Recording provenance of workflow runs with RO-Crate

Authors: Leo, Simone, Crusoe, Michael R., Rodríguez-Navas, Laura, Sirvent, Raül, Kanitz, Alexander, De Geest, Paul, Wittner, Rudolf, Pireddu, Luca, Garijo, Daniel, Fernández, José M., Colonnelli, Iacopo, Gallo, Matej, Ohta, Tazro, Suetake, Hirotaka, Capella-Gutierrez, Salvador, de Wit, Renske, Kinoshita, Bruno P., Soiland-Reyes, Stian

Source: PLoS ONE vol. 19, iss. 9, pp. 1-35, 2024

Subject Terms: Computer Science - Digital Libraries

Access URL: http://arxiv.org/abs/2312.07852

Best practices for multimodal clinical data management and integration: An atopic dermatitis research case

Authors: Ohta, Tazro, Hananoe, Ayaka, Fukushima-Nomura, Ayano, Ashizaki, Koichi, Sekita, Aiko, Seita, Jun, Kawakami, Eiryo, Sakurada, Kazuhiro, Amagai, Masayuki, Koseki, Haruhiko, Kawasaki, Hiroshi

Source: In Allergology International April 2024 73(2):255-263

Intercloud brokerages based on PLS method for deploying infrastructures for big data analytics

Authors: Miura, Katsunori, Ohta, Tazro, Powell, Courtney, Munetomo, Masaharu

Source: 2016 IEEE International Conference on Big Data (Big Data) Big Data (Big Data), 2016 IEEE International Conference on. :2097-2102 Dec, 2016

Relation: 2016 IEEE International Conference on Big Data (Big Data)

Reproducible Scientific Computing Environment with Overlay Cloud Architecture

Authors: Yokoyama, Shigetoshi, Masatani, Yoshinobu, Ohta, Tazro, Ogasawara, Osamu, Yoshioka, Nobukazu, Liu, Kai, Aida, Kento

Source: 2016 IEEE 9th International Conference on Cloud Computing (CLOUD) CLOUD Cloud Computing (CLOUD), 2016 IEEE 9th International Conference on. :774-781 Jun, 2016

Relation: 2016 IEEE 9th International Conference on Cloud Computing (CLOUD)

TogoID: an exploratory ID converter to bridge biological datasets

Authors: Ikeda, Shuya, Ono, Hiromasa, Ohta, Tazro, Chiba, Hirokazu, Naito, Yuki, Moriya, Yuki, Kawashima, Shuichi, Yamamoto, Yasunori, Okamoto, Shinobu, Goto, Susumu, Katayama, Toshiaki

Source: Bioinformatics. 38(17):4194-4199

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100162694801.0x000001&indx=1&recIds=ETOCvdc_100162694801.0x000001

A Near Complete Genome Assembly of the Oshima Cherry Cerasus speciosa.

Authors: Fujiwara, Kazumichi, Toyoda, Atsushi, Biswa, Bhim B., Kishida, Takushi, Tsuruta, Momi, Nakamura, Yasukazu, Kimura, Noriko, Kawamoto, Shoko, Sato, Yutaka, Katsuki, Toshio, Kimura, Akatsuki, Nonomura, Ken-Ichi, Niki, Hironori, Yano, Hiroyuki, Umehara, Kinji, Ohta, Tazro, Suzuki, Chikahiko, Koide, Tsuyoshi

Source: Scientific Data; 2/4/2025, Vol. 12 Issue 1, p1-16, 16p

Subject Terms: GENOMICS, GENETIC variation, LIFE sciences, CULTURAL values, GENOMES

Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features.

Authors: Ikeda, Shuya, Aoki-Kinoshita, Kiyoko F., Chiba, Hirokazu, Goto, Susumu, Hosoda, Masae, Kawashima, Shuichi, Kim, Jin-Dong, Moriya, Yuki, Ohta, Tazro, Ono, Hiromasa, Takatsuki, Terue, Yamamoto, Yasunori, Katayama, Toshiaki

Source: Journal of Biomedical Semantics; 1/8/2025, Vol. 16 Issue 1, p1-10, 10p

Subject Terms: LIFE sciences, INFORMATION storage & retrieval systems, SCIENCE databases, DATABASES, WEB-based user interfaces

Recording provenance of workflow runs with RO-Crate.

Authors: Leo, Simone, Crusoe, Michael R., Rodríguez-Navas, Laura, Sirvent, Raül, Kanitz, Alexander, De Geest, Paul, Wittner, Rudolf, Pireddu, Luca, Garijo, Daniel, Fernández, José M., Colonnelli, Iacopo, Gallo, Matej, Ohta, Tazro, Suetake, Hirotaka, Capella-Gutierrez, Salvador, de Wit, Renske, Kinoshita, Bruno P., Soiland-Reyes, Stian

Source: PLoS ONE; 9/10/2024, Vol. 19 Issue 9, p1-35, 35p

Subject Terms: IMAGE analysis, DIGITAL learning, MACHINE learning, WORKFLOW management systems, INFORMATION sharing, DATA modeling, WORKFLOW

ChIP-Atlas 3.0: a data-mining suite to explore chromosome architecture together with large-scale regulome data.

