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BioThesaurus specifications
Information
Unique identifier | OMICS_26486 |
---|---|
Name | BioThesaurus |
Restrictions to use | None |
Community driven | No |
Data access | File download, Browse |
User data submission | Not allowed |
Version | 7.0 |
Maintained | Yes |
Maintainer
- person_outline Hongfang Liu
Publication for BioThesaurus
BioThesaurus citations
(7)A method for integrating and ranking the evidence for biochemical pathways by mining reactions from text
[…] A+ indexes concepts from the abstracts including genes, proteins, diseases, symptoms, drugs, enzymes and simple chemical compounds, identified using biological databases and thesauri such as UniProt, BioThesaurus, Unified Medical Language System (UMLS), KEGG and DrugBank. The user interacts with the system by issuing queries in the form of a word, a concept identifier or any Boolean combination of […]
Novel semantic similarity measure improves an integrative approach to predicting gene functional associations
[…] d drugs), and presents them in a tabular format ranked based on co-occurrence statistics. The concept IDs and their names and synonyms are collected from several biomedical databases such as UniProt, BioThesaurus, UMLS, and DrugBank.We queried FACTA with all human protein-coding genes and stored for each query gene the set of related gene IDsc, UMLS and DrugBank terms.GoPubMed[]—developed by the T […]
The BioLexicon: a large scale terminological resource for biomedical text mining
[…] tatistical machine learning method. The dictionary consists of 266,000 entries for general English words extracted from WordNet [], together with 1.3 million entries for protein names, extracted from BioThesaurus []. The tool is available at http://text0.mib.man.ac.uk/~sasaki/bootstrep/nemine.html.Text mining techniques are typically evaluated against 'gold standards' []. We evaluated the NER tool […]
Moara: a Java library for extracting and normalizing gene and protein mentions
[…] ext and the synonyms in the dictionaries. It is flexible because the mention and the synonyms are previously pre-processed by dividing the token according to punctuations, numbers, Greek letters, and BioThesaurus terms, and finally ordering the parts of the token alphabetically. The initial lists of synonyms for the four organisms were available in the two editions of the BioCreative challenge: Bi […]
Incorporating rich background knowledge for gene named entity classification and recognition
[…] The dictionary was built from two resources: BioThesaurus 2.0 [] and ABGene lexicon []. To improve the dictionary coverage, we converted all the dictionary entries to lowercases, removed hyphens and tokenized the terms from non-letter and non-di […]
Integrating protein protein interactions and text mining for protein function prediction
[…] e, we enriched this retrieval by additional references that are contained in the BioLexicon (work in progress). The BioLexicon is a new data resource that combines the protein term repository called "BioThesaurus" with other terminological resources (e.g., NCBI taxonomy, ChEBI) and adds linguistically relevant information []. We used terms from the BioLexicon to retrieve additional references to M […]
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