Text Mining and Semantics

Links to tools for more complex searching and for making connections between text and other scientific information. This section focuses specifically on text such as scientific publications, article abstracts, or NCBI GenBank records. It also covers the role of growing field of semantic web content in biological data integration.

Found 58 links

Displaying 15 links

Acromine DisambiguatorTool Content

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Given a biomedical text, Acromine Disambiguator correctly predicts expanded full forms of acronoyms appearing in the text. As acronyms appearing in biomedical texts are often ambiguous, such a disambiguation process is important to ensure the correct interpretation of the text.

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AlkemioTool Content

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Alkemio: association of chemicals with biomedical topics by text and data mining

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TitlePublication YearGoogle Scholar Citation Count

BeeSpace NavigatorTool Content

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BeeSpace Navigator is a tool for exploratory analysis of gene function using biological literature. It is an automated version of the curation process to extract gene function.

BioLabelerTool Content

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BioLabeler extracts UMLS concepts from Biomedical texts such as scientific paper abstracts, experiments descriptions or medical notes and can be use to automatically curate and annotate BioMedical Literature or to index large documents databases and improve searches or discover relationships between them

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TitlePublication YearGoogle Scholar Citation Count

BioLitTool Content

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BioLit is a web sever resource that integrates scientific publications with existing biological databases. To perform this link, BioLit searches the full text of the article for metadata such as database identifiers and ontology terms.

links directory index: 23
TitlePublication YearGoogle Scholar Citation Count
BioLit: integrating biological literature with databases200823

bioNMFTool Content

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A web-based tool based on nonnegative matrix factorization (NMF) that can be used to provide new information from multi-dimensional biological data sets.

BIOSMILETool Content

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BIOSMILE is a web-based NCBI PubMed search tool. Users input keywords to be searched and BIOSMILE retrieves matching PubMed abstracts.

botXminerDatabase Content

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botXminer is a literature searching tool that allows you to search BotDB. BotDB citations contain only those articles with either \'botulinum\' or \'tetanus\' anywhere in their text. botXminer is an interface to this subset of complete medline xml files loaded into an Oracle XMLDB.

BSQATool Content

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BeeSpace Question/Answering (BSQA) system is a web server that performs integrated text mining for insect biology, covering diverse aspects from molecular interactions of genes to insect behavior. BSQA recognizes a number of entities and relations in Medline documents about the model insect, Drosophila melanogaster.

CARGOTool Content

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CARGO (Cancer And Related Genes Online) is a portal that uses widgets to allow users to mine literature using iHOP, retrieve disease information from OMIM, visualize 3D SNPs, query protein interactions, and view summarized gene annotation information for cancer related genes in human.

ChilibotTool Content

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Chilibot searches the PubMed literature database based on specific relationships between proteins, genes, or keywords. The results are returned as a graph.

CoPubTool Content

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CoPub is a text mining tool for the detection of biomedical terms that co-occur in abstracts with the list of input genes (human, rat, and mouse genes). CoPub also graphically displays differentially expressed genes and over-represented keywords in a network for better visualization of relationships. CoPub 5.0 uses a new thesauri. It allows for searching of keywords, provides highlighting and sorting mechanisms and statistics. It also searches for indirect relations between genes, pathways, drugs and diseases.

DECATool Content

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DECA is a species disambiguation system for biological named entities. The system will identify protein entities and disambiguate them according to species, by assigning NCBI Taxonomy organism IDs.

This content is being maintained by pthompson.

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