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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
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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
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
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.