Difference between revisions of "FlyBase:ID Validator"
| Line 20: | Line 20: | ||
* GenBank nucleotide/protein accessions | * GenBank nucleotide/protein accessions | ||
* Uniprot (Swiss-Prot/TrEMBL) 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 results in conversion errors if chossing to 'Validate and Convert'.) The available 'convert to' options are: | 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 results in conversion errors if chossing to 'Validate and Convert'.) The available 'convert to' options are: | ||
| Line 34: | Line 35: | ||
* References | * References | ||
Note that only a subset of all possible conversions make sense - attempting to make non-sensical conversions (e.g. transcripts -> alleles) will result in a blank output table. A table showing common/useful conversion types is shown below. | Note that only a subset of all possible conversions make sense - attempting to make non-sensical conversions (e.g. transcripts -> alleles) will result in a blank output table. A table showing common/useful conversion types is shown below. | ||
| + | |||
3. Click on the 'Submit Query' button. | 3. Click on the 'Submit Query' button. | ||
| + | |||
4. The resulting table has three sections: | 4. The resulting table has three sections: | ||
| − | i) A header line listing the number of | + | i) A header line listing the number of: |
* Submitted IDs | * Submitted IDs | ||
* Validated/Updated IDs | * Validated/Updated IDs | ||
| Line 48: | Line 51: | ||
* a local file of the conversion table in TSV format | * a local file of the conversion table in TSV format | ||
iii) The conversion table, comprising 4 columns showing the: | iii) The conversion table, comprising 4 columns showing the: | ||
| − | * Submitted ID | + | * Submitted symbol/ID |
| − | * Current ID | + | * Current FlyBase ID |
| − | * Converted ID | + | * Converted FlyBase ID |
| − | * | + | * The FlyBase symbol, hyperlinked to the relevant FlyBase record |
| + | |||
| + | The table is color-coded: | ||
| + | * current FlyBase IDs are colored green | ||
| + | * other recognized (i.e. updateable/convertible) IDs/symbols are colored yellow | ||
| + | * unknown (ie. unconvertible) IDs/symbols are colored red | ||
Revision as of 13:43, 12 December 2017
Overview
You can use the ID Converter tool to either:
(i) validate a set of symbols/IDs, which will update any old symbols/IDs to their current equivalents (where possible); or
(ii) validate and convert a set of symbols/IDs, which will additionally convert the submitted list from one data class to another (where feasible), such as converting a list of allele or transcript IDs to their corresponding gene IDs.
This tool can also be used to simply upload ID lists, as the set of validated/converted IDs can be exported to a HitList for further analysis/processing within FlyBase.
Usage
1. Either type/paste in a set of IDs/symbols into the 'Enter IDs or Symbols:' box, or choose to Upload an 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 names
- 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 results in conversion errors if chossing to 'Validate and Convert'.) The available 'convert to' options are:
- Genes
- Alleles
- Aberrations
- Balancers
- Transgenic constructs
- Natural transposons
- Insertions
- Transcripts
- Polypeptides
- Clones
- References
Note that only a subset of all possible conversions make sense - attempting to make non-sensical conversions (e.g. transcripts -> alleles) will result in a blank output table. A table showing common/useful conversion types is shown below.
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:
- current FlyBase IDs are colored green
- other recognized (i.e. updateable/convertible) IDs/symbols are colored yellow
- unknown (ie. unconvertible) IDs/symbols are colored red