Ingenuity Systems, Inc.

Qiagen Redwood City, Inc.

Qiagen Gmbh

Daniel R Richards

Ramon M Felciano

Raymond J Cho

Richard O Chen

Keith Steward

Sushma Selvarajan

Sara Tanenbaum Schneider

Viresh Patel

Philippa Norman

Bret Holley

Douglas E Bassett, Jr

Peer M Schatz

Douglas E Bassett

Brett Holley

Disclosed herein are system, method, and computer program product embodiments for aiding in the interpretation of variants observed in clinical sequencing data. An embodiment operates by receiving clinical trial enrollment criteria from a user, including but not limited to genetic targeting criteria; searching a knowledge base of patient test information received from a plurality of independent entities for patients that match the clinical trial enrollment criteria; and providing to the user search results for consented patients that match the clinical trial enrollment criteria.

Methods and systems for interpretation and reporting of sequence-based genetic tests

Disclosed herein are system, method, and computer program product embodiments for building a community database of allele counts. An embodiment operates by receiving human variant datasets derived from samples generated by distinct users, wherein the users consented to share pooled variant observations with other users; determining that a plurality of variant observations meet the inclusion criteria for a pool; and calculating one or more anonymized allele statistics from the pool.

Methods and systems for interpretation and reporting of sequence-based genetic tests using pooled allele statistics

Methods for identifying disease-related pathways that can used to identify drug discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes.

Drug discovery methods

Methods for identifying disease-related pathways that can be used to identify drug discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes.

Methods for constructing and maintaining knowledge representation systems are disclosed herein. The knowledge representation system is initially organized and populated using knowledge engineers. After the initial organization, scientific domain experts digest and structure source texts for direct entry into the knowledge representation system using templates created by the knowledge engineers. These templates constrain both the form and content of the digested information, allowing it to be entered directly into the knowledge representation system. Although knowledge engineers are available to evaluate and dispose of those instances when the digested information cannot be entered in the form required by the templates, their role is much reduced from conventional knowledge representation system construction methods. The methods disclosed herein permit the construction and maintenance of a much larger knowledge representation system than could be constructed and maintained using known methods.

Constructing and maintaining a computerized knowledge representation system using fact templates

Method for identifying disease-related pathways that can used to identify discovery targets, to identify new uses for known drugs, to identify markers for drug response, and related purposes.

Methods for constructing and maintaining knowledge representation systems (KRS) are disclosed. The KRS is initially organized and populated using knowledge engineers. After initial organization, scientific domain experts digest and structure source texts for direct entry into the KRS using templates. These templates constrain both the form and content of the digested information, allowing it to be entered directly into the KRS. The methods disclosed herein permit the construction and maintenance of a much larger KRS than could be constructed and maintained using known methods. Fact type specific fact templates are completed, accepting predefined fact types found in predetermined information sources. Fact template may comprise a user interface that constrains user entry to one of a predetermined set of valid entries. The user interface may include a user field that permits entry of new information not included in the predetermined set of valid user entries.

Computerized knowledge representation system with flexible user entry fields

A method, system, and computer program product are provided for extracting information from a plurality of articles in a distributed manner and for storing the extracted information in an information store. The invention identifies a plurality of articles from which information is to be extracted and a plurality of information extractors for extracting the information from the articles. Each article is assigned a priority score and ranking the articles from highest to lowest priority, thereby generating a queue; wherein the priority score for each article is calculated using a user-configurable priority calculation algorithm. The plurality of articles is assigned to the plurality of information extractors based on order in the queue, wherein an article with a higher rank is presented for information extraction before an article with a lower rank. Information extracted by information extractors from the articles is stored in the information store.

Techniques for facilitating information acquisition and storage

Methods for the construction and maintenance of a knowledge representation system

The method and system for extracting information from a plurality of articles and for storing the extracted information in a knowledge-based information store. The method and system identify a plurality of articles from which information is to be extracted. The method and system identify and assign a plurality of information extractors for extracting information from the plurality of articles. The method and system receive information extracted by an information extractor from an article assigned to the information extractor. The method and system enable a content reviewer to review the extracted information received from the information extractor and the content reviewer identifies errors associated with the extracted information. If the error count is above the threshold level, the article may be reassigned for information extraction. If the error count is equal to or below the threshold level, the content reviewer may change the extracted information to correct the errors.

A system and method of information extraction and storage extracts information from a plurality of articles in a distributed manner and stores the extracted information in an information store. In one embodiment, the system includes identification of a plurality of articles from which information is to be extracted and a plurality of information extractors for extracting the information from the articles. A database is provided for storing information related to the plurality of articles and the plurality of information extractors. The plurality of articles are assigned to the plurality of information extractors for information extraction and the extracted information is then stored in the information store.

Growing community of inventors

Palo Alto, CA, United States of America

Daniel R Richards