Genomics & Informatics

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Application note

June 11, 2019

Fully connecting the Observational Health Data Science and Informatics (OHDSI) initiative with the world of linked open data

Juan M. Banda

Genomics Inform. 2019;17(2):e13.

The usage of controlled biomedical vocabularies is the cornerstone that enables seamless interoperability when using a common data model across multiple data sites. The Observational Health Data Science and Informatics...

Application note

June 19, 2019

Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications

Leyla Garcia, Olga Giraldo, Alexander Garcia, Dietrich Rebholz-Schuhmann

Genomics Inform. 2019;17(2):e14.

The total number of scholarly publications grows day by day, making it necessary to explore and use simple yet effective ways to expose their metadata. Schema.org supports adding structured metadata...

Application note

June 19, 2019

PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts

Jordi Armengol-Estapé, Felipe Soares, Montserrat Marimon, Martin Krallinger

Genomics Inform. 2019;17(2):e15.

Automatically detecting mentions of pharmaceutical drugs and chemical substances is key for the subsequent extraction of relations of chemicals with other biomedical entities such as genes, proteins, diseases, adverse reactions...

Mini review

June 27, 2019

Resources for assigning MeSH IDs to Japanese medical terms

Yuka Tateisi

Genomics Inform. 2019;17(2):e16.

Medical Subject Headings (MeSH), a medical thesaurus created by the National Library of Medicine (NLM), is a useful resource for natural language processing (NLP). In this article, the current status...

Application note

June 26, 2019

OryzaGP: rice gene and protein dataset for named-entity recognition

Pierre Larmande, Huy Do, Yue Wang

Genomics Inform. 2019;17(2):e17.

Text mining has become an important research method in biology, with its original purpose to extract biological entities, such as genes, proteins and phenotypic traits, to extend knowledge from scientific...

Mini review

June 27, 2019

A review of drug knowledge discovery using BioNLP and tensor or matrix decomposition

Mina Gachloo, Yuxing Wang, Jingbo Xia

Genomics Inform. 2019;17(2):e18.

Prediction of the relations among drug and other molecular or social entities is the main knowledge discovery pattern for the purpose of drug-related knowledge discovery. Computational approaches have combined the...

Application note

June 26, 2019

Towards cross-platform interoperability for machine-assisted text annotation

Richard Eckart de Castilho, Nancy Ide, Jin-Dong Kim, Jan-Christoph Klie, Keith Suderman

Genomics Inform. 2019;17(2):e19.

In this paper we investigate cross-platform interoperability for natural language processing (NLP) and, in particular, annotation of textual resources, with an eye toward identifying the design elements of annotation models...

Application note

June 27, 2019

Improving the CONTES method for normalizing biomedical text entities with concepts from an ontology with (almost) no training data

Arnaud Ferré, Mouhamadou Ba, Robert Bossy

Genomics Inform. 2019;17(2):e20.

Entity normalization, or entity linking in the general domain, is an information extraction task that aims to annotate/bind multiple words/expressions in raw text with semantic references, such as concepts of...

Application note

June 24, 2019

Improving spaCy dependency annotation and PoS tagging web service using independent NER services

Nico Colic, Fabio Rinaldi

Genomics Inform. 2019;17(2):e21.

Dependency parsing is often used as a component in many text analysis pipelines. However, performance, especially in specialized domains, suffers from the presence of complex terminology. Our hypothesis is that...

