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Toward an Ontological Database for Subcellular Neuroanatomy [chapter]

Amarnath Gupta, Stephen D. Larson, Christopher Condit, Sandeep Gupta, Lisa Fong, Li Chen, Maryann E. Martone
Advances in Conceptual Modeling – Foundations and Applications  
We present the semantic data model for an ontological database for subcellular anatomy for Neurosciences.  ...  ontological models in their databases.  ...  in developing ontology-based databases for neuroscience.  ... 
doi:10.1007/978-3-540-76292-8_8 dblp:conf/er/GuptaLCGFCM07 fatcat:ke4habueszb53myafdaygxr6ze

Informatics in neuroscience

L. French, P. Pavlidis
2007 Briefings in Bioinformatics  
The continuing development of standards for data exchange and interoperability, together with increasing awareness and acceptance of the importance of data sharing, are among the key efforts required to  ...  Acknowledgements The authors thank Jesse Gillis for input on computational neuroscience, and Bill Bug for suggestions on the manuscript.  ...  P.P. is supported by a career award from the Michael Smith Foundation for Health Research and a Human Brain Project grant from the National Institutes of Health (GM076990).  ... 
doi:10.1093/bib/bbm047 pmid:17932081 fatcat:2jeejrqeczhyzb7yzcv7cigncm

Terminology for Neuroscience Data Discovery: Multi-tree Syntax and Investigator-Derived Semantics

Daniel Gardner, David H. Goldberg, Bernice Grafstein, Adrian Robert, Esther P. Gardner
2008 Neuroinformatics  
Core NIF terminologies use a straightforward syntax designed for ease of use and for navigation by familiar web interfaces, and readily exportable to aid development of relational-model databases for neuroscience  ...  Datasets, data analysis tools, web resources, and other entities are characterized by multiple descriptors, each addressing core concepts, including data type, acquisition technique, neuroanatomy, and  ...  These included five Society for Neuroscience Presidents: Michael E. Goldberg, Bernice Grafstein, Edward G.  ... 
doi:10.1007/s12021-008-9029-7 pmid:18958630 pmcid:PMC2663521 fatcat:tmzuulzx3vdu3euurvy7hbqjea

A formal ontology of subcellular neuroanatomy

Stephen D. Larson
2007 Frontiers in Neuroinformatics  
In this paper, we describe the structure and content of a formal ontology whose scope is the subcellular anatomy of the nervous system (SAO), covering nerve cells, their parts, and interactions between  ...  In an effort to make better tools to assist humans in this endeavor, create a more accessible and permanent record of their data, and to aid the process of constructing complex and detailed computational  ...  Bushong for his help with glial cell types and Sarah M. Maynard for her help with biological entities relevant to neurodegenerative diseases.  ... 
doi:10.3389/neuro.11.003.2007 pmid:18974798 pmcid:PMC2525993 fatcat:tezok7nrgzfapcoehbutsr5zae

e-Neuroscience: challenges and triumphs in integrating distributed data from molecules to brains

Maryann E Martone, Amarnath Gupta, Mark H Ellisman
2004 Nature Neuroscience  
In this perspective, we discuss the importance of spatial systems and ontologies for proper modeling of neuroscience data and their use in a large-scale data integration effort, the Biomedical Informatics  ...  Many web-accessible resources have been created, ranging from simple data collections to highly structured databases.  ...  Further funding was provided by NSF grants supporting the National Partnership for Advanced Computational Infrastructure (NSF-ASC 97-5249 and MCB-9728338).  ... 
doi:10.1038/nn1229 pmid:15114360 fatcat:dy3ntxg5zfdlrepd5z27sktpbu

A knowledge based approach to matching human neurodegenerative disease and animal models

Sarah M. Maynard, Christopher J. Mungall, Suzanna E. Lewis, Fahim T. Imam, Maryann E. Martone
2013 Frontiers in Neuroinformatics  
with an advanced knowledge of neuroanatomy.  ...  As proof of concept, we built a Neurodegenerative Disease Phenotype Ontology (NDPO) and an associated Phenotype Knowledge Base (PKB) using an entity-quality model that incorporates descriptions for both  ...  with an advanced knowledge of neuroanatomy.  ... 
doi:10.3389/fninf.2013.00007 pmid:23717278 pmcid:PMC3653101 fatcat:d5tkyljc2bcqxacfycjkat4q34

The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience

William J. Bug, Giorgio A. Ascoli, Jeffrey S. Grethe, Amarnath Gupta, Christine Fennema-Notestine, Angela R. Laird, Stephen D. Larson, Daniel Rubin, Gordon M. Shepherd, Jessica A. Turner, Maryann E. Martone
2008 Neuroinformatics  
This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically Neuroinform (  ...  ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious.  ...  Some progress towards an automated solution has been achieved, as shown in the following example for the NIF Molecule module.  ... 
doi:10.1007/s12021-008-9032-z pmid:18975148 pmcid:PMC2743139 fatcat:5xu3gqt2hndotmmjru4xwnwaqu

