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Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase
2020
Database: The Journal of Biological Databases and Curation
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WormBase (WB), the authoritative repository for research data on Caenorhabditis elegans and other nematodes, uses text mining (TM) to semi-automate its curation pipeline. ...
In this paper, we present a new WB AFP system that combines TM and AFP into a single application to enhance community curation. ...
Acknowledgements We would particularly like to thank all authors who participated in testing and all WB curators who helped validate author submissions. ...
doi:10.1093/database/baaa006
pmid:32185395
pmcid:PMC7078066
fatcat:rqgg4d73ufb5xmkusxfyhj6tzi
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges
2016
Database: The Journal of Biological Databases and Curation
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We then describe related efforts within the text-mining community, with a special focus on the BioCreative series of challenge workshops. ...
We describe four large scale applications of text mining, as showcased during a recent panel discussion at the BioCreative V Challenge Workshop. ...
Recently, Fluck and colleagues developed BELIEF, a text-mining work flow to improve the efficiency of BEL curation (25) . ...
doi:10.1093/database/baw161
pmid:28025348
pmcid:PMC5199160
fatcat:q22gw7owfjejznsrom3c4xnlem
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report
2012
Database: The Journal of Biological Databases and Curation
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Acknowledgements We thank Edith Wong and Benjamin Hitz for their assistance in track setup and GBrowse configuration; Gail Binkley and Stuart Miyasato for adding the Genome Map data files to the downloads ...
server; Dianna Fisk for assistance in defining dataset metadata; Craig Amundsen for aid with the UCSC liftOver tool; Shuai Weng and Kalpana Karra for helpful discussions and the SGD biocurators for their ...
We regularly communicate with our users and data providers through email and at conferences and meetings to ensure data accessibility, accuracy and availability is maintained at a favourable level. ...
doi:10.1093/database/bar057
pmid:22434826
pmcid:PMC3308148
fatcat:wwzz7etezvho3hd4fpbe4b44ia
The BioGRID interaction database: 2019 update
2018
Nucleic Acids Research
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The Biological General Repository for Interaction Datasets (BioGRID: https://thebiogrid.org) is an open access database dedicated to the curation and archival storage of protein, genetic and chemical interactions ...
A new dedicated aspect of BioGRID annotates genome-wide CRISPR/Cas9-based screens that report gene-phenotype and gene-gene relationships. ...
ACKNOWLEDGEMENTS The authors thank John Aitchison, Brenda Andrews, Gary Bader, Anastasia Baryshnikova ...
doi:10.1093/nar/gky1079
pmid:30476227
pmcid:PMC6324058
fatcat:72ppbdg3vbbhzfeugxmqu7athm
The Resource Identification Initiative: a cultural shift in publishing
2015
Brain and Behavior
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A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. ...
To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve ...
many other editors who wrote letters to their authors and the staff at various publishers and many other community projects that wrote blogs and press releases about this initiative. ...
doi:10.1002/brb3.417
pmid:27110440
pmcid:PMC4834942
fatcat:5mhmxpdvzbcehp22jkvsm4uf2q
The Resource Identification Initiative: A cultural shift in publishing
2015
F1000Research
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A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. ...
To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve ...
many other editors who wrote letters to their authors and the staff at various publishers and many other community projects that wrote blogs and press releases about this initiative. ...
doi:10.12688/f1000research.6555.2
pmid:26594330
pmcid:PMC4648211
fatcat:vajtceajmjebhlqr35sqthiwc4
The Resource Identification Initiative: A Cultural Shift in Publishing
2015
Neuroinformatics
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A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. ...
To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve ...
many other editors who wrote letters to their authors and the staff at various publishers and many other community projects that wrote blogs and press releases about this initiative. ...
doi:10.1007/s12021-015-9284-3
pmid:26589523
pmcid:PMC5072392
fatcat:q6spoj26ljcnbpaftnx2ecvc4a
The Resource Identification Initiative: A cultural shift in publishing
2015
Journal of Comparative Neurology
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A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. ...
