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Associated diseases

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BioC specifications

Information


Unique identifier OMICS_04858
Name BioC
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Donald C. Comeau <>

Publication for BioC

BioC in publications

 (16)
PMCID: 5737204
PMID: 29220479
DOI: 10.1093/database/bax090

[…] the results of automated identification and relation extraction tools are considered useful as the basis of annotation., currently, markyt is able to import raw, unannotated documents in tsv and bioc inline xml []. moreover, the tool is able to import annotations following the formats brat standoff annotation [], bioc inline xml [], bionlp standoff representation [] and biocreative tsv []. […]

PMCID: 5691355
PMID: 29220478
DOI: 10.1093/database/bax088

[…] expressions and data parsers such as xpath (xml path language). currently, the system supports the integration of most bionlp workshop’s (http://bionlp.org) formats out-of-the-box such as the bioc and standoff formats, with it also being possible to additionally customize new formats., after this selection and extraction processes, annotations objects are semantically enriched by using […]

PMCID: 5482438
PMID: 28644863
DOI: 10.1371/journal.pone.0179488

[…] phenotype, and adverse reactions in different text sources literature, clinical records and social media; methods to achieve interoperability, generalisability, and scalability in text mining: bioc [], rdf and semantic web, among others; and the application of ontologies in text mining and text mining as an ontology builder., from an overview of the existing information extraction methods […]

PMCID: 5199186
PMID: 27888231
DOI: 10.1093/database/baw145

[…] programming interface and refers to whether there is a suitable library for use with this format. the domain column denotes the typical category of information encoded with thisformat.ahttp://bioc.sourceforge.net/bhttp://2011.bionlp-st.org/home/file-formatschttp://brat.nlplab.org/standoff.htmldhttp://www.ncbi.nlm.nih.gov/cbbresearch/lu/demo/pubtator/ehttp://www.tei-c.org/guidelines/p5/fhtt […]

PMCID: 5029005
PMID: 27650402
DOI: 10.1186/s12859-016-1249-5

[…] and disease entities and relationships between them for the biocreative v challenge of recognizing disease name entities and extracting chemical-induced disease relationship. the corpus in the bioc xml format currently contains 1,500 pubmed articles with 4,409 chemicals, 5,818 diseases, and 3,116 chemical–disease interactions, all manually annotated. they used some annotation tools […]


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BioC institution(s)
National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD, USA

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