An ontological approach to describing neurons and their relationships

David J. Hamilton, Gordon M. Shepherd, Maryann E. Martone, Giorgio A. Ascoli
2012 Frontiers in Neuroinformatics  
This article provides an overview of the problem and outlines a solution approach utilizing ontological characterizations.  ...  Progress toward this goal is hampered by the multiplicity of names for cells and by lack of a consensus on the criteria for defining neuron types.  ...  This work was supported in part by NIH R01 NS39600 and an INCF contract to Giorgio A. Ascoli, NIH R01 DC009977, NIDA SSSAB-2008, and R01 DC000086 to Gordon M.  ... 
doi:10.3389/fninf.2012.00015 pmid:22557965 pmcid:PMC3338117 fatcat:lowhh4moprd37kvatajqdnwgw4

Challenges and Opportunities in Mining Neuroscience Data

H. Akil, M. E. Martone, D. C. Van Essen
2011 Science  
To address the terminology problem, the NIF has assembled an expansive lexicon and ontology covering the broad domains of neuroscience by synthesizing open-access community ontologies (36) .  ...  The Neurolex and accompanying NIFSTD (NIF-standardized) ontologies provide definitions of over 50,000 concepts, using formal languages to represent brain regions, cells, subcellular structures, molecules  ... 
doi:10.1126/science.1199305 pmid:21311009 pmcid:PMC3102049 fatcat:aiy6d5motvc2hd3qn6f5ujmt7i

Application of neuroanatomical ontologies for neuroimaging data annotation

Turner
2010 Frontiers in Neuroinformatics  
This representation was also used to augment the neuroanatomical axis of RadLex, the ontology for clinical imaging.  ...  The annotation of functional neuroimaging results for data sharing and re-use is particularly challenging, due to the diversity of terminologies of neuroanatomical structures and cortical parcellation  ...  toward summarized, standardized results, as might be found in clinical reports of fMRI scans or from research databases (such as Bockholt et al., 2009 or Keator et al., 2008 .  ... 
doi:10.3389/fninf.2010.00010 pmid:20725521 pmcid:PMC2912099 fatcat:oodol6ftmndl5g5folq6uknbmi

NeuroLex.org: an online framework for neuroscience knowledge

Stephen D. Larson, Maryann E. Martone
2013 Frontiers in Neuroinformatics  
Today, few information systems are able to provide detailed answers to complex questions about neuroscience that account for multiple spatial scales, and which cross the boundaries of diverse parts of  ...  As a result, investigators still primarily seek answers to their questions in an increasingly densely populated collection of articles in the literature, each of which must be digested individually.  ...  Why work with ontologies instead of relying on databases?  ... 
doi:10.3389/fninf.2013.00018 pmid:24009581 pmcid:PMC3757470 fatcat:vveea5jjtjbrhdbgzx745vdhr4

Highlights from the Era of Open Source Web-Based Tools

Kristin R. Anderson, Julie A. Harris, Lydia Ng, Pjotr Prins, Sara Memar, Bengt Ljungquist, Daniel Fürth, Robert W. Williams, Giorgio A. Ascoli, Dani Dumitriu
2021 Journal of Neuroscience  
High digital connectivity and a focus on reproducibility are contributing to an open science revolution in neuroscience.  ...  Repositories and platforms have emerged across the whole spectrum of subdisciplines, paving the way for a paradigm shift in the way we share, analyze, and reuse vast amounts of data collected across many  ...  To achieve this, a protocol was established for systematic, standardized viral tracer injections, serial two-photon tomography imaging and an informatics pipeline to generate a large database of mouse  ... 
doi:10.1523/jneurosci.1657-20.2020 pmid:33472826 pmcid:PMC7880282 fatcat:gsdfjetgafboflmnr23txfywuy

Neuron Names: A Gene- and Property-Based Name Format, With Special Reference to Cortical Neurons

Gordon M. Shepherd, Luis Marenco, Michael L. Hines, Michele Migliore, Robert A. McDougal, Nicholas T. Carnevale, Adam J. H. Newton, Monique Surles-Zeigler, Giorgio A. Ascoli
2019 Frontiers in Neuroanatomy  
Using a tested format of parent-child relations for the region and subregion for naming a neuron, we show how the format can be extended so that these additional properties can become an explicit part  ...  of a neuron's identity and name, or archived in a linked properties database.  ...  ACKNOWLEDGMENTS grateful to the Editor and the reviewers for many valuable suggestions and for keeping the focus on the proposed neuron names.  ... 
doi:10.3389/fnana.2019.00025 pmid:30949034 pmcid:PMC6437103 fatcat:hrkahov67fb4rj64r6tji5fkru

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

Michael Hawrylycz, Jyl Boline, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky
2009 Nature Precedings  
All of the above should take into consideration existing solutions; for example, those demonstrated by BioMoby, myGrid and BIRN.  ...  Integration of databases has been an active research area for decades. Approaches vary depending on the level of autonomy each database retains. A commonly used approach is the database mediator.  ...  for the individual databases.  ... 
doi:10.1038/npre.2009.4000 fatcat:zgzee4e5ivfo5gt6ouemrwfdsu

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

Michael Hawrylycz, Jyl Boline, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky
2009 Nature Precedings  
All of the above should take into consideration existing solutions; for example, those demonstrated by BioMoby, myGrid and BIRN.  ...  Integration of databases has been an active research area for decades. Approaches vary depending on the level of autonomy each database retains. A commonly used approach is the database mediator.  ...  for the individual databases.  ... 
doi:10.1038/npre.2009.4000.1 fatcat:fezgneezbray5fwphzirvaw67a
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