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 any file of IDs 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)
- FlyBase symbols (for most data classes)
- FlyBase gene annotation symbols (CG#)
- clone symbols
- PubMed IDs
- GenBank nucleotide/protein accessions
- UniProt (Swiss-Prot/TrEMBL) accessions
2. Choose to 'Validate Only' or 'Validate and Convert', choosing the desired conversion data class from the drop-down menu. (Note that IDs/symbols pertaining to different data classes (e.g. gene and alleles) may be submitted if choosing to 'Validate Only', but will result in conversion errors if choosing to 'Validate and Convert'.) The available 'convert to' options are:
- Genes
- Alleles
- Aberrations
- Balancers
- Transgenic constructs
- Natural transposons
- Insertions
- Transcripts
- Polypeptides
- Clones
- References
A table showing common/useful conversion types is shown below:
| Input (example) | Output (example) | Logic |
|---|---|---|
| Genes (FBgn ID or FlyBase symbol) | Polypeptides (FBpp ID and symbol) | List all polypeptides corresponding to each gene |
| Genes (FBgn ID or FlyBase symbol) | Alleles (FBal ID and symbol) | List all alleles corresponding to each gene |
| Alleles (FBal ID or FlyBase symbol) | Genes (FBgn ID and FlyBase symbol) | List all genes corresponding to each allele |
| Clones (FBcl ID or FlyBase symbol) | Genes (FBgn ID and FlyBase symbol) | List all genes associated with each clone |
| Genes (FBgn ID or FlyBase symbol) | References (FBrf ID) | List all references associated with each gene |
| References (FBrf ID or PMID) | Genes (FBgn ID and FlyBase symbol) | List all genes associated with each reference |
| References (PMID) | References (FBrf ID) | Convert PubMed IDs (PMIDs) to FlyBase reference (FBrf) IDs |
| Genes (GenBank nucleotide accession) | Genes (FBgn ID and FlyBase symbol) | Convert GenBank nucleotide accessions to FlyBase gene IDs |
| Proteins (UniProt or GenBank Protein accession) | Genes (FBgn ID and FlyBase symbol) | Convert external protein accessions to FlyBase gene IDs |
3. Click on the 'Submit Query' button.
4. The resulting table has three sections:
i) A header line listing the number of:
- Submitted IDs
- Validated/Updated IDs
- Unknown IDs
- Unique converted IDs
ii) Buttons to export/download the final list of converted IDs to:
- a FlyBase HitList
- a local file of unique FB IDs only
- a local file of the conversion table in TSV format
iii) The conversion table, comprising 4 columns showing the:
- Submitted symbol/ID
- Current FlyBase ID
- Converted FlyBase ID
- The FlyBase symbol, hyperlinked to the relevant FlyBase record
The table is color-coded as follows:
- converted FlyBase IDs are colored green
- other recognized (i.e. updateable/convertible) IDs/symbols are colored yellow
- unknown (ie. unconvertible) IDs/symbols are colored red
Caveats/Disclaimers
- Only a subset of all possible conversions make sense - attempting to make non-sensical conversions (e.g. 'transcripts' converted to 'alleles') will only result in a blank output table.
- Entering an FBgn ID or CG annotation symbol that has become a secondary ID for two current genes (e.g. FBgn0053520 or CG33520), or entering a CG annotation symbol that is current for one gene but a synonym of another (e.g. CG10602), generates two separate rows in the output table - one for each matching gene.
- 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.