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 23 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.

• OMIM
  OMIM ^® (Online Mendelian Inheritance in Man ^® ) is a comprehensive, authoritative, and timely compendium of human genes and genetic phenotypes.

• UniProt
  The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information. (See "what we provide" and "site tour".)

• 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.

• EMBL
  The EMBL Nucleotide Sequence Database (also known as EMBL-Bank) constitutes Europe's primary nucleotide sequence resource.

• 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.

• 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.

• Medical/Clinical Datasets:

  • Physionet
    Research resource for complex physiologic signals.

  • UCI's Cardiotocography Data Set

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.

Information Source Integration, Platforms, and Existing Software

• GQuery: Global cross-database NCBI search
  Simultaneously search multiple life sciences databases at the National Center for Biotechnology Information (NCBI). (Formerly known as "Entrez"?)

• 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.

• iHOP
  Information Hyperlinked Over Proteins. Gene centric search Engine.

• EBIMed
  EBIMed is a web application that combines Information Retrieval and Extraction from MEDLINE

• GoPubMed
  Clusters documents based on Gene/MesH Ontology

• Textpresso
  The Textpresso project serves the biological and biomedical research community by providing: (1) Full text literature searches of model organism research and subject-specific articles at individual sites. (2) Text classification and mining of biomedical literature for database curation. (3) Linking biological entities in PDF and online journal articles to online databases.

• MeSH
  U.S. National Library of Medicine's Medical Subject Headings.

• ABNER: A Biomedical Named Entity Recognizer
  ABNER is a software tool for molecular biology text analysis.

• The Stanford Natural Language Processing Group
  Their research has resulted in state-of-the-art technology for robust, broad-coverage natural-language processing in many languages. These technologies include a part-of-speech tagger; a high performance probabilistic parser; a competition-winning biological named entity recognition system; and algorithms for processing Arabic, Chinese, and German text.

• 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.

OTHER USEFUL BIOINFORMATICS COURSE WEBSITES

• Prof. Kellis' Algorithms for Computational Biology course (MIT)

• Profs. Alterovitz's, Kellis', and Ramoni's Bioinformatics and Proteomics course (MIT)

• Prof. Yemini's Computational Genomics course (Columbia Univ.)

• Prof. Mneimneh's Computational Biology course (Hunter College)

• Prof. Moran's Algorithms in Computational Biology course (Technion Univ.)

• Prof. Subramanian's From Sequence to Structure: An Introduction to Computational Biology course (Rice Univ.)

• Rosalind is a joint project between the University of California at San Diego and Saint Petersburg Academic University along with the Russian Academy of Sciences.

  ruiz@cs.wpi.edu