HPO / http://www.human-phenotype-ontology.org/ / The HPO is currently
being developed using
the medical
literature, Orphanet,
DECIPHER, and
OMIM. HPO currently
contains approximately
11,000 terms and over
115,000 annotations to
hereditary diseases.
PhenX Toolkit / https://www.phenxtoolkit.org / The PhenX Toolkit
offers well-established,
broadly validated
measures of
phenotypes
and exposures relevant
to investigators in
human genomics,
epidemiology, and
biomedical research.
PhenoDb / http://phenodb.net / myPhenoDB is a
freely-accessible website that
allows clinical
researchers to store
standardized
phenotypic
information,
diagnosis, and pedigree
data and then run
analyses on VCF
files from individuals,
families or cohorts with
suspected Mendelian
disease.
PhenomeCentral / https://phenomecentral.org / PhenomeCentral is a
repository for secure
data sharing targeted to
clinicians and scientists
working in the rare
disorder community.
dbGAP / http://www.ncbi.nlm.nih.gov/gap / The database of
Genotypes and
Phenotypes (dbGaP)
was developed to
archive and
distribute the results of
studies that have
investigated the
interaction of genotype
and phenotype.
GeneMatcher / https://genematcher.org / GeneMatcher is a
freely accessible web
site designed to enable
connections between
clinicians and
researchers from
around the world who
share an interest in the
same gene or genes
International
Consortium of
Human
Phenotype
Terminologies
(ICHPT) / The International
Consortium for Human
Phenotype
Terminologies
(ICHPT), sorts the
thousands of
phenotypic terms
appearing in the
literature into a
common vocabulary.
Orphanet / http://www.orpha.net/consor/cgi-bin/index.php / Orphanet is the
Reference portal for
information on rare
diseases and orphan
drugs, for all audiences.
Orphanet’s aim is to
help improve the
diagnosis, care and
treatment of patients
with rare diseases.
London
Dysmorphology
Database –
Winter-
Baraitser
Dysmorphology
Database
(WBDD) / http://www.lmdatabases.com / The London
Dysmorphology
Database or Winter-
Baraitser
Dysmorphology
Database (WBDD)
currently contains
information on over
4700 dysmorphic,
multiple congenital anomaly and
mental retardation
syndromes. It includes
single gene disorders,
sporadic conditions,
and those caused by
environmental agents.
DECIPHER / https://decipher.sanger.ac.uk / DECIPHER (DatabasE
of genomiC varIation
and Phenotype in
Humans using Ensembl
Resources) is an
interactive web-based
database which
incorporates a suite of
tools designed to aid
the interpretation of
genomic variants.
Elements of
Morphology / https://elementsofmorphology.nih.gov / International effort
towards standardization
of terms used to
describe human
morphology.
OMIM / http://www.ncbi.nlm.nih.gov/omim / OMIM is a
comprehensive,
authoritative
compendium of
human genes and
genetic phenotypes that
is freely available
and updated daily.
SNOMED / http://www.ihtsdo.org/snomed-ct/get-snomed-ct / SNOMED CT
(Systematized
Nomenclature of
Medicine—
Clinical Terms) is a
comprehensive clinical
terminology.
POSSUMweb / http://www.possum.net.au / A dysmorphology
database of multiple
malformations,
metabolic, teratogenic,
chromosomal and
skeletal syndromes
and their images - for
learning and diagnosis
Simulconsult / http://www.simulconsult.com / Genomic labs can use
the Genome-Phenome
Analyzer version
to combine a genome
variant table with the
phenotype data
entered by the referring
clinician (or the lab
genetic counselor),
thereby using the full
power of genome and
phenome to converge
quickly on a diagnosis.
ClinGen / http://clinicalgenome.org / The Clinical Genome
Resource (ClinGen) is
A National Institutes of
Health (NIH)-funded
program dedicated to
harnessing the data
from both research
efforts and clinical
genetic testing,
and using it to propel
expert and machine-
driven curation
activities.
PheWAS / http://phewas.mc.vanderbilt.edu/ / Phenome-wide
association studies
(PheWAS) analyze
many phenotypes
compared to a single
genetic variant (or
other attribute).
ClinVar / http://www.ncbi.nlm.nih.gov/clinvar/ / ClinVar is a freely
accessible, public
archive of reports of
the relationships among
human variations and
phenotypes, with
supporting evidence.
PheKB / https://phenotype.mc.vanderbilt.edu/ / The Phenotype
Knowledgebase
website, PheKB, is a
collaborative
environment to
building and validating
electronic phenotype
algorithms.
PhenoTIPS / http://phenotips.org/ / PhenoTips is a software
tool for collecting and
analyzing phenotypic
information for patients
with genetic disorders.
Phenomizer / http://compbio.charite.de/phenomizer/ / Assists in finding the
correct clinical
diagnosis by exploiting
the semantic structure
of the Human
Phenotype Ontology.
PhenIX, / http://compbio.charite.de/PhenIX/ / PhenIX, Phenotypic
Interpretation of
eXomes, is a pipeline
for ranking
(prioritizing)
candidate genes in
exomes or NGS
panels with
comprehensive
coverage of human
Mendelian disease
genes.
Exomiser / https://www.sanger.ac.uk/resources/databases/exomiser/ / The Exomiser is a Java
program that
functionally annotates
variants from whole-
exome sequencing data
starting from a
VCF file (version 4).
NCBO / http://www.bioontology.org/annotator-service / The goal of the
National Center for
Biomedical Ontology is
to support biomedical
researchers in their
knowledge-intensive
work, by providing
online tools and a Web
portal enabling
them to access, review,
and integrate disparate
ontological
resources in all aspects
of biomedical
investigation and
clinical practice.
OBO Foundry / http://www.obofoundry.org/ / The OBO Foundry is a
collaborative
experiment involving
developers of science-
based ontologies who
are establishing a
set of principles for
ontology development
with the goal of
creating a suite of
orthogonal
interoperable
reference ontologies in
the biomedical
domain.
Disease Ontology / http://disease-ontology.org/ / The Disease Ontology
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. The Disease
Ontology semantically
integrates
disease and medical
vocabularies through
extensive cross
mapping of DO terms
to MeSH, ICD, NCI’s
thesaurus,
SNOMED and OMIM.
Sequence Ontology / http://www.sequenceontology.org/ / The Sequence
Ontology is a set of
terms and relationships
used to describe the
features and attributes
of biological sequence.
Table 3 – Summary of Online Phenotype-Genotype resources