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The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine [article]

Julius OB Jacobsen, Michael Baudis, Gareth S Baynam, Jacques S Beckmann, Sergi Beltran, Tiffany J Callahan, Christopher G Chute, Melanie Courtot, Daniel Danis, Olivier Elemento, Robert R Freimuth, Michael A Gargano (+35 others)
2021 medRxiv   pre-print
Here, we introduce the Global Alliance for Genomics and Health (GA4GH) Phenopacket schema, which supports exchange of computable longitudinal case-level phenotypic information for diagnosis and research  ...  , and this has impeded the sharing of phenotypic information for computational analysis.  ...  Acknowledgements The authors gratefully acknowledge insight and feedback from Marian H. Adly, Orion J. Buske, Pier Luigi Buttigieg, Nour Gazzaz, Janine Lewis, Manuel Posada de la Paz and Maria Taboada  ... 
doi:10.1101/2021.11.27.21266944 fatcat:rv7ksvht45dn5idczjwxdgjy5y

Monarch Initiative Data and Resource Sharing Plan

Julie McMurry, Nomi Harris, Moni Munoz-Torres, Melissa Haendel
2020 Zenodo  
Data Sharing Plan as proposed for Monarch  ...  To this end, we have successfully piloted the use of Mondo in the context of semantic search for discovery within the NHLBI STAGE Data Commons.  ...  annotating cases and PhenoPackets.  ... 
doi:10.5281/zenodo.3604521 fatcat:yzifku7k6jfkrkdhxcg5gbp2vu

The COVID-19 epidemiology and monitoring ontology

Núria Queralt-Rosinach, Paul N. Schofield, Robert Hoehndorf, Claus Weiland, Erik Schultes, César H. Bernabé, Marco Roos
2021 Zenodo  
In this study we present our findings and contributions for the bio-ontologies community.  ...  However, this pandemic revealed that we lack tools for an efficient and timely exchange of this epidemiological data which is necessary to assess the impact of disease outbreaks, the efficacy of mitigating  ...  To build an interoperable biomedical ontology, we decided to build an OBO ontology and use the OWL 2, a DL-based formalism and semantic web standard for knowledge representation to enable data sharing  ... 
doi:10.5281/zenodo.5752959 fatcat:7b2eq2mq7jcbvjttaegklpyaqq

CINECA_Semantic and harmonisation best practice_D3.2

Melanie Courtot, Isuru Liyanage
2021 Zenodo  
We provide best practices for cohort metadata harmonisation, using the semantic platform we deployed in the cloud to enable cohort owners to map their data and harmonise against the GECKO (GEnomics Cohorts  ...  Finally, we highlight ongoing work for alignment with other efforts in the community and future opportunities.  ...  repository for biomedical ontologies that provides a single point of access to the latest ontology versions, as well as a simple web interface and a rich set of restful APIs to access its data.  ... 
doi:10.5281/zenodo.5055308 fatcat:laaidf3kz5bxfdxqpflljmzmw4

B1MG D3.7 - Documented best practices in sharing and linking phenotypic and genetic data - 2v0 (revised)

Jeroen Belien, Catia Pinto, Maarten Ligtvoet, Milena Urbini, Pim Volkert, Wei Gu, Michela Tebaldi, Attila Patocs, K.Joeri van der Velde, Marielle E van Gijn, Jan O Korbel, Antonella Padella (+6 others)
2021 Zenodo  
It identifies and describes best practices on sharing and linking phenotypic and genetic data in both the healthcare sector and in the research setting.  ...  The idea is to, as much as possible, avoid reinventing the wheel, learn from previous/current existing projects to improve performance and avoid mistakes made by others.  ...  OBO Foundry principles and developed using the W3C Web Ontology Language.It is being used in by the European Genome-phenome Archive (EGA) at EMBL-EBI/CRG as well as the Broad Institute for the Data Use  ... 
doi:10.5281/zenodo.5780228 fatcat:o4nwshib2fhgbfx5usikk6n23a

B1MG D3.7 - Documented best practices in sharing and linking phenotypic and genetic data - 1v0

