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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


No version available

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 citations

 (4)
library_books

Sperm Proteome Maturation in the Mouse Epididymis

2015
PLoS One
PMCID: 4640836
PMID: 26556802
DOI: 10.1371/journal.pone.0140650

[…] oteome 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 in […]

library_books

Self training in significance space of support vectors for imbalanced biomedical event data

2015
BMC Bioinformatics
PMCID: 4423724
PMID: 25952719
DOI: 10.1186/1471-2105-16-S7-S6

[…] m 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 MEDLI […]

library_books

Collective Instance Level Gene Normalization on the IGN Corpus

2013
PLoS One
PMCID: 3839972
PMID: 24282506
DOI: 10.1371/journal.pone.0079517

[…] ngine, 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 the reco […]

library_books

Cataloging the biomedical world of pain through semi automated curation of molecular interactions

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

[…] In total there were 1 578 654 event chains from the BioContext database present in P1. After grouping these event chains, there were 356 499 unique event chains, with 261 438 single events, 93 271 containing two participants (i.e. molecular interaction […]

Citations

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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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