Archived assemblies

Older assemblies are archived on the archives server. However, some metadata about the archived assemblies is kept in the hgcentral database in order to offer liftOver to and from the older assemblies.

NOTE: the following setup describes the database setup that should take effect with the v172 cgis. The old setup used a separate database, hgcentarchive, with its own dbDb table. This entire database is being replaced by the single table dbDbArch in hgcentral.

hgcentral setup

liftOverChain

Entries in liftOverChain should be kept for archived assemblies in order to keep nets/chains from other browsers that point to the archived assemblies from breaking. Also, the entries make it possible for hgLiftOver and hgConvert to continue to work for archived assemblies on the main site (not genome-archive).

dbDb

A line in dbDb for an archived assembly should be maintained if:

1. Any other organism's nets and chains are still pointing to it.

2. The conservation track of another organism was built using the archived assembly. The conservation track needs the dbDb entry in order to find the organism name for the hgc page (it uses it to write "Rhesus" rather than "rheMac1", for instance).

dbDbArch

If a line in dbDb is no longer needed for another assembly's net, chain, or conservation track, it can be removed and added to hgcentral.dbDbArch instead. The dbDbArch table is present to support hgLiftOver and hgConvert, which will continue to work for archived assemblies as long as the pertinent information in /gbdb is still available.