Question: Is the DAVID knowledgebase not updated any more?
9
gravatar for Christian
4.1 years ago by
Christian2.6k
Cambridge, US
Christian2.6k wrote:

Looking at the update information at http://david.abcc.ncifcrf.gov/helps/update.html, the latest update was Sept 2009.

Also, a question in the DAVID user forum (http://david.abcc.ncifcrf.gov/forum/viewtopic.php?f=8&t=1153) dating back to November 2013 and asking why the knowledgebase is not updated more regularily did not receive any answer by the database maintainers.

All this is rather worrysome and makes me wonder how appropriate it is to continue using DAVID for gene set enrichment analysis.

Edit: I should add that I find DAVID a great resource and it would be very sad to see it go.

ADD COMMENTlink modified 2.1 years ago • written 4.1 years ago by Christian2.6k
1

Did you try contacting the DAVID bioinformatics team? http://david.abcc.ncifcrf.gov/content.jsp?file=Contact.html There are three personal email addresses there. Perhaps you could try that and report back what you find.

ADD REPLYlink written 4.1 years ago by seidel6.5k

Yes, sent an e-mail today and will post the answer here.

ADD REPLYlink written 4.1 years ago by Christian2.6k

Soooo... anything?

ADD REPLYlink written 4.1 years ago by Georg Summer140

No reply yet from any of the three DAVID Bioinformatic Team members listed at http://david.abcc.ncifcrf.gov/content.jsp?file=Contact.html. Does not look good so far.

ADD REPLYlink written 4.1 years ago by Christian2.6k
1

I called the numbers for Rich Lempicki, and Da-Wei Huang listed on the contact page last week. Both had voice mail boxes identifying themselves as being from the "DAVID bioinformatics lab" as if it is still an active and staffed entity. They haven't returned my calls. I've approached Rich Lempicki twice via google-plus in reference to the DAVID update issue over the last few months. No response. I don't have time to continue with a dialing campaign at the moment, but I'm curious to know if there is some empirical way to determine if the database has been updated by looking at the data itself. i.e. is there some piece of information that can be mined from the database that can be tied to a date. For instance some GO term or a GO term/gene relationship that didn't exist in 2009, but was introduced in 2011, would suggest that the database was updated in 2011.

ADD REPLYlink written 3.9 years ago by seidel6.5k

I'm also keen to hear thoughts on this. DAVID is often recommended (including on this website) but it does seem quite out of date. I'd be quite interested if anyone has good data comparing using DAVID to something like topGO with the current version of GO.db from Bioconductor (updated bi-annually).

ADD REPLYlink written 4.0 years ago by johnstantongeddes380
1

The software was written by people contracted to NIAID by SAIC-Frederick. It might be that the contract expired or has since changed. The lab that wrote this software was also contracted to do Affy arrays for NIAID. I was under the impression that the NIAID array service lab was not located at NCI, but they may have split their Affy and Agilent facilites.

NIH has the head of that lab Richard A. Lempicki listed under DHHS/NIH/NIAID/DCR/CCRB. However the CCRB doesn't list him on the webpage: http://www.niaid.nih.gov/about/findingpeople/dcr/Pages/CCRB.aspx The linkedin profile of the DAVID bioinformatics lab, Da-Wei Huang, M.D., still has his linkedin page listed as such. So I'm not sure.

I sent an email too, but worse case I can always walk over there and knock on the door.

ADD REPLYlink written 4.0 years ago by pld4.7k

>...I can always walk over there and knock on the door.

Oh, that's the best case. You should totally do it. I was thinking of sending email to Richard A. Lempicki at Leidos Biomedical (his current affiliation) to see what's up. If I could walk over there I'd do it in a second. I might start calling phone numbers, there are a few listed.

ADD REPLYlink written 4.0 years ago by seidel6.5k

yes please, would be great if you could walk over and let us know about the current status and future plans here.

ADD REPLYlink written 4.0 years ago by Christian2.6k

Thanks for the background info. Look forward to anything you might here!

ADD REPLYlink written 4.0 years ago by johnstantongeddes380

Soooo... did you find anyone?

ADD REPLYlink written 4.0 years ago by Georg Summer140

Haven't had a chance yet, I'll try to get over during lunch today.

ADD REPLYlink written 4.0 years ago by pld4.7k

yes, please

ADD REPLYlink written 4.0 years ago by Christian2.6k

I looked into this and I can confirm with 90% certainty that DAVID is dead. First, the forum has not had new "news" since March 2015: https://david.ncifcrf.gov/forum/viewforum.php?f=10

Second, at the bottom of the announcement of their award in 2013, it says Dr. Dawei Huang is the lead, not the names on the contact page. https://david.ncifcrf.gov/forum/viewtopic.php?f=10&t=1254

Third, I was able to find Dr. Huang's LinkedIn page, which indicates he left in February 2015, which correlates to the forum ceasing updates. https://www.linkedin.com/in/huang-da-wei-5723295

Is there a suitable replacement yet?

ADD REPLYlink written 2.4 years ago by Tom Koch110

In terms of replacements, MyGene.info serves up gene annotations as a web service and can provide a lot of the same data types as DAVID, and is kept up-to-date. It's fast, there's an API, and there are clients for it in R and python. Other peeps on Biostar have used it for Gene ID conversion, get GO terms, pathways, and more.

ADD REPLYlink written 2.4 years ago by gtsueng140

I can't see how MyGene.info is currently a replacement for DAVID. It is for querying/retrieving gene annotation data, whereas DAVID performs gene set enrichment analysis.

ADD REPLYlink written 23 months ago by Christian2.6k
0
gravatar for Christian
2.1 years ago by
Christian2.6k
Cambridge, US
Christian2.6k wrote:

The update arrived (DAVID 6.8):

https://david.ncifcrf.gov/content.jsp?file=release.html

See also related discussion on Biostars here:

Finally the much awaited DAVID update has taken place. Thoughts in the community will be appreciated

ADD COMMENTlink written 2.1 years ago by Christian2.6k

It is not working! the link is thee, but my wheel just keep on turning.

ADD REPLYlink written 14 months ago by Assa Yeroslaviz1.1k

Must be a local issue (firewall?). DAVID site came up fine and is working.

ADD REPLYlink written 14 months ago by genomax49k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1411 users visited in the last hour