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BLAH7 | Application note

September 30, 2021


A biomedically oriented automatically annotated Twitter COVID-19 dataset
Luis Alberto Robles Hernandez, Tiffany J. Callahan, Juan M. Banda
Genomics Inform. 2021;19(3):e21.

The use of social media data, like Twitter, for biomedical research has been gradually increasing over the years. With the coronavirus disease 2019 (COVID-19) pandemic, researchers have turned to more...

BLAH7 | Application note

September 30, 2021


Improving classification of low-resource COVID-19 literature by using Named Entity Recognition
Oscar Lithgow-Serrano, Joseph Cornelius, Vani Kanjirangat, Carlos-Francisco Méndez-Cruz, Fabio Rinaldi
Genomics Inform. 2021;19(3):e22.

Automatic document classification for highly interrelated classes is a demanding task that becomes more challenging when there is little labeled data for training. Such is the case of the coronavirus...

BLAH7 | Application note

September 30, 2021


LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19
Sizhuo Ouyang, Yuxing Wang, Kaiyin Zhou, Jingbo Xia
Genomics Inform. 2021;19(3):e23.

Currently, coronavirus disease 2019 (COVID-19) literature has been increasing dramatically, and the increased text amount make it possible to perform large scale text mining and knowledge discovery. Therefore, curation of...

BLAH7 | Application note

September 30, 2021


COVID-19 recommender system based on an annotated multilingual corpus
Márcia Barros, Pedro Ruas, Diana Sousa, Ali Haider Bangash, Francisco M. Couto
Genomics Inform. 2021;19(3):e24.

Tracking the most recent advances in Coronavirus disease 2019 (COVID-19)‒related research is essential, given the disease's novelty and its impact on society. However, with the publication pace speeding up, researchers...

BLAH7 | Application note

September 30, 2021


Constructing Japanese MeSH term dictionaries related to the COVID-19 literature
Atsuko Yamaguchi, Terue Takatsuki, Yuka Tateisi, Felipe Soares
Genomics Inform. 2021;19(3):e25.

The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information has been updated with considerable frequency. For society to derive benefits from this...

BLAH7 | Application note

September 30, 2021


O-JMeSH: creating a bilingual English-Japanese controlled vocabulary of MeSH UIDs through machine translation and mutual information
Felipe Soares, Yuka Tateisi, Terue Takatsuki, Atsuko Yamaguchi
Genomics Inform. 2021;19(3):e26.

Previous approaches to create a controlled vocabulary for Japanese have resorted to existing bilingual dictionary and transformation rules to allow such mappings. However, given the possible new terms introduced due...

BLAH7 | Application note

September 30, 2021


OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition
Pierre Larmande, Yusha Liu, Xinzhi Yao, Jingbo Xia
Genomics Inform. 2021;19(3):e27.

Due to the rapid evolution of high-throughput technologies, a tremendous amount of data is being produced in the biological domain, which poses a challenging task for information extraction and natural...

BLAH7 | Opinion

September 30, 2021


Visualizing the phenotype diversity: a case study of Alexander disease
Eisuke Dohi, Ali Haider Bangash
Genomics Inform. 2021;19(3):e28.

Since only a small number of patients have a rare disease, it is difficult to identify all of the features of these diseases. This is especially true for patients presenting...

Original article

September 30, 2021


Molecular insights into the role of genetic determinants of congenital hypothyroidism
Yedukondalu Kollati, Radha Rama Devi Akella, Shaik Mohammad Naushad, Rajesh K. Patel, G. Bhanuprakash Reddy, Vijaya R. Dirisala
Genomics Inform. 2021;19(3):e29.

In our previous studies, we have demonstrated the association of certain variants of the thyroid-stimulating hormone receptor (TSHR), thyroid peroxidase (TPO), and thyroglobulin (TG) genes with congenital hypothyroidism. Herein, we...

