FTP README

The files in this directory contain all of the data that can be viewed in the interaction explorer plus supplemental information from the external data source(s) which was not displayed in the interaction explorer. Supplemental data included will vary by external data source in accordance with what information is provided by each external data source.

In many cases there will be additional rows of data in the download file that were not loaded into MGI and therefore not available in the interaction explorer. This may arise for example, when anmiRNA targets several areas on a single transcript or when an miRNA targets several different transcripts. Since representation of features in MGI is at the gene level, these types of records will map back to a single MGI id. Display of this data in the interaction explorer would appear as duplicates lines since the information that makes the rows unique not displayed.

At this time, these supplemental data include:

For all sources that include a prediction score:

  • the original unscaled score.It can be found in the last (Unscaled score) column on sheet.
  • the mature stem product for which the prediction was made. These can be found in the column titled Property:Organizer_product_id and will be in the format RNA:miRBase:mmu-mir-207(18) indicating that it is an RNA, and the name (mmu-mir-207) is the official miRBase name for the stem product. The value in parentheses (18) indicates the miRBase version if available.

For validated data sources:

  • the actual stem product for which the interaction validated.
  • the validation method can be found in the notes column
  • references for the validation method can be found in the Property:Other_refs column in the format Reference Source:Reference Number. For example PMID:19536157.

For both predicted and validated sources:

  • Where available, the id of the predicted/validated target transcript is provided in the column titled Property:Participant_product_id. The format will be T(Transcript):ID source:ID. For example T:ENSEMBL:ENSMUST00000167091 indicating a transcript id from Ensembl with the value of ENSMUST00000167091.
  • The JNumber is an internal JAX reference which links to publications by the data source describing the algorithm/data. Navigate to enter the internal JNumber in the quick search. The internal reference will provide additional JNumber(s) which can be used in the quick search to findreferences to the articles by the external data providers.