Amarnath Gupta | University of California, San Diego (original) (raw)

Papers by Amarnath Gupta

Research paper thumbnail of Content-Based Image Retrieval at the End of the Early Years

Pattern Analysis …, Jan 1, 2002

AbstractÐThe paper presents a review of 200 references in content-based image retrieval. The pape... more AbstractÐThe paper presents a review of 200 references in content-based image retrieval. The paper starts with discussing the working conditions of content-based retrieval: patterns of use, types of pictures, the role of semantics, and the sensory gap. Subsequent sections discuss computational steps for image retrieval systems.

Research paper thumbnail of Virage image search engine: an open framework for image management

Proceedings of …, Jan 1, 1996

Until recently, the management of large image databases has relied exclusively on manually entere... more Until recently, the management of large image databases has relied exclusively on manually entered alphanumeric annotations. Systems are beginning to emerge in both the research and commercial sectors based on 'content-based' image retrieval, a technique which explicitly ...

Research paper thumbnail of Visual Information Retrieval

Communications of the ACM, Jan 1, 1997

Amarnath Gupta (amarnath@virage.com) is a senior software scientist in Virage, Inc., a developer ... more Amarnath Gupta (amarnath@virage.com) is a senior software scientist in Virage, Inc., a developer and vendor of VIR systems in San Mateo, Calif.

Research paper thumbnail of XML-based information mediation with MIX

Proceedings of the …, Jan 1, 1999

Research paper thumbnail of Virage video engine

Proceedings of …, Jan 1, 1997

The temporal and multi-modal nature of video increases the dimensionality of content based retrie... more The temporal and multi-modal nature of video increases the dimensionality of content based retrieval problem. This places new demands on the indexing and retrieval tools required. The Virage Video Engine (VVE) with the default set of primitives provide the necessary frame ...

Research paper thumbnail of Emergent Semantics Through Interaction In Image Databases

Knowledge and Data Engineering, …, Jan 1, 2002

AbstractÐIn this paper, we briefly discuss some aspects of image semantics and the role that it p... more AbstractÐIn this paper, we briefly discuss some aspects of image semantics and the role that it plays for the design of image databases. We argue that images don't have an intrinsic meaning, but that they are endowed with a meaning by placing them in the context of other images and by the user interaction. From this observation, we conclude that, in an image, database users should be allowed to manipulate not only the individual images, but also the relation between them. We present an interface model based on the manipulation of configurations of images.

Research paper thumbnail of Collection-based persistent digital archives-part 1

D-Lib Magazine, Jan 1, 2000

The preservation of digital information for long periods of time is becoming feasible through the... more The preservation of digital information for long periods of time is becoming feasible through the integration of archival storage technology from supercomputer centers, data grid technology from the computer science community, information models from the digital library ...

Research paper thumbnail of Model-based mediation with domain maps

Data Engineering, 2001. …, Jan 1, 2001

We propose an extension to current view-based mediator systems called model-based mediation, in w... more We propose an extension to current view-based mediator systems called model-based mediation, in which views are defined and executed at the level of conceptual models (CMs) rather than at the structural level. Structural integration and lifting of data to the conceptual level is "pushed down" from the mediator to wrappers which in our system export classes, associations, constraints, and query capabilities of a source. Another novel feature of our architecture is the use of domain maps, semantic nets of concepts and relationships that are used to mediate across sources from multiple worlds (i.e., whose data are related in indirect and often complex ways). As part of registering a source's CM with the mediator, the wrapper creates a "semantic index" of its data into the domain map. We show that these indexes not only semantically correlate the multiple worlds data and thereby support the definition of the integrated CM, but that they are also useful during query processing, for example, to select relevant sources. A first prototype of the system has been implemented for a complex Neuroscience mediation problem.

