SELECTED DATA/TEXT SOURCES, ONTOLOGIES, AND SYSTEMS

Data / Text / Information Sources

• NCBI
  The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information.

• GenBank
  

  GenBank^® is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.

• Pubmed
  PubMed comprises more than 21 million citations for biomedical articles from MEDLINE and life science journals. Citations may include links to full-text articles from PubMed Central or publisher web sites.

• Registry of standard biological parts
  The Registry is a continuously growing collection of genetic parts that can be mixed and matched to build synthetic biology devices and systems.

• Saccharomyces Genome Database
  SGD^TM is a scientific database of the molecular biology and genetics of the yeast Saccharomyces cerevisiae, which is commonly known as baker's or budding yeast.

• Worm Database
  Online bioinformatics database of the biology and genome of the model organism Caenorhabditis elegans (C. elegans) and related nematodes.
  • See Wormbase's User Guide.

Ontologies

• Gene Ontology
  The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases.

• PAMGO
  PAMGO extends Gene Ontology to include terms describing various processes related to microbe-host interactions.

• See Trends in Microbiology (July 2009 V. 17 Issue 7) for articles about uses and extensions of Gene Ontology in the microbial domain.

Data Source Integration, Platforms, and Existing Software

• Entrez cross-database search
  Simultaneously search multiple life sciences databases at the National Center for Biotechnology Information (NCBI).

• VBI Genome Browser
  The VBI Genome Browser is a tool that allows viewing of genomic data that adheres to the Genomics Unified Schema (GUSDB) data storage standard.

• GeneCards
  GeneCards is a searchable, integrated database of human genes that provides concise genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes.

• eTBLAST
  eTBLAST is a unique search engine for searching biomedical literature that lets you input an entire paragraph and returns MEDLINE abstracts that are similar to it.

• ISI Web of Knowledge
  ISI Web of Knowledge is an online academic database provided by Thomson Scientific.s Institute for Scientific Information. It provides access to many databases and other resources.

• W3C
  The World Wide Web Consortium (W3C) is an international community where member organizations, a full-time staff, and the public work together to develop web standards.

EMBL, NCBI

  ruiz@cs.wpi.edu