2015-07-01
2016-09-01
v.1.0
v.1.0
RDF representation of biomedical and genomic information related to inherited diseases of glycan metabolism provided by NCBI and available from ftp://ftp.ncbi.nlm.nih.gov/pub/medgen/, ftp://ftp.ncbi.nih.gov/gene/, and ftp://ftp.ncbi.nlm.nih.gov/pub/clinvar/
Information from NCBI's MedGen, NCBI Gene, ClinVar, and PubMed databases
This RDF document includes entries from NCBI (National Center for Biotechnology Information) Databases such as MedGen, NCBI Gene, ClinVar, and PubMed. MedGen is the portal of information related to medical genetics. MedGen includes the lists of terms from the multiple sources organized in groups and hierarchical structures
Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
Glycoscience and Glycotechnology Research Group, Biotechnology Research Institute for Drug Discovery, National Institute of Advanced Industrial Science and Technology (AIST)
Hisashi Narimatsu
Toshihide Shikanai
Elena Solovieva
Noriaki Fujita
This concept scheme includes the concepts that represent entries from MedGen related to inherited diseases of glycan metabolism.
This concept scheme includes the concepts that represent entries from MedGen related to inherited diseases of glycan metabolism.
http://jcggdb.jp/rdf/diseases/gmncbi
This concept scheme includes the concepts that represent entries from MedGen, such as link information between UMLS Concept Unique Identifiers for inherited diseases of glycan metabolism and PubMed unique identifiers.
This concept scheme includes the concepts that represent entries from MedGen, such as link information between UMLS Concept Unique Identifiers for inherited diseases of glycan metabolism and PubMed unique identifiers.
http://jcggdb.jp/rdf/diseases/pmncbi
This concept scheme includes the concepts that represent entries from Gene and ClinVar, such as information about the relationships between MIM numbers (OMIM), GeneIDs, and Records in MedGen.
This concept scheme includes the concepts that represent entries from Gene and ClinVar, such as information about the relationships between MIM numbers (OMIM), GeneIDs, and Records in MedGen.
http://jcggdb.jp/rdf/diseases/dgncbi
This concept scheme includes the concepts that represent entries from NCBI (National Center for Biotechnology Information) Gene database.
This concept scheme includes the concepts that represent entries from NCBI (National Center for Biotechnology Information) Gene database.
http://jcggdb.jp/rdf/diseases/gincbi
NCBI Disease Description
For describing information about diseases from the NCBI.
For description data from NAMES.RRF, MGDEF.RFF, MedGen_HPO_OMIM_Mapping.txt files
PubMed Disease Data
For describing information about diseases from the PubMed.
For description data from medgen_pubmed.lnk file
Disease and Gene Data from NCBI
For describing information about diseases and genes from the NCBI.
For description data from gene_condition_source_id and mim2gene_medgen files
Name from Source
Disease name from UMLS sources.
For description data from NAMES.RRF file
Definition from Source
Disease definition from UMLS sources.
For description data from MGDEF.RFF file
HPO Data
Data from HPO.
For description data from MedGen_HPO_OMIM_Mapping.txt file
NCBI Gene Data
Data from NCBI Gene and ClinVar.
For description data from gene_condition_source_id file
Information Sources
Medical and biological information sources that are created or used in NCBI
Data sources that are used in NCBI Databases
Semantic Relations UMLS
For describing information about semantic relations between concepts in this ontology, by using relations from UMLS.
Disease and Phenotype description
Disease name and PubMed link information
Disease name and NCBI gene data
Disease and gene data from NCBI and OMIM
NCBI gene info
Name from source property
Disease name from UMLS sources.
For description data from NAMES.RRF file
Definition from source property
Disease definition from UMLS sources.
For description data from MGDEF.RFF file
HPO data property
Data from HPO.
For description data from MedGen_HPO_OMIM_Mapping.txt file
NCBI Gene data property
Data from NCBI Gene and ClinVar.
For description data from gene_condition_source_id file
UMLS UI
UMLS: Unique Identifier of the Relation.
