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A Common Dialect for Infrastructure and Services in Translator

Melissa Haendel, Julie McMurry, Anne Thessen, Chris Bizon, Nomi Harris, Chris Mungall
2019 Zenodo  
The BioLink model will define the standard entity types, relationship types, and a schema shared by all Translator components.  ...  A continually-updated knowledge graph and data lake will provide Translator with a standardized and integrated global view of the whole information landscape.  ...  KG Knowledge graph and data lake TS Next-generation shared Translator Services TR A registry of Translator KPs, ARAs, and shared services Oregon State University/Oregon Health & Science University  ... 
doi:10.5281/zenodo.3546914 fatcat:uzgj6bckgbdyxb43a4yneu3kcm

RTX-KG2: a system for building a semantically standardized knowledge graph for translational biomedicine [article]

E. C. Wood, Amy K. Glen, Lindsey G. Kvarfordt, Finn Womack, Liliana Acevedo, Timothy S. Yoon, Chunyu Ma, Veronica Flores, Meghamala Sinha, Jared C. Roach, Luis Mendoza, Andrew S. Hoffman (+3 others)
2021 bioRxiv   pre-print
The semantic layer and schema for RTX-KG2 follow the standard Biolink metamodel to maximize interoperability within Translator.  ...  Results: To create a knowledge provider system within the Translator project, we have developed RTX-KG2, an open-source software system for building—and hosting a web API for querying—a biomedical knowledge  ...  David Wishart and Carin Li for providing a download link for the SMPDB PubMed annotations and Noel Southall and NCATS for help with hosting RTX-KG2 on GitHub.  ... 
doi:10.1101/2021.10.17.464747 fatcat:2maw4bch2rcv7bwsf7id2tknhy

Transforming the study of organisms: Phenomic data models and knowledge bases

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel (+1 others)
2020 PLoS Computational Biology  
Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable.  ...  The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their  ...  Acknowledgments The authors would like to acknowledge the organizers and sponsors of the 2019 US2TS Conference held at Duke University who created space for this discussion.  ... 
doi:10.1371/journal.pcbi.1008376 pmid:33232313 pmcid:PMC7685442 fatcat:d36yhdezgnbblbj4sy62jiqw3m

A Biomedical Open Knowledge Network Harnesses the Power of AI to Understand Deep Human Biology

Sergio Baranzini, Katy Börner, John Morris, Charlotte Nelson, Karthik Soman, Erica Schleimer, Michael Keiser, Mark Musen, Roger Pearce, Tahsin Reza, Brett Smith, Bruce Herr II (+8 others)
2022 The AI Magazine  
databases into a single property graph, with 3 million nodes and 15 million edges to date.  ...  Knowledge representation and reasoning (KR&R) has been successfully implemented in many fields to enable computers to solve complex problems with AI methods.  ...  He completed the PhD degree in Electrical and Computer Engineering at The University of British Columbia, Vancouver. Brett  ... 
doi:10.1609/aimag.v43i1.19125 fatcat:cstlwsr2aretlcvl2j6xmx4w5y

The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment

Haendel Melissa, Chute Christopher, Gersing Kenneth
2020 JAMIA Journal of the American Medical Informatics Association  
Methods The Clinical and Translational Science Award (CTSA) Program and scientific community created N3C to overcome technical, regulatory, policy, and governance barriers to sharing and harmonizing individual-level  ...  Organized in inclusive workstreams, in two months we created: legal agreements and governance for organizations and researchers; data extraction scripts to identify and ingest positive, negative, and possible  ...  NCATS Biomedical Data Translator Translational integration with basic research data and literature knowledge.  ... 
doi:10.1093/jamia/ocaa196 pmid:32805036 pmcid:PMC7454687 fatcat:rgaafgl6k5hjvlbpphcdcdr6ie

Decentralized Infrastructure for (Neuro)science [article]

Jonny L. Saunders
2022 arXiv   pre-print
for both science and society.  ...  Based on a system of peer-to-peer linked data, I sketch interoperable systems for shared data, tools, and knowledge that map onto three domains of platform capture: storage, computation and communication  ...  This isn't speculative -it can just strap whatever clinical data Translator gains access to into its existing biomedical knowledge graph.  ... 
arXiv:2209.07493v1 fatcat:yazadgtvtvedtiqhfg3f32aqq4

The National COVID Cohort Collaborative (N3C): Rationale, Design, Infrastructure, and Deployment

Melissa A Haendel, Chris Chute, N3C Consortium (See Attached Document)
2020 Zenodo  
Methods The Clinical and Translational Science Award (CTSA) Program and scientific community created N3C to overcome technical, regulatory, policy, and governance barriers to sharing and harmonizing individual-level  ...  Organized in inclusive workstreams, in two months we created: legal agreements and governance for organizations and researchers; data extraction scripts to identify and ingest positive, negative, and possible  ...  ACKNOWLEDGEMENTS STATEMENT We acknowledge the Oregon Clinical and Translational Research Institute for their guidance and review of N3C plans and regulatory processes as they unfolded.  ... 
doi:10.5281/zenodo.3979622 fatcat:ocgmyerqtvfdhnw23r3jjy7r6i

