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BioC specifications


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


No version available


  • person_outline Donald C. Comeau

Publications for BioC

BioC citations


Collaborative relation annotation and quality analysis in Markyt environment

PMCID: 5737204
PMID: 29220479
DOI: 10.1093/database/bax090
call_split See protocol

[…] r when 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 []. Bo […]


A semantic based workflow for biomedical literature annotation

PMCID: 5691355
PMID: 29220478
DOI: 10.1093/database/bax088
call_split See protocol

[…] regular expressions and data parsers such as XPath (XML Path Language). Currently, the system supports the integration of most BioNLP Workshop’s ( 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 ontol […]


SciLite: a platform for displaying text mined annotations as a means to link research articles with biological data

Wellcome Open Res
PMCID: 5527546
PMID: 28948232
DOI: 10.21956/wellcomeopenres.10999.r18949

[…] in some cases integration, the annotations generated are hard to share across different platforms. In part this is due to the lack of a common standard to exchange annotations. Although formats like BioC ( ) and Biological Expression Language ( BEL) are used to represent text-mined outputs, they are highly specific to the domain and their uptake is limited beyond the life sciences text mining com […]


The BioC BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

PMCID: 5225395
PMID: 28077563
DOI: 10.1093/database/baw147
call_split See protocol

[…] Annotation guidelines for the BioC-BioGRID corpus can be summarized as follows: For each full text article, BioGRID curators curated PPIs and/or GIs described in the article, as specified by the BioGRID curation guidelines.Curator […]


Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges

PMCID: 5199160
PMID: 28025348
DOI: 10.1093/database/baw161

[…] ls written in a system-independent language such as Java or Python do not require a specific operating system. Format incompatibilities can be addressed by creating a standard data format. The recent BioC project is such an example, which has created an interoperable data format that is both straightforward and sufficiently expressive to represent a wide variety of text-mining tasks (, ). Another […]


Text mining resources for the life sciences

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

[…] ated into the pivot model, conversely the annotations expressed in the pivot model are translated into the native tool input format. Performance is one of the main design principles of these formats. BioC (), GATE annotation format, LIF () and CAS () are formats designed to be processed by BioC, GATE (), LAPPS () and UIMA () workflows, respectively.These formats present the advantage of giving dir […]


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

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