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 medical information technology (IT) system includes a plurality of medical information systems storing medical reports in different respective medical information system-specific medical report formats. An integrated diagnostics system includes: a medical report transform operative to transform text of medical reports stored in the different respective system report formats to an integrated diagnostics representation which represents the text of the medical reports as vocabulary category values of a vocabulary of categories; and a plurality of document processing tasks each operative to invoke the medical report transform to transform one or more medical reports processed by the task to the integrated diagnostics representation and to perform the task on the vocabulary category values of the integrated diagnostics representation of the one or more medical reports processed by the task.

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: Various embodiments relate to a method and non-transitory computer readable medium for genome spelling correction, the method including the steps of performing pre-processing on a sentence, storing a first adjacent word to an unknown word and a second adjacent word to the unknown word, generating a plurality of candidate words for the unknown word, forming a plurality of trigrams with the first adjacent word to the unknown word and the second adjacent word to the unknown word and each of the plurality of candidate words, searching a trigram table for each of the plurality of trigrams and outputting the candidate word from the trigram with a highest trigram count in the trigram table.

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.