CGD Help: Batch Data Download

Contents

Description
Using the Batch Data Download Tool

Description

This resource allows simultaneous retrieval of DNA and protein sequences for a list of Standard gene names or Feature names or CGDIDs (identifiers assigned at CGD). Data that can be retrieved using this tool are included in one or more files on our Download site.

Using the Batch Download Tool

The Batch Download tool allows you to enter a list of Standard gene names or Feature names or CGDIDs and select the types of data that you want to retrieve.

Step 1: Your Input
Two options are available in Step 1.

Option 1: You can either enter Feature names (e.g., orf19.2203)/Standard Gene names (e.g., ACT1)/CGDIDs (e.g., CAL0001571) in the input box or upload a file of Feature/Standard names/CGDIDs.
OR
Option 2: Enter chromosomal coordinates (from Assembly 21 or 20) or contig coordinates (from Assembly 19) to retrieve all features between these coordinates. In this option you can either pick one chromosome/contig at a time or upload a file of chromosomal regions in the following format.
```
 chromosome_number[tab]start_coordinate[tab]stop_coordinate
```
If no coordinates are entered, all the features in the selected chromosome will be retrieved. This latter option will not retrieve data for features that are partially within and partially outside of the input coordinates. If you are uploading a file, note that there should be one Feature/Standard gene name/CGDID per line and the file should be saved as a text file.

Step 2: Choosing a Data type
For a given set of Feature names/Standard names/CGDIDs, you can simultaneously retrieve data for multiple data types. Data are always output in FASTA format except when using the Chromosomal Coordinates option. The following types of data may be retrieved:

Genomic DNA (DNA sequence, including introns and any gap regions)
Genomic DNA + 1 kb upstream and 1 kb downstream of flanking sequence
Coding Sequence
ORF translation- retrieves the translation of the coding sequence (i.e., protein sequence). Note that non-coding DNA features such as ARS and CEN elements are not translated in this option

Chromosomal Coordinates- retrieves data on chromosomal features, similar to the Chromosomal Feature file found on the CGD Download site. The columns in this file are as follows.

Column
1) Feature name (mandatory); this is the primary orf19 name, if available
2) Standard gene name (locus name)
3) Aliases (multiples separated by \|)
4) Feature type
5) Chromosome
6) Start_coordinate
7) Stop_coordinate
8) Strand
9) Primary CGDID
10) Secondary CGDID (if any)
11) Description
12) Date Created
13) Sequence Coordinate Version Date (if any)
14-15) Blank
16) Date of gene name reservation (if any)
17) Has the reserved gene name become the standard name? (Y/N)
18) Name of S. cerevisiae ortholog(s) (multiples separated by \|)

Gene Ontology (GO) Annotations- retrieves GO annotations for features, in the gene_association.CGD file format found in CGD's FTP site. This is the standard file format for gene_association files of the Gene Ontology (GO) Consortium. A more complete description of the file format can be found at the GO Consortium's website.
The columns in this file are as follows.

Column	Description
1) DB	database contributing the file (always "CGD" for this file)
2) DB_Object_ID	CGDID
3) DB_Object_Symbol	see below
4) NOT (optional)	'NOT' qualifier for a GO annotation, when needed
5) GO ID	unique numeric identifier for the GO term
6) DB:Reference(\|DB:Reference)	the reference associated with the GO annotation
7) Evidence	the evidence code for the GO annotation
8) With (or) From (optional)	any With or From qualifier for the GO annotation
9) Aspect	which ontology the GO term belongs in
10) DB_Object_Name(\|Name) (optional)	a name for the gene product in words, e.g. 'acid phosphatase'
11) DB_Object_Synonym(\|Synonym) (optional)	see below
12) DB_Object_Type	type of object annotated, e.g. gene, protein, etc.
13) taxon(\|taxon)	taxonomic identifier of species encoding gene product
14) Date	date GO annotation was made
15) Assigned_by	source of the annotation (always "CGD" for this file)

Phenotypes- retrieves phenotype data in a file format similar to the phenotype.tab file on CGD's FTP site. The columns in this file are:

Column	Contents
1) ORF (mandatory)	Systematic name of the ORF
2) Gene (optional)	Gene name, if one exists
3) CGDID (mandatory)	the CGDID, unique database identifier, for the ORF
4) Phenotype_type (mandatory)	classification of the phenotype
5) Phenotype (mandatory)	the phenotype
6) Description (optional)	a description of the type of experiment, if available
7) Reference (optional)	the unique PubMed identifer (PMID:) or the unique CGD identifier (CGD_ref:) for a reference

Orthologs and Best hits- retrieves S. cerevisiae orthologs and best hits in a tab-delimited file format. See this page for details on the method used to identify orthologs and best hits. The columns in this file are:

Column	Contents
1) ORF (mandatory)	Systematic name of the C. albicans ORF
2) Gene (optional)	CGD standard gene name, if one exists
3) SGDID (mandatory)	SGDID, unique database identifier, for the S. cerevisiae ortholog or best hit match
4) SGD Gene (mandatory)	SGD standard gene name or systematic name of the S. cerevisiae ortholog or best hit match
5) Ortholog or Best hit? (mandatory)	Indication whether the S. cerevisiae gene is an ortholog or best hit

Interpreting the results

If your input list of Feature/Gene names includes names that are Alias names, names that have been deleted or merged or non-existing gene names, an error message will be displayed. From this intermediate page you can either go back, edit your list to exclude those names, and resubmit, or click 'Proceed' which will retrieve the data for your input list by excluding those invalid names.

The different types of data that you requested are retrieved and stored in separate files that are listed in a table on the results page. Please note that data for all the types of information requested may not be available or may not be applicable for all the input Gene/Feature name(s). For example, the phenotype data type may not be available for all the features, while the data type 'ORF translation' is not applicable for DNA features like ARS elements or RNA genes. A Gene/Feature is not included in the file if there is no data for that feature. The number of features included in each file is shown in the table on the results page.
The file name, which has the process ID appended to it, is descriptive of the type of data it contains and the size of the file is displayed in the last column of the table. Clicking on the file name should download the file to the desktop of your local machine (depending on the browser). The file that contains your data will be available for 6 hours from the time it was requested. Go to the Batch Download Tool

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