To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the Methods sections of articles and thereby improve ...
many other editors who wrote letters to their authors and the staff at various publishers and many other community projects that wrote blogs and press releases about this initiative. ...
doi:10.1002/cne.23913
pmid:26599696
pmcid:PMC4684178
fatcat:7ffobrbycrfwten6m7awoymuoi
The Resource Identification Initiative: A cultural shift in publishing
2015
F1000Research
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2017; you can also visit the original URL.
The file type is application/pdf.
A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. ...
To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in the methods sections of papers and thereby improve ...
many other editors who wrote letters to their authors and the staff at various publishers and many other community projects that wrote blogs and press releases about this initiative. ...
doi:10.12688/f1000research.6555.1
pmid:26594330
pmcid:PMC4648211
fatcat:we4gxrrksrcsdm37f4gzdze63i
BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services
2019
F1000Research
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The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. ...
By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. ...
Acknowledgements BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience ...
doi:10.12688/f1000research.18238.1
fatcat:mdt6bijqlveanplh4bmca5towu
The European Bioinformatics Institute's data resources
2009
Nucleic Acids Research
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It has also put the need for unrestricted access to biological data at the centre of biology. ...
Here, we describe how the EMBL-EBI's biomolecular databases are evolving to cope with increasing levels of submission, a growing and diversifying user base, and the demand for new types of data. ...
The authors would like to thank Guy Cochrane, Paul Flicek, Sarah Hunter, Paul Kersey, Gerard Kleywegt, Claire O'Donovan and Juan Vizcaı´no for their constructive feedback on this manuscript. ...
doi:10.1093/nar/gkp986
pmid:19934258
pmcid:PMC2808956
fatcat:lha7vmv3fnhipb7kunhmvunveu
Unlocking Big Data for better health
2017
Nature Biotechnology
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a central consultancy for web development and User Experience Design (UXD) at the institute. ...
We worked with the ORCID Foundation to improve both data management protocols and user experience design. ...
doi:10.1038/nbt.3918
pmid:28700551
fatcat:oqiurm5cgzec7lfenvjvlemxoy
Clinical decision support systems for improving diagnostic accuracy and achieving precision medicine
2015
Journal of Clinical Bioinformatics
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As a result, invaluable and newly discovered knowledge is difficult to access. ...
As research laboratories and clinics collaborate to achieve precision medicine, both communities are required to understand mandated electronic health/medical record (EHR/EMR) initiatives that will be ...
We also thank the Elyssa and Jack Schecter Family Fund, Leon Lowenstein Foundation and Newman's Own Foundation for supporting research at the Genomics and Biomarkers Program. ...
doi:10.1186/s13336-015-0019-3
pmid:25834725
pmcid:PMC4381462
fatcat:fgufkkvxf5bwdj7otmpdqgct7e
Integrating Bioinformatics and Computational Biology: Perspectives and Possibilities for In Silico Network Reconstruction in Molecular Systems Biology
2008
Current Bioinformatics
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In this paper we discuss how different computational tools and methods can be made to work together integrating different types of data, mining these data for biological information, and assisting in pathway ...
We analyze issues regarding the design of such automated tools and discuss what limitations and pitfalls can be foreseen for the automation and what solutions can computer science and biologists provide ...
RA was supported by a Ramon y Cajal award from the Spanish Ministerio de Educacin y Ciencia. We also thank two anonymous reviewers for helpful suggestions that significantly improved this paper. ...
doi:10.2174/157489308784340694
fatcat:zqewv6cmkze6bfrxlteojj7xem
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]
2019
Preserved Fulltext
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The first section describes how we developed RDF data, ontologies and tools in genomics, proteomics, metabolomics, glycomics and by literature text mining. ...
By enhancing the harmonization of these two layers of machine-readable data and knowledge, we improve the way community wide resources are developed and published. ...
Acknowledgements BioHackathon 2013 and 2014 are supported by the Integrated Database Project (Ministry of Education, Culture, Sports, Science and Technology of Japan) and hosted by the National Bioscience ...
doi:10.5256/f1000research.19950.r54207
fatcat:xwkwhbcrzbcojgtuskhpyftsay
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