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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  
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

Ayush Singhal, Robert Leaman, Natalie Catlett, Thomas Lemberger, Johanna McEntyre, Shawn Polson, Ioannis Xenarios, Cecilia Arighi, Zhiyong Lu
2016 Database: The Journal of Biological Databases and Curation  
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

E. T. Chan, J. M. Cherry
2012 Database: The Journal of Biological Databases and Curation  
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

Rose Oughtred, Chris Stark, Bobby-Joe Breitkreutz, Jennifer Rust, Lorrie Boucher, Christie Chang, Nadine Kolas, Lara O'Donnell, Genie Leung, Rochelle McAdam, Frederick Zhang, Sonam Dolma (+5 others)
2018 Nucleic Acids Research  
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

Anita Bandrowski, Matthew Brush, Jeffery S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena C. Tan, Nicole Washington, Elena Zudilova-Seinstra (+1 others)
2015 Brain and Behavior  
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

Anita Bandrowski, Matthew Brush, Jeffery S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena Tan, Nicole Washington, Elena Zudilova-Seinstra (+1 others)
2015 F1000Research  
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

Anita Bandrowski, Matthew Brush, Jeffery S Grethe, Melissa A Haendel, David N Kennedy, Sean Hill, Patrick R Hof, Maryann E Martone, Maaike Pols, Serena S Tan, Nicole Washington, Elena Zudilova-Seinstra (+1 others)
2015 Neuroinformatics  
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

Anita Bandrowski, Matthew Brush, Jeffery S. Grethe, Melissa A Haendel, David N. Kennedy, Sean Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena C. Tan, Nicole Washington, Elena Zudilova-Seinstra (+1 others)
2015 Journal of Comparative Neurology  
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

Anita Bandrowski, Matthew Brush, Jeffery S. Grethe, Melissa A. Haendel, David N. Kennedy, Sean Hill, Patrick R. Hof, Maryann E. Martone, Maaike Pols, Serena Tan, Nicole Washington, Elena Zudilova-Seinstra (+1 others)
2015 F1000Research  
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

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  
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

Catherine Brooksbank, Graham Cameron, Janet Thornton
2009 Nucleic Acids Research  
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

Steven Munevar
2017 Nature Biotechnology  
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

Christian Castaneda, Kip Nalley, Ciaran Mannion, Pritish Bhattacharyya, Patrick Blake, Andrew Pecora, Andre Goy, K Stephen Suh
2015 Journal of Clinical Bioinformatics  
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

Rui Alves, Ester Vilaprinyo, Albert Sorribas
2008 Current Bioinformatics  
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]

Todd J. Vision
2019
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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