For description of new individuals for #SemanticRelationsUMLS class
UMLS RL
UMLS: Name of the Relation.
For description of new individuals for #SemanticRelationsUMLS class
UMLS ABR
UMLS: Abbreviation of the Relation.
For description of new individuals for #SemanticRelationsUMLS class
UMLS RIN
UMLS: Name of the inverse of the Relation.
For description of new individuals for #SemanticRelationsUMLS class
UMLS RTN
UMLS: Tree Number of the Relation.
For description of new individuals for #SemanticRelationsUMLS class
UMLS Relation Definition
UMLS: Definition of the Relation.
For description of new individuals for #SemanticRelationsUMLS class
UMLS HL
UMLS: Hierarchical links of the Relation to its parent ({isa}) and its children ({inverse_isa}). If there are no hierarchical links, then the value "none" is assigned.
For description of new individuals for #SemanticRelationsUMLS class
UMLS Concept name
Concept name from UMLS
For concepts that are recorded in the UMLS Metathesaurus
For description of concepts in RDF representation of biomedical and genomic information provided in MedGen
UMLS Concept definition
Concept definition from UMLS
For concepts that are recorded in the UMLS Metathesaurus
For description of concepts in RDF representation of biomedical and genomic information provided in MedGen
UMLS sources
Sources that contribute strings or relationships to the UMLS Metathesaurus.
For concepts that are recorded in the UMLS Metathesaurus
For description of concepts in RDF representation of biomedical and genomic information provided in MedGen
MIM number
MIM number defining the record from OMIM.
For description data from mim2gene_medgen and gene_condition_source_id files
OMIM disease name
Preferred term for disease from OMIM.
For description data from MedGen_HPO_OMIM_Mapping.txt file
UMLS HPO CUI
UMLS: Concept UID (CUI) assiged to the term from HPO.
For description data from MedGen_HPO_OMIM_Mapping.txt file
HPO ID
Identifier from HPO.
For description data from MedGen_HPO_OMIM_Mapping.txt file
HPO name
Preferred term from HPO.
For description data from MedGen_HPO_OMIM_Mapping.txt file
MedGen name
UMLS: Preferred term used in MedGen.
For description data from MedGen_HPO_OMIM_Mapping.txt file
MedGen sources
Property that represent MedGen sources. Sources of the term used preferentially by MedGen.
For description data from MedGen_HPO_OMIM_Mapping.txt, mim2gene_medgen and gene_condition_source_id files
UML STY
UMLS: Semantic type
For description data from MedGen_HPO_OMIM_Mapping.txt file
UMLS RELA (Additional Relationship Label)
Relationship
UMLS: Relationship of the term from HPO to the record from OMIM. Constructions like 'not_manifestation_of' are used to represent the 'not' qualifier for a relationship.
For description data from MedGen_HPO_OMIM_Mapping.txt file
MedGen CUI
Concept unique identifier assigned by MedGen. If the accession starts with a C followed by integers, the identifier is a concept ID (CUI) from UMLS. If it starts with a CN, no CUI in UMLS was identified, and NCBI created a placeholder.
For description data from mim2gene_medgen and gene_condition_source_id files
Concept UI in MedGen sources
Property that represent the concept identifier used by MedGen source and the name of this source is recorded in "gmsch:medgenSource" property.
For description data from gene_condition_source_id file
Name in source
Concept name (gene or disease name) from UMLS and MedGen sources.
For description data from gene_condition_source_id file
OMIM type
Type of relationship between the MIM number and the GeneID. Current values are: 'gene' the MIM number associated with a Gene, 'phenotype' the MIM number associated with a disease that is associated with a gene.
For description data from mim2gene_medgen file
NCBI Gene symbol
Preferred symbol corresponding to the GeneID.
Source Abbreviation in NCBI
Source Abbreviation in NCBI
Source Official Name
Source Official Name
Source Official Abbreviation
Source Official Abbreviation
Source URI
Source URI
has_manifestationT150
has_manifestation
MF
manifestation_of
R3.6
That part of a phenomenon which is directly observable or concretely or visibly expressed, or which gives evidence to the underlying process. This includes expression of, display of, and exhibition of.