Jeroen Belien, Catia Pinto, Maarten Ligtvoet, Milena Urbini, Pim Volkert, Wei Gu, Michela Tebaldi, Attila Patocs, K.Joeri van der Velde, Marielle E van Gijn, Jan O Korbel, Antonella Padella (+5 others)
2021 Zenodo  
It identifies and describes best practices on sharing and linking phenotypic and genetic data in both the healthcare sector and in the research setting.  ...  The idea is to, as much as possible, avoid reinventing the wheel, learn from previous/current existing projects to improve performance and avoid mistakes made by others.  ...  DUO is based on the OBO Foundry principles and developed using the W3C Web Ontology Language.  ... 
doi:10.5281/zenodo.4819148 fatcat:emq7g3lcinbxjcsqjokjw3ehpa

Exploring JSON-LD as an Executable Definition of FHIR RDF to Enable

Harold R Solbrig, Harold R Solbrig, Eric Prud'hommeaux, David Booth, Cory M Endle, Daniel J Stone, Guoqian Jiang
2021 AMIA Annual Symposium Proceedings  
, in preparation for updating the FHIR RDF standard.  ...  We first demonstrated that this JSON-LD 1.1 approach can produce the same output as the current FHIR RDF standard.  ...  Background RDF is the foundational data representation for "Semantic Web", "Linked Data", or the "Web of Data", originally envisioned by Tim Berners-Lee and articulated in a feature article of Semantic  ... 
pmid:33936490 pmcid:PMC8075421 fatcat:47v6b22uj5bz7olctyyoc7x2tq

The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species

2019 Nucleic Acids Research  
Our algorithms and tools are widely used to identify animal models of human disease through phenotypic similarity, for differential diagnostics and to facilitate translational research.  ...  The Monarch Initiative (https://monarchinitiative.org) integrates information on genes, variants, genotypes, phenotypes and diseases in a variety of species, and allows powerful ontology-based search.  ...  ACKNOWLEDGEMENTS We would like to thank the many people who have contributed to the improvements and updates we have reported here, including (but not limited to) Donna Maglott, Anne Pariser and Janine  ... 
doi:10.1093/nar/gkz997 pmid:31701156 pmcid:PMC7056945 fatcat:tramusfgz5eufn2aguuzzasafi

The case for open science: rare diseases

Yaffa R Rubinstein, Peter N Robinson, William A Gahl, Paul Avillach, Gareth Baynam, Helene Cederroth, Rebecca M Goodwin, Stephen C Groft, Mats G Hansson, Nomi L Harris, Vojtech Huser, Deborah Mascalzoni (+13 others)
2020 JAMIA Open  
Here, we describe how the RD community has adopted the core pillars of Open Science, adding new initiatives to promote care and research for RD patients and, ultimately, for all of medicine.  ...  The value of Open Science is nowhere more important and appreciated than in the rare disease (RD) community.  ...  The lay HPO should also enable RD patients to share their phenotyping profiles openly on the web using standards such as Phenopackets (see below), which allows the use of informatics to support open querying  ... 
doi:10.1093/jamiaopen/ooaa030 pmid:33426479 pmcid:PMC7660964 fatcat:63cfktcyqvea3ff3yiushhkoze

A Common Dialect for Infrastructure and Services in Translator

Melissa Haendel, Julie McMurry, Anne Thessen, Chris Bizon, Nomi Harris, Chris Mungall
2019 Zenodo  
These services will provide validation, lookup, and mapping functionality for use across Translator.  ...  together different components and data/information sources at scale, with community buy-in, and with a plan for sustainabil [...]  ...  " web interface.  ... 
doi:10.5281/zenodo.3546914 fatcat:uzgj6bckgbdyxb43a4yneu3kcm

D5.1 - Data homogenization requirements and specifications

Haridimos Kondylakis, Valia Kalokyri, Kostas Marias, Víctor Mateos, José Luis Bravo
2021 Zenodo  
This deliverable sets the requirements for the data homogenization processes paving the way to a common approach for a data lake, based on the FHIR standard.  ...  Considering the wide range of repositories that GenoMed4All will need, homogenizing data formats from different sources and systems (e.g. EHRs, images, genomic data, etc.) is essential.  ...  Although the semantic web and the linked open data (LOD) paradigms provide the means to open, connect and integrate the available data, still a huge amount of them exists in many different formats, ranging  ... 
doi:10.5281/zenodo.5862874 fatcat:pqka7lubvndpdiaxjrp2gdjw64

Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources

Sebastian Köhler, Leigh Carmody, Nicole Vasilevsky, Julius O B Jacobsen, Daniel Danis, Jean-Philippe Gourdine, Michael Gargano, Nomi L Harris, Nicolas Matentzoglu, Julie A McMurry, David Osumi-Sutherland, Valentina Cipriani (+57 others)
2018 Nucleic Acids Research  
Its detailed descriptions of clinical abnormalities and computable disease definitions have made HPO the de facto standard for deep phenotyping in the field of rare disease.  ...  record systems around the world.  ...  Within the Solve-RD project (https://solve-rd.eu), RD-Connect worked with Orphanet and HPO to implement the first version of the Phenopackets standard (https://github.com/phenopackets) and export ∼600  ... 
doi:10.1093/nar/gky1105 pmid:30476213 pmcid:PMC6324074 fatcat:rsd6cv3i7jgjrgidg5ywtnxowa

The GA4GH Phenopacket schema: A computable representation of clinical data for precision medicine

Julius O B Jacobsen, Michael Baudis, Gareth S Baynam, Jacques S Beckmann, Sergi Beltran, Tiffany J Callahan, Christopher G Chute, Mélanie Courtot, Daniel Danis, Olivier Elemento, Robert R Freimuth, Michael A Gargano (+19 others)
2021
Acknowledgements The authors gratefully acknowledge insight and feedback from Marian H. Adly, Orion J. Buske, Pier Luigi Buttigieg, Nour Gazzaz, Janine Lewis, Manuel Posada de la Paz and Maria Taboada  ...  To improve the interoperability of Phenopackets within the FAIR platform, the project is providing Semantic Phenopackets based on Semantic Web standards and ontologies from the Open Biological and Biomedical  ...  To achieve full interoperability of ERNs rare disease patient registries with Phenopackets, the Semantic Phenopackets developed for the EJP RD virtual research platform will be further extended to include  ... 
doi:10.5167/uzh-210475 fatcat:6cyu5mspsne2pf5urhshgt3b5m

Reuse of design pattern measurements for health data [article]

N Queralt-Rosinach, M Wilkinson, R Kaliyaperumal, CH Bernabé, Q Long, M Dumontier, Paul Schofield, M Roos, Apollo-University Of Cambridge Repository
2021
The application of ontologies, Semantic Web technologies and the FAIR principles is an approach used by different life science research projects, such as the European Joint Programme on Rare Diseases,  ...  Here, we show the reuse of a pattern for measurements to model diverse health data, to demonstrate and raise visibility of the usefulness of this pattern for biomedical research.  ...  We would also like to thank to the EJP RD, the GO FAIR VODAN, and the ZonMW Health Holland under the Trusted World of Corona, for supporting the research on FAIR data that was reused here.  ... 
doi:10.17863/cam.77969 fatcat:kqxx3crz4necbaph2bu77si7vq

BioSamples database: an updated sample metadata hub

Mélanie Courtot, Luca Cherubin, Adam Faulconbridge, Daniel Vaughan, Matthew Green, David Richardson, Peter Harrison, Patricia L Whetzel, Helen Parkinson, Tony Burdett
2018 Nucleic Acids Research  
The BioSamples database is now the authoritative repository for all INSDC sample metadata, an ELIXIR Deposition Database for Biomolecular Data and the EMBL-EBI sample metadata hub.  ...  The BioSamples database at EMBL-EBI provides a central hub for sample metadata storage and linkage to other EMBL-EBI resources.  ...  We thank many of the EBI staff, in particular, Simon Jupp, Olga Vrousgou for their help with ontology services, and all past members of the BioSamples database team, Marco Brandizi, Mikhail Gostev, Flavia  ... 
doi:10.1093/nar/gky1061 pmid:30407529 pmcid:PMC6323949 fatcat:dow5tdpfu5h3vhyjvvphk57j7i
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