Recent Advances

Guangya Chen, Shengjie Li, Jiuping Xu, Xinmin Yang
2018 Journal of Optimization Theory and Applications  
We thank Mr Jef Lay for developing the OCR error correction tool shown in Figure 2 .  ...  We would like to thank Sebastian Walter for his help in the experiments. Acknowledgments The work was funded by JISC through the Digital Infrastructure programme, Managing Research Data call.  ...  In Proceedings of BioLINK 2013: Roles for text min- ing in biomedical knowledge discovery and transla- tional medicine, pages 32-38. Luke McCarthy, Ben Vandervalk, and Mark Wilkinson. 2012.  ... 
doi:10.1007/s10957-018-1316-3 fatcat:6mmzisl7jbhsvi5dhblc3jqimq

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

Lisa Harper, Jacqueline Campbell, Ethalinda K S Cannon, Sook Jung, Monica Poelchau, Ramona Walls, Carson Andorf, Elizabeth Arnaud, Tanya Z Berardini, Clayton Birkett, Steve Cannon, James Carson (+40 others)
2018 Database: The Journal of Biological Databases and Curation  
Governmental agencies, publishers and science funders require data management plans for publicly funded research.  ...  AgBioData (https://www.agbiodata.org) is a consortium of people working at agricultural biological databases, data archives and knowledgbases who strive to identify common issues in database development  ...  Acknowledgements We acknowledge with thanks The National Science Foundation Plant Genome Research Program Award # 1444573 for funding the AgBioData Workshop and development and hosting of the AgBio-Data  ... 
doi:10.1093/database/bay088 pmid:30239679 pmcid:PMC6146126 fatcat:spcxmd66qrgdnos4larqfvf6ai

Transforming the study of organisms: Phenomic data models and knowledge bases [article]

Anne E. Thessen, Ramona L. Walls, Lars Vogt, Jessica Singer, Robert Warren, Pier Luigi Buttigieg, James P. Balhoff, Christopher J. Mungall, Deborah L. McGuinness, Brian J. Stucky, Matthew J. Yoder, Melissa A. Haendel (+1 others)
2021
Some phenotypic and trait data are available in a semantic language from knowledge bases, but these are often not interoperable.  ...  The rapidly decreasing cost of gene sequencing has resulted in a deluge of genomic data from across the tree of life; however, outside a few model organism databases, genomic data are limited in their  ...  Acknowledgments The authors would like to acknowledge the organizers and sponsors of the 2019 US2TS Conference held at Duke University who created space for this discussion.  ... 
doi:10.34657/5073 fatcat:qn453aa37vdzpgs6qzyog5ss54

SLLS 2013 Amsterdam Conference Abstracts

Jane Raimes
2014 Longitudinal and life course studies  
In a US national, longitudinal sample (N=3,014), structural equation modeling was used to examine effects of 8th and 10th grade conduct problems and depressive symptoms on increases in alcohol, cigarette  ...  , USA; Kelley Sittner Hartshorn, Oklahoma State University, USA Perceived discrimination has been identified as a risk factor for poor psychosocial (e.g., suicide ideation, depression) and behavioural  ...  We analyse retrospective union and fertility histories from 16 standardised surveys in a dataset called the Harmonized--Histories.  ... 
doi:10.14301/llcs.v5i1.285 fatcat:7mlrd3avnbewni5oh3kybncrxu

Linguistic Linked Open Data (LLOD)-Building the cloud

Christian Chiarcos
2013 Proceedings of the Joint Workshop on NLP&LOD and SWAIE   unpublished
We thank Mr Jef Lay for developing the OCR error correction tool shown in Figure 2 .  ...  We would like to thank Sebastian Walter for his help in the experiments. Acknowledgments The work was funded by JISC through the Digital Infrastructure programme, Managing Research Data call.  ...  In Proceedings of BioLINK 2013: Roles for text min- ing in biomedical knowledge discovery and transla- tional medicine, pages 32-38. Luke McCarthy, Ben Vandervalk, and Mark Wilkinson. 2012.  ... 
fatcat:3wczc43tgrgjvfy7bt44cb24si

Strategies for amassing, characterizing, and applying third-party metadata in bioinformatics

Benjamin McGee Good
2009
For biomedical researchers, the vital data they contain is often difficult to locate and to integrate.  ...  In particular, these standards define languages for the provision of the metadata that facilitates both discovery and integration of distributed resources.  ...  I thank him for standing by me in the face of adversity, for patiently putting up with my first (and second and sixteenth) drafts, for his unrelenting attempts to 'deflower' my scientific writing, for  ... 
doi:10.14288/1.0067124 fatcat:3sjde2ud3ngpzl4fdd73v5qdoa

The Sentinel Initiative as a Knowledge Commons [chapter]

Ryan Abbott, Katherine J. Strandburg, Brett M. Frischmann, Michael J. Madison
Governing Medical Knowledge Commons  
a practical introduction to the knowledge commons framework and a synthesis of conclusions and lessons.  ...  for accumulating evidence about how knowledge commons succeed.  ...  that fosters translational research projects in the reproductive sciences.  ... 
doi:10.1017/9781316544587.007 fatcat:lefya2gjp5hwnfdvl4fnjqdrvq