Organizing an in-class hackathon to correct pdf-to-text conversion errors of genomics & informatics 1.0

Sunho Kim; Royoung Kim; Hee Jo Nam; Ryeo Gyeong Kim; Enjin Ko; Han Su Kim; Jihye Shin; Daeun Cho; Yurhee Jin; Soyeon Bae; Ye Won Jo; San Ah Jeong; Yena Kim; Seoyeon Ahn; Bomi Jang; Jiheyon Seong; Yujin Lee; Si Eun Seo; Yujin Kim; Ha Jeong Kim; Hyeji Kim; Hye Lynn Sung; Hyoyoung Lho; Jaywon Koo; Jion Chu; Juwon Lim; Youngju Kim; Kyungyeon Lee; Yuri Lim; Meongeun Kim; Seonjeong Hwang; Shinhye Han; Sohyeun Bae; Sua Kim; Suhyeon Yoo; Yeonjeong Seo; Yerim Shin; Yonsoo Kim; You Jung Ko; Jihee Baek; Hyejin Hyun; Hyemin Choi; Ji Hye Oh; Da Young Kim; Hyun Seok Park

doi:10.5808/GI.2020.18.3.e33

Organizing an in-class hackathon to correct pdf-to-text conversion errors of genomics & informatics 1.0

Sunho Kim, Royoung Kim, Hee Jo Nam, Ryeo Gyeong Kim, Enjin Ko, Han Su Kim, Jihye Shin, Daeun Cho, Yurhee Jin, Soyeon Bae, Ye Won Jo, San Ah Jeong, Yena Kim, Seoyeon Ahn, Bomi Jang, Jiheyon Seong, Yujin Lee, Si Eun Seo, Yujin Kim, Ha Jeong KimHyeji Kim, Hye Lynn Sung, Hyoyoung Lho, Jaywon Koo, Jion Chu, Juwon Lim, Youngju Kim, Kyungyeon Lee, Yuri Lim, Meongeun Kim, Seonjeong Hwang, Shinhye Han, Sohyeun Bae, Sua Kim, Suhyeon Yoo, Yeonjeong Seo, Yerim Shin, Yonsoo Kim, You Jung Ko, Jihee Baek, Hyejin Hyun, Hyemin Choi, Ji Hye Oh, Da Young Kim, Hyun Seok Park

Research output: Contribution to journal › Article › peer-review

1 Scopus citations

Abstract

This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-col-umn biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.

Original language	English
Article number	e33
Pages (from-to)	1-8
Number of pages	8
Journal	Genomics and Informatics
Volume	18
Issue number	3
DOIs	https://doi.org/10.5808/GI.2020.18.3.e33
State	Published - 2020

Bibliographical note

Publisher Copyright:
© 2020, Korea Genome Organization.

Keywords

Biomedical text mining
Corpus
Text analytics

Access to Document

10.5808/GI.2020.18.3.e33

Cite this

Kim, S., Kim, R., Nam, H. J., Kim, R. G., Ko, E., Kim, H. S., Shin, J., Cho, D., Jin, Y., Bae, S., Jo, Y. W., Jeong, S. A., Kim, Y., Ahn, S., Jang, B., Seong, J., Lee, Y., Seo, S. E., Kim, Y., ... Park, H. S. (2020). Organizing an in-class hackathon to correct pdf-to-text conversion errors of genomics & informatics 1.0. Genomics and Informatics, 18(3), 1-8. Article e33. https://doi.org/10.5808/GI.2020.18.3.e33

@article{495017bc9142488b89b1842c9dd69d9e,

title = "Organizing an in-class hackathon to correct pdf-to-text conversion errors of genomics & informatics 1.0",

abstract = "This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-col-umn biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.",

keywords = "Biomedical text mining, Corpus, Text analytics",

author = "Sunho Kim and Royoung Kim and Nam, {Hee Jo} and Kim, {Ryeo Gyeong} and Enjin Ko and Kim, {Han Su} and Jihye Shin and Daeun Cho and Yurhee Jin and Soyeon Bae and Jo, {Ye Won} and Jeong, {San Ah} and Yena Kim and Seoyeon Ahn and Bomi Jang and Jiheyon Seong and Yujin Lee and Seo, {Si Eun} and Yujin Kim and Kim, {Ha Jeong} and Hyeji Kim and Sung, {Hye Lynn} and Hyoyoung Lho and Jaywon Koo and Jion Chu and Juwon Lim and Youngju Kim and Kyungyeon Lee and Yuri Lim and Meongeun Kim and Seonjeong Hwang and Shinhye Han and Sohyeun Bae and Sua Kim and Suhyeon Yoo and Yeonjeong Seo and Yerim Shin and Yonsoo Kim and Ko, {You Jung} and Jihee Baek and Hyejin Hyun and Hyemin Choi and Oh, {Ji Hye} and Kim, {Da Young} and Park, {Hyun Seok}",

