Dynamic Semantic Metadata in Biomedical Communications

is there life between standards? Data interoperability for AI.

Data Visualization to Enhance our Understanding of the Cancer Genome

Nils Gehlenborg

The integration of computational and statistical approaches with visualization tools is becoming crucial as biomedical data sets are rapidly growing in size. Finding efficient solutions that address the interplay between data management, algorithmic and visual analysis tools is challenging. I will discuss some of these challenges and demonstrate how we are addressing them in our Refinery Platform project (http://www.refinery-platform.org).

Connected Data for Machine Learning | Paul Groth

Connected Data World

PROTEIN DATABASE

naveed ul mushtaq

Opening up pharmacological space, the OPEN PHACTs api

Evaluation of beef production and consumption ontology and presentatio...Robert Trypuz

Improving links between Human Proteome Atlas (HPA) and EMBL-EBI resources

Rafael C. Jimenez

Bioinformatics Final ReportShruthi Choudary

Data retrieval tools

Vidya Kalaivani Rajkumar

Global phenotypic data sharing standards to maximize diagnostic discovery

Use of open_linked_data_in_bioinformaticsRemzi Çelebi

Containerized attribute indexing and graph genomes for federated data access

Ben Busby

Analysis with biological pathways:

Chibucos annot go_final

Sucheta Tripathy

Final Acb All Hands 26 11 07.Key

guest3d0531

Phenopackets as applied to variant interpretation

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

2016 ACS Semantic Approaches for Biochemical Knowledge Discovery

Michel Dumontier

Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...

RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to chemists. We will discuss some of the challenges associated with validating data quality and examine how ChemSpider is a part of the new “semantic web for chemistry”. ChemSpider has also spawned a number of additional projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles, Learn Chemistry Wiki for students learning chemistry and SpectraSchool for learning spectroscopy.

Database in bioinformatics

VinaKhan1

Ontologies for life sciences: examples from the gene ontology

Melanie Courtot

Semantic Web for Health Care and Biomedical Informatics

Amit Sheth

Data analysis & integration challenges in genomics

mikaelhuss

What's hot

Connecting life sciences data at the European Bioinformatics Institute

Connected Data World

Approaches for the Integration of Visual and Computational Analysis of Biomed...

Nils Gehlenborg

Connected Data for Machine Learning | Paul Groth

Connected Data World

PROTEIN DATABASE

naveed ul mushtaq

Opening up pharmacological space, the OPEN PHACTs api

Evaluation of beef production and consumption ontology and presentatio...Robert Trypuz

Improving links between Human Proteome Atlas (HPA) and EMBL-EBI resources

Rafael C. Jimenez

Bioinformatics Final ReportShruthi Choudary

Data retrieval tools

Vidya Kalaivani Rajkumar

Global phenotypic data sharing standards to maximize diagnostic discovery

Use of open_linked_data_in_bioinformaticsRemzi Çelebi

Containerized attribute indexing and graph genomes for federated data access

Ben Busby

Analysis with biological pathways:

Chibucos annot go_final

Sucheta Tripathy

Final Acb All Hands 26 11 07.Key

guest3d0531

Phenopackets as applied to variant interpretation

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

2016 ACS Semantic Approaches for Biochemical Knowledge Discovery

Michel Dumontier

Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...

Database in bioinformatics

VinaKhan1

Ontologies for life sciences: examples from the gene ontology

Melanie Courtot

What's hot (20)

Connecting life sciences data at the European Bioinformatics Institute

Approaches for the Integration of Visual and Computational Analysis of Biomed...

Connected Data for Machine Learning | Paul Groth

PROTEIN DATABASE

Opening up pharmacological space, the OPEN PHACTs api

Evaluation of beef production and consumption ontology and presentatio...

Improving links between Human Proteome Atlas (HPA) and EMBL-EBI resources

Bioinformatics Final Report

Data retrieval tools

Global phenotypic data sharing standards to maximize diagnostic discovery

Use of open_linked_data_in_bioinformatics

Containerized attribute indexing and graph genomes for federated data access

Analysis with biological pathways:

Chibucos annot go_final

Final Acb All Hands 26 11 07.Key

Phenopackets as applied to variant interpretation

2016 ACS Semantic Approaches for Biochemical Knowledge Discovery

Delivering Curated Chemistry to the World via Crowdsourced Deposition and Ann...

