BioContext statistics

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BioContext specifications

Information


Unique identifier OMICS_04826
Name BioContext
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License BSD 2-clause “Simplified” License
Computer skills Advanced
Version 1.0
Stability Stable
Maintained Yes

Versioning


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Maintainer


  • person_outline Martin Gerner <>

Information


Unique identifier OMICS_04826
Name BioContext
Interface Web user interface
Restrictions to use None
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Martin Gerner <>

Publication for BioContext

BioContext in pipeline

2013
PMCID: 3662864
PMID: 23707966
DOI: 10.1093/database/bat033

[…] event chain to each disease term match and from these the overall disease relevancy of each grouped event chain (without the term weighting)., we did not repeat the existing evaluations performed in biocontext () for anatomy, negation and speculation contexts. similarly, mutation detection and normalization had also been previously evaluated for mutationfinder (). however, to evaluate […]


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BioContext in publications

 (4)
PMCID: 4640836
PMID: 26556802
DOI: 10.1371/journal.pone.0140650

[…] during the maturation process, we wished to validate the dataset by comparing our high-throughput analyses with previously described studies. to this end we utilized an online text mining tool biocontext [] that identified 102 literature references containing contextual information on proteins in the mammalian epididymis (). manual curation found 19 references that studied proteins found […]

PMCID: 4423724
PMID: 25952719
DOI: 10.1186/1471-2105-16-S7-S6

[…] literature are indexed to support a deeper semantic search in comparison to traditional keyword-based search engines. thus, such a search system can provide results with a high precision to a user. biocontext [] and medie [] systems are example of event-based search engines. medie has an intelligent interface for retrieving biomedical events referenced with their literature from the entire […]

PMCID: 3839972
PMID: 24282506
DOI: 10.1371/journal.pone.0079517

[…] even more complex results are obtained, inferring that distinguishing the true identity of named entities is indeed an indispensable process. recently, some advanced retrieval systems, such as biocontext and evex , have begun to integrate entity normalization/disambiguation components e.g., genetukit and gennorm to deal with the ambiguity issues. entity normalization goes beyond […]

PMCID: 3662864
PMID: 23707966
DOI: 10.1093/database/bat033

[…] 692 documents from medline and pubmed central, from which we extracted 356 499 unique normalized molecular events, with 261 438 single protein events and 93 271 molecular interactions supplied by biocontext. event chains are annotated with negation, speculation, anatomy, gene ontology terms, mutations, pain and disease relevance, which collectively provide detailed insight into how that event […]


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BioContext institution(s)
Faculty of Life Sciences, University of Manchester, Manchester, UK; School of Computer Science, University of Manchester, Manchester, UK

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