note = "Publisher Copyright: {\textcopyright} 2020, Korea Genome Organization.",

year = "2020",

doi = "10.5808/GI.2020.18.3.e33",

language = "English",

volume = "18",

pages = "1--8",

journal = "Genomics and Informatics",

issn = "2234-0742",

publisher = "Korea Genome Organization",

number = "3",

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Kim, S, Kim, R, Nam, HJ, Kim, RG, Ko, E, Kim, HS, Shin, J, Cho, D, Jin, Y, Bae, S, Jo, YW, Jeong, SA, Kim, Y, Ahn, S, Jang, B, Seong, J, Lee, Y, Seo, SE, Kim, Y, Kim, HJ, Kim, H, Sung, HL, Lho, H, Koo, J, Chu, J, Lim, J, Kim, Y, Lee, K, Lim, Y, Kim, M, Hwang, S, Han, S, Bae, S, Kim, S, Yoo, S, Seo, Y, Shin, Y, Kim, Y, Ko, YJ, Baek, J, Hyun, H, Choi, H, Oh, JH, Kim, DY & Park, HS 2020, 'Organizing an in-class hackathon to correct pdf-to-text conversion errors of genomics & informatics 1.0', Genomics and Informatics, vol. 18, no. 3, e33, pp. 1-8. https://doi.org/10.5808/GI.2020.18.3.e33

TY - JOUR

T1 - Organizing an in-class hackathon to correct pdf-to-text conversion errors of genomics & informatics 1.0

AU - Kim, Sunho

AU - Kim, Royoung

AU - Nam, Hee Jo

AU - Kim, Ryeo Gyeong

AU - Ko, Enjin

AU - Kim, Han Su

AU - Shin, Jihye

AU - Cho, Daeun

AU - Jin, Yurhee

AU - Bae, Soyeon

AU - Jo, Ye Won

AU - Jeong, San Ah

AU - Kim, Yena

AU - Ahn, Seoyeon

AU - Jang, Bomi

AU - Seong, Jiheyon

AU - Lee, Yujin

AU - Seo, Si Eun

AU - Kim, Yujin

AU - Kim, Ha Jeong

AU - Kim, Hyeji

AU - Sung, Hye Lynn

AU - Lho, Hyoyoung

AU - Koo, Jaywon

AU - Chu, Jion

AU - Lim, Juwon

AU - Kim, Youngju

AU - Lee, Kyungyeon

AU - Lim, Yuri

AU - Kim, Meongeun

AU - Hwang, Seonjeong

AU - Han, Shinhye

AU - Bae, Sohyeun

AU - Kim, Sua

AU - Yoo, Suhyeon

AU - Seo, Yeonjeong

AU - Shin, Yerim

AU - Kim, Yonsoo

AU - Ko, You Jung

AU - Baek, Jihee

AU - Hyun, Hyejin

AU - Choi, Hyemin

AU - Oh, Ji Hye

AU - Kim, Da Young

AU - Park, Hyun Seok

PY - 2020

Y1 - 2020

N2 - This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-col-umn biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.

AB - This paper describes a community effort to improve earlier versions of the full-text corpus of Genomics & Informatics by semi-automatically detecting and correcting PDF-to-text conversion errors and optical character recognition errors during the first hackathon of Genomics & Informatics Annotation Hackathon (GIAH) event. Extracting text from multi-col-umn biomedical documents such as Genomics & Informatics is known to be notoriously difficult. The hackathon was piloted as part of a coding competition of the ELTEC College of Engineering at Ewha Womans University in order to enable researchers and students to create or annotate their own versions of the Genomics & Informatics corpus, to gain and create knowledge about corpus linguistics, and simultaneously to acquire tangible and transferable skills. The proposed projects during the hackathon harness an internal database containing different versions of the corpus and annotations.

KW - Biomedical text mining

KW - Corpus

KW - Text analytics

UR - http://www.scopus.com/inward/record.url?scp=85092103087&partnerID=8YFLogxK

U2 - 10.5808/GI.2020.18.3.e33

DO - 10.5808/GI.2020.18.3.e33

M3 - Article

AN - SCOPUS:85092103087

SN - 2234-0742

VL - 18

SP - 1

EP - 8

JO - Genomics and Informatics

JF - Genomics and Informatics

IS - 3

M1 - e33

ER -

Organizing an in-class hackathon to correct pdf-to-text conversion errors of genomics & informatics 1.0

Abstract

Bibliographical note

Keywords

Access to Document

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