urlget

Function

Description

Retrieves one or more URLs for further information about an identifier in a data resource.

EMBOSS can retrieve specific data types (sequences, features, taxonomy, resources, ontology terms) as defined ACD types.

Where there is no defined ACD inpu type, EMBOSS can retrieve the text of a database entry where the information is provided in a human-readable text format.

For many data resources there is no retrievable data format. In these cases EMBOSS can use the Data Resource Catalogue to construct URLs that can be viewed in the user's preferred browser which should be able to render them in a meaningful way.

Algorithm

urlget constructs the URL using the information in the Data Resource Catalogue entry which can be retrieved in its original format using drget.

The Query records are searched to find a query that returns HTML data (not parseable as text). The user-supplied identifier is inserted in the query to construct a URL.

If the identifier is specified as a swissprot (-swiss) or EMBL (-embl) cross-reference the defiitions of swissprot or EMBL cross-references in the DRCAT entry are used to select queries matching the identifier type.

Alternatively, the EDAM term name describing the identifier can be provided by the user to resolve the selection from multiple queries.

Usage

Command line arguments


Input file format

urlget reads a query containing a database name from DRCAT and an identifier.

Output file format

urlget returns a file containing one or more URLs with a description.

The -oformat qualifier provides a choice of formats which may be extended in future releases.

Data files

urlget uses the Data Resource Catalogue to retrieve information on URLs for the specified database name.

Notes

None.

References

None.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with status 0.

Known bugs

None.

Author(s)

History

Target users

Comments