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System and method for scientific information knowledge management

  • US 10,275,711 B2
  • Filed: 08/17/2012
  • Issued: 04/30/2019
  • Est. Priority Date: 12/16/2005
  • Status: Active Grant
First Claim
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1. A method, implemented using one or more computers comprising one or more processors and system memory, of integrating data in a database of scientific information, the method comprising:

  • (a) receiving, by the one or more processors, an input feature set, said input feature set comprising a data structure comprising a table comprising (i) a list of input features and (ii) a list of associated statistical information, wherein the features comprise genes, SNPs, SNP patterns, portions of genes, regions of a genome, proteins, compounds, metabolites, or phenotypes;

    (b) receiving, by the one or more processors, an index set comprising (i) a plurality of feature identifiers representing a plurality of features, and (ii) a plurality of globally unique mapping identifiers,whereineach feature identifier points to one or more globally unique mapping identifiers,two or more feature identifiers of the plurality of feature identifiers point to a same globally unique mapping identifier, the two or more feature identifiers are related to each other by at least one of;

    nomenclature-based, sequence-based, activity-based, regulatory-based, function-based, or structure-based relationships, andeach globally unique mapping identifier has a unique address in the index set;

    (c) automatically mapping, by the one or more processors, the input features in the input feature set to a subset of feature identifiers in the index set, wherein the subset of feature identifiers represents the input features and points to a subset of globally unique mapping identifiers in the index set, thereby providing first mapping information between the input features and the subset of globally unique mapping identifiers;

    (d) providing, by the one or more processors, second mapping information between at least some pre-existing features of a plurality of pre-existing feature sets in the database and at least some of the subset of globally unique mapping identifiers, wherein the input feature set and the plurality of pre-existing feature sets are obtained from different experiments, platforms, or organisms;

    (e) generating, by the one or more processors, an alignment scheme between the input feature set and the plurality of pre-existing feature sets in the database using the first mapping information and the second mapping information;

    (f) automatically correlating, by the one or more processors, the input feature set with the plurality of pre-existing feature sets in the database using the alignment scheme; and

    (g) automatically storing, by the one or more processors, the correlation information in (f) on a non-transitory machine readable medium for use in responding to queries involving feature sets.

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