Research paper thumbnail of In Search of Information In Visual Media

Communications of the ACM, Jan 1, 1997

Research paper thumbnail of Visual information retrieval technology: A virage perspective

white paper, Virage Inc, Jan 1, 1995

A significant event in the world of information systems in the past few years is the development ... more A significant event in the world of information systems in the past few years is the development of multimedia information systems. A multimedia information system goes beyond traditional database systems to incorporate various modes of non-textual digital data, such as digitized images and videos, in addition to textual information. It allows a user the same (or better) ease of use and flexibility of storage and access as traditional database systems. Today, thanks to an ever-increasing number of application areas like stock photography, medical imaging, digital video production, document imaging and so forth, gigabytes of image and video information are being produced every day. The need to handle this information has resulted in new technological requirements and challenges: s Image and video data are much more voluminous than text, and need supporting technology for rapid and efficient storage and retrieval.

Research paper thumbnail of E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains

Nature neuroscience, Jan 1, 2004

Imaging, from magnetic resonance imaging (MRI) to localization of specific macromolecules by micr... more Imaging, from magnetic resonance imaging (MRI) to localization of specific macromolecules by microscopies, has been one of the driving forces behind neuroinformatics efforts of the past decade. Many web-accessible resources have been created, ranging from simple data collections to highly structured databases. Although many challenges remain in adapting neuroscience to the new electronic forum envisioned by neuroinformatics proponents, these efforts have succeeded in formalizing the requirements for effective data sharing and data integration across multiple sources. 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 Research Network (BIRN).

Research paper thumbnail of Stack-based algorithms for pattern matching on dags

… of the 31st international conference on …, Jan 1, 2005

Existing work for query processing over graph data models often relies on pre-computing the trans... more Existing work for query processing over graph data models often relies on pre-computing the transitive closure or path indexes. In this paper, we propose a family of stack-based algorithms to handle path, twig, and dag pattern queries for directed acyclic graphs (DAGs) in particular. Our algorithms do not precompute the transitive closure nor path indexes for a given graph, however they achieve an optimal runtime complexity quadratic in the average size of the query variable bindings. We prove the soundness and completeness of our algorithms and present the experimental results.

Research paper thumbnail of Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease

Studies in health …, Jan 1, 2005

Through support from the National Institutes of Health&am... more Through support from the National Institutes of Health's National Center for Research Resources, the Biomedical Informatics Research Network (BIRN) is pioneering the use of advanced cyberinfrastructure for medical research. By synchronizing developments in advanced wide area networking, distributed computing, distributed database federation, and other emerging capabilities of e-science, the BIRN has created a collaborative environment that is paving the way for biomedical research and clinical information management. The BIRN Coordinating Center (BIRN-CC) is orchestrating the development and deployment of key infrastructure components for immediate and long-range support of biomedical and clinical research being pursued by domain scientists in three neuroimaging test beds.

Research paper thumbnail of Knowledge-based integration of neuroscience data sources

Scientific and Statistical …, Jan 1, 2000

The need for information integration is paramount in many biological disciplines, because of the ... more The need for information integration is paramount in many biological disciplines, because of the large heterogeneity in both the types of data involved and in the diversity of approaches (physiological, anatomical, biochemical, etc.) taken by biologists to study the same or correlated phenomena. However, the very heterogeneity makes the task of information integration very difficult since two approaches studying different aspects of the same phenomena may not even share common attributes in their schema description. This paper develops a wrapper-mediator architecture which extends the conventional data-and vieworiented information mediation approach by incorporating additional knowledge-modules that bridge the gap between the heterogeneous data sources. The semantic integration of the disparate local data sources employs F-logic as a data and knowledge representation and reasoning formalism. We show that the rich object-oriented modeling features of F-logic together with its declarative rule language and the uniform treatment of data and metadata (schema information) make it an ideal candidate for complex integration tasks. We substantiate this claim by elaborating on our integration architecture and illustrating the approach using real world examples from the neuroscience domain. The complete integration framework is currently under development; a first prototype establishing the viability of the approach is operational.

