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Help: Batch Extract Interface and Results


Contents


Description

The batch extract interface for SOURCE allows retrieval of a subset of the data available in SOURCE for many entries at once. This function will be useful to users who are interested in large sets of genes or clones (such as those present on DNA microarrays).


Identifier Input

You must input a list of identifiers for which you wish to extract data. These identifiers can be GenBank Accessions, dbEST cloneIDs, UniGene ClusterIDs, UniGene gene names, or UniGene gene symbols. To upload your data you can select a file on your local computer using the "Input File" field or "Browse..." button. This file must only contain one column and each line must contain a separate identifier. Alternatively, you can type your list of identifiers into the text field, separated by the "Return" or "Enter" key.

After submitting the identifiers, you must chose which type of identifier you are using and also from which species they stem. The species designation will be ignored in the case of CloneIDs, GenBank Accessions, or UniGene ClusterIDs, since for these the organism of orgin is intrinsic to the identifier. CloneIDs solely consisting of digits (i.e. not containing a prefix identifying the source of the clone such as 'IMAGE:' or 'ATCC:') that are not found in the SOURCE database will be assumed to be IMAGE clones and also searched for with the 'IMAGE:' prefix.


Choice of data for retrieval

You can choose to extract one or more of the types of data described below.


Error Conditions

Since SOURCE is currently using UniGene as the central database to which all other databases are linked, a gene of interest must be in UniGene in order for data to be available for it. If an identifier is not found in UniGene, the batch extract script will return a warning stating that it was not found. Similarly, if a cloneID or accession number maps to multiple UniGene clusters, the script will not extract data but rather return a warning stating that the identifier does not map to a single UniGene cluster. In order to suppress these warnings (i.e. to leave those identifiers out of the final results file) you can check the appropriate box in the "Error Conditions" section of the form. Note that you can also choose to see the cluster IDs for chimeric clusters by selecting the "Show all Cluster IDs if in multiple Clusters" choice. If you concurrently chose to suppress the entries that map to multiple UniGene clusters, the suppression takes presedence.


Downloading the results

Once your request has been processed you will see a link to the results file. In order to save it to your computer, please right-click on the word "results" and chose the "Save target as" (Internet Explorer) or "Save link as" (Netscape) option.


Relevant Links

External Sites

  1. UniGene
  2. dbEST
  3. SwissProt
  4. LocusLink
  5. GeneCards
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    Please send comments or questions to: array@genomics.princeton.edu