Biomedical Text Mining - Examples

Examples

• KLEIO - an advanced information retrieval system providing knowledge enriched searching for biomedicine.
• FACTA+ - a MEDLINE search engine for finding associations between biomedical concepts. The FACTA+ Visualizer helps intuitive understanding of FACTA+ search results through graphical visualization of the results.
• U-Compare - U-Compare is an integrated text mining/natural language processing system based on the UIMA Framework, with an emphasis on components for biomedical text mining.
• TerMine - a term management system that identifies key terms in biomedical and other text types.
• MEDIE - an intelligent search engine to retrieve biomedical correlations from MEDLINE, based on indexing by Natural Language Processing and Text Mining techniques
• AcroMine - an acronym dictionary which can be used to find distinct expanded forms of acronyms from MEDLINE.
• AcroMine Disambiguator - Disambiguates abbreviations in biomedical text with their correct full forms.
• GENIA tagger - Analyses biomedical text and outputs base forms, part-of-speech tags, chunk tags, and named entity tags
• NEMine - Recognises gene/protein names in text
• Yeast MetaboliNER - Recognizes yeast metabolite names in text.
• Smart Dictionary Lookup - machine learning-based gene/protein name lookup.
• TPX - A concept-assisted search and navigation tool for biomedical literature analyses - runs on PubMed/PMC and can be configured, on request, to run on local literature repositories too.
• Chilibot — A tool for finding relationships between genes or gene products.
• EBIMed - EBIMed is a web application that combines Information Retrieval and Extraction from Medline.
• FABLE — A gene-centric text-mining search engine for MEDLINE
• GOAnnotator, an online tool that uses Semantic similarity for verification of electronic protein annotations using GO terms automatically extracted from literature.
• GoPubMed — retrieves PubMed abstracts for your search query, then detects ontology terms from the Gene Ontology and Medical Subject Headings in the abstracts and allows the user to browse the search results by exploring the ontologies and displaying only papers mentioning selected terms, their synonyms or descendants.
• Anne O'Tate Retrieves sets of PubMed records, using a standard PubMed interface, and analyzes them, arranging content of PubMed record fields (MeSH, author, journal, words from title and abtsracts, and others) in order of frequency.
• Information Hyperlinked Over Proteins (iHOP): "A network of concurring genes and proteins extends through the scientific literature touching on phenotypes, pathologies and gene function. iHOP provides this network as a natural way of accessing millions of PubMed abstracts. By using genes and proteins as hyperlinks between sentences and abstracts, the information in PubMed can be converted into one navigable resource, bringing all advantages of the internet to scientific literature research."
• LitInspector — Gene and signal transduction pathway data mining in PubMed abstracts.
• NextBio- Life sciences search engine with a text mining functionality that utilizes PubMed abstracts (ex: literature search) and clinical trials (example) to return concepts relevant to the query based on a number of heuristics including ontology relationships, journal impact, publication date, and authorship.
• PubAnatomy — An interactive visual search engine that provides new ways to explore relationships among Medline literature, text mining results, anatomical structures, gene expression and other background information.
• PubGene — Co-occurrence networks display of gene and protein symbols as well as MeSH, GO, PubChem and interaction terms (such as "binds" or "induces") as these appear in MEDLINE records (that is, PubMed titles and abstracts).
• Whatizit - Whatizit is great at identifying molecular biology terms and linking them to publicly available databases.
• XTractor — Discovering Newer Scientific Relations Across PubMed Abstracts. A tool to obtain manually annotated,expert curated relationships for Proteins, Diseases, Drugs and Biological Processes as they get published in PubMed.
• Medical Abstract — Medical Abstract is an aggregator for medical abstract journal from PubMed Abstracts.
• MuGeX — MuGeX is a tool for finding disease specific mutation-gene pairs.
• MedCase — MedCase is an experimental tool of Faculties of Veterinary Medicine and Computer Science in Cluj-Napoca, designed as a homeostatic serving sistem with natural language support for medical applications.