We propose a method to automatically extract templates from biomedical literature without background knowledge. The proposed method automatically extracts verbs and templates indicating interactions between biomolecules with a large dictionary called an extensional ontology. We applied our method to two datasets: one comprised 299 full texts from Cell (1998– 2002) and 13,818 entries from OMIM (...

Entrez is the text-based search and retrieval system used at NCBI for all of the major databases, including PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, OMIM, and many others. Entrez is at once an indexing and retrieval system, a collection of data from many sources, and an organizing principle for biomedical information. These general concepts are t...

Huge unrealized post-genome opportunities remain in the understanding of detailed molecular mechanisms for Alzheimer Disease (AD). In this work, we developed a computational method to rank-order AD-related proteins, based on an initial list of AD-related genes and public human protein interaction data. In this method, we first collected an initial seed list of 65 AD-related genes from the OMIM ...

Online Mendelian Inheritance in Man (OMIMTM) is a timely, authoritative compendium of bibliographic material and observations on inherited disorders and human genes. It is the continuously updated electronic version of Mendelian Inheritance in Man (MIM). MIM was last published in 1998 (1) and is authored and edited by Dr. Victor A. McKusick and a team of science writers, editors, scientists, an...

throughout his long life, man has always imagined creating a creature with the same capabilities of his own or much higher than that; a creature in his service. at the end of the 20th century, gaining the logical and mathematical model for man’s actions and reactions has caused man to be the creator of a virtual intelligence himself; the intelligence by which a machine can think like a man, hav...

Databases such as MEDLINE, OMIM, RefSeq and LocusLink serve as important information sources for biomedical studies. A search of several databases can yield vast quantities of information, so much in fact that the searcher may struggle to pinpoint the important information. This has highlighted the desirability of a specific tool to facilitate efficient database searching and extraction of info...

McKusick's Online Mendelian Inheritance in Man (OMIM; http://www.ncbi.nlm.nih.gov/omim), a knowledgebase of human genes and phenotypes, was originally published as a book, Mendelian Inheritance in Man, in 1966. The content of OMIM is derived exclusively from the published biomedical literature and is updated daily. It currently contains 18,961 full-text entries describing phenotypes and genes. ...

Manual annotation of biological data cannot keep up with data production. Open annotation models using wikis have been proposed to address this problem. In this empirical study we analyse 36 years of knowledge collection by 738 authors in two Molecular Biology wikis (EcoliWiki and WikiPathways) and two knowledge bases (OMIM and Reactome). We rst investigate authorship metrics (authors per entry...

Researchers in the biomedical and molecular biology fields are faced with a wide variety of information sources. These are presented in the form of images, free text, and structured data files that include medical records, gene and protein sequence data, and whole genome microarray data, all gathered from a variety of experimental organisms and clinical subjects. The need to organize and relate...

Ziel dieser Bachelorarbeit ist die Erstellung und Visualisierung einer Krankheitsontologie basierend auf Daten der “Disease Ontology“ [1] und die Abbildung von KrankheitsMutations-Relationen aus den Datenbanken OMIM [2], COSMIC [3],GAD [4] und GeneView [5] auf diese Ontologie. Anschließend soll eine Netzwerkanalyse auf Krankheits-Gen Ebene durchgeführt und mit Daten anderer Paper [6] [7] [8] ve...