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Biomedical text summarization to support genetic database curation: using Semantic MEDLINE to create a secondary database of genetic information

T. Elizabeth Workman, Marcelo Fiszman, John F Hurdle, Thomas C Rindflesch
2010 Journal of the Medical Library Association  
A gold standard was produced using records from Genetics Home Reference and Online Mendelian Inheritance in Man. Genes in text found by the system were compared to the gold standard.  ...  Methods: An existing summarization system was modified for identifying biomedical text relevant to the genetic etiology of disease.  ...  Then, the query was issued a second time after modifying the OMIM interface limits options to retrieve only records that included a clinical synopsis.  ... 
doi:10.3163/1536-5050.98.4.003 pmid:20936065 pmcid:PMC2947139 fatcat:4gy4a6c5undsfpm32flvjes3b4

Molecularly and clinically related drugs and diseases are enriched in phenotypically similar drug-disease pairs

Ingo Vogt, Jeanette Prinz, Mónica Campillos
2014 Genome Medicine  
We assessed and visualized the enrichment over random of clinical and molecular relationships among drug-disease pairs that share phenotypes using lift plots.  ...  The phenotypic similarity between 4,869 human diseases and 1,667 drugs was evaluated using an ontology-based semantic similarity approach to compare disease symptoms with drug side effects.  ...  We removed terms based on term types (given by the UMLS Metathesaurus) suggested to be removed for concept recognition purposes in text [22] .  ... 
doi:10.1186/s13073-014-0052-z pmid:25276232 pmcid:PMC4165361 fatcat:3j3xn2zig5hqrkkowsaz7ojvkq

Computational methods for identifying similar diseases

Liang Cheng, Hengqiang Zhao, Pingping Wang, Wenyang Zhou, Meng Luo, Tianxin Li, Junwei Han, Shulin Liu, Qinghua Jiang
2019 Molecular Therapy: Nucleic Acids  
To this end, the associations between diseases at the molecular, phenotypic, and taxonomic levels were used to measure the pairwise similarity in diseases.  ...  Then, frequently used methods were evaluated using a benchmark-data-based strategy.  ...  The index "etiology" is based on clinical signs and laboratory or pathological findings related to a disease. The index "tissue" is compiled as the anatomic location of phenotype.  ... 
doi:10.1016/j.omtn.2019.09.019 pmid:31678735 pmcid:PMC6838934 fatcat:43gylxprhnfihlhzr2ociquapy

Task-Driven Dynamic Text Summarization

Terri Elizabeth Workman
Acknowledgements and Funding We wish to acknowledge Thomas Rindflesch and Marcelo Fiszman for their essential work in developing SemRep and the Summarization concept.  ...  Acknowledgements The authors express their gratitude to Graciela Rosemblat for assisting with the study's evaluation, to Jeanne Le Ber for editorial assistance, and to Joyce Mitchell for advice and suggestions  ...  the UMLS [22] Metathesaurus preferred concepts Taurolidine and infection.  ... 
doi:10.26053/0h-3p7a-bkg0 fatcat:o3lypokeqvhf7khl7q2he3wdhq

An intelligent digital library system for biologists

J. Stone, Xindong Wu, M. Greenblatt
Proceedings. 2004 IEEE Computational Systems Bioinformatics Conference, 2004. CSB 2004.  
System (UMLS).  ...  The digital library is based on a framework used for conventional libraries and an objectoriented paradigm, and provides personalized user-centered services based on the user's areas of interests and preferences  ...  This information includes allelic variants, gene map disorders, and clinical synopsis, and references.  ... 
doi:10.1109/csb.2004.1332471 dblp:conf/csb/StoneWG04 fatcat:z62l7u2wm5hcfijnxgblrjof3u

A network-based analysis of the cellular and genetic etiology of disease

Alexander John Cornish, Michael Sternberg, British Heart Foundation
In order to use data specific to a disease-manifesting cell type to identify disease- associated genes, it is first necessary to identify the disease-manifesting cell types.  ...  The performance of many of these methods may however be limited by their failure to use data specific to the tissues and cell types that manifest each disease.  ...  Robinson et al. (2008) used the text and clinical synopsis parts of disease records in OMIM to annotate human diseases with HPO terms.  ... 
doi:10.25560/61577 fatcat:5cr3lt5nfrbflc5rvcey22stji