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Building a pipeline to solicit expert knowledge from the community to aid gene summary curation

2019 Database: The Journal of Biological Databases and Curation  
Here, we describe how we solicited help from the research community to generate manually written summaries of D. melanogaster gene function.  ...  Based on the data within the FlyBase database, we developed a computational pipeline to identify researchers who have worked extensively on each gene.  ...  We greatly appreciate the willingness of our expert authors to respond to our request and provide helpful gene snapshots.  ... 
doi:10.1093/database/baz152 pmid:31960022 pmcid:PMC6971343 fatcat:cci3gb6iovbkdbzinb2yr4w6pi

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

Lishuang Shen, Maria Angela Diroma, Michael Gonzalez, Daniel Navarro-Gomez, Jeremy Leipzig, Marie T. Lott, Mannis van Oven, Douglas C. Wallace, Colleen Clarke Muraresku, Zarazuela Zolkipli-Cunningham, Patrick F. Chinnery, Marcella Attimonelli (+3 others)
2016 Human Mutation  
A central Web portal (https://mseqdr.org) integrates community knowledge from expert-curated databases with genomic and phenotype data shared by clinicians and researchers.  ...  MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical  ...  Acknowledgments We are grateful to the late Dr. Richard Cotton for his guidance and support of the MSeqDR community effort from its inception.  ... 
doi:10.1002/humu.22974 pmid:26919060 pmcid:PMC4846568 fatcat:bzp3d5hrffb7hb4dupropvddka

Automated generation of gene summaries at the Alliance of Genome Resources

Ranjana Kishore, Valerio Arnaboldi, Ceri E Van Slyke, Juancarlos Chan, Robert S Nash, Jose M Urbano, Mary E Dolan, Stacia R Engel, Mary Shimoyama, Paul W Sternberg, the Alliance of Genome Resources
2020 Database: The Journal of Biological Databases and Curation  
The method uses sentence templates for each data category included in the gene summary in order to build a natural language sentence from the list of terms associated with each gene.  ...  The gene data used for this purpose include curated associations (annotations) to ontology terms from the Gene Ontology, Disease Ontology, model organism knowledgebase (MOK)-specific anatomy ontologies  ...  Special thanks to all the Alliance developers and technical staff for helping integrate the gene summaries software into the Alliance portal.  ... 
doi:10.1093/database/baaa037 pmid:32559296 pmcid:PMC7304461 fatcat:sqmafymva5htzjv3sauiipkote

Natural Language Processing in aid of FlyBase curators

Nikiforos Karamanis, Ruth Seal, Ian Lewin, Peter McQuilton, Andreas Vlachos, Caroline Gasperin, Rachel Drysdale, Ted Briscoe
2008 BMC Bioinformatics  
that was previously available to the curators.  ...  Results: PaperBrowser is the first NLP-powered interface that was developed under a usercentered approach to improve the way in which FlyBase curators navigate an article.  ...  Acknowledgements FlySlip is funded by the UK Biotechnology and Biological Sciences Research Council (BBSRC grant No 38688).  ... 
doi:10.1186/1471-2105-9-193 pmid:18410678 pmcid:PMC2375127 fatcat:mkbkdp2ld5ge7ia4s4274odta4

A Community-Based Annotation Framework for Linking Solanaceae Genomes with Phenomes

N. Menda, R. M. Buels, I. Tecle, L. A. Mueller
2008 Plant Physiology  
SGN has recently spearheaded a new approach by developing community annotation tools to expand its curational capacity.  ...  Since the inception of this project in late 2006, interest and participation from the Solanaceae research community has been strong and growing continuously to the extent that we plan to expand the framework  ...  for contributing to the development of the Solanaceae Phenotype Ontology.  ... 
doi:10.1104/pp.108.119560 pmid:18539779 pmcid:PMC2492603 fatcat:idtk3vqar5he7j5756socytbiy

FaceBase 3: analytical tools and FAIR resources for craniofacial and dental research

Bridget D Samuels, Robert Aho, James F Brinkley, Alejandro Bugacov, Eleanor Feingold, Shannon Fisher, Ana S Gonzalez-Reiche, Joseph G Hacia, Benedikt Hallgrimsson, Karissa Hansen, Matthew P Harris, Thach-Vu Ho (+27 others)
2020 Development  
Summaries of the datasets generated by the FaceBase projects from 2014 to 2019 are provided here.  ...  Over the past decade, researchers have deposited hundreds of annotated and curated datasets on both normal and disordered craniofacial development in FaceBase, all freely available to the research community  ...  Acknowledgements The HGAI Spoke thanks the staff of the University of Pittsburgh Center for Craniofacial and Dental Genetics who contributed to the Marazita FaceBase 2 project, notably Nandita Mukhopadhyay  ... 
doi:10.1242/dev.191213 pmid:32958507 pmcid:PMC7522026 fatcat:leylsvenfngm3nsbmspnfyybru

Extending gene ontology in the context of extracellular RNA and vesicle communication

Kei-Hoi Cheung, Shivakumar Keerthikumar, Paola Roncaglia, Sai Lakshmi Subramanian, Matthew E. Roth, Monisha Samuel, Sushma Anand, Lahiru Gangoda, Stephen Gould, Roger Alexander, David Galas, Mark B. Gerstein (+16 others)
2016 Journal of Biomedical Semantics  
To address the lack of standard terminology to describe extracellular RNA (exRNA) data/metadata, we have launched an inter-community effort to extend the Gene Ontology (GO) with subcellular structure concepts  ...  Association File (GAF) format for batch submission to GO, and curation of the submitted annotations by the GO Consortium.  ...  Finally we would like to acknowledge the community support offered by the following Consortiums: Extracellular RNA Communication (ERC) Consortium, Gene Ontology Consortium (GOC), and International Society  ... 
doi:10.1186/s13326-016-0061-5 pmid:27076901 pmcid:PMC4830068 fatcat:2pww24s4ajf3zpui3ueo3d7kau