Research paper thumbnail of A cell-centered database for electron tomographic data

Journal of Structural …, Jan 1, 2002

Electron tomography is providing a wealth of 3D structural data on biological components ranging ... more Electron tomography is providing a wealth of 3D structural data on biological components ranging from molecules to cells. We are developing a web-accessible database tailored to high-resolution cellular level structural and protein localization data derived from electron tomography. The Cell Centered Database or CCDB is built on an object-relational framework using Oracle 8i and is housed on a server at the San Diego Supercomputer Center at the University of California, San Diego. Data can be deposited and accessed via a web interface. Each volume reconstruction is stored with a full set of descriptors along with tilt images and any derived products such as segmented objects and animations. Tomographic data are supplemented by high-resolution light microscopic data in order to provide correlated data on higher-order cellular and tissue structure. Every object segmented from a reconstruction is included as a distinct entity in the database along with measurements such as volume, surface area, diameter, and length and amount of protein labeling, allowing the querying of image-specific attributes. Data sets obtained in response to a CCDB query are retrieved via the Storage Resource Broker, a data management system for transparent access to local and distributed data collections. The CCDB is designed to provide a resource for structural biologists and to make tomographic data sets available to the scientific community at large. Ó

Research paper thumbnail of Integrating Gis and Imagery Through Xml-Based Information Mediation

Integrated Spatial Databases, Jan 1, 1999

Research paper thumbnail of BiologicalNetworks: visualization and analysis tool for systems biology

Nucleic acids research, Jan 1, 2006

Systems level investigation of genomic scale information requires the development of truly integr... more Systems level investigation of genomic scale information requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properties of genes or other database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes. Towards that goal, we recently constructed PathSys, a data integration platform for systems biology, which provides dynamic integration over a diverse set of databases [Baitaluk et al. (2006) BMC Bioinformatics 7, 55]. Here we describe a server, BiologicalNetworks, which provides visualization, analysis services and an information management framework over PathSys. The server allows easy retrieval, construction and visualization of complex biological networks, including genome-scale integrated networks of protein–protein, protein–DNA and genetic interactions. Most importantly, BiologicalNetworks addresses the need for systematic presentation and analysis of high-throughput expression data by mapping and analysis of expression profiles of genes or proteins simultaneously on to regulatory, metabolic and cellular networks. BiologicalNetworks Server is available at http://brak.sdsc.edu/pub/BiologicalNetworks.

Research paper thumbnail of The Cell-Centered Database

Neuroinformatics, Jan 1, 2003

The creation of structured shared data repositories for molecular data in the form of webaccessib... more The creation of structured shared data repositories for molecular data in the form of webaccessible databases like GenBank has been a driving force behind the genomic revolution. These resources serve not only to organize and manage molecular data being created by researchers around the globe, but also provide the starting point for data mining operations to uncover interesting information present in the large amount of sequence and structural data. To realize the full impact of the genomic and proteomic efforts of the last decade, similar resources are needed for structural and biochemical complexity in biological systems beyond the molecular level, where proteins and macromolecular complexes are situated within their cellular and tissue environments. In this review, we discuss our efforts in the develop-ment of neuroinformatics resources for managing and mining cell level imaging data derived from light and electron microscopy. We describe the main features of our web-accessible database, the Cell Centered Database (CCDB; http://ncmir.ucsd.edu/CCDB/), designed for structural and protein localization information at scales ranging from large expanses of tissue to cellular microdomains with their associated macromolecular constituents. The CCDB was created to make 3D microscopic imaging data available to the scientific community and to serve as a resource for investigating structural and macromolecular complexity of cells and tissues, particularly in the rodent nervous system.

Research paper thumbnail of The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience

Neuroinformatics, Jan 1, 2008

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, fle... more A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.

Research paper thumbnail of The neuroscience information framework: a data and knowledge environment for neuroscience

Neuroinformatics, Jan 1, 2008

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research,... more With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience's Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultantcollaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line.

Research paper thumbnail of Content-Based Image Retrieval at the End of the Early Years

Pattern Analysis …, Jan 1, 2002

AbstractÐThe paper presents a review of 200 references in content-based image retrieval. The pape... more AbstractÐThe paper presents a review of 200 references in content-based image retrieval. The paper starts with discussing the working conditions of content-based retrieval: patterns of use, types of pictures, the role of semantics, and the sensory gap. Subsequent sections discuss computational steps for image retrieval systems.

