Evidence map›Paper›PMID 32308977›Full record

ArticleF1000Research2020

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 and 67 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in F1000Research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. A Simple Standard for Sharing Ontological Mappings (SSSOM).Database : the journal of biological databases and curation · 2022
    Article
  2. Review
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

77 authors.

Rutger A VosInstitute of Biology Leiden, Leiden University, Leiden, The Netherlands.ORCID 0000-0001-9254-7318
Toshiaki KatayamaDatabase Center for Life Science, Tokyo, Japan.ORCID 0000-0003-2391-0384
Hiroyuki MishimaDepartment of Human Genetics, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, Japan.
Shin KawanoDatabase Center for Life Science, Tokyo, Japan.ORCID 0000-0002-7969-2972
Shuichi KawashimaDatabase Center for Life Science, Tokyo, Japan.
Jin-Dong KimDatabase Center for Life Science, Tokyo, Japan.
Yuki MoriyaDatabase Center for Life Science, Tokyo, Japan.
Toshiaki TokimatsuDDBJ Center, National Institute of Genetics, Mishima, Japan.
Atsuko YamaguchiDatabase Center for Life Science, Tokyo, Japan.ORCID 0000-0001-7538-5337
Yasunori YamamotoDatabase Center for Life Science, Tokyo, Japan.
Hongyan WuShenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
Peter AmstutzCuroverse, Somerville, USA.
Erick AntezanaDepartment of Biology, Norwegian University of Science and Technology, Trondheim, Norway.ORCID 0000-0002-2497-8236
Nobuyuki P AokiFaculty of Science and Engineering, SOKA University, Tokyo, Japan.
Kazuharu ArakawaInstitute for Advanced Biosciences, Keio University, Tokyo, Japan.
Jerven T BollemanSIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Lausanne, Switzerland.ORCID 0000-0002-7449-1266
Evan BoltonNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.
Raoul J P BonnalIstituto Nazionale Genetica Molecolare, Romeo ed Enrica Invernizzi, Milan, Italy.
Hidemasa BonoDatabase Center for Life Science, Tokyo, Japan.ORCID 0000-0003-4413-0651
Kees BurgerDutch Techcentre for Life Sciences, Utrecht, The Netherlands.
Hirokazu ChibaNational Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.
Kevin B CohenComputational Bioscience Program, University of Colorado School of Medicine, Denver, USA.
Eric W DeutschInstitute for Systems Biology, Seattle, USA.
Jesualdo T Fernández-BreisUniversidad de Murcia, IMIB-Arrixaca, Murcia, Spain.
Gang FuNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.
Takatomo FujisawaNational Institute of Genetics, Mishima, Japan.
Atsushi FukushimaRIKEN Center for Sustainable Resource Science, Yokohama, Japan.ORCID 0000-0001-9015-1694
Alexander GarcíaPolytechnic University of Madrid, Madrid, Spain.
Naohisa GotoResearch Institute for Microbial Diseases, Osaka University, Osaka, Japan.
Tudor GrozaSt Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Darlinghurst, Australia.
Colin HercusNovocraft Technologies Sdn. Bhd., Selangor, Malaysia.
Robert HoehndorfComputational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
Kotone ItayaInstitute for Advanced Biosciences, Keio University, Tokyo, Japan.
Nick JutyEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
Takeshi KawashimaNational Institute of Genetics, Mishima, Japan.
Jee-Hyub KimEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.
Akira R KinjoInstitute for Protein Research, Osaka University, Osaka, Japan.
Masaaki KoteraSchool of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
Kouji KozakiThe Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan.ORCID 0000-0003-4578-4980
Sadahiro KumagaiHitachi Ltd., Tokyo, Japan.
Tatsuya KushidaNational Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan.
Thomas LüttekeInstitute of Veterinary Physiology and Biochemistry, Justus-Liebig University Giessen, Giessen, Germany.ORCID 0000-0002-7140-9933