{isa} functionally_related_to
This semantic relation is used for linking the Genetic Glyco-Diseases Ontologies (GGDonto) ontology to the RDF representation of biomedical and genomic information from NCBI.
manifestation_ofT150
manifestation_of
MF
has_manifestation
R3.6
That part of a phenomenon which is directly observable or concretely or visibly expressed, or which gives evidence to the underlying process. This includes expression of, display of, and exhibition of.
{isa} functionally_related_to
This semantic relation is used for linking the Genetic Glyco-Diseases Ontologies (GGDonto) ontology to the RDF representation of biomedical and genomic information from NCBI.
causesT147
causes
CA
caused_by
R3.2.2
Brings about a condition or an effect. Implied here is that an agent, such as for example, a pharmacologic substance or an organism, has brought about the effect. This includes induces, effects, evokes, and etiology.
{isa} brings_about
This semantic relation is used for linking the Genetic Glyco-Diseases Ontologies (GGDonto) ontology to the RDF representation of biomedical and genomic information from NCBI.
caused_byT147
caused_by
CA
causes
R3.2.2
Brings about a condition or an effect. Implied here is that an agent, such as for example, a pharmacologic substance or an organism, has brought about the effect. This includes induces, effects, evokes, and etiology.
{isa} brings_about
This semantic relation is used for linking the Genetic Glyco-Diseases Ontologies (GGDonto) ontology to the RDF representation of biomedical and genomic information from NCBI.
conceptual_part_ofT160
conceptual_part_of
CP
has_conceptual_part
R5.11
Conceptually a portion, division, or component of some larger whole.
{isa} conceptually_related_to
This semantic relation is used for linking the Genetic Glyco-Diseases Ontologies (GGDonto) ontology to the RDF representation of biomedical and genomic information from NCBI.
has_conceptual_partT160
has_conceptual_part
CP
conceptual_part_of
R5.11
Conceptually a portion, division, or component of some larger whole.
{isa} conceptually_related_to
This semantic relation is used for linking the Genetic Glyco-Diseases Ontologies (GGDonto) ontology to the RDF representation of biomedical and genomic information from NCBI.
conceptually_related_toT158
conceptually_related_to
CR
conceptually_related_to
R5
Conceptually a portion, division, or component of some larger whole.
{isa} conceptually_related_to
This semantic relation is used for linking the Genetic Glyco-Diseases Ontologies (GGDonto) ontology to the RDF representation of biomedical and genomic information from NCBI.
MeSH
Medical Subject Headings
MSH
Medical Subject Headings
MeSH
http://www.ncbi.nlm.nih.gov/mesh/
HPO
Human Phenotype Ontology
HPO
Human Phenotype Ontology
HPO
http://www.human-phenotype-ontology.org/
SNOMEDCT
Systematized Nomenclature of Medicine - Clinical Terms
SNOMEDCT
Systematized Nomenclature of Medicine - Clinical Terms
SNOMED CT
http://www.nlm.nih.gov/research/umls/Snomed/snomed_main.html
OMIM
Online Mendelian Inheritance in Man
OMIM
Online Mendelian Inheritance in Man
OMIM
http://www.omim.org/
GTR
Genetic Testing Registry
GTR
Genetic Testing Registry
GTR
http://www.ncbi.nlm.nih.gov/gtr/
MTH
UMLS Metathesaurus
MTH
UMLS Metathesaurus
http://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/
MDR
Medical Dictionary for Regulatory Activities Terminology
MDR
Medical Dictionary for Regulatory Activities Terminology
MedDRA
http://www.meddra.org/
GeneReviews
GeneReviews
GeneReviews
GeneReviews
http://www.ncbi.nlm.nih.gov/books/NBK1116/
NCI
National Cancer Institute Thesaurus
NCI
National Cancer Institute Thesaurus
NCIt
http://ncit.nci.nih.gov/
Genetics Home Reference
Genetics Home Reference
Genetics Home Reference
Genetics Home Reference
http://ghr.nlm.nih.gov/