Authors: Zou, Zhaonan, Ohta, Tazro, Oki, Shinya

Source: Nucleic Acids Research; 7/5/2024, Vol. 52 Issue W1, pW45-W53, 9p

GWAS of mosaic loss of chromosome Y highlights genetic effects on blood cell differentiation

Authors: Terao, Chikashi, Momozawa, Yukihide, Ishigaki, Kazuyoshi, Kawakami, Eiryo, Akiyama, Masato, Loh, Po-Ru, Genovese, Giulio, Sugishita, Hiroki, Ohta, Tazro, Hirata, Makoto, Perry, John, Matsuda, Koichi, Murakami, Yoshinori, Kubo, Michiaki, Kamatani, Yoichiro

Source: Nature communications. 10(1):1-10

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100190854444.0x000001&indx=1&recIds=ETOCvdc_100190854444.0x000001

Collaborative environmental DNA sampling from petal surfaces of flowering cherry Cerasus × yedoensis 'Somei-yoshino' across the Japanese archipelago

Authors: Ohta, Tazro, Kawashima, Takeshi, Shinozaki, Natsuko O., Dobashi, Akito, Hiraoka, Satoshi, Hoshino, Tatsuhiko, Kanno, Keiichi, Kataoka, Takafumi, Kawashima, Shuichi, Matsui, Motomu, Nemoto, Wataru, Nishijima, Suguru, Suganuma, Natsuki, Suzuki, Haruo, Taguchi, Y-h., Takenaka, Yoichi, Tanigawa, Yosuke, Tsuneyoshi, Momoka, Yoshitake, Kazutoshi, Sato, Yukuto, Yamashita, Riu, Arakawa, Kazuharu, Iwasaki, Wataru

Source: Journal of plant research. 131(4):709-717

Availability: http://explore.bl.uk/primo_library/libweb/action/display.do?tabs=detailsTab&gathStatTab=true&ct=display&fn=search&doc=ETOCvdc_100119723378.0x000001&indx=1&recIds=ETOCvdc_100119723378.0x000001

A workflow reproducibility scale for automatic validation of biological interpretation results.

Authors: Suetake, Hirotaka, Fukusato, Tsukasa, Igarashi, Takeo, Ohta, Tazro

Source: GigaScience; 2023, Vol. 12 Issue 1, p1-11, 11p

Subject Terms: WORKFLOW, WORKFLOW management systems, RESEARCH personnel, DATA analysis

Workflow sharing with automated metadata validation and test execution to improve the reusability of published workflows.

Authors: Suetake, Hirotaka, Fukusato, Tsukasa, Igarashi, Takeo, Ohta, Tazro

Source: GigaScience; 2023, Vol. 12 Issue 1, p1-10, 10p

Subject Terms: WORKFLOW, WORKFLOW software, METADATA, COST shifting, RESEARCH personnel, HUMAN resources departments, PROOF of concept, SHARING

ChIP-Atlas 2021 update: a data-mining suite for exploring epigenomic landscapes by fully integrating ChIP-seq, ATAC-seq and Bisulfite-seq data.

Authors: Zou, Zhaonan, Ohta, Tazro, Miura, Fumihito, Oki, Shinya

Source: Nucleic Acids Research; 7/5/2022, Vol. 50 Issue W1, pW175-W182, 8p

Experimental Design-Based Functional Mining and Characterization of High-Throughput Sequencing Data in the Sequence Read Archive.

Authors: Nakazato, Takeru¹ nakazato@dbcls.rois.ac.jp, Ohta, Tazro¹, Bono, Hidemasa¹

Source: PLoS ONE. Oct2013, Vol. 8 Issue 10, p1-7. 7p.

Subject Terms: *NUCLEOTIDE sequence, *DATA mining, *EXPERIMENTAL design, *ACQUISITION of data, *GENOMES, *NATURAL language processing, *BIOINFORMATICS

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Improving the trans-ancestry portability of polygenic risk scores by prioritizing variants in predicted cell-type-specific regulatory elements

Authors: Amariuta, Tiffany, Ishigaki, Kazuyoshi, Sugishita, Hiroki, Ohta, Tazro, Koido, Masaru, Dey, Kushal K., Matsuda, Koichi, Murakami, Yoshinori, Price, Alkes L., Kawakami, Eiryo, Terao, Chikashi, Raychaudhuri, Soumya

Source: Nature Genetics; December 2020, Vol. 52 Issue: 12 p1346-1354, 9p

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