Question: How To Know When A Ucsc Annotation Track Has Been Updated
5
gravatar for User 6659
7.8 years ago by
User 6659960
User 6659960 wrote:

Dear All

How do you know when a UCSC annotation track has been updated or when new tracks have been released. I have looked on the FAQ but I can't see any obvious answers except for the section about when Genbank updates are done. I imagine in some cases it might depend on the specific data source (e.g. dbSNP tracks are probably updated for each dbSNP release). Is there a mailing list or anything equivalent?

thanks a lot

ucsc • 1.7k views
ADD COMMENTlink modified 5.4 years ago by Biostar ♦♦ 20 • written 7.8 years ago by User 6659960
7
gravatar for Mary
7.8 years ago by
Mary11k
Boston MA area
Mary11k wrote:

You can check the release log: http://genome.ucsc.edu/goldenPath/releaseLog.html

We've asked in the past for something like an RSS feed of this, but I don't remember that ever coming together.

There are mailing lists of various types. But the "announce" is usually only big things like a whole new species. ENCODE announce sometimes does individual tracks. But not consistently.

Release log is your best best.

Mailing lists: Main: http://genome.ucsc.edu/contacts.html ENCODE: https://lists.soe.ucsc.edu/mailman/listinfo/encode-announce

There's also a mirror list if you maintain a mirror site, probably not relevant--but FYI.

ADD COMMENTlink written 7.8 years ago by Mary11k
1

good idea about the RSS, too bad they didn't implement it.

ADD REPLYlink written 7.8 years ago by Giovanni M Dall'Olio26k
1

thanks mary (and also for the excellent open helix tutorials too which i watched the other week!)

ADD REPLYlink written 7.8 years ago by User 6659960

Yeah, we had people ask us for that in workshops and at a conference, I remember mentioning it to the UCSC team. I'll use this opportunity to mention it again :)

ADD REPLYlink written 7.8 years ago by Mary11k
6
gravatar for Jennifer Hillman Jackson
7.8 years ago by
Bay Area, CA
Jennifer Hillman Jackson360 wrote:

To add to Mary's great answer, there is a field on each track's description page called "Data last updated:" that may be helpful for those wanting update information directly from the Genome Browser [GB] or database tables.

To web browse/extract this update tag in the GB, and example would be: [?]- UCSC browser [?]- select "Human Feb. 2009 (GRCh37/hg19)" aka hg19 [?]- on the assembly browser page, click on any track name [?]- in the top section, bottom field is "Data last updated:"

Please note that for composite tracks you will need to click into one of the sub-tracks to view the update date, as each is independently created/updated.

A way to retrieve the data in a table/file format is to use the Table Browser [TB] (or direct FTP, or the public mySQL database) and navigate to the database.table == hgFixed.trackVersion. The database, track name, update time, etc. is all there.

The path in the TB is a bit different than a regular database query: [?]- start with any database [?]- select group: all tables, database: hgFixed, and table: hgFixed.trackVersion [?]- download the table

Hopefully this is helpful! [?]jen

ADD COMMENTlink written 7.8 years ago by Jennifer Hillman Jackson360

Excellent--thanks for coming by! I was going to mail this thread to you guys with a request for the RSS feed again. That could be handy way to push that info out to the people who might need to know that.

ADD REPLYlink written 7.8 years ago by Mary11k

hi - i don't know if you are still looking at this question but the table hgFixed.trackVersion seems to give the date when the assembly track e.g. Hg18, hg19 etc was last modified and not the annotation tracks?

ADD REPLYlink written 7.8 years ago by User 6659960

hi i don't know if you are still looking at this question but i'm a bit confused by the database structure. there looks as if there is one database per genome assembly which has tables per annotation tracks (e.g. there are databases hg18, hg19 etc). But what is the hgFixed database? The trackVersion table looks like it contains information for each assembly, not the annotation tracks of an assembly which was what the question was about. Is this correct? Thanks for taking the time to answer this post :)

ADD REPLYlink written 7.8 years ago by User 6659960

Wow - two year later - but to see what the table contains, click on "describe table schema" (once you have navigated to it). The top of the page has the schema, sample rows will be underneath. There are multiple rows per database, one per track, tagged by date the data was loaded along with other comments (data author, etc.). The database "hgFixed" is a global database - it spans across assemblies/genomes. One way to understand it is to pick a small region and download a slice - is a 9 column tab file (if you count the bin/index leading field). - J

ADD REPLYlink written 5.8 years ago by Jennifer Hillman Jackson360
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