Question: What Happened To The Bind (Biological Interaction Network) Database And Is Access Guaranteed In The Future?
8
gravatar for Chris Evelo
5.2 years ago by
Chris Evelo9.8k
Maastricht, The Netherlands
Chris Evelo9.8k wrote:

BIND the Biological Interaction Network Database was described here: http://dx.doi.org/doi:10.1093/nar/29.1.242

The original link http://binddb.org is dead, may have been dead for a while. I used to use http://bind.ca but that now forwards to http://bond.unleashedinformatics.com the BOND (Biological Object database Network) Database which is operated by Thomson Reuters. That is free (after registration) and is said to have BIND inside. But I was wondering what has happened, and whether we need to worry about the future. Especially since the ftp link given in the original paper also appears to be dead.

ADD COMMENTlink modified 21 months ago by bounlu90 • written 5.2 years ago by Chris Evelo9.8k

sounds like a pretty convincing obituary to me...

ADD REPLYlink written 5.2 years ago by Andrew Su4.6k
11
gravatar for Pierre Lindenbaum
5.2 years ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum91k