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The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows

Toshiaki Katayama, Kazuharu Arakawa, Mitsuteru Nakao, Keiichiro Ono, Kiyoko F Aoki-Kinoshita, Yasunori Yamamoto, Atsuko Yamaguchi, Shuichi Kawashima, Hong-Woo Chun, Jan Aerts, Bruno Aranda, Load Hendrix Barboza (+45 others)
2010 Journal of Biomedical Semantics  
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient  ...  software developers are still necessary for an effective advance in bioinformatics web service technologies.  ...  Authors' contributions All authors attended the BioHackathon 2008. TK and KAr primarily wrote the manuscript. TK, YY, SK, MN, HC, AY, TNo, KAs and TTak organized the BioHackathon 2008.  ... 
doi:10.1186/2041-1480-1-8 pmid:20727200 pmcid:PMC2939597 fatcat:ytcct7auwbexdf4qwcvhl4ac4a

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications

Toshiaki Katayama, Mark D Wilkinson, Rutger Vos, Takeshi Kawashima, Shuichi Kawashima, Mitsuteru Nakao, Yasunori Yamamoto, Hong-Woo Chun, Atsuko Yamaguchi, Shin Kawano, Jan Aerts, Kiyoko F Aoki-Kinoshita (+45 others)
2011 Journal of Biomedical Semantics  
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability between such tools.  ...  Results: Developers in attendance came from diverse backgrounds, with experts in Web services, workflow tools, text mining and visualization.  ...  The first DBCLS BioHackathon [2] focused on standardization of bioinformatics Web services, and in particular on standardizing data-exchange formats to increase interoperability in support of simplified  ... 
doi:10.1186/2041-1480-2-4 pmid:21806842 pmcid:PMC3170566 fatcat:k7sl6kqe55h2jmb2tz4a53nqs4

BioHackathon 2012 report
BioHackathon 2012報告

2012 Journal of Information Processing and Management  
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. Journal of Biomedical Semantics. 2010, vol. 1, no. 8, doi: 10.1186/2041-1480-  ... 
doi:10.1241/johokanri.55.606 fatcat:7pymsrsbybctfeakrdrx7illau

The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies

Toshiaki Katayama, Mark D Wilkinson, Gos Micklem, Shuichi Kawashima, Atsuko Yamaguchi, Mitsuteru Nakao, Yasunori Yamamoto, Shinobu Okamoto, Kenta Oouchida, Hong-Woo Chun, Jan Aerts, Hammad Afzal (+54 others)
2013 Journal of Biomedical Semantics  
BioHackathon 2010 was the third in a series of meetings hosted by the Database Center for Life Sciences (DBCLS) in Tokyo, Japan.  ...  We discussed on topics including guidelines for designing semantic data and interoperability of resources. We consequently developed tools and clients for analysis and visualization.  ...  Furthermore, to fully utilize these RDF data in analytical workflows, further efforts were made to support native RDF-consuming Web services.  ... 
doi:10.1186/2041-1480-4-6 pmid:23398680 pmcid:PMC3598643 fatcat:fm5xaotu3nbafibe3pm3js4d7u

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz (+65 others)
2020 F1000Research  
We share our perspective on the state of the art, continued challenges, and goals for future research and development for the life sciences Semantic Web.  ...  We report on the activities of the 2015 edition of the BioHackathon, an annual event that brings together researchers and developers from around the world to develop tools and technologies that promote  ...  ) and the Database Center for Life Science (DBCLS).  ... 
doi:10.12688/f1000research.18236.1 pmid:32308977 pmcid:PMC7141167 fatcat:oaglnztjrrhpvgluujl3reudoe

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services

Toshiaki Katayama, Shuichi Kawashima, Gos Micklem, Shin Kawano, Jin-Dong Kim, Simon Kocbek, Shinobu Okamoto, Yue Wang, Hongyan Wu, Atsuko Yamaguchi, Yasunori Yamamoto, Erick Antezana (+64 others)
2019 F1000Research  
Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively.  ...  The second section describes how we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery.  ...  We thank Yuji Kohara, the director of DBCLS, for his supporting the BioHackathons.  ... 
doi:10.12688/f1000research.18238.1 fatcat:mdt6bijqlveanplh4bmca5towu

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains

Toshiaki Katayama, Mark D Wilkinson, Kiyoko F Aoki-Kinoshita, Shuichi Kawashima, Yasunori Yamamoto, Atsuko Yamaguchi, Shinobu Okamoto, Shin Kawano, Jin-Dong Kim, Yue Wang, Hongyan Wu, Yoshinobu Kano (+73 others)
2014 Journal of Biomedical Semantics  
, and the development of applications for Semantic Web data.  ...  The application of semantic technologies to the integration of biological data and the interoperability of bioinformatics analysis and visualization tools has been the common theme of a series of annual  ...  Initially, the focus was on Web services and workflows to enable efficient data retrieval.  ... 
doi:10.1186/2041-1480-5-5 pmid:24495517 pmcid:PMC3978116 fatcat:hyb4sddegjbjncdhugr5lm4wu4

TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services

T. Katayama, M. Nakao, T. Takagi
2010 Nucleic Acids Research  
Web services have become widely used in bioinformatics analysis, but there exist incompatibilities in interfaces and data types, which prevent users from making full use of a combination of these services  ...  The TogoWS SOAP API resolves compatibility issues found on the server and client-side SOAP implementations. The TogoWS service is freely available at: http://  ...  in the current Web services in bioinformatics and determined the required infrastructure to make these services interoperable.  ... 
doi:10.1093/nar/gkq386 pmid:20472643 pmcid:PMC2896079 fatcat:fwil2d32vvgm5ewyrcmc6dm7ea

