FlyBase:ID Validator

Overview

This tool will accept a list of FlyBase symbols/IDs (for any data type) and, where necessary/possible, update them to their current versions. It will also convert certain external IDs (GenBank nucleotide/protein accessions, UniProt accessions, PubMed IDs) into their equivalent FlyBase IDs. The output is provided as a validation table that can either be downloaded as a file or exported to a FlyBase HitList for futher processing (including conversion between data types).

Usage

1. Either type/paste in a set of IDs/symbols into the 'Enter IDs or Symbols' box, or choose to 'Upload File of Identifiers' by clicking the Browse button. Spaces or returns should be used to separate the IDs/symbols (no commas or other text separators). The supported input types include:

• FlyBase IDs (for most data classes; e.g. FBgn (gene), FBal (allele), FBrf (reference) IDs)
• FlyBase symbols (for most data classes)
• FlyBase gene annotation symbols (eg. CG# or CR# for D. melanogaster)
• PubMed IDs (with or without a 'PMID' prefix)
• GenBank nucleotide/protein accessions
• UniProt (Swiss-Prot/TrEMBL) accessions

2. Choose whether to 'Return non-melanogaster' matches' (i.e. FlyBase entries matching the query ID/symbol from a species other than D. melanogaster) and whether to 'Match synonyms' (i.e. include ID/symbol synonyms when matching the submitted and FlyBase entries.) The default setting is to 'match synonyms' but not 'Return non-melanogaster matches'.

3. Click on the 'Submit Query' button.

4. The resulting table has four sections:

i) A header line listing the number of:

• Submitted IDs
• Unique Validated/Updated IDs
• Unknown IDs

ii) Buttons to export the list of validated IDs to:

• a FlyBase HitList (for further processing, including conversion between data types)
• the FlyBase Batch Download tool (to obtain and download additional data associated with each entry - NOTE: this option is enabled only for output lists comprising a single data class, such as 'genes')

iii) Buttons to download/save a file of:

• all unique validated IDs
• all unknown (unvalidated) IDs
• a TSV file of the entire validation report

iv) The validation table, comprising 4 columns showing:

• a checkbox indicated whether that row should be included in any 'export' request (see (ii) above)
• the submitted symbol/ID
• the validated (current) FlyBase ID
• the current FlyBase symbol, hyperlinked to the relevant FlyBase record

If one or more entered symbols/IDs mapped to multiple current FlyBase entries, then a WARNING message is displayed above the validation table, and the affected entries are marked with an exclamation mark (!).

The rows of the validation table are color-coded as follows:

• entered symbols/IDs that match current FlyBase symbols/IDs are colored green
• entered symbols/IDs that match non-current FlyBase symbol/ID synonyms and weresucessfully updated are colored yellow
• entered symbols/IDs that were unknown/unvalidated are colored red

Caveats/Disclaimers

• If the 'Match synonyms' box is checked, then entering an FBgn ID or CG number that has become a secondary ID for two current genes (e.g. FBgn0053520 or CG33520), or entering a CG number that is current for one gene but a synonym of another (e.g. CG10602), will generate two separate rows in the output table - one for each matching gene. A warning will appear above the validation table and the affected rows will be marked with an exclamation mark (!).

• Secondary IDs from 3rd party sources (UniProt, GenBank, PubMed) do not work (e.g. UniProt Q9VE67 does not work, but Q8IN81 does) - such IDs need to be updated at the 3rd party site before using the FlyBase ID converter.