Difference between revisions of "FlyBase:ID Validator"

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===Usage===
 
===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:
+
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)
+
* FlyBase IDs (for most data classes; e.g. FBgn (gene), FBal (allele), FBrf (reference) IDs)
 
* FlyBase symbols (for most data classes)
 
* FlyBase symbols (for most data classes)
−
* FlyBase gene annotation symbols (CG#)
+
* FlyBase gene annotation symbols (eg. CG# or CR# for ''D. melanogaster'')
−
* clone symbols
 
 
* PubMed IDs
 
* PubMed IDs
 
* GenBank nucleotide/protein accessions
 
* GenBank nucleotide/protein accessions
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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:
+
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 in the search to match the submitted entry and database entries.) The default setting is  to 'match synonyms' but '''not''' 'Return non-melanogaster matches'.
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* Genes
 
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* Alleles
 
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* Aberrations
 
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* Balancers
 
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* Transgenic constructs
 
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* Natural transposons
 
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* Insertions
 
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* Transcripts
 
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* Polypeptides
 
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* Clones
 
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* References
 
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A table showing common/useful conversion types is shown below:
 
−
 
 
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{| class="wikitable"
 
−
|-
 
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! Input (example) !! Output (example) !! Logic
 
−
|-
 
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| '''Genes''' (FBgn ID or FlyBase symbol) || '''Polypeptides''' (FBpp ID and symbol) || List all polypeptides corresponding to each gene
 
−
|-
 
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| '''Genes''' (FBgn ID or FlyBase symbol) || '''Alleles''' (FBal ID and symbol) || List all alleles corresponding to each gene
 
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|-
 
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| '''Alleles''' (FBal ID or FlyBase symbol) || '''Genes''' (FBgn ID and FlyBase symbol) || List all genes corresponding to each allele
 
−
|-
 
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| '''Clones''' (FBcl ID or FlyBase symbol) || '''Genes''' (FBgn ID and FlyBase symbol) || List all genes associated with each clone
 
−
|-
 
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| '''Genes''' (FBgn ID or FlyBase symbol) || '''References''' (FBrf ID) || List all references associated with each gene
 
−
|-
 
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| '''References''' (FBrf ID or PMID) || '''Genes''' (FBgn ID and FlyBase symbol) || List all genes associated with each reference
 
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|-
 
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| '''References''' (PMID) || '''References''' (FBrf ID) || Convert PubMed IDs (PMIDs) to FlyBase reference (FBrf) IDs
 
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|-
 
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| '''Genes''' (GenBank nucleotide accession) || '''Genes''' (FBgn ID and FlyBase symbol) || Convert GenBank nucleotide accessions to FlyBase gene IDs
 
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|-
 
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| '''Proteins''' (UniProt or GenBank Protein accession) || '''Genes''' (FBgn ID and FlyBase symbol) || Convert external protein accessions to FlyBase gene IDs
 
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|-
 
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|}
 
  
  
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4. The resulting table has three sections:
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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
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* Unique Validated/Updated IDs
 
* Unknown IDs
 
* Unknown IDs
−
* Unique converted IDs
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ii) Buttons to export the list of validated IDs to:
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ii) Buttons to export/download the final list of converted IDs to:
 
 
* a FlyBase HitList
 
* a FlyBase HitList
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* a local file of unique FB IDs only
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* the FlyBase BatchDownload tool
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* a local file of the conversion table in TSV format
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iii) Buttons to download/save a file of:
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iii) The conversion table, comprising 4 columns showing the:
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* all unique validated IDs
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* Submitted symbol/ID
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* all unknown (unvalidated) IDs
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* Current FlyBase ID
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* a TSV file of the entire validation report
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* Converted FlyBase ID
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iv) The validation table, comprising 4 columns showing:
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* The FlyBase symbol, hyperlinked to the relevant FlyBase record
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* 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 table is color-coded as follows:
+
The rows of the validation table are color-coded as follows:
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* converted FlyBase IDs are colored '''green'''
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* entered symbols/IDs that match current FlyBase symbols/IDs are colored '''green'''
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* other recognized (i.e. updateable/convertible) IDs/symbols are colored '''yellow'''
+
* entered symbols/IDs that match non-current FlyBase symbol/ID synonyms and weresucessfully updated are colored '''yellow'''
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* unknown (ie. unconvertible) IDs/symbols are colored '''red'''
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* entered symbols/IDs that were unknown/unvalidated are colored '''red'''
  
 
===Caveats/Disclaimers===
 
===Caveats/Disclaimers===

Revision as of 12:16, 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
  • 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 in the search to match the submitted entry and database 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
  • the FlyBase BatchDownload tool

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

  • 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.
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