Example: retrieve resources from bio.tools

resources/external/biotools/clinvar.yaml

@@ -0,0 +1,21 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: A freely accessible, public archive of reports of relationships
+  among medically important variants and phenotypes hosted by the NCBI. It integrates
+  and cross-references data from multiple databases at NCBI. In addition to dbSNP
+  and dbVar, it depends on MedGen to represent phenotype, Gene to represent genes,
+  and on human RefSeqs to represent the location of sequence variation. Each record
+  represents the submitter, the variation and the phenotype. Metadata for this resource
+  was programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:clinvar
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Deposition
+- Query and retrieval
+- Aggregation
+- Genetic variation analysis
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: ClinVar'
+resourceUrl: https://www.ncbi.nlm.nih.gov/clinvar/

resources/external/biotools/coeus.yaml

@@ -0,0 +1,19 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Semantic web application network that combines a set of algorithms
+  to streamline the creation of new semantic web-based knowledge management systems.
+  In a single package, it provides the tools to create new applications, including
+  advanced integration connectors for different data sources along with ontology mapping
+  techniques. Metadata for this resource was programmatically retrieved from elixir's
+  bio.tools registry.
+resourceID: biotools:coeus
+resourceKeywords:
+- Developed_RD-Connect
+- Rare Disease
+- Data retrieval
+- Aggregation
+- Formatting
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: COEUS'
+resourceUrl: https://bioinformatics.ua.pt/coeus/

resources/external/biotools/cosmic.yaml

@@ -0,0 +1,17 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Catalogue Of Somatic Mutations In Cancer (COSMIC) - resource
+  for exploring the impact of somatic mutations in human cancer. Metadata for this
+  resource was programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:cosmic
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Polymorphism detection
+- Data retrieval
+- Protein modelling
+- Text mining
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: COSMIC'
+resourceUrl: https://www.sanger.ac.uk/genetics/CGP/cosmic/

resources/external/biotools/dbgap.yaml

@@ -0,0 +1,20 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: The Database of Genotypes and Phenotypes (dbGAP) is a National
+  Institutes of Health-sponsored repository charged to archive and distribute the
+  data and results from studies that have investigated the interaction of genotype
+  and phenotype in humans. Information in dbGaP is organized as a hierarchical structure
+  and includes the accessioned objects, phenotypes (as variables and datasets), various
+  molecular assay data (SNP and Expression Array data, Sequence and Epigenomic marks),
+  analyses and documents. Metadata for this resource was programmatically retrieved
+  from elixir's bio.tools registry.
+resourceID: biotools:dbgap
+resourceKeywords:
+- Rare Disease
+- Deposition
+- Data retrieval
+- Genotyping
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: dbGAP'
+resourceUrl: https://www.ncbi.nlm.nih.gov/gap

resources/external/biotools/dgva.yaml

@@ -0,0 +1,17 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: The Database of Genomic Variants archive ((DGVa) is a repository
+  that provides archiving, accessioning and distribution of publicly available genomic
+  structural variants, in all species. Metadata for this resource was programmatically
+  retrieved from elixir's bio.tools registry.
+resourceID: biotools:dgva
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Deposition
+- Data retrieval
+- Structural variation detection
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: DGVa'
+resourceUrl: https://www.ebi.ac.uk/dgva

resources/external/biotools/disease_ontology.yaml

@@ -0,0 +1,18 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: The Disease Ontology (DO) has been developed as a standardized
+  ontology for human disease with the purpose of providing the biomedical community
+  with consistent, reusable and sustainable descriptions of human disease terms, phenotype
+  characteristics and related medical vocabulary disease concepts. Metadata for this
+  resource was programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:disease_ontology
+resourceKeywords:
+- Rare Disease
+- Annotation
+- Ontology comparison
+- Query and retrieval
+- Ontology visualisation
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: DO'
+resourceUrl: https://disease-ontology.org/