Research paper thumbnail of Virage image search engine: an open framework for image management

Proceedings of …, Jan 1, 1996

Until recently, the management of large image databases has relied exclusively on manually entere... more Until recently, the management of large image databases has relied exclusively on manually entered alphanumeric annotations. Systems are beginning to emerge in both the research and commercial sectors based on 'content-based' image retrieval, a technique which explicitly ...

Research paper thumbnail of Visual Information Retrieval

Communications of the ACM, Jan 1, 1997

Amarnath Gupta (amarnath@virage.com) is a senior software scientist in Virage, Inc., a developer ... more Amarnath Gupta (amarnath@virage.com) is a senior software scientist in Virage, Inc., a developer and vendor of VIR systems in San Mateo, Calif.

Research paper thumbnail of XML-based information mediation with MIX

Proceedings of the …, Jan 1, 1999

Research paper thumbnail of Virage video engine

Proceedings of …, Jan 1, 1997

The temporal and multi-modal nature of video increases the dimensionality of content based retrie... more The temporal and multi-modal nature of video increases the dimensionality of content based retrieval problem. This places new demands on the indexing and retrieval tools required. The Virage Video Engine (VVE) with the default set of primitives provide the necessary frame ...

Research paper thumbnail of Emergent Semantics Through Interaction In Image Databases

Knowledge and Data Engineering, …, Jan 1, 2002

AbstractÐIn this paper, we briefly discuss some aspects of image semantics and the role that it p... more AbstractÐIn this paper, we briefly discuss some aspects of image semantics and the role that it plays for the design of image databases. We argue that images don't have an intrinsic meaning, but that they are endowed with a meaning by placing them in the context of other images and by the user interaction. From this observation, we conclude that, in an image, database users should be allowed to manipulate not only the individual images, but also the relation between them. We present an interface model based on the manipulation of configurations of images.

Research paper thumbnail of Collection-based persistent digital archives-part 1

D-Lib Magazine, Jan 1, 2000

The preservation of digital information for long periods of time is becoming feasible through the... more The preservation of digital information for long periods of time is becoming feasible through the integration of archival storage technology from supercomputer centers, data grid technology from the computer science community, information models from the digital library ...

Research paper thumbnail of Model-based mediation with domain maps

Data Engineering, 2001. …, Jan 1, 2001

We propose an extension to current view-based mediator systems called model-based mediation, in w... more We propose an extension to current view-based mediator systems called model-based mediation, in which views are defined and executed at the level of conceptual models (CMs) rather than at the structural level. Structural integration and lifting of data to the conceptual level is "pushed down" from the mediator to wrappers which in our system export classes, associations, constraints, and query capabilities of a source. Another novel feature of our architecture is the use of domain maps, semantic nets of concepts and relationships that are used to mediate across sources from multiple worlds (i.e., whose data are related in indirect and often complex ways). As part of registering a source's CM with the mediator, the wrapper creates a "semantic index" of its data into the domain map. We show that these indexes not only semantically correlate the multiple worlds data and thereby support the definition of the integrated CM, but that they are also useful during query processing, for example, to select relevant sources. A first prototype of the system has been implemented for a complex Neuroscience mediation problem.

Research paper thumbnail of In Search of Information In Visual Media

Communications of the ACM, Jan 1, 1997

Research paper thumbnail of Visual information retrieval technology: A virage perspective

white paper, Virage Inc, Jan 1, 1995

A significant event in the world of information systems in the past few years is the development ... more A significant event in the world of information systems in the past few years is the development of multimedia information systems. A multimedia information system goes beyond traditional database systems to incorporate various modes of non-textual digital data, such as digitized images and videos, in addition to textual information. It allows a user the same (or better) ease of use and flexibility of storage and access as traditional database systems. Today, thanks to an ever-increasing number of application areas like stock photography, medical imaging, digital video production, document imaging and so forth, gigabytes of image and video information are being produced every day. The need to handle this information has resulted in new technological requirements and challenges: s Image and video data are much more voluminous than text, and need supporting technology for rapid and efficient storage and retrieval.

