Difference between revisions of "Phenoscape data loader"

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(New page: One of the chief objectives of the Phenoscape project is to present a centralized repository to store annotations entered by ichthyologists. These annotations can be queried from a user in...)
 
(→‎Functioning of the Phenoscape Data Loader)
 
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One of the chief objectives of the Phenoscape project is to present a centralized repository to store annotations entered by ichthyologists. These annotations can be queried from a user interface and used to answer [[Driving_Research_Questions]] and for Advanced [[Phenoscape_use_cases]]. The following tools which are under various stages of development, will serve to realize this objective.
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The Phenoscape Data Loader is being developed as a Perl module. This section offers an overview of the functioning of the Phenoscape Data Loader. The data loader has been installed on the dev application server at NESCent and can be found at /usr/local/projects/phenoscape-data-loader
  
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==Phenoscape Data loader==
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==The Phenoscape data loader - A step by step review==
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A data loader application to refresh the data in the Phenoscape database on a daily basis is under development. The application is being developed as a Perl module, which in sequential order:
 
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* '''Downloads curated NeXML files from the Phenoscape SVN repositories'''
 
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** Ichthyologists curate scientific publications using the [[Phenex]] character matrix annotator and these curations are stored in an SVN repository. The data loader downloads these data files on a daily basis for subsequent uploading into the relational database
 
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* '''Drops and recreates the database'''
 
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* '''Loads the requisite ontologies into the database'''
 
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** The annotations of character matrices use terms that are defined in life science ontologies. These ontologies include the [http://bioportal.bioontology.org/ontologies/38703 Teleost Taxonomy Ontology (TTO)], the [http://www.obofoundry.org/ro/ Relations Ontology],  the [[Teleost_Anatomy_Ontology|Teleost Anatomy Ontology (TAO)]], and the [http://bioontology.org/wiki/index.php/PATO:Main_Page Phenotype and Trait Ontology (PATO)]. The data loader loads all these definitions into the relational database
 
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* '''Loads the data from the curated NeXML files into the database''',
 
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** The data loader transforms the curated data from NeXML syntax to a set of relational tuples (records), which are then sequentially inserted into the database
 
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* '''Invokes the OBD reasoner to elicit implicit information from the data and adds them to the database'''
 
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** The OBD reasoner uses definitions of transitive relations, relation hierarchies, and relation compositions to infer implicit information. These inferences are added to the relational database in the final step
 
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* '''Logs incomplete annotations into a log file'''
 
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** The data loader does not load incomplete annotations from the NeXML files into the database. Incomplete annotations contain null values for taxa or phenotype or both. Instead, it logs these incomplete annotations on a file-specific basis in this [[Problem Log Format]]. Curators can then work on finishing these annotations which will be subsequently loaded into the database in the next execution of the data loader.
 
  
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For status updates
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The Phenoscape data loader performs the following steps in sequence
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* '''[[Cartik's notes on the Phenoscape Data Loader]]'''
 
  
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===Downloads curated NeXML files from the Phenoscape SVN repositories===
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Ichthyologists curate scientific publications using the [[Phenex]] character matrix annotator and these curations are stored in an SVN repository. The data loader downloads these data files for subsequent uploading into the relational database
 +
 +
===Loads the requisite ontologies into the database===
 +
The annotations of character matrices use terms that are defined in life science ontologies. These ontologies include the [http://bioportal.bioontology.org/ontologies/38703 Teleost Taxonomy Ontology (TTO)], the [http://www.obofoundry.org/ro/ Relations Ontology],  the [[Teleost_Anatomy_Ontology|Teleost Anatomy Ontology (TAO)]], and the [http://bioontology.org/wiki/index.php/PATO:Main_Page Phenotype and Trait Ontology (PATO)]. The data loader loads all these definitions into the relational database
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===Loads the data from ZFIN model organism database ===
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[http://zfin.org ZFIN] hosts data relating mutant phenotypes of the ''Danio Rerio'' (Zebrafish) organism to specific genes and genotypes. The data loader transcribes this data into OBD format and loads it into the database
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===Loads the data from the curated NeXML files into the database===
 +
The data loader transforms the curated data from NeXML syntax to a set of relational tuples (records), which are then sequentially inserted into the database
 +
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===Reasons with the data ===
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The data loader invokes the [[OBD Reasoner]] to infer implicit knowledge from the assertions, in the form of new assertions. These inferred assertions are also added to the database.
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===Populates the data warehouse===
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The data warehouse is necessary for speedy execution of queries invoked from the user interface. The data warehouse is populated by running stored procedures on the data, after the reasoning process has completed. As an additional step, the loader invokes a labelmaker procedure, which generates readable labels for "post composed" terms
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===Loads the homology data===
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Homology data from the Phenoscape SVN files are loaded into the database. This includes assertions about homologies, the publications from which these are sourced, and the evidence codes used for these assertions.
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==Refreshing the data with the Phenoscape data loader==
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The Phenoscape data loader runs as a cron job on the kb-dev server every Friday at 6 PM EST. Given that the application WAR points to one of two copies of the Phenoscape knowledgebase, the data loader refreshes the other copy of the knowledgebase, so the application is never "offline". After the data refresh is completed, the application WAR is redeployed so that it points to the newer version of the data.
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==[[OBD API Documentation]]==
 