Original article

September 30, 2021


Rapid and sensitive detection of Salmonella species targeting the hilA gene using a loop-mediated isothermal amplification assay
Jiyon Chu, Juyoun Shin, Shinseok Kang, Sun Shin, Yeun-Jun Chung
Genomics Inform. 2021;19(3):e30.

Salmonella species are among the major pathogens that cause foodborne illness outbreaks. In this study, we aimed to develop a loop-mediated isothermal amplification (LAMP) assay for the rapid and sensitive...

Original article

September 30, 2021


Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients
Songtham Anuntakarun, Vorthon Sawaswong, Rungrat Jitvaropas, Kesmanee Praianantathavorn, Witthaya Poomipak, Yupin Suputtamongkol, Chintana Chirathaworn, Sunchai Payungporn
Genomics Inform. 2021;19(3):e31.

Leptospirosis is a zoonotic disease caused by spirochetes from the genus Leptospira. In Thailand, Leptospira interrogans is a major cause of leptospirosis. Leptospirosis patients present with a wide range of...

Original article

September 30, 2021


Draft genome of Semisulcospira libertina, a species of freshwater snail
Jeong-An Gim, Kyung-Wan Baek, Young-Sool Hah, Ho Jin Choo, Ji-Seok Kim, Jun-Il Yoo
Genomics Inform. 2021;19(3):e32.

Semisulcospira libertina, a species of freshwater snail, is widespread in East Asia. It is important as a food source. Additionally, it is a vector of clonorchiasis, paragonimiasis, metagonimiasis, and other...

Original article

September 30, 2021


Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation
Maheswari Patturaj, Aiswarya Munusamy, Nithishkumar Kannan, Ulaganathan Kandasamy, Yasodha Ramasamy
Genomics Inform. 2021;19(3):e33.

Eucalyptus is one of the major plantation species with wide variety of industrial uses. Polymorphic and informative simple sequence repeats (SSRs) have broad range of applications in genetic analysis. ...

Application note

September 30, 2021


High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array
Haeun Lee, Cherl-Joon Lee, Dong Hee Kim, Chun-Sung Cho, Wonseok Shin, Kyudong Han
Genomics Inform. 2021;19(3):e34.

Digital PCR (dPCR) is the third-generation PCR that enables real-time absolute quantification without reference materials. Recently, global diagnosis companies have developed new dPCR equipment. In line with the development, the...
Current Issue
Volume 19(3); Sep 2021
Editor’s introduction to the special section on the 7th Biomedical Linked Annotation Hackathon (BLAH7)
Jin-Dong Kim, Kevin Bretonnel Cohen, Fabio Rinaldi, Zhiyong Lu, Hyun-Seok Park
Genomics Inform. 2021;19(3):e20.

Editorial

September 30, 2021
A biomedically oriented automatically annotated Twitter COVID-19 dataset
Luis Alberto Robles Hernandez, Tiffany J. Callahan, Juan M. Banda
Genomics Inform. 2021;19(3):e21.

BLAH7 | Application note

September 30, 2021
Improving classification of low-resource COVID-19 literature by using Named Entity Recognition
Oscar Lithgow-Serrano, Joseph Cornelius, Vani Kanjirangat, Carlos-Francisco Méndez-Cruz, Fabio Rinaldi
Genomics Inform. 2021;19(3):e22.

BLAH7 | Application note

September 30, 2021
LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19
Sizhuo Ouyang, Yuxing Wang, Kaiyin Zhou, Jingbo Xia
Genomics Inform. 2021;19(3):e23.

BLAH7 | Application note

September 30, 2021
COVID-19 recommender system based on an annotated multilingual corpus
Márcia Barros, Pedro Ruas, Diana Sousa, Ali Haider Bangash, Francisco M. Couto
Genomics Inform. 2021;19(3):e24.

BLAH7 | Application note

September 30, 2021
Constructing Japanese MeSH term dictionaries related to the COVID-19 literature
Atsuko Yamaguchi, Terue Takatsuki, Yuka Tateisi, Felipe Soares
Genomics Inform. 2021;19(3):e25.