Research paper thumbnail of E-neuroscience: challenges and triumphs in integrating distributed data from molecules to brains

Nature neuroscience, Jan 1, 2004

Imaging, from magnetic resonance imaging (MRI) to localization of specific macromolecules by micr... more Imaging, from magnetic resonance imaging (MRI) to localization of specific macromolecules by microscopies, has been one of the driving forces behind neuroinformatics efforts of the past decade. Many web-accessible resources have been created, ranging from simple data collections to highly structured databases. Although many challenges remain in adapting neuroscience to the new electronic forum envisioned by neuroinformatics proponents, these efforts have succeeded in formalizing the requirements for effective data sharing and data integration across multiple sources. 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 Research Network (BIRN).

Research paper thumbnail of Stack-based algorithms for pattern matching on dags

… of the 31st international conference on …, Jan 1, 2005

Existing work for query processing over graph data models often relies on pre-computing the trans... more Existing work for query processing over graph data models often relies on pre-computing the transitive closure or path indexes. In this paper, we propose a family of stack-based algorithms to handle path, twig, and dag pattern queries for directed acyclic graphs (DAGs) in particular. Our algorithms do not precompute the transitive closure nor path indexes for a given graph, however they achieve an optimal runtime complexity quadratic in the average size of the query variable bindings. We prove the soundness and completeness of our algorithms and present the experimental results.

Research paper thumbnail of Biomedical informatics research network: building a national collaboratory to hasten the derivation of new understanding and treatment of disease

Studies in health …, Jan 1, 2005

Through support from the National Institutes of Health&am... more Through support from the National Institutes of Health's National Center for Research Resources, the Biomedical Informatics Research Network (BIRN) is pioneering the use of advanced cyberinfrastructure for medical research. By synchronizing developments in advanced wide area networking, distributed computing, distributed database federation, and other emerging capabilities of e-science, the BIRN has created a collaborative environment that is paving the way for biomedical research and clinical information management. The BIRN Coordinating Center (BIRN-CC) is orchestrating the development and deployment of key infrastructure components for immediate and long-range support of biomedical and clinical research being pursued by domain scientists in three neuroimaging test beds.

Research paper thumbnail of Knowledge-based integration of neuroscience data sources

Scientific and Statistical …, Jan 1, 2000

The need for information integration is paramount in many biological disciplines, because of the ... more The need for information integration is paramount in many biological disciplines, because of the large heterogeneity in both the types of data involved and in the diversity of approaches (physiological, anatomical, biochemical, etc.) taken by biologists to study the same or correlated phenomena. However, the very heterogeneity makes the task of information integration very difficult since two approaches studying different aspects of the same phenomena may not even share common attributes in their schema description. This paper develops a wrapper-mediator architecture which extends the conventional data-and vieworiented information mediation approach by incorporating additional knowledge-modules that bridge the gap between the heterogeneous data sources. The semantic integration of the disparate local data sources employs F-logic as a data and knowledge representation and reasoning formalism. We show that the rich object-oriented modeling features of F-logic together with its declarative rule language and the uniform treatment of data and metadata (schema information) make it an ideal candidate for complex integration tasks. We substantiate this claim by elaborating on our integration architecture and illustrating the approach using real world examples from the neuroscience domain. The complete integration framework is currently under development; a first prototype establishing the viability of the approach is operational.

Research paper thumbnail of A cell-centered database for electron tomographic data

Journal of Structural …, Jan 1, 2002

Electron tomography is providing a wealth of 3D structural data on biological components ranging ... more Electron tomography is providing a wealth of 3D structural data on biological components ranging from molecules to cells. We are developing a web-accessible database tailored to high-resolution cellular level structural and protein localization data derived from electron tomography. The Cell Centered Database or CCDB is built on an object-relational framework using Oracle 8i and is housed on a server at the San Diego Supercomputer Center at the University of California, San Diego. Data can be deposited and accessed via a web interface. Each volume reconstruction is stored with a full set of descriptors along with tilt images and any derived products such as segmented objects and animations. Tomographic data are supplemented by high-resolution light microscopic data in order to provide correlated data on higher-order cellular and tissue structure. Every object segmented from a reconstruction is included as a distinct entity in the database along with measurements such as volume, surface area, diameter, and length and amount of protein labeling, allowing the querying of image-specific attributes. Data sets obtained in response to a CCDB query are retrieved via the Storage Resource Broker, a data management system for transparent access to local and distributed data collections. The CCDB is designed to provide a resource for structural biologists and to make tomographic data sets available to the scientific community at large. Ó

