Difference between revisions of "FlyBase:ID Validator"
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===Overview=== | ===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'. | ||
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| − | + | 3. Click on the 'Submit Query' button. | |
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| − | + | 4. The resulting table has four sections: | |
| − | + | i) A header line listing the number of: | |
| − | i) A header line listing the number of | ||
* Submitted IDs | * Submitted IDs | ||
| − | * Validated/Updated IDs | + | * Unique Validated/Updated IDs |
* Unknown IDs | * Unknown IDs | ||
| − | + | ii) Buttons to export the list of validated IDs to: | |
| − | ii) Buttons to export | + | * a FlyBase [[FlyBase:Tools_Overview#HitList_Refinement|HitList]] (for further processing, including conversion between data types) |
| − | * a FlyBase HitList | + | * the FlyBase [[FlyBase:Batch_Download|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') |
| − | * a | + | iii) Buttons to download/save a file of: |
| − | * a | + | * 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. | ||
Latest revision as of 12:44, 15 April 2020
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.