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A semantic search engine for biomedical knowledge. GeneView is built upon a comprehensively annotated version of PubMed abstracts and openly available PubMed Central full texts. This semi-structured representation of biomedical texts enables a number of features extending classical search engines. For instance, users may search for entities using unique database identifiers or they may rank documents by the number of specific mentions they contain. To semantically enrich these articles and provide convenient user access, GeneView uses several inter-operating components: (i) named entity recognition and PPI extraction modules; (ii) an inverted index for efficient searching; (iii) a customizable ranking algorithm taking the extracted entity-centric information into account and (iv) a web front end for querying and visualization.
Facilitates the easy interrogation of omics datasets holistically to improve ‘findability’ of relevant data. Omicseq uses an algorithm for ranking omics datasets that fully uses the numerical content of the dataset to determine relevance to the query entity. It aims to enhance findability of omics datasets, to facilitate re-utilization, or re-purposing of existing data for secondary, tertiary analyses. The tool can facilitate discoveries using existing and emerging genomic datasets.
Allows detection of proteins homologous and identification of the reference proteins. Seq2Ref is a homology-based web server to identify reference proteins from PubMed, Protein Data Bank (PDB) and Swiss-Prot (SP) databases. The software can be used to find PubMed references relevant to proteins of unknown function, and to obtain a deeper understanding of proteins than that revealed by short annotations. Thus, it can contribute to precisely inferring unknown protein function and developing detailed functional interpretation.
Chrawler / Chemistry and Crawler
Federates search of chemical structures and reactions across various data sources in an enterprise environment. Chrawler is an innovative chem-informatics tool and an enterprise search solution for a variety of data sources, including Microsoft Sharepoint, network drives, Documentum, Electronic Lab Notebook, compound databases, Outlook email servers. Chrawler's powerful search options include (i) substructure, full structure, exact full structure, similarity search for chemical structures and reactions, (ii) sequence search for biologics, (iii) combined structure/sequence and text search.
PhenDisco / Phenotype Discoverer
Allows users to retrieve data from the database of genotypes and phenotypes (dbGaP). PhenDisco is a web-based information retrieval system that consists of two main components: (1) text processing tools that standardize both phenotype variables and study metadata, and (2) information retrieval tools that support queries from users and return ranked results. The software also integrates tools to enhance query processing and phenotype variable mapping. It augments background knowledge from domain experts by adding meta-data for the studies.
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