Efforts Towards Accessible And Reliable Bioinformatics

Matúš Kalaš, Inge Jonassen
2015 Zenodo  
We aimed at utilising the World-Wide-Web and industrial standards, in order to increase compatibility and maintainability, and foster shared effort.  ...  broad topic of integrative bioinformatics, in particular with respect to bioinformatics software and services.  ...  EDAM can serve as a Semantic-Web vocabulary for bioinformatics data, what was enabled and tested at the 4 th DBCLS BioHackathon, in 2011 ).  ... 
doi:10.5281/zenodo.33715 fatcat:2pxqpqu5yvat3ctdedqam3sjsi

Workshop on FAIR Computational Workflows - ECCB 2020

Ignacio Eguinoa, Carole Goble, Michael R Crusoe, Stian Soiland-Reyes, Salvador Capella-Gutierrez, Sarah Cohen-Boulakia, Björn Grüning, Alexander Peltzer, Simone Leo, Frederik Coppens, Mateusz Kuzak
2020 Zenodo  
Slides used to present the Workshop on FAIR Computational Workflows during ECCB 2020 pre meetings (New Trends in Bioinformatics).  ...  at the 2018 American Geophysical Union (AGU) Fall Meeting "FAIRness assessment for software" at the 2018 DBCLS/NBDC BioHackathon "Making Software FAIR" at the DTL Communities@Work 2018 Conference  ...  Exchange format for Workflow Hub Snapshot and versioning entries Marking up workflows with metadata Metadata provided about a workflow highly variable Web-based markup.  ... 
doi:10.5281/zenodo.4071482 fatcat:trc6bjczfrd7vohlad54fzw7ey

Enriched biodiversity data as a resource and service

Rutger Vos, Jordan Biserkov, Bachir Balech, Niall Beard, Matthew Blissett, Christian Brenninkmeijer, Tom van Dooren, David Eades, George Gosline, Quentin Groom, Thomas Hamann, Hannes Hettling (+23 others)
2014 Biodiversity Data Journal  
Acknowledgements The Biodiversity Data Enrichment Hackathon was supported by the EU-funded pro-iBiosphere project (Coordination and policy development in preparation for a European Open Biodiversity Knowledge  ...  Management System, addressing Acquisition, Curation, Synthesis, Interoperability and Dissemination, grant No 312848) and Naturalis Biodiversity Center.  ...  The approach is akin to Open Space Technology (Owen 1997) , whose application was pioneered in the bioinformatics domain by the DBCLS BioHackathons.  ... 
doi:10.3897/bdj.2.e1125 pmid:25057255 pmcid:PMC4092319 fatcat:knyjmsmbcnbrpai6awxgfhrrgy

Sapporo: A workflow execution service that encourages the reuse of workflows in various languages in bioinformatics

Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita, Takeshi Fujino, Tsuyoshi Hachiya, Yuichi Kodama, Takatomo Fujisawa, Osamu Ogasawara, Atsushi Shimizu, Masanori Arita, Tsukasa Fukusato (+2 others)
2022 F1000Research  
The API follows the Workflow Execution Service API standard proposed by the Global Alliance for Genomics and Health.  ...  Workflow systems, or so-called workflow languages, are used for the description and execution of a set of data analysis steps.  ...  the project: the Pitagora Meetup, Workflow Meetup Japan, NBDC/DBCLS BioHackathon Series, Elixir's BioHackathon Europe Series, GA4GH Cloud WorkStream, Common Workflow Language Community, Nextflow Community  ... 
doi:10.12688/f1000research.122924.1 fatcat:yss5w5lwfbgmzp3wzxv44b3kby

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

J. Ison, M. Kalas, I. Jonassen, D. Bolser, M. Uludag, H. McWilliam, J. Malone, R. Lopez, S. Pettifer, P. Rice
2013 Bioinformatics  
It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to  ...  Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats.  ...  We thank the Bio-jETI, eSysbio, SEQanswers, BioCatalogue and SoftWare Ontology developers, the participants of BioHackathon'11 and all Web service providers that have annotated their services, for their  ... 
doi:10.1093/bioinformatics/btt113 pmid:23479348 pmcid:PMC3654706 fatcat:l4b736gzizf2xjgy6aneqlokwy

Referee report. For: BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services [version 1; peer review: 1 approved with reservations]

Todd J. Vision
Here we report advancements made in the 6th and 7th annual BioHackathons which were held in Tokyo and Miyagi respectively.  ...  we defined descriptions of datasets, the provenance of data, and quality assessment of services and service discovery.  ...  We thank Yuji Kohara, the director of DBCLS, for his supporting the BioHackathons.  ... 
doi:10.5256/f1000research.19950.r54207 fatcat:xwkwhbcrzbcojgtuskhpyftsay

Towards FAIR principles for research software

Anna-Lena Lamprecht, Leyla Garcia, Mateusz Kuzak, Carlos Martinez, Ricardo Arcila, Eva Martin Del Pico, Victoria Dominguez Del Angel, Stephanie van de Sandt, Jon Ison, Paula Andrea Martinez, Peter McQuilton, Alfonso Valencia (+7 others)
2019 Data Science  
We also thank the Japan BioHackathon for sponsoring a FAIR software related project for the 2018 edition.  ...  NCH and CAG were supported by EP/N006410/1 and EP/S021779/1 for the UK Software Sustainability Institute. AV, JLG, SCG and CAG were supported by ELIXIR-EXCELERATE 676559.  ...  Better community software development practices will help here. [72] "FAIRness assessment for software" ( dbcls/bh18/wiki/ FAIRnessassessment-for-software) at the ELIXIR 2018 BioHackathon  ... 
doi:10.3233/ds-190026 fatcat:jgsnuasx5faalnm5jl45vcytni
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