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Semantic Web-based integration of cancer pathways and allele frequency data.

Holford ME, Rajeevan H, Zhao H, Kidd KK, Cheung KH - Cancer Inform (2009)

Bottom Line: The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions.This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine.It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA.

ABSTRACT
We demonstrate the use of Semantic Web technology to integrate the ALFRED allele frequency database and the Starpath pathway resource. The linking of population-specific genotype data with cancer-related pathway data is potentially useful given the growing interest in personalized medicine and the exploitation of pathway knowledge for cancer drug discovery. We model our data using the Web Ontology Language (OWL), drawing upon ideas from existing standard formats BioPAX for pathway data and PML for allele frequency data. We store our data within an Oracle database, using Oracle Semantic Technologies. We then query the data using Oracle's rule-based inference engine and SPARQL-like RDF query language. The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions. Among the possibilities is the ability to identify genetic variants which are associated with cancer pathways and whose frequency varies significantly between ethnic groups. This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine. It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies.

No MeSH data available.


Related in: MedlinePlus

The Starpath ontology. (Generated using Protege—Ontoviz plugin).
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f4-cin-08-19: The Starpath ontology. (Generated using Protege—Ontoviz plugin).

Mentions: Figure 4 shows the full Starpath ontology. Each of the SPElement subclasses defines a few custom properties. Compounds indicate their cas-id from the Chemical Abstract Services and their chemical formula. Events designate their type and use object properties to point to their constituent party1 and party2. These object properties are members of a special class called EventParty which joins Event and Party and further specifies which side of the Event the Party occupies and in which direction the Event proceeds. The EventParty also holds references to masked-events. A MaskedEvent is an event as described by a pathway where only a portion of the event in question is significant to definition of the pathway. For example, though by definition any biochemical reaction is reversible given the necessary conditions, often the reaction will only proceed in one direction within a metabolic pathway. An instance of the Mask class is used to indicate given a certain pathway from a particular reference what masked-events are in effect. The MaskedEvent class in turn indicates given the event-party and mask, which members will participate and on which side and direction. The Gene class holds datatype properties that provide the common symbol for a gene and whether this symbol is governed by a particular authority such as HUGO for human genes. Gene also specifies zero to many grelated objects that are associated with it and zero to many orthologs. Orthologs are described by the Orthology class which delineates their provenance through a Reference object and their ref-id from that provenance. The organism of a gene is an instance of an Organism class, which provides its biological-name, common-name and taxon-id. As mentioned above, the GRelated class can describe any of several objects that can be linked to a gene. Its actual type is indicated by datatype property and its organism by the organism object property defined for Gene. A common type of GRelated in Starpath is the microarray probe; for GRelateds of this type, the parent chip is specified in an object property whose range is the Chip class. The Chip class indicates its full name, short-name and type using datatype properties. The Party class adds no additional properties to its base class other than zero to many members whose range is any subclass of SPElement. Finally, we have the Pathway class, which contains object properties that list the events that comprise them, the organism in question and what mask if any is to be applied.


Semantic Web-based integration of cancer pathways and allele frequency data.

Holford ME, Rajeevan H, Zhao H, Kidd KK, Cheung KH - Cancer Inform (2009)

The Starpath ontology. (Generated using Protege—Ontoviz plugin).
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC2664696&req=5

f4-cin-08-19: The Starpath ontology. (Generated using Protege—Ontoviz plugin).
Mentions: Figure 4 shows the full Starpath ontology. Each of the SPElement subclasses defines a few custom properties. Compounds indicate their cas-id from the Chemical Abstract Services and their chemical formula. Events designate their type and use object properties to point to their constituent party1 and party2. These object properties are members of a special class called EventParty which joins Event and Party and further specifies which side of the Event the Party occupies and in which direction the Event proceeds. The EventParty also holds references to masked-events. A MaskedEvent is an event as described by a pathway where only a portion of the event in question is significant to definition of the pathway. For example, though by definition any biochemical reaction is reversible given the necessary conditions, often the reaction will only proceed in one direction within a metabolic pathway. An instance of the Mask class is used to indicate given a certain pathway from a particular reference what masked-events are in effect. The MaskedEvent class in turn indicates given the event-party and mask, which members will participate and on which side and direction. The Gene class holds datatype properties that provide the common symbol for a gene and whether this symbol is governed by a particular authority such as HUGO for human genes. Gene also specifies zero to many grelated objects that are associated with it and zero to many orthologs. Orthologs are described by the Orthology class which delineates their provenance through a Reference object and their ref-id from that provenance. The organism of a gene is an instance of an Organism class, which provides its biological-name, common-name and taxon-id. As mentioned above, the GRelated class can describe any of several objects that can be linked to a gene. Its actual type is indicated by datatype property and its organism by the organism object property defined for Gene. A common type of GRelated in Starpath is the microarray probe; for GRelateds of this type, the parent chip is specified in an object property whose range is the Chip class. The Chip class indicates its full name, short-name and type using datatype properties. The Party class adds no additional properties to its base class other than zero to many members whose range is any subclass of SPElement. Finally, we have the Pathway class, which contains object properties that list the events that comprise them, the organism in question and what mask if any is to be applied.

Bottom Line: The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions.This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine.It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies.

View Article: PubMed Central - PubMed

Affiliation: Department of Biostatistics, School of Public Health, Yale University, New Haven, CT, USA.

ABSTRACT
We demonstrate the use of Semantic Web technology to integrate the ALFRED allele frequency database and the Starpath pathway resource. The linking of population-specific genotype data with cancer-related pathway data is potentially useful given the growing interest in personalized medicine and the exploitation of pathway knowledge for cancer drug discovery. We model our data using the Web Ontology Language (OWL), drawing upon ideas from existing standard formats BioPAX for pathway data and PML for allele frequency data. We store our data within an Oracle database, using Oracle Semantic Technologies. We then query the data using Oracle's rule-based inference engine and SPARQL-like RDF query language. The ability to perform queries across the domains of population genetics and pathways offers the potential to answer a number of cancer-related research questions. Among the possibilities is the ability to identify genetic variants which are associated with cancer pathways and whose frequency varies significantly between ethnic groups. This sort of information could be useful for designing clinical studies and for providing background data in personalized medicine. It could also assist with the interpretation of genetic analysis results such as those from genome-wide association studies.

No MeSH data available.


Related in: MedlinePlus