This section describes how to download and add ontology terms to your Persephone database.

1. Download the trait ontology terms you need in Open Biomedical Ontologies (OBO) format from Gramene at http://archive.gramene.org/plant_ontology/ontology_browse.html.

2. Review the "add_TraitOntology.ini" control file, which is included in the PersephoneShell zip file archive "Samples/Ontology" folder and is shown below.


[ProcessRun]
; Run ID: if specified, it uses the existing run.
;RunId=12345
; Run description: if specified, a custom description will be used. Will be ignored if a RunId is specified.
;                  otherwise, "Added sequences for {MapSet Accession No.} from {Sources}." will be used.
RunDescription="Added trait ontology from http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=co."

[Ontology]
; Source (required): an OBO file located locally or remotely accessible via URL.
Source="http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/gramene/traits/trait.obo?view=co"
; XrefDbs: comma delimited. Create outer link for 'xref' in OBO.
;          If specified, corresponding section(s) named the same must exist.
;          If the same db key already exists, update; otherwise, insert as new.
XrefDbs="TO"

[TO]
; DbKey (required): database xref key. case-sensitive. e.g. TO of TO:1234
XrefDbKey=TO
; DbName (required): title of database
XrefDbName="Gramene Trait Ontology DB"
; HomeUrl: database home url
HomeUrl="http://archive.gramene.org"
; LinkUrl (required): database link url with the placeholder char %s
LinkUrlPattern="http://archive.gramene.org/db/ontology/search?id=%s"
; LinkUrlSample: sample identifier used to check its validity.
LinkUrlSample=0060866

Note

The Ontology and TO sections are described in Ontology Section and TO Section, respectively.

3. Copy the control file "add_TraitOntology.ini" to the directory where you installed PersephoneShell (e.g., C:\PersephoneShell).

4. Add the trait ontology terms in interactive or command line mode (see Running PersephoneShell). In the interactive mode, enter command as shown below.

PS> add ontology -c add_TraitOntology.ini

In the command line mode, enter

C:\PersephoneShell> psh -s ********** add ontology -c add_TraitOntology.ini

A verification message will be displayed.

Ontology Section

The Ontology section contains a source consisting of a single OBO file. The source can be a local file or accessible via FTP or HTTP. The XrefDbs field lists section names separated by commas that should be defined in the same INI file.

TO Section

The TO (Trait Ontology) cross-reference database section consists of the following fields:

  • daXrefDbKey. A database key that is used in accession (e.g., "TO:123456").
  • XrefDbName. The name of the database.
  • HomeUrl. The main page URL of the database.
  • LinkUrlPattern. The database link URL with the placeholder character "%s".
  • LinkUrlSample. A sample identifier to be used to validate the LinkUrlPattern field.