BioCconvert: A Conversion Tool Between BioC and PubAnnotation

نویسندگان

  • Donald C. Comeau
  • Rezarta Islamaj Dogan
  • Sun Kim
  • Chih-Hsuan Wei
  • W. John Wilbur
  • Zhiyong Lu
چکیده

BioC is a simple XML data format for text, annotations, and relations. PubAnnotation is a repository of text annotations focused on the life science literature. A conversion tool between BioC XML and the JSON import / export format of PubAnnotation has been developed, BioCconvert. As a demonstration, the Ab3P gold standard abbreviation annotations are being made available through PubAnnotation. Keywords—BioC, PubAnnotation, interoperability, biomedical annotations

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

منابع مشابه

tmBioC: improving interoperability of text-mining tools with BioC

The lack of interoperability among biomedical text-mining tools is a major bottleneck in creating more complex applications. Despite the availability of numerous methods and techniques for various text-mining tasks, combining different tools requires substantial efforts and time owing to heterogeneity and variety in data formats. In response, BioC is a recent proposal that offers a minimalistic...

متن کامل

PubAnnotation-query: a search tool for corpora with multi-layers of annotation

PubAnnotation provides a convenient platform to collect and align corpora with various annotations. However, corpora must be searchable to be useful, but there has been no standard way to search corpora, particularly when multiple layers of annotations are present. PubAnnotation-query is designed to provide an interface for searching corpora annotated with multiple layers. This paper describes ...

متن کامل

A Visual Tool for Displaying Annotations in BioC

To support data interoperability for annotation results, we developed BioC-Viewer (http://viewer.bioqrator.org/). BioC-Viewer is a web-based interactive curation tool to visualize annotation results from text mining tools and to easily curate entities and relationships with supporting BioC format. Since our focus was on a visual tool for BioGRID curators in BioCreative V BioC Track, BioC-Viewer...

متن کامل

BioC viewer: a web-based tool for displaying and merging annotations in BioC

BioC is an XML-based format designed to provide interoperability for text mining tools and manual curation results. A challenge of BioC as a standard format is to align annotations from multiple systems. Ideally, this should not be a major problem if users follow guidelines given by BioC key files. Nevertheless, the misalignment between text and annotations happens quite often because different...

متن کامل

Overview of BioCreative V BioC Track

BioC is a simple XML format for text, annotations and relations, and was developed to achieve interoperability for biomedical text processing. Following the success of BioC in BioCreative IV, the BioCreative V BioC track addressed a collaborative task to build an assistant tool for BioGRID curation. For this track, we divided the whole task into 8 different subtopics including gene/protein/orga...

متن کامل

ذخیره در منابع من


  با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید

برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید

ثبت نام

اگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید

عنوان ژورنال:

دوره   شماره 

صفحات  -

تاریخ انتشار 2016