Neo4j Bloom
Neo4j Bloom is an easy-to-use graph exploration application for visually interacting with Neo4j graphs. A public version is available at:
https://db.covidgraph.org/browser/bloom
User: public
Password: corona
Visual Graph Explorer
This application is provided by yWorks and allows you to explore the knowledge data in a visual way.
Launch App
Neo4j Browser
The Neo4j browser is a user interface for querying the graph directly on database level by pattern matching via Cypher. It offers a basic visualization of the result graph as well as data export and API access. A public version is available at:
https://db.covidgraph.org/browser
User: public
Password: corona
SemSpect
The new SemSpect Graph App for Neo4j is used for data quality checking as well as query tool by the CovidGraph development team. A public version is available at:
https://db.covidgraph.org/semspect/
User: public
Password: corona
COVID-19 Open Research Dataset (CORD-19)
In response to the COVID-19 pandemic, the Allen Institute for AI has partnered with leading research groups to prepare and distribute the COVID-19 Open Research Dataset (CORD-19), a free resource of over 44,000 scholarly articles, including over 29,000 with full text, about COVID-19 and the coronavirus family of viruses for use by the global research community.
https://pages.semanticscholar.org/coronavirus-research
The Lens COVID-19 Datasets
The Lens has assembled free and open datasets of patent documents, scholarly research works metadata and biological sequences from patents, and deposited them in a machine-readable and explorable form.
https://about.lens.org/covid-19/
Ensembl Genome Browser
Ensembl is a genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data. Ensembl tools include BLAST, BLAT, BioMart and the Variant Effect Predictor (VEP) for all supported species.
http://www.ensembl.org
NCBI Gene Database
Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
https://www.ncbi.nlm.nih.gov/gene
The Gene Ontology Resource
The Gene Ontology (GO) knowledgebase is the world’s largest source of information on the functions of genes. This knowledge is both human-readable and machine-readable, and is a foundation for computational analysis of large-scale molecular biology and genetics experiments in biomedical research.
http://geneontology.org
2019 Novel Coronavirus COVID-19 (2019-nCoV) Data Repository by Johns Hopkins CSSE
This is the data repository for the 2019 Novel Coronavirus Visual Dashboard operated by the Johns Hopkins University Center for Systems Science and Engineering (JHU CSSE). Also, Supported by ESRI Living Atlas Team and the Johns Hopkins University Applied Physics Lab (JHU APL).
https://github.com/CSSEGISandData/COVID-19
United Nations World Population Prospects 2019
The 2019 Revision of World Population Prospects is the twenty-sixth round of official United Nations population estimates and projections that have been prepared by the Population Division of the Department of Economic and Social Affairs of the United Nations Secretariat.
https://population.un.org/wpp/
Systems Biology Models
Systems biology data is integrated from MaSyMoS (Management System for Models and Simulations), a Neo4j graph database. MaSyMoS stores computational models, simulation descriptions and associated meta-data, including a collection of COVID-19 models from BioModels.
https://masymos.readthedocs.io/en/latest/
https://www.ebi.ac.uk/biomodels/covid-19
ClinicalTrials.gov
The ClinicalTrials.gov resource provides clinical trial data, including clinical trials concerning COVID-19
https://clinicaltrials.gov/
NCBI RefSeq
The NCBI Reference Sequence Database is a collection of reference sequences including transcripts
https://www.ncbi.nlm.nih.gov/refseq/
UniProt
The Universal Protein Resource contains protein sequences and associated functional data.
https://www.uniprot.org/
Reactome
Reactome is a pathway database that stores information about biological pathways
https://reactome.org/
GTEx Portal
The GTEx Portal is a tissue database containing gene expression data
https://gtexportal.org/home/
Disease Ontology
The Infectious Disease Ontology is an ontology for human diseases
https://disease-ontology.org/
Human Phenotype Ontology
Terms in the Human Phenotype Ontology represent phenotypes of human hereditary diseases
https://hpo.jax.org/app/
Phenotype and Trait Ontology
The Phenotype and Trait Ontology contains information about phenotypic qualities
http://www.obofoundry.org/ontology/pato.html
Mammalian Phenotype Ontology
The Mammalian Phenotype Ontology describes mammalian phenotypes
http://www.informatics.jax.org/vocab/mp_ontology/
ChEBI
ChEBI, short for Chemical Entities of Biological Interest, is an ontology for molecular entities such as metabolites
https://www.ebi.ac.uk/chebi/
Hetionet
The biomedical data network Hetionet includes information about diseases and anatomy
https://het.io/