Research paper thumbnail of Integrating Gis and Imagery Through Xml-Based Information Mediation

Integrated Spatial Databases, Jan 1, 1999

Research paper thumbnail of BiologicalNetworks: visualization and analysis tool for systems biology

Nucleic acids research, Jan 1, 2006

Systems level investigation of genomic scale information requires the development of truly integr... more Systems level investigation of genomic scale information requires the development of truly integrated databases dealing with heterogeneous data, which can be queried for simple properties of genes or other database objects as well as for complex network level properties, for the analysis and modelling of complex biological processes. Towards that goal, we recently constructed PathSys, a data integration platform for systems biology, which provides dynamic integration over a diverse set of databases [Baitaluk et al. (2006) BMC Bioinformatics 7, 55]. Here we describe a server, BiologicalNetworks, which provides visualization, analysis services and an information management framework over PathSys. The server allows easy retrieval, construction and visualization of complex biological networks, including genome-scale integrated networks of protein–protein, protein–DNA and genetic interactions. Most importantly, BiologicalNetworks addresses the need for systematic presentation and analysis of high-throughput expression data by mapping and analysis of expression profiles of genes or proteins simultaneously on to regulatory, metabolic and cellular networks. BiologicalNetworks Server is available at http://brak.sdsc.edu/pub/BiologicalNetworks.

Research paper thumbnail of The Cell-Centered Database

Neuroinformatics, Jan 1, 2003

The creation of structured shared data repositories for molecular data in the form of webaccessib... more The creation of structured shared data repositories for molecular data in the form of webaccessible databases like GenBank has been a driving force behind the genomic revolution. These resources serve not only to organize and manage molecular data being created by researchers around the globe, but also provide the starting point for data mining operations to uncover interesting information present in the large amount of sequence and structural data. To realize the full impact of the genomic and proteomic efforts of the last decade, similar resources are needed for structural and biochemical complexity in biological systems beyond the molecular level, where proteins and macromolecular complexes are situated within their cellular and tissue environments. In this review, we discuss our efforts in the develop-ment of neuroinformatics resources for managing and mining cell level imaging data derived from light and electron microscopy. We describe the main features of our web-accessible database, the Cell Centered Database (CCDB; http://ncmir.ucsd.edu/CCDB/), designed for structural and protein localization information at scales ranging from large expanses of tissue to cellular microdomains with their associated macromolecular constituents. The CCDB was created to make 3D microscopic imaging data available to the scientific community and to serve as a resource for investigating structural and macromolecular complexity of cells and tissues, particularly in the rodent nervous system.

Research paper thumbnail of The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience

Neuroinformatics, Jan 1, 2008

A critical component of the Neuroscience Information Framework (NIF) project is a consistent, fle... more A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.

Research paper thumbnail of The neuroscience information framework: a data and knowledge environment for neuroscience

Neuroinformatics, Jan 1, 2008

With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research,... more With support from the Institutes and Centers forming the NIH Blueprint for Neuroscience Research, we have designed and implemented a new initiative for integrating access to and use of Web-based neuroscience resources: the Neuroscience Information Framework. The Framework arises from the expressed need of the neuroscience community for neuroinformatic tools and resources to aid scientific inquiry, builds upon prior development of neuroinformatics by the Human Brain Project and others, and directly derives from the Society for Neuroscience's Neuroscience Database Gateway. Partnered with the Society, its Neuroinformatics Committee, and volunteer consultantcollaborators, our multi-site consortium has developed: (1) a comprehensive, dynamic, inventory of Web-accessible neuroscience resources, (2) an extended and integrated terminology describing resources and contents, and (3) a framework accepting and aiding concept-based queries. Evolving instantiations of the Framework may be viewed at http://nif.nih.gov, http://neurogateway.org, and other sites as they come on line.