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...)
 
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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.
 
 
 
==Phenoscape Data loader==
 
==Phenoscape Data loader==
 
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:
 
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:

Revision as of 00:26, 9 January 2009

Phenoscape Data loader

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:

  • 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 on a daily basis for subsequent uploading into the relational database
  • Drops and recreates the database
  • Loads the requisite ontologies 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
  • Invokes the OBD reasoner to elicit implicit information from the data and adds them to the database
    • 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
  • Logs incomplete annotations into a log file
    • 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.

For status updates

For code specific details

  • OBD API Documentation
    • 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 The OBOEdit Javadoc