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Comprehensive Overview of Bioinformatics Databases and Resources for Genomic Research

This document provides a detailed overview of various bioinformatics databases and resources critical for genomic and proteomic research. Key databases highlighted include Gene Ontology, EBI InterPro, NCBI Taxonomy, RefSeq, and PlasmoDB, each serving unique purposes in gene and protein analysis. The structured network facilitates the integration and retrieval of biological data, enhancing the understanding of gene functions and protein characteristics. Simplified schemas are used for clarity, and data is curated from prestigious global laboratories for comprehensive insights.

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Comprehensive Overview of Bioinformatics Databases and Resources for Genomic Research

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  1. Peers description • Overview • Full copies of all these databases are hosted on the Penn DbGroup servers • The demo: • Uses simplified schemas for easier understanding • Initial state is filled with a subset of the real data • Gene OntologyThe Gene Ontology project provides a controlled vocabulary to describe gene and gene product attributes in any organism.http://www.geneontology.org/Incoming mappings: None

  2. Peers desription • EBI Interpro(European Bioinformatics Institute)http://www.ebi.ac.uk/interpro/A database of protein families, domains and functional sites, in which identifiable features found in known proteins can be applied to unknown protein sequences.Incoming mappings: None in this simplified peer network. However Interpro could use a lot of incoming mappings since it imports data from all major domain databases such as PFAM, PRODOM… • NCBI(National Center for Biotechnology Information)http://www.ncbi.nlm.nih.gov/ • Taxonomy The NCBI Taxonomy attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources.Incoming mappings: None in this simplified peer network • RefSeqThe Reference Sequence collection aims to provide a comprehensive, integrated, non-redudant set of sequencesIncoming mappings:M0: Get the Taxonomy updates from the Taxonomy schema

  3. Peers description • PCBI PlasmoDb: Plasmodium Genome Resourcehttp://www.plasmodb.org/DescriptionHosts genomic and proteomic data (and more) for the cause of Malaria. Brings together data provided by numerous laboratories worldwide, and adds its own data analysis. Mappings • M1: Import NCBI Taxonomy updates (referenced from each entry) • M2: Imports the RefSeq catalog, used for computation and references. • M3: Used to flag entries still used in PlasmoDB but that have been discarded from RefSeq. • M4 & M5: PlasmoDB annotators reference the relevant Interpro data for each PlasmoDB entry. Then the details from the Interpro database are used for different computations and/or shown to the website users. M4: Imports the domain cross-references given by Interpro M5: Imports into PlasmoDB the references to the Gene Ontology given by Interpro; and gets the latest labels from Gene Ontology at the same time.

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