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PhenoMining Services

Wesley W. Chu Computer Science Department UCLA. PhenoMining Services. PhenoMining Services. A set of Web-based text mining services, including: Concept Explorer: Find the distributions of concept terms and their phenotypes in the corpus

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PhenoMining Services

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  1. Wesley W. Chu Computer Science Department UCLA PhenoMining Services

  2. PhenoMining Services • A set of Web-based text mining services, including: • Concept Explorer: Find the distributions of concept terms and their phenotypes in the corpus • PhenoPath Mining: Identify links between phenotypes at different levels, and display relevant text passages • Table and Figure Assertion Mining: Display tables and figures whose captions match input concepts/phenotypes • Cross-species Concept Explorer: Bridge cognition-level concepts across species using links with gene and neuroanatomical concepts • Analysis of the CNP/LA2K Multi-Level Phenome

  3. Limitations of PubMed Query for CNP • PubMed does NOT provide: • Ranking of retrieved documents • Display of relevant Sentences and Paragraphs • Display of relevant Figures and Tables • Retrieval of documents by Phenotype • Retrieval of documents that match a Multi-level Phenome • CNP PhenoMining services use knowledge from text mining to remedy these shortcomings • CNP/LA2K Multi-Level Phenome of 61 concepts in six levels (syndrome, symptom, cognitive concept, task, brain region, gene) • CNP Corpus of 7000 full-text documents from PubMed Central (PMC) chosen for relevance to CNP research (e.g. schizophrenia, working memory, prefrontal cortex, reversal learning, 22q11.2, SYN3, dopamine)

  4. Figure and Table Mining Result phenomining.org/ftm

  5. PhenoPath Mining • PhenoPaths are sequences of related concepts involving intermediate phenotypes in a Multi-level Phenome. • Phenome Queries take a Phenome specified by multiple lexica, and generates a graph of PhenoPaths using conditional co-occurrence of concept terms by text mining at the sentence, paragraph, or article level. • PhenoPath Mining yields a set of paragraphs or sentences from the corpus, corresponding to phenotypes in the paths

  6. PhenoPath Example with 4 Levels phenomining.org/pm

  7. PhenoPath Mining Result

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