PubAnatomy 3D: Integrating Medline Exploration with the Allen Mouse Brain Atlas
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1
University of Michigan, United States
PubAnatomy 3D: Integrating Medline Exploration with the Allen Mouse Brain Atlas
Yang Gang1, Manhong Dai1, Jean Song2, Barbara Mirel3, Fan Meng1,4,5
1Molecular and Behavioral Neuroscience Institute, 2Health Sciences Library, 3School of Education, 4Psychiatry Department and 5Center for Computational Medicine and Bioinformatics, University of Michigan
Neurobiology data generated by the big science approaches, such the Allen brain atlases and the NIH Human Connectome Project, provide the opportunity for understanding how brain works at both molecular and anatomical levels with unprecedented resolution and completeness. For example, researchers can now use the Brain Explorer and the NeuroBlast tools developed by the Allen Institute for Brain Science to explore genes and their spatial expression pattern across the whole brain for learning the potential biological implications of genes identified in their experiments as well as designing follow-up experiments, such as knockout/knockin mouse for modeling human diseases. However, since it is impossible for individual scientists to grasp all the known functional roles of genes, anatomical structures and the functional relationships among them, researchers frequently need to perform literature searches to guide such big brain data set explorations. Similarly, literature exploration can also benefit significantly from the relationships among genes and anatomical structures presented in such data sets. The need to use two separate data exploration tools such as the Brain Explorer and PubMed leads to technical hurdles as well as gaps in the thinking process that can significantly constrain the hypothesis development process.
PubAnatomy is 3D is designed to provide a seamless exploration environment across the Allen Mouse Atlas data and the Medline literature for iterative data- and literature guided hypothesis development. We mapped genes and anatomical structures in the Allen Mouse Atlas data set to individual Medline records and developed a flexible web-based search interface for iterative Medline and mouse atlas data exploration. A typical use case is a researcher starting with Medline search for their interested topic, such as diseases and brain structures (Fig 1, upper part), to obtain a list of Medline records, which is annotated with different concept categories such as genes as well as summary statistics such as number of Medline records associated with each gene in the search results (Fig 1, lower part). Researchers can use the summary statistics, various filtering criteria as well as the content of relevant Medline records to select genes and anatomical structures they want to explore through simple drag-and-drop for 3D brain exploration (Fig2). Besides displaying the voxel level data for selected brain structures, users can also select multiple arbitrary 2D intersections in the coronal and sagittal directions to view the raw in situ images together with brain structure annotations for each 2D intersection (Fig 3). Two or more genes can be displayed side-by-side for detailed raw in situ data inspection (Fig 4). Users can use new structures or additional genes identified in the exploration process to filter Medline research results or start new search/modify existing search through simple drag-and-drop, greatly facilitating the iterative literature and data exploration during hypothesis development.
Pubanatomy3D is available at http://brainarray.mbni.med.umich.edu/PubAnatomy3D/. We plan to define and publish the Application Programming Interface for Pubanatomy 3D to enable third party developers to access data and functions PubAnatomy as well as passing their own data such as gene or SNP lists to PubAnatomy 3D. We will also integrate more data sets, such as connectome, pathway and protein interaction, Gene Ontology, etc. into PubAnatomy to further enhance its usefulness for hypothesis development in neurobiology.
Acknowledgements
This project is supported by NIH grant 1R01LM009812 and the Pritzker Neuropsychiatric Disorders Research Consortium.
Keywords:
MEDLINE,
Brain Atlas,
Gene Expression,
Anatomy,
exploration
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Oral presentation
Topic:
General neuroinformatics
Citation:
Yang
G,
Dai
M,
Song
J,
Mirel
B and
Meng
F
(2013). PubAnatomy 3D: Integrating Medline Exploration with the Allen Mouse Brain Atlas.
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00082
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Received:
07 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Mr. Gang Yang, University of Michigan, Ann Arbor, United States, flashflexpro@gmail.com
Mr. Fan Meng, University of Michigan, Ann Arbor, United States, mengf@umich.edu