resources/external/biotools/diseasecard.yaml

@@ -0,0 +1,19 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Information retrieval tool for accessing and integrating genetic
+  and medical information for health applications. Resorting to this integrated environment,
+  clinicians are able to access and relate diseases data already available in the
+  Internet, scattered along multiple databases. Metadata for this resource was programmatically
+  retrieved from elixir's bio.tools registry.
+resourceID: biotools:diseasecard
+resourceKeywords:
+- Developed_RD-Connect
+- Rare Disease
+- Database search
+- Data retrieval
+- Pathway or network analysis
+- Aggregation
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: Diseasecard'
+resourceUrl: https://bioinformatics.ua.pt/diseasecard/

resources/external/biotools/disgenet.yaml

@@ -0,0 +1,38 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: "DisGeNET is a discovery platform containing one of the largest\
+  \ publicly available collections of genes and variants associated to human diseases.\
+  \ DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal\
+  \ models and the scientific literature. DisGeNET data are homogeneously annotated\
+  \ with controlled vocabularies and community-driven ontologies. Additionally, several\
+  \ original metrics are provided to assist the prioritization of genotype\u2013phenotype\
+  \ relationships.\n\nThe current version of DisGeNET (v7.0) contains 1,134,942 gene-disease\
+  \ associations (GDAs), between 21,671 genes and 30,170 diseases, disorders, traits,\
+  \ and clinical or abnormal human phenotypes, and 369,554 variant-disease associations\
+  \ (VDAs), between 194,515 variants and 14,155 diseases, traits, and phenotypes.\
+  \ Metadata for this resource was programmatically retrieved from elixir's bio.tools\
+  \ registry."
+resourceID: biotools:disgenet
+resourceKeywords:
+- Drug Research and Development
+- Rare Disease
+- COVID-19
+- Complex Disease
+- Mendelian Disease
+- ELIXIR-ES
+- RIS3CAT VEIS
+- TransQST
+- IMPaCT-Data
+- Database search
+- Variant prioritisation
+- Pathway or network visualisation
+- Aggregation
+- Data retrieval
+- Gene ID (NCBI)
+- UniProt accession
+- dbSNP ID
+- Database search results
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: DisGeNET'
+resourceUrl: https://www.disgenet.org/

resources/external/biotools/dvd.yaml

@@ -0,0 +1,21 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Diagnostic Variant Database (DVD) is a nation-wide human genomic
+  variant database launched by Dutch University Medical Centers. Its purpose is to
+  share all genetic variants detected in the course of next-generation sequencing
+  (NGS) applications between collaborators. It helps medical researchers to distinguish
+  between functionally relevant and benign genetic variants. DVD also allows users
+  to contact the researcher who originally identified a particular genetic mutation.
+  Metadata for this resource was programmatically retrieved from elixir's bio.tools
+  registry.
+resourceID: biotools:dvd
+resourceKeywords:
+- Rare Disease
+- Deposition
+- Query and retrieval
+- Aggregation
+- Genetic variation analysis
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: DVD'
+resourceUrl: https://trac.nbic.nl/dvd/

resources/external/biotools/ega.yaml

@@ -0,0 +1,19 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: European genome-phenome Archive (EGA) - service for permanent
+  archiving and sharing of all types of personally identifiable genetic and phenotypic
+  data resulting from biomedical research projects. Metadata for this resource was
+  programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:ega
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Deposition
+- Query and retrieval
+- Aggregation
+- EGA accession
+- Experiment report
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: EGA'
+resourceUrl: https://ega-archive.org/

resources/external/biotools/ensembl.yaml

@@ -0,0 +1,16 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Genome databases for vertebrates genomes. Metadata for this resource
+  was programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:ensembl
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Deposition
+- Genome visualisation
+- Query and retrieval
+- Genome annotation
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: Ensembl'
+resourceUrl: https://www.ensembl.org/

resources/external/biotools/entrez.yaml

@@ -0,0 +1,19 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: NCBI information retrieval system, including GenBank, MMDB (structures),
+  genomes, population sets, OMIM, taxonomy and PubMed. Metadata for this resource
+  was programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:entrez
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Sequence similarity search
+- Service invocation
+- Query and retrieval
+- Mapping
+- Deposition
+- Sequence analysis
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: Entrez'
+resourceUrl: https://www.ncbi.nlm.nih.gov/Entrez/