BLAH7 | Application note

September 30, 2021
O-JMeSH: creating a bilingual English-Japanese controlled vocabulary of MeSH UIDs through machine translation and mutual information
Felipe Soares, Yuka Tateisi, Terue Takatsuki, Atsuko Yamaguchi
Genomics Inform. 2021;19(3):e26.

BLAH7 | Application note

September 30, 2021
OryzaGP 2021 update: a rice gene and protein dataset for named-entity recognition
Pierre Larmande, Yusha Liu, Xinzhi Yao, Jingbo Xia
Genomics Inform. 2021;19(3):e27.

BLAH7 | Application note

September 30, 2021
Visualizing the phenotype diversity: a case study of Alexander disease
Eisuke Dohi, Ali Haider Bangash
Genomics Inform. 2021;19(3):e28.

BLAH7 | Opinion

September 30, 2021
Molecular insights into the role of genetic determinants of congenital hypothyroidism
Yedukondalu Kollati, Radha Rama Devi Akella, Shaik Mohammad Naushad, Rajesh K. Patel, G. Bhanuprakash Reddy, Vijaya R. Dirisala
Genomics Inform. 2021;19(3):e29.

Original article

September 30, 2021
Rapid and sensitive detection of Salmonella species targeting the hilA gene using a loop-mediated isothermal amplification assay
Jiyon Chu, Juyoun Shin, Shinseok Kang, Sun Shin, Yeun-Jun Chung
Genomics Inform. 2021;19(3):e30.

Original article

September 30, 2021
Comparative genome characterization of Leptospira interrogans from mild and severe leptospirosis patients
Songtham Anuntakarun, Vorthon Sawaswong, Rungrat Jitvaropas, Kesmanee Praianantathavorn, Witthaya Poomipak, Yupin Suputtamongkol, Chintana Chirathaworn, Sunchai Payungporn
Genomics Inform. 2021;19(3):e31.

Original article

September 30, 2021
Draft genome of Semisulcospira libertina, a species of freshwater snail
Jeong-An Gim, Kyung-Wan Baek, Young-Sool Hah, Ho Jin Choo, Ji-Seok Kim, Jun-Il Yoo
Genomics Inform. 2021;19(3):e32.

Original article

September 30, 2021
Chromosome-specific polymorphic SSR markers in tropical eucalypt species using low coverage whole genome sequences: systematic characterization and validation
Maheswari Patturaj, Aiswarya Munusamy, Nithishkumar Kannan, Ulaganathan Kandasamy, Yasodha Ramasamy
Genomics Inform. 2021;19(3):e33.

Original article

September 30, 2021
High-accuracy quantitative principle of a new compact digital PCR equipment: Lab On An Array
Haeun Lee, Cherl-Joon Lee, Dong Hee Kim, Chun-Sung Cho, Wonseok Shin, Kyudong Han
Genomics Inform. 2021;19(3):e34.

Application note

September 30, 2021

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LitCovid-AGAC: cellular and molecular level annotation data set based on COVID-19 Sizhuo Ouyang, Yuxing Wang, Kaiyin Zhou, Jingbo Xia Genomics Inform. 2021;19(3):e23. Sol A Jeon, Jong Lyul Park, Jong-Hwan Kim, Jeong Hwan Kim, Yong Sung Kim, Jin Cheon Kim, Seon-Young Kim Genomics Inform. 2019;17(3):e32. Cited By 16
Improving classification of low-resource COVID-19 literature by using Named Entity Recognition Oscar Lithgow-Serrano, Joseph Cornelius, Vani Kanjirangat, Carlos-Francisco Méndez-Cruz, Fabio Rinaldi Genomics Inform. 2021;19(3):e22. Seungyeoun Lee, Heeju Lim Genomics Inform. 2019;17(4):e41. Cited By 14
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