Innovative Capabilities of Patomics Knowledgebase DNA Patent Analysis:

Patomics represents a significant advance over existing patent sequence databases. In addition to commonly available features such as flexible search criteria, sequence-based searching, and customizable statistical summaries, we offer more advanced search functions than currently available from our competitors that enable researchers to perform more sophisticated concept and clustering searches. Patomics will provide four unique features which are not currently available in any existing patent database service. These are:

• Detailed annotation of claims associated with sequences
• Patent clustering based on pathway and disease data
• Patent Landscape Protocols
• Genome-Patent Browser

Detailed claim annotation of claims associated with sequences: The PKB goes much further than any existing database in explaining the nature of the IP associated with a gene. First, we distinguish between the mere listing of a sequence as part of a patent’s documentation (which entails no IP claims on the sequence) and the occurrence of a sequence in a patent claim (which does entail an IP protection of the sequence). Next, we distinguish between patent claims involving the composition of the sequences and claims involving a process in which the sequence is used. We provide detailed annotation of the IP associated with a gene, making it possible to answer such question as the following: Does the IP involve an exact match of the sequence or a partial match? Does the IP involve methods for diagnosis or treatment? These additional levels of annotation will permit a much deeper understanding of the patent landscape associated with a given gene, and support the development of the other unique database tools, as follows:

Patent Clustering: Clustering is the partitioning of data into subsets based on common traits and characteristics. Patomics will be the first patent bioinformatics database that will offer clustering features based on physiological pathway and disease information that is extracted from external data sources and used to cluster patent information. Thus, an IP searcher seeking to build a landscape around a particular gene will not be limited to that gene – but will be able to link it with genes in the same pathway and diseases associated with the gene and physiological pathway. This important feature will enable researchers to identify patents which may not mention a gene by name or sequence, but which cover diseases and pathways in which the targeted gene is involved. For instance, there may be broad claims to treating a certain disease that would be infringed by the gene, but because the gene is not mentioned in the patent, searchers would not have identified the patent in searches conducted in competing databases. These unique features provide Patomics with a competitive advantage over existing databases and addressing pressing market needs for patent tools that integrate bioinformatics analysis. The information provided in the Patomics database will facilitate a systemic study of the categories of claims that have issued on human genes.

Patent Scope: Patent scope and breadth is another issue that requires consideration: do narrow patents (covering one sequence) have the same effects on commerce and healthcare provision as broad patents (covering a family of sequences related by sequence identity or the ability to hybridize to one another). The Patomics database will be a tool to readily access the patent, and then understand the nature of rights it gives the patent holder.

Patent Landscape Protocols: The Patent Landscape query tool enables users to construct a picture of the intellectual property terrain for any desired aspect of the human genome. By making selective queries of the Patomics database, a table of information will be retrieved that will display a summary of information on existing patents in the field of the query. This will allow users to identify the existing intellectual property in their targeted field, as well as competitors engaged in the same technology. In addition to this, we provide links to scientific literature which will enable validity and priority studies. For example, suppose one is interested in investigating the patent landscape associated with a specific disease.

Genome Patent Browser: A typical genome browser will provide chromosome ideograms aligned with annotated “tracks” that permit users to visualize the chromosome landscape of any feature they are interested in viewing. GenBank’s browser has tracks for over thirty different features, including BES clones, Genes, RefSeq transcripts, STS markers, and Morbid Diseases. We have developed an annotated track for Patents, which will enable users to survey the patent landscape on a chromosome at a glance. The Genome Patent Browser will enable users to display the Patent Track alongside the Clone Track – providing instant visualization of all patents that cover sequences which are present in the 3q probe. To our knowledge, there is no existing way to accomplish this as simply and quickly as proposed with the Patomics Genome Patent Browser feature.

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