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iTools: a framework for classification, categorization and integration of computational biology resources.

PloS one | May 28, 2008

The advancement of the computational biology field hinges on progress in three fundamental directions--the development of new computational algorithms, the availability of informatics resource management infrastructures and the capability of tools to interoperate and synergize. There is an explosion in algorithms and tools for computational biology, which makes it difficult for biologists to find, compare and integrate such resources. We describe a new infrastructure, iTools, for managing the query, traversal and comparison of diverse computational biology resources. Specifically, iTools stores information about three types of resources--data, software tools and web-services. The iTools design, implementation and resource meta-data content reflect the broad research, computational, applied and scientific expertise available at the seven National Centers for Biomedical Computing. iTools provides a system for classification, categorization and integration of different computational biology resources across space-and-time scales, biomedical problems, computational infrastructures and mathematical foundations. A large number of resources are already iTools-accessible to the community and this infrastructure is rapidly growing. iTools includes human and machine interfaces to its resource meta-data repository. Investigators or computer programs may utilize these interfaces to search, compare, expand, revise and mine meta-data descriptions of existent computational biology resources. We propose two ways to browse and display the iTools dynamic collection of resources. The first one is based on an ontology of computational biology resources, and the second one is derived from hyperbolic projections of manifolds or complex structures onto planar discs. iTools is an open source project both in terms of the source code development as well as its meta-data content. iTools employs a decentralized, portable, scalable and lightweight framework for long-term resource management. We demonstrate several applications of iTools as a framework for integrated bioinformatics. iTools and the complete details about its specifications, usage and interfaces are available at the iTools web page http://iTools.ccb.ucla.edu.

Pubmed ID: 18509477 RIS Download

Mesh terms: Computational Biology | Databases, Factual | Internet | Systems Integration

Research resources used in this publication

None found

Research tools detected in this publication

Data used in this publication

None found

Associated grants

  • Agency: NIDA NIH HHS, Id: U54-DA021519
  • Agency: NCI NIH HHS, Id: U54-CA121852
  • Agency: NIGMS NIH HHS, Id: U54-GM072970
  • Agency: NIBIB NIH HHS, Id: U54 EB005149
  • Agency: NHGRI NIH HHS, Id: U54 HG004028
  • Agency: NIBIB NIH HHS, Id: U54-EB005149
  • Agency: NCRR NIH HHS, Id: U54-RR021813
  • Agency: NCI NIH HHS, Id: U54 CA121852
  • Agency: NCRR NIH HHS, Id: P41 RR013218
  • Agency: NLM NIH HHS, Id: U54 LM008748
  • Agency: NHGRI NIH HHS, Id: U54-HG004028
  • Agency: NCRR NIH HHS, Id: U54 RR021813
  • Agency: NLM NIH HHS, Id: U54-LM008748
  • Agency: NIDA NIH HHS, Id: U54 DA021519
  • Agency: NIGMS NIH HHS, Id: U54 GM072970

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This is a list of tools and resources that we have found mentioned in this publication.


Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.


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Internet Analysis Tools Registry

A centrally available listing of all image analysis tools that are available to the neuroscience community in order to facilitate the development, identification, and sharing of tools. It is hoped that this helps the tool developers to get their tools to a larger user community and to reduce redundancy (or at least utilize tool redundancy to facilitate optimal tool design) in tool development. This also helps tool users in identification of the existing tools for specific problems as they arise. The registry is designed to be self-moderated. This means that all tool entries are owned by some responsible party who enters the tool information, and keeps it up to date via the Web.


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