Phenoscape data loader

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

Functioning of the Phenoscape Data Loader

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 on a daily basis 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

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.

Reasons with the data

Lastly, 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.

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