Database in bioinformatics

Ontologies for life sciences: examples from the gene ontology

Similar to Dynamic Semantic Metadata in Biomedical Communications

Semantic Web for Health Care and Biomedical Informatics

Amit Sheth

Data analysis & integration challenges in genomics

mikaelhuss

2011-10-11 Open PHACTS at BioIT World Europe

open_phacts

Results Vary: The Pragmatics of Reproducibility and Research Object Frameworks

Carole Goble

Dynamic Integration of Semantic Metadata in Biomedical Communications

Pistoia Alliance

Pistoia talk apr 12 2011Tim Clark

Online Resources to Support Open Drug Discovery Systems

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

This is a presentation given at the Opal Events meeting ""Drug Discovery Partnerships: Filling the Pipeline". I was speaking in a session with Jean-Claude Bradley regarding "Pre-competitive Collaboration: Sharing Data to Increase Predictability". This presentation discussed some of the work we are doing on Open PHACTS. My thanks especially to Carole Goble, Lee Harland and Sean Ekins for their comments.

Why the world needs phenopacketeers, and how to be one

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Keynote presented at the the Ninth International Biocuration Conference Geneva, Switzerland, April 10-14, 2016 The health of an individual organism results from complex interplay between its genes and environment. Although great strides have been made in standardizing the representation of genetic information for exchange, there are no comparable standards to represent phenotypes (e.g. patient disease features, variation across biodiversity) or environmental factors that may influence such phenotypic outcomes. Phenotypic features of individual organisms are currently described in diverse places and in diverse formats: publications, databases, health records, registries, clinical trials, museum collections, and even social media. In these contexts, biocuration has been pivotal to obtaining a computable representation, but is still deeply challenged by the lack of standardization, accessibility, persistence, and computability among these contexts. How can we help all phenotype data creators contribute to this biocuration effort when the data is so distributed across so many communities, sources, and scales? How can we track contributions and provide proper attribution? How can we leverage phenotypic data from the model organism or biodiversity communities to help diagnose disease or determine evolutionary relatedness? Biocurators unite in a new community effort to address these challenges.

Semantic (Web) Technologies for Translational Research in Life SciencesArtificial Intelligence Institute at UofSC

Driving Deep Semantics in Middleware and Networks: What, why and how?

Amit Sheth

Emerging challenges in data-intensive genomics

mikaelhuss

2011-11-28 Open PHACTS at RSC CICAG

open_phacts

The seven-deadly-sins-of-bioinformatics3960mare34

The Seven Deadly Sins of Bioinformatics

Duncan Hull

Una estrategia para la integración de ontologías, servicios web y PLN en el a...

Anubis Hosein

Methods to enhance the validity of precision guidelines emerging from big data

Chirag Patel

Improving online chemistry one structure at a time

RSC|ChemSpider is one of the world’s largest online resources for chemistry related data and services. Developed with the intention of delivering access to structure-based chemistry data via the internet the ChemSpider platform hosts over 26 million unique chemical compounds aggregated from over 400 data sources and provides an environment for the community to both annotate and curate these existing data as well as deposit new data to the system. The search system delivers flexible querying capabilities together with links to external sites for publication and patent data. ChemSpider has spawned a number of projects include ChemSpider SyntheticPages for hosting openly peer-reviewed chemical synthesis articles. This presentation will review the present capabilities of the ChemSpider system providing direct examples of how to use the system to source high quality data of value to pharmaceutical companies. We will discuss some of the challenges associated with validating data quality, examine how ChemSpider is a part of the semantic web for chemistry and investigate approaches to using ChemSpider integrated to analytical instrumentation.

ISMB/ECCB 2013 Keynote Goble Results may vary: what is reproducible? why do o...

Carole Goble

Keynote given by Carole Goble on 23rd July 2013 at ISMB/ECCB 2013 http://www.iscb.org/ismbeccb2013 How could we evaluate research and researchers? Reproducibility underpins the scientific method: at least in principle if not practice. The willing exchange of results and the transparent conduct of research can only be expected up to a point in a competitive environment. Contributions to science are acknowledged, but not if the credit is for data curation or software. From a bioinformatics view point, how far could our results be reproducible before the pain is just too high? Is open science a dangerous, utopian vision or a legitimate, feasible expectation? How do we move bioinformatics from one where results are post-hoc "made reproducible", to pre-hoc "born reproducible"? And why, in our computational information age, do we communicate results through fragmented, fixed documents rather than cohesive, versioned releases? I will explore these questions drawing on 20 years of experience in both the development of technical infrastructure for Life Science and the social infrastructure in which Life Science operates.

The Monarch Initiative: From Model Organism to Precision Medicine

NIH BD2K all-hands meeting poster November 12, 2015. Attempts at correlating phenotypic aspects of disease with causal genetic influences are often confounded by the challenges of interpreting diverse data distributed across numerous resources. New approaches to data modeling, integration, tooling, and community practices are needed to make efficient use of these data. The Monarch Initiative is an international consortium working on the development of shared data, tools, and standards to enable direct translation of integrated genotype, phenotype, and environmental data from human and model organisms to enhance our understanding of human disease. We utilize sophisticated semantic mapping techniques across a diverse set of standardized ontologies to deeply integrate data across species, sources, and modalities. Using phenotype similarity matching algorithms across these data enables disorder prediction, variant prioritization, and patient matching against known diseases and model organisms. These similarity algorithms form the core of several innovative tools. The Exomiser, which enables exome variant prioritization by combining pathogenicity, frequency, inheritance, protein interaction, and cross-species phenotype data. Our Phenotype Sufficiency tool provides clinicians the ability to compare patient phenotypic profiles using the Human Phenotype Ontology to determine uniqueness and specificity in support of variant prioritization. The PhenoGrid visualization widget illustrates phenotype similarity between patients, known diseases, and model organisms. Monarch develops models in collaboration with the community in support of the burgeoning genotype-phenotype disease research community. We have successfully used Exomiser to solve a number of undiagnosed patient cases in collaboration with the NIH Undiagnosed Disease Program. Ongoing development in coordination with the Global Alliance for Genetic Health (GA4GH) and other groups will catalyze the realization of our goal of a vital translational community focused on the collaborative application of integrated genotype, phenotype, and environmental data to human disease.

Prosdocimi ucb cdao

Francisco Prosdocimi

CDAO presentation. The idea of the comparative analysis ontoloty has been presented worldwide, including: NESCent (USA), IGBMC (France), UFRJ (Brazil). Providing a semantic framework for evolutionary analysis in a high-throughtput way after the next and third generation sequencing is the way to approach evolutionary-based studies into genome-wide analysis. The darwinian core of reasoning also allows CDAO to be used with other entities.

Similar to Dynamic Semantic Metadata in Biomedical Communications (20)

Semantic Web for Health Care and Biomedical Informatics

Data analysis & integration challenges in genomics

2011-10-11 Open PHACTS at BioIT World Europe

Results Vary: The Pragmatics of Reproducibility and Research Object Frameworks

Dynamic Integration of Semantic Metadata in Biomedical Communications

Pistoia talk apr 12 2011

Online Resources to Support Open Drug Discovery Systems

Why the world needs phenopacketeers, and how to be one

Semantic (Web) Technologies for Translational Research in Life Sciences

Driving Deep Semantics in Middleware and Networks: What, why and how?

Emerging challenges in data-intensive genomics

2011-11-28 Open PHACTS at RSC CICAG

The seven-deadly-sins-of-bioinformatics3960

The Seven Deadly Sins of Bioinformatics

Una estrategia para la integración de ontologías, servicios web y PLN en el a...

Methods to enhance the validity of precision guidelines emerging from big data

Improving online chemistry one structure at a time

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The Monarch Initiative: From Model Organism to Precision Medicine

Prosdocimi ucb cdao

More from Tim Clark

Reproducibility, argument and data in translational medicine

Failures in reproducibility and robustness of scientific findings are explored from statistical, historical, and argumentation theory perspectives. The impact of false positives in the literature is connected to failures in T1 and T2 biomedical translation, and is shown to have a significant impact on the costs of therapeutic development and availability of needed treatments to the public. Technological and social approaches to resolve these issues are presented. "Reproducibility" initiatives are critiqued as unsustainable and non-authoritative; improved requirements and methods for scientific communication of findings including data, methods and material are supported as the best approaches for improved reproducibility.

Fairport domain specific metadata using w3 c dcat & skos w ontology views

FAIRPORT is an international project to develop a lightweight interoperability architecture for biomedical - and potentially other - data repositories. This slide deck is a presentation to the FAIRPORT technical team. It describes a proposed model for supporting domain-specific search metadata using a common schema model across all repositories. The proposal makes use of the following existing technologies, with minor extensions: - the W3C DCAT model for dataset description - the W3C SKOS knowledge organization system - OWL2 Ontology Language - Dublin Core Vocabulary - NCBO Bioportal biomedical ontologies collection

Annotopia open annotation services platform

Annotopia is an open-access, open-source, open annotation services platform developed for scientific annotation of documents and datasets on the web using the W3C Open Annotation model http://www.openannotation.org/spec/core/. Using Annotopia, virtually any client application including lightweight web clients, can create, selectively share, and access annotation of web documents and data. This can be done regardless of the ownership of the base objects being annotated. Annotopia supports unstructured, semi-structured and fully-structured (semantic) annotation; manual and automated (textmining) annotation; permissions, groups, and sharing. It also provides access to specialized vocabulary and text analytics services. Annotopia is an open source platform licensed under Apache 2.0.

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