Abstract: A method (100) for standardizing gene nomenclature, comprising: (i) receiving (110) a source; (ii) tokenizing (120) the source; (iii) comparing (130) a first token to a prefix tree structure with a root node, edges, and leaf nodes; (iv) determining (140) which edge extending from the root node to associated first leaf nodes the first token matches; (v) updating (150) an identification pointer with the location of the first leaf node; (vi) determining (160) which of one or more edges that a second token matches; (vii) updating (170) the identification pointer with the location of the second leaf node; (viii) repeating (172) the determining (160) and updating (170) steps with subsequent tokens until a subsequent token fails to match an edge extending from a leaf node or there is no edge extending from the leaf node; and (ix) providing (180) an identification of a canonical gene name.

Abstract: A method (100) for generating a standardized cancer stage from a text-based source using an annotation system (400), comprising: (i) extracting (130), by a stage annotator, information from the text-based source relative to a stage of the patients cancer to generate cancer annotations; (ii) identifying (140), by a disease annotator, information from the text-based source indicative of a type of cancer; (iii) extracting (150), by a stage synonym annotator, information from the text-based source synonymous with a cancer to generate cancer annotations; (iv) converting (160), by a stage canonicalizer, the cancer annotations from the stage annotator and the stage synonym annotator to a standardized cancer stage; and (v) reporting (170) the standardized cancer stage, the report comprising the standardized cancer stage, the cancer annotations extracted sources from the text-based source, and/or the location of each of the cancer annotations within the text-based source.

Abstract: A method (100) for standardizing gene nomenclature, comprising: (i) receiving (110) a source; (ii) tokenizing (120) the source; (iii) comparing (130) a first token to a prefix tree structure with a root node, edges, and leaf nodes; (iv) determining (140) which edge extending from the root node to associated first leaf nodes the first token matches; (v) updating (150) an identification pointer with the location of the first leaf node; (vi) determining (160) which of one or more edges that a second token matches; (vii) updating (170) the identification pointer with the location of the second leaf node; (viii) repeating (172) the determining (160) and updating (170) steps with subsequent tokens until a subsequent token fails to match an edge extending from a leaf node or there is no edge extending from the leaf node; and (ix) providing (180) an identification of a canonical gene name.

Abstract: Methods and systems for constructing a query. The methods and systems described herein provide novel techniques for constructing queries by mapping ontologies to each other. Accordingly, systems and methods described herein may map an otherwise unmappable term to an ontology in order to capitalize on the knowledge contained therein.

Abstract: A method (100) for recruiting a patient for a clinical trial, comprising: receiving (110) a dataset comprising information about one or more clinical trials each including patient eligibility criteria; extracting (120) the patient eligibility criteria from each of the clinical trials; converting (130) the patient eligibility criteria to a standardized patient eligibility criterion using a structured clinical trial mark-up language; storing (140) the patient eligibility criterion in a database (862), each of the criterion associated with one or more clinical trials; receiving (150) patient-specific data values about a patient; querying (160) the clinical trial eligibility criteria database using the patient-specific data values to identify eligibility criterion satisfied by the patient-specific data value; identifying (170) a clinical trial associated with the one or more standardized patient eligibility criterion satisfied by a received patient-specific data value; and providing (180) a report of the identifi