Masaaki MatsubaraThe Noguchi Institute, Tokyo, Japan.ORCID 0000-0001-8188-3623
Joe MiyamotoNational Cancer Center Japan, Tokyo, Japan.
Attayeb MohsenNational Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.ORCID 0000-0003-0690-8012
Hiroshi MoriCenter for Information Biology, National Institute of Genetics, Mishima, Japan.
Yuki NaitoDatabase Center for Life Science, Tokyo, Japan.
Takeru NakazatoDatabase Center for Life Science, Tokyo, Japan.
Jeremy Nguyen-XuanLawrence Berkeley National Laboratory, Berkeley, USA.
Kozo NishidaRIKEN Quantitative Biology Center, Osaka, Japan.
Naoki NishidaDepartment of Systems Science, Osaka University, Osaka, Japan.
Hiroyo NishideNational Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.
Soichi OgishimaTohoku Medical Megabank Organization, Tohoku University, Sendai, Japan.
Tazro OhtaDatabase Center for Life Science, Tokyo, Japan.
Shujiro OkudaNiigata University Graduate School of Medical and Dental Sciences, Niigata, Japan.
Benedict PatenUC Santa Cruz Genomics Institute, University of California, Santa Cruz, USA.
Jean-Luc PerretINVENesis, Neuchâtel, Switzerland.
Philip PrathipatiNational Institutes of Biomedical Innovation, Health and Nutrition, Osaka, Japan.
Pjotr PrinsUniversity Medical Center Utrecht, Utrecht, The Netherlands.
Núria Queralt-RosinachDepartment of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA.ORCID 0000-0003-0169-8159
Daisuke ShinmachiFaculty of Science and Engineering, SOKA University, Tokyo, Japan.
Shinya SuzukiSchool of Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.ORCID 0000-0002-1816-4260
Tsuyosi TabataGraduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
Terue TakatsukiRIKEN BioResource Center, Ibaraki, Japan.
Kieron TaylorEuropean Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK.ORCID 0000-0002-6575-5223
Mark ThompsonLeiden University Medical Center, Leiden, The Netherlands.
Ikuo UchiyamaNational Institute for Basic Biology, National Institutes of Natural Sciences, Okazaki, Japan.
Bruno VieiraWurmLab, School of Biological & Chemical Sciences, Queen Mary University of London, London, UK.
Chih-Hsuan WeiNational Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, USA.
Mark WilkinsonEscuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain.ORCID 0000-0001-6960-357X
Issaku YamadaThe Noguchi Institute, Tokyo, Japan.ORCID 0000-0001-9504-189X
Ryota YamanakaOracle Corporation, Tokyo, Japan.
Kazutoshi YoshitakeGraduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
Akiyasu C YoshizawaGraduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan.
Michel DumontierInstitute of Data Science, Maastricht University, Maastricht, The Netherlands.
Kenjiro KosakiCenter for Medical Genetics, Keio University School of Medicine, Tokyo, Japan.
Toshihisa TakagiNational Bioscience Database Center, Japan Science and Technology Agency, Tokyo, Japan.

Funding

National Biomedical Information ServicesZIHLM200888 · NLM · NATIONAL LIBRARY OF MEDICINE · PI PALTOO, DINA · 2009 to 2025
$5200.7M
6 · The paper itself

Abstract

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 the reusability of biological data. We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences, including chemistry, genotypes and phenotypes, orthology and phylogeny, proteomics, genomics, glycomics, and metabolomics. We describe our progress to address ongoing challenges to the reusability and reproducibility of research results, and identify outstanding issues that continue to impede the progress of bioinformatics research. 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.

Indexed as

Biological Science DisciplinesComputational BiologySemantic WebData MiningMetadataReproducibility of ResultsBioHackathonBioinformaticsDatabasesLinked Open DataMetadataOntologySemantic WebVisualizationWeb ServicesWorkflows

Identifiers

PMID32308977
PMCPMC7141167

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.