Spo: An Ontology for Describing Host-pathogen Interactions Inherent to Streptococcus Pneumoniae Infections Talk by Cátia Vaz INESC-ID / ISEL-IPL Joint work with Alexandre Francisco, Susana Vinga, Pedro Reis, Ana Teresa Freitas and Pneumopath Consorcium
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Spo: Spo: An Ontology for Describing Host-pathogen Interactions Inherent to Streptococcus Pneumoniae Infections Talk by Cátia Vaz INESC-ID / ISEL-IPL Joint.
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Spo:An Ontology for Describing Host-pathogen Interactions Inherent to Streptococcus Pneumoniae Infections
Talk by Cátia Vaz
INESC-ID / ISEL-IPL
Joint work with Alexandre Francisco, Susana Vinga, Pedro Reis, Ana Teresa Freitas
and Pneumopath Consorcium
host-pathogen interactions
Over the past twenty years, the study of infection has tended to consider individual virulence factors or host factors.
For finding new targets for diagnosis and treatment it is important to take into account more that one factor It is important to study the host-pathogen interactions
during infection of Streptococcus pneumonaie. This is one of the main goals of the Pneumopath
project.
host-pathogen interactions
The infection can be determined by multiple attributes of both host and pathogen. It is important to take into account:
epidemiological and genomic characterization of pneumococcal strains;
the results from experiments that evaluate host or pneumococcal responses to infection or different environmental challenges;
the results from experiments that identify host genetic susceptibility factors.
Data
The data to be considered to describe the host-pathogen interactions during infection of Streptococcus pneumonaie includes: characterization of pneumococcal strains, typing information data of in vitro and in vivo experiments with animals and
cell models. Some of these data are scattered across numerous
information systems and repositories, each with its own terminologies, identifier schemes, and data formats.
Data Integration
Thererefore, it is needed to have a common understanding of the concepts that describes host-pneumococcal interactions and thus it is need to: Define a vocabulary
The concepts and relations The semantic interconections
Relations between concepts and relations :. Define an Ontology!
Modeling Information
We have defined a model based on the information We have defined the concepts and their relations It allows more sharing of data and interoperability
We express data using knowledge representation languages We define a less coupled model to technology, making simpler
data integration
The model is very adaptive With the appearance of new concepts and new relations, it is
only necessary to add that new information avoid processes of data migration
Modeling Information
Thus, semantic annotation and interoperability become an absolute necessity for the integration of such diverse biomolecular data.
ExperimentsWorkpackage
Experiment
AnimalExperiment
Assay
GrowthExperiment
Participant
Institution
GeographicInformation
hasWorkpackage hasParticipant
“is-a”“is-a”
“is-a”belongsToInstitution
hasGeographicInformation
hasParticipant
ExperimentsWorkpackage
Experiment
AnimalExperiment
Assay
GrowthExperiment
Participant
Institution
GeographicInformation
hasWorkpackage hasParticipant
“is-a”“is-a”
“is-a”belongsToInstitution
hasGeographicInformation
hasParticipant
Name
DateRawFile Name
Name
AddressCountryCountryISOCodeRegion
Common Understanding...For instance, in experiences with animals:
And in experiences of Growth:
Two different Time Series?
Common Understanding...And with the same measurements in the same kind of experience: