A5013316336- Biomedical Text Mining and Ontologies
- Scientific Computing and Data Management
- Data-Driven Disease Surveillance
- SARS-CoV-2 and COVID-19 Research
- Genetics, Bioinformatics, and Biomedical Research
- SARS-CoV-2 detection and testing
- Research Data Management Practices
- Bioinformatics and Genomic Networks
- Genomics and Phylogenetic Studies
- COVID-19 diagnosis using AI
- Viral Infections and Outbreaks Research
- Reproductive tract infections research
- Computational Drug Discovery Methods
- Cell Image Analysis Techniques
- Cloud Computing and Resource Management
- Data Quality and Management
- Gut microbiota and health
- Distributed and Parallel Computing Systems
- Gene expression and cancer classification
- COVID-19 epidemiological studies
- Plant and fungal interactions
- Misinformation and Its Impacts
Scripps Research Institute
2019-2023
Scripps (United States)
2021-2023
Scripps Institution of Oceanography
2021-2023
Universidad de Málaga
2012
Abstract The emergence of SARS-CoV-2 variants concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response this need, global scientific community, through unprecedented effort, sequenced and shared over 10 million genomes GISAID, as May 2022. This extraordinarily high sampling rate provides a unique opportunity track evolution virus in real-time. Here, we present outbreak.info , platform that currently tracks 40 combinations PANGO...
To combat the ongoing COVID-19 pandemic, scientists have been conducting research at breakneck speeds, producing over 52,000 peer-reviewed articles within first year. address challenge in tracking vast amount of new located separate repositories, we developed outbreak.info Research Library, a standardized, searchable interface and SARS-CoV-2 resources. Unifying metadata from sixteen assembled collection 350,000 publications, clinical trials, datasets, protocols, other resources as October...
To meet the increased need of making biomedical resources more accessible and reusable, Web Application Programming Interfaces (APIs) or web services have become a common way to disseminate knowledge sources. The BioThings APIs are collection high-performance, scalable, annotation as service that automate integration biological annotations from disparate data This currently includes MyGene.info, MyVariant.info MyChem.info for integrating on genes, variants chemical compounds, respectively....
Abstract Biomedical datasets are increasing in size, stored many repositories, and face challenges FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices promote transparency, encourage reproducibility, accelerate research advances through data reuse. To improve our computational tools, evaluated metadata standards across established biomedical repositories. The vast...
Abstract The emergence of SARS-CoV-2 variants concern has prompted the need for near real-time genomic surveillance to inform public health interventions. In response this need, global scientific community, through unprecedented effort, sequenced and shared over 11 million genomes GISAID, as May 2022. This extraordinarily high sampling rate provides a unique opportunity track evolution virus in real-time. Here, we present outbreak.info, platform that currently tracks 40 combinations PANGO...
Abstract Background Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical readily accessible through open data efforts, finding relevant remains a significant challenge. Schema.org is metadata vocabulary standardization project that enables web content creators FAIR. Leveraging could benefit resource providers, but it can be challenging apply standards outputs. We created an online...
Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge can easily represent heterogeneous types of information, and many algorithms tools exist querying analyzing graphs. Biomedical have been used in a variety applications, including drug repurposing, identification targets, prediction side effects, clinical decision support. Typically, constructed by centralization integration from multiple disparate sources. Here, we describe...
The petabyte scale of the Big Data generation in bioinformatics requires introduction advanced computational techniques to enable efficient knowledge discovery from data. Many data analysis tools have been developed but few adapted take advantage high performance computing (HPC) resources. For some these tools, an attractive option is employ a map/reduce strategy. On other hand, Cloud Computing could be important platform run such parallel because it provides on-demand, elastic This paper...
The accelerating growth of genomic and proteomic information for Chlamydia species, coupled with unique biological aspects these pathogens, necessitates bioinformatic tools features that are not provided by major public databases. To meet growing needs, we developed ChlamBase, a model organism database is built upon the WikiGenomes application framework, Wikidata, community-curated database. ChlamBase was designed to serve as central access point research community. integrates from numerous...
Abstract Background Biomedical researchers are strongly encouraged to make their research outputs more Findable, Accessible, Interoperable, and Reusable (FAIR). While many biomedical readily accessible through open data efforts, finding relevant remains a significant challenge. Schema.org is metadata vocabulary standardization project that enables web content creators FAIR. Leveraging schema.org could benefit resource providers, but it can be challenging apply standards outputs. We created...
Abstract To combat the ongoing COVID-19 pandemic, scientists have been conducting research at breakneck speeds, producing over 52,000 peer-reviewed articles within first year. address challenge in tracking vast amount of new located separate repositories, we developed outbreak.info Research Library, a standardized, searchable interface and SARS-CoV-2 resources. Unifying metadata from fourteen assembled collection 270,000 publications, clinical trials, datasets, protocols, other resources as...
Abstract Gene definitions and identifiers can be painful to manage–more so when trying include gene function annotations as this highly context-dependent. Creating groups of genes or sets help provide such context, but it compounds the issue each within set map multiple have derived from sources. We developed MyGeneset.info an API for integrated suitable use in analytical pipelines web servers. Leveraging our previous work with MyGene.info (a server that provides gene-centric identifiers),...
Abstract Summary To meet the increased need of making biomedical resources more accessible and reusable, Web APIs or web services have become a common way to disseminate knowledge sources. The BioThings are collection high-performance, scalable, annotation as service that automate integration biological annotations from disparate data This currently includes MyGene.info, MyVariant.info, MyChem.info for integrating on genes, variants, chemical compounds, respectively. These used by both...
Knowledge graphs are an increasingly common data structure for representing biomedical information. These knowledge can easily represent heterogeneous types of information, and many algorithms tools exist querying analyzing graphs. Biomedical have been used in a variety applications, including drug repurposing, identification targets, prediction side effects, clinical decision support. Typically, constructed by centralization integration from multiple disparate sources. Here, we describe...
Abstract Biomedical datasets are increasing in size, stored many repositories, and face challenges FAIRness (findability, accessibility, interoperability, reusability). As a Consortium of infectious disease researchers from 15 Centers, we aim to adopt open science practices promote transparency, encourage reproducibility, accelerate research advances through data reuse. To improve our computational tools, evaluated metadata standards across established biomedical repositories. The vast...