EMBnet.journal 19 Suppl. B

EMBnet Journal
2013 EMBnet journal  
This work was supported by a PRIN awarded to Prof. Stefano Ceri.  ...  We believe that the adoption of the technologies presented here can benefits to the whole scientific community by improving the quality of web tools while diminishing the time spent on software development  ...  The efforts of expert curators will be efficiently allocated to resolving controversial annotations, while NLP pipeline developers can further train their algorithms from gold standard corpora solicited  ... 
doi:10.14806/ej.19.b.749 fatcat:h6kgq2g4ljbn7jrq6xpkbh2eie

D5.1 Interoperability Implementation Regulations

Carol Goble, Chris Evelo, Helen Parkinson, ELIXIR Interoperability Community
2018 Zenodo  
APIs for the data repositories and biological knowledge bases agreed and implemented in the field with WP6 to 9 (Use Cases), and WP3 (Data)", as well has ensuring that resources were registered in appropriate  ...  During the execution of EXCELERATE we have significantly refined and adapted this vision to offer a flexible and practical open framework for developing and deploying interoperability across the WPs, working  ...  A prerequisite for knowledge transfer is that a data steward working on the side of the domain expert is committed to each case.  ... 
doi:10.5281/zenodo.1452414 fatcat:j6bod5nlinadhl623uez7x46m4

Crowdsourcing biomedical research: leveraging communities as innovation engines

Julio Saez-Rodriguez, James C. Costello, Stephen H. Friend, Michael R. Kellen, Lara Mangravite, Pablo Meyer, Thea Norman, Gustavo Stolovitzky
2016 Nature reviews genetics  
Challenges also encourage open innovation, create collaborative communities to solve diverse and important biomedical problems, and foster the creation and dissemination of well-curated data repositories  ...  Crowdsourcing the analysis of complex and massive data has emerged as a framework to find robust methodologies.  ...  The authors also thank the DREAM Challenges community, who taught them everything about Challenges that they have tried to share in this Review.  ... 
doi:10.1038/nrg.2016.69 pmid:27418159 pmcid:PMC5918684 fatcat:tap77ocblrbydl3fc6connsnwi

Therapeutics Data Commons: Machine Learning Datasets and Tasks for Drug Discovery and Development [article]

Kexin Huang, Tianfan Fu, Wenhao Gao, Yue Zhao, Yusuf Roohani, Jure Leskovec, Connor W. Coley, Cao Xiao, Jimeng Sun, Marinka Zitnik
2021 arXiv   pre-print
Here, we introduce Therapeutics Data Commons (TDC), the first unifying platform to systematically access and evaluate machine learning across the entire range of therapeutics.  ...  To date, TDC includes 66 AI-ready datasets spread across 22 learning tasks and spanning the discovery and development of safe and effective medicines.  ...  TDC's Tools, Libraries, and Resources TDC has a flexible ecosystem of tools, libraries, and community resources to let researchers push the state-ofthe-art in ML and go from model building and training  ... 
arXiv:2102.09548v2 fatcat:i5f5vrbaxnehhmhqiuwkkx2s6y

The Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols

Denis Yuen, Louise Cabansay, Andrew Duncan, Gary Luu, Gregory Hogue, Charles Overbeck, Natalie Perez, Walt Shands, David Steinberg, Chaz Reid, Nneka Olunwa, Richard Hansen (+6 others)
2021 Nucleic Acids Research  
practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few.  ...  Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific  ...  ACKNOWLEDGEMENTS We would like to acknowledge numerous contributors to Dockstore.  ... 
doi:10.1093/nar/gkab346 pmid:33978761 fatcat:zwvges37mva2hfc4aaa4w5dkyy

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

Michael Hawrylycz, Jyl Boline, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky
2009 Nature Precedings  
All of the above should take into consideration existing solutions; for example, those demonstrated by BioMoby, myGrid and BIRN.  ...  However, in order to tackle tasks specific to a community, experts from those communities will be required.  ...  We believe this group can continue to lead the development of these resources; however, in order to tackle tasks specific to a community, experts from those groups will be required.  ... 
doi:10.1038/npre.2009.4000 fatcat:zgzee4e5ivfo5gt6ouemrwfdsu

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain

Michael Hawrylycz, Jyl Boline, Albert Burger, Tsutomu Hashikawa, G. Allan Johnson, Maryann Martone, Lydia Ng, Jonathan Nissanov, Luis Puelles, Seth Ruffins, Fons Verbeek, Ilya Zaslavsky
2009 Nature Precedings  
All of the above should take into consideration existing solutions; for example, those demonstrated by BioMoby, myGrid and BIRN.  ...  However, in order to tackle tasks specific to a community, experts from those communities will be required.  ...  We believe this group can continue to lead the development of these resources; however, in order to tackle tasks specific to a community, experts from those groups will be required.  ... 
doi:10.1038/npre.2009.4000.1 fatcat:fezgneezbray5fwphzirvaw67a

From Open Data to Open Science

Rahul Ramachandran, Kaylin Bugbee, Kevin Murphy
2021 Earth and Space Science  
Acknowledgments Authors would like to thank Derek Koehl for his assistance in editing and improving the manuscript.  ...  They also thank all our colleagues within the Earth Science Data Systems Program NASA who provided insight and expertise that greatly assisted this research.  ...  First, the study provides a summary of the drivers behind open science and an overview of the current state of various open science activities across the community.  ... 
doi:10.1029/2020ea001562 fatcat:md6esg4eabbs5cpkaxkqrn7cly
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