resources/external/biotools/genecards.yaml

@@ -0,0 +1,17 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Database of human genes, their products, and involvement in diseases.
+  It automatically integrates gene-centric data from ~150 web sources, including genomic,
+  transcriptomic, proteomic, genetic, clinical and functional information. Metadata
+  for this resource was programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:genecards
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Service discovery
+- Data retrieval
+- Aggregation
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: GeneCards'
+resourceUrl: https://www.genecards.org/

resources/external/biotools/gnomad.yaml

@@ -0,0 +1,19 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Genome Aggregation Database (gnomAD) - browser that aggregates
+  exome and whole-genome sequencing data from a wide variety of large-scale sequencing
+  projects. It enables search of genetic variation information by gene, variant or
+  region. Metadata for this resource was programmatically retrieved from elixir's
+  bio.tools registry.
+resourceID: biotools:gnomad
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Database search
+- Data retrieval
+- Aggregation
+- Genetic variation analysis
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: gnomAD'
+resourceUrl: https://gnomad.broadinstitute.org/

resources/external/biotools/gtex.yaml

@@ -0,0 +1,18 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Genotype-Tissue Expression (GTEx) - database which helps to study
+  the relationship between genetic variation and gene expression in human tissues.
+  Metadata for this resource was programmatically retrieved from elixir's bio.tools
+  registry.
+resourceID: biotools:gtex
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Data retrieval
+- Gene expression analysis
+- Aggregation
+- Genetic variation analysis
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: GTEx'
+resourceUrl: https://www.gtexportal.org/home/

resources/external/biotools/lovd.yaml

@@ -0,0 +1,18 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: The Leiden Open Variation Database (LOVD) provides a flexible,
+  freely available tool for gene-centered collection and display of DNA variations.
+  LOVD 3.0 extends this idea to also provide patient-centered data storage and storage
+  of NGS data, even of variants outside of genes. Metadata for this resource was programmatically
+  retrieved from elixir's bio.tools registry.
+resourceID: biotools:lovd
+resourceKeywords:
+- NBIC
+- Rare Disease
+- ELIXIR-NL
+- Data retrieval
+- Genetic variation analysis
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: LOVD'
+resourceUrl: https://www.lovd.nl/3.0/home

resources/external/biotools/mint.yaml

@@ -0,0 +1,22 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Molecular interaction Database (MINT) - public repository for
+  protein-protein interactions (PPI) reported in peer-reviewed journals. The web interface
+  allows the users to search, visualize and download interactions data. Metadata for
+  this resource was programmatically retrieved from elixir's bio.tools registry.
+resourceID: biotools:mint
+resourceKeywords:
+- Core Data Resources
+- RD-connect
+- Rare Disease
+- COVID-19
+- Deposition
+- Data retrieval
+- Pathway or network analysis
+- Deposition
+- Text data
+- Protein interaction data
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: MINT'
+resourceUrl: https://mint.bio.uniroma2.it/

resources/external/biotools/ncbi_resources.yaml

@@ -0,0 +1,17 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: The National Center for Biotechnology Information (NCBI) provides
+  analysis and retrieval resources for the data in GenBank and other biological data
+  made available through the NCBI web site. Metadata for this resource was programmatically
+  retrieved from elixir's bio.tools registry.
+resourceID: biotools:ncbi_resources
+resourceKeywords:
+- Rare Disease
+- Deposition
+- Service discovery
+- Query and retrieval
+- PCR primer design
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: NCBI Resources'
+resourceUrl: https://www.ncbi.nlm.nih.gov

resources/external/biotools/omim.yaml

@@ -0,0 +1,19 @@
+resourceCategory: Data Management and Stewardship
+resourceDescription: Online Mendelian inheritance in Man (OMIM) - catalog of human
+  genes and genetic disorders with descriptive text, references, and links to many
+  NCBI resources including GenBank and PubMed. Metadata for this resource was programmatically
+  retrieved from elixir's bio.tools registry.
+resourceID: biotools:omim
+resourceKeywords:
+- RD-connect
+- Rare Disease
+- Service invocation
+- Query and retrieval
+- Genetic mapping
+- Aggregation
+- Genetic variation analysis
+resourceSubcategory: Databases and catalogues
+resourceTags:
+- database
+resourceTitle: 'External resource registered at bio.tools: OMIM'
+resourceUrl: https://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM