Timothy Sheils
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View article: 349 Rare Disease Alert System (RDAS) to promote rare disease research
349 Rare Disease Alert System (RDAS) to promote rare disease research Open
Objectives/Goals: Rare disease patients often face lengthy delays in receiving accurate diagnoses or experience misdiagnoses due to a lack of available information. The NCATS Rare Disease Alert System (RDAS) is a public, comprehensive rare…
View article: SmartGraph API: Programmatic Knowledge Mining in Network-Pharmacology Setting
SmartGraph API: Programmatic Knowledge Mining in Network-Pharmacology Setting Open
The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication we identified the need for the development of an Applicati…
View article: TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets
TIN-X version 3: update with expanded dataset and modernized architecture for enhanced illumination of understudied targets Open
TIN-X (Target Importance and Novelty eXplorer) is an interactive visualization tool for illuminating associations between diseases and potential drug targets and is publicly available at newdrugtargets.org . TIN-X uses natural language pro…
View article: SmartGraph API: Programmatic Knowledge Mining in Network- Pharmacology Setting
SmartGraph API: Programmatic Knowledge Mining in Network- Pharmacology Setting Open
The recent SmartGraph platform facilitates the execution of complex drug-discovery workflows with ease in the network-pharmacology paradigm. However, at the time of its publication, we identified the need for the development of an Applicat…
View article: Pharos 2023: an integrated resource for the understudied human proteome
Pharos 2023: an integrated resource for the understudied human proteome Open
The Illuminating the Druggable Genome (IDG) project aims to improve our understanding of understudied proteins and our ability to study them in the context of disease biology by perturbing them with small molecules, biologics, or other the…
View article: RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from metabolites, proteins, and genes Open
Motivation Functional interpretation of high-throughput metabolomic and transcriptomic results is a crucial step in generating insight from experimental data. However, pathway and functional information for genes and metabolites are distri…
View article: RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites
RaMP-DB 2.0: a renovated knowledgebase for deriving biological and chemical insight from genes, proteins, and metabolites Open
RaMP-DB 2.0 is a web interface, API, relational database and R package designed for straightforward and comprehensive functional interpretation of metabolomic and multi-omic data. Since its first release in 2018, RaMP-DB 2.0 has been upgra…
View article: Getting Started with the IDG KMC Datasets and Tools
Getting Started with the IDG KMC Datasets and Tools Open
The Illuminating the Druggable Genome (IDG) consortium is a National Institutes of Health (NIH) Common Fund program designed to enhance our knowledge of under‐studied proteins, more specifically, proteins unannotated within the three most …
View article: Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite
Erratum: CATMoS: Collaborative Acute Toxicity Modeling Suite Open
In this article, the “ Acknowledgments ” section was missing the text below: H.C., D.P.R., and H.Z. at Rutgers University at Camden were partially supported by the NIEHS (grants R01ES031080 and R15ES023148).The authors regret the error.
View article: NCATS Inxight Drugs: a comprehensive and curated portal for translational research
NCATS Inxight Drugs: a comprehensive and curated portal for translational research Open
The United States has a complex regulatory scheme for marketing drugs. Understanding drug regulatory status is a daunting task that requires integrating data from many sources from the United States Food and Drug Administration (FDA), US g…
View article: CATMoS: Collaborative Acute Toxicity Modeling Suite
CATMoS: Collaborative Acute Toxicity Modeling Suite Open
BACKGROUND: Humans are exposed to tens of thousands of chemical substances that need to be assessed for their potential toxicity. Acute systemic toxicity testing serves as the basis for regulatory hazard classification, labeling, and risk …
View article: Additional file 1 of Scientific evidence based rare disease research discovery with research funding data in knowledge graph
Additional file 1 of Scientific evidence based rare disease research discovery with research funding data in knowledge graph Open
Additional file 1. 32 root disease categories from MONDO.
View article: TCRD and Pharos 2021: mining the human proteome for disease biology
TCRD and Pharos 2021: mining the human proteome for disease biology Open
In 2014, the National Institutes of Health (NIH) initiated the Illuminating the Druggable Genome (IDG) program to identify and improve our understanding of poorly characterized proteins that can potentially be modulated using small molecul…
View article: SmartGraph: a network pharmacology investigation platform
SmartGraph: a network pharmacology investigation platform Open
Motivation Drug discovery investigations need to incorporate network pharmacology concepts while navigating the complex landscape of drug-target and target-target interactions. This task requires solutions that integrate high-quality biome…
View article: How to Illuminate the Druggable Genome Using Pharos
How to Illuminate the Druggable Genome Using Pharos Open
Pharos is an integrated web‐based informatics platform for the analysis of data aggregated by the Illuminating the Druggable Genome (IDG) Knowledge Management Center, an NIH Common Fund initiative. The current version of Pharos (as of Octo…
View article: Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models
Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models Open
Advances in the development of high-throughput screening and automated chemistry have rapidly accelerated the production of chemical and biological data, much of them freely accessible through literature aggregator services such as ChEMBL …
View article: SmartGraph: A Network Pharmacology Investigation Platform
SmartGraph: A Network Pharmacology Investigation Platform Open
Motivation Drug discovery investigations need to incorporate network pharmacology concepts while navigating the complex landscape of drug-target and target-target interactions. This task requires solutions that integrate high-quality biome…
View article: Collaborative Use Repurposing Engine (CURE): FDA-NCATS/NIH Effort to Capture the Global Clinical Experience of Drug Repurposing to Facilitate Development of New Treatments for Neglected and Emerging Infectious Diseases
Collaborative Use Repurposing Engine (CURE): FDA-NCATS/NIH Effort to Capture the Global Clinical Experience of Drug Repurposing to Facilitate Development of New Treatments for Neglected and Emerging Infectious Diseases Open
Background Repurposing approved products has proven a critical strategy to serve unmet medical needs. Historically, 40% of drugs approved for treatment of tropical diseases were repurposed, including albendazole for echinococcosis and neur…
View article: Pharos: Collating protein information to shed light on the druggable genome
Pharos: Collating protein information to shed light on the druggable genome Open
The 'druggable genome' encompasses several protein families, but only a subset of targets within them have attracted significant research attention and thus have information about them publicly available. The Illuminating the Druggable Gen…