical approach to reliably and automatically annotate metabolites with the concepts defined in MeSH, the National Library of Medicine's controlled vocabulary for biomedical concepts |
MiSearch{{cite journal |last1=States |first1=D. J. |last2=Ade |first2=A. S. |last3=Wright |first3=Z. C. |last4=Bookvich |first4=A. V. |last5=Athey |first5=B. D. |title=MiSearch adaptive pubMed search tool |journal=Bioinformatics |volume=25 |issue=7 |pages=974–6 |year=2009 |pmid=18326507 |pmc=2660869 |doi=10.1093/bioinformatics/btn033}}
| A literature search tool that works with the National Center for Biotechnology Information's (NCBI) Entrez to rapidly search PubMed citations and display them ranked by relevancy to research interests |
PubAnatomy{{cite journal |last1=Xuan |first1=Weijian |last2=Dai |first2=Manhong |last3=Mirel |first3=Barbara |last4=Song |first4=Jean |last5=Athey |first5=Brian |last6=Watson |first6=Stanley J |last7=Meng |first7=Fan |title=Open Biomedical Ontology-based Medline exploration |journal=BMC Bioinformatics |volume=10 |pages=S6 |year=2009 |issue=Suppl 5 |doi=10.1186/1471-2105-10-S5-S6 |pmid=19426463 |pmc=2679406 |doi-access=free }}
| A literature exploration tool that provides new ways to explore relationships among anatomical structures, pathophysiological processes, gene expression levels and protein–protein interactions in the context of Medline literature and experimental data |
PubOnto
| A literature exploration tool that provides multiple ontologies from the Open Biomedical Ontologies to help researchers explore literature from different perspectives |
See also
Notes
{{Reflist}}
References
- {{cite journal |last1=Shannon |first1=P. |last2=Markiel |first2=A |last3=Ozier |first3=O |last4=Baliga |first4=NS |last5=Wang |first5=JT |last6=Ramage |first6=D |last7=Amin |first7=N |last8=Schwikowski |first8=B |last9=Ideker |first9=T |title=Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks |journal=Genome Research |volume=13 |issue=11 |pages=2498–504 |year=2003 |pmid=14597658 |pmc=403769 |doi=10.1101/gr.1239303 }}
External links
- [http://www.ncibi.org/ National Center for Integrative Biomedical Informatics homepage]
- [http://cytoscape.org/ Cytoscape]
{{authority control}}
Category:Research institutes in Michigan
Category:Medical research institutes in the United States
Category:Bioinformatics organizations