Current Issue: Volume 17(2); Jun 2019

Introduction to BLAH5 special issue: recent progress on interoperability of biomedical text mining Jin-Dong Kim, Kevin Bretonnel Cohen, Nigel Collier, Zhiyong Lu, Fabio Rinaldi Genomics Inform. 2019;17(2):e12. Editorial June 24, 2019 Full text PubReader ePub PDF	Fully connecting the Observational Health Data Science and Informatics (OHDSI) initiative with the world of linked open data Juan M. Banda Genomics Inform. 2019;17(2):e13. Application note June 24, 2019 Full text PubReader ePub PDF
Biotea-2-Bioschemas, facilitating structured markup for semantically annotated scholarly publications Leyla Garcia, Olga Giraldo, Alexander Garcia, Dietrich Rebholz-Schuhmann Genomics Inform. 2019;17(2):e14. Application note June 24, 2019 Full text PubReader ePub PDF	PharmacoNER Tagger: a deep learning-based tool for automatically finding chemicals and drugs in Spanish medical texts Jordi Armengol-Estapé, Felipe Soares, Montserrat Marimon, Martin Krallinger Genomics Inform. 2019;17(2):e15. Application note June 24, 2019 Full text PubReader ePub PDF
Resources for assigning MeSH IDs to Japanese medical terms Yuka Tateisi Genomics Inform. 2019;17(2):e16. Mini review June 24, 2019 Full text PubReader ePub PDF	OryzaGP: rice gene and protein dataset for named-entity recognition Pierre Larmande, Huy Do, Yue Wang Genomics Inform. 2019;17(2):e17. Application note June 24, 2019 Full text PubReader ePub PDF
A review of drug knowledge discovery using BioNLP and tensor or matrix decomposition Mina Gachloo, Yuxing Wang, Jingbo Xia Genomics Inform. 2019;17(2):e18. Mini review June 24, 2019 Full text PubReader ePub PDF	Towards cross-platform interoperability for machine-assisted text annotation Richard Eckart de Castilho, Nancy Ide, Jin-Dong Kim, Jan-Christoph Klie, Keith Suderman Genomics Inform. 2019;17(2):e19. Application note June 24, 2019 Full text PubReader ePub PDF
Improving the CONTES method for normalizing biomedical text entities with concepts from an ontology with (almost) no training data Arnaud Ferré, Mouhamadou Ba, Robert Bossy Genomics Inform. 2019;17(2):e20. Application note June 24, 2019 Full text PubReader ePub PDF	Improving spaCy dependency annotation and PoS tagging web service using independent NER services Nico Colic, Fabio Rinaldi Genomics Inform. 2019;17(2):e21. Application note June 24, 2019 Full text PubReader ePub PDF

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Towards cross-platform interoperability for machine-assisted text annotation Richard Eckart de Castilho, Nancy Ide, Jin-Dong Kim, Jan-Christoph Klie, Keith Suderman Genomics Inform. 2019;17(2):e19.	Use of Graph Database for the Integration of Heterogeneous Biological Data Byoung-Ha Yoon, Seon-Kyu Kim, Seon-Young Kim Genomics Inform. 2017;15(1):19-27. Cited By 9
Use of Graph Database for the Integration of Heterogeneous Biological Data Byoung-Ha Yoon, Seon-Kyu Kim, Seon-Young Kim Genomics Inform. 2017;15(1):19-27.	Evaluation of Digital PCR as a Technique for Monitoring Acute Rejection in Kidney Transplantation Hyeseon Lee, Young-Mi Park, Yu-Mee We, Duck Jong Han, Jung-Woo Seo, Haena Moon, Yu-Ho Lee, Yang-Gyun Kim, Ju-Young Moon, Sang-Ho Lee, et al. Genomics Inform. 2017;15(1):2-10. Cited By 9
A review of drug knowledge discovery using BioNLP and tensor or matrix decomposition Mina Gachloo, Yuxing Wang, Jingbo Xia Genomics Inform. 2019;17(2):e18.	A ChIP-Seq Data Analysis Pipeline Based on Bioconductor Packages Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim Genomics Inform. 2017;15(1):11-18. Cited By 6
MergeReference: A Tool for Merging Reference Panels for HLA Imputation Seungho Cook, Buhm Han Genomics Inform. 2017;15(3):108-111.	Roles of Oncogenic Long Non-coding RNAs in Cancer Development Hyunhee Do, Wanyeon Kim Genomics Inform. 2018;16(4):e18. Cited By 4
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