For code specific details
 
For code specific details
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* '''[[OBD API Documentation]]'''
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Specific details of OBD related classes and interfaces as documented by CK. These will be updated very often and are meant to be used as an addendum to the [http://oboedit.org/?page=javadocs The OBOEdit Javadoc]
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** Specific details of OBD related classes and interfaces as documented by Cartik Kothari. These will be updated very often and are meant to be used as an addendum to the [http://oboedit.org/?page=javadocs The OBOEdit Javadoc]
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[[Category:Informatics]]
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[[Category:Database]]

Latest revision as of 16:05, 29 October 2009

The Phenoscape Data Loader is being developed as a Perl module. This section offers an overview of the functioning of the Phenoscape Data Loader. The data loader has been installed on the dev application server at NESCent and can be found at /usr/local/projects/phenoscape-data-loader

The Phenoscape data loader - A step by step review

The Phenoscape data loader performs the following steps in sequence

Downloads curated NeXML files from the Phenoscape SVN repositories

Ichthyologists curate scientific publications using the Phenex character matrix annotator and these curations are stored in an SVN repository. The data loader downloads these data files for subsequent uploading into the relational database

Loads the requisite ontologies into the database

The annotations of character matrices use terms that are defined in life science ontologies. These ontologies include the Teleost Taxonomy Ontology (TTO), the Relations Ontology, the Teleost Anatomy Ontology (TAO), and the Phenotype and Trait Ontology (PATO). The data loader loads all these definitions into the relational database

Loads the data from ZFIN model organism database

ZFIN hosts data relating mutant phenotypes of the Danio Rerio (Zebrafish) organism to specific genes and genotypes. The data loader transcribes this data into OBD format and loads it into the database

Loads the data from the curated NeXML files into the database

The data loader transforms the curated data from NeXML syntax to a set of relational tuples (records), which are then sequentially inserted into the database

Reasons with the data

The data loader invokes the OBD Reasoner to infer implicit knowledge from the assertions, in the form of new assertions. These inferred assertions are also added to the database.

Populates the data warehouse

The data warehouse is necessary for speedy execution of queries invoked from the user interface. The data warehouse is populated by running stored procedures on the data, after the reasoning process has completed. As an additional step, the loader invokes a labelmaker procedure, which generates readable labels for "post composed" terms

Loads the homology data

Homology data from the Phenoscape SVN files are loaded into the database. This includes assertions about homologies, the publications from which these are sourced, and the evidence codes used for these assertions.

Refreshing the data with the Phenoscape data loader

The Phenoscape data loader runs as a cron job on the kb-dev server every Friday at 6 PM EST. Given that the application WAR points to one of two copies of the Phenoscape knowledgebase, the data loader refreshes the other copy of the knowledgebase, so the application is never "offline". After the data refresh is completed, the application WAR is redeployed so that it points to the newer version of the data.

OBD API Documentation

For code specific details Specific details of OBD related classes and interfaces as documented by CK. These will be updated very often and are meant to be used as an addendum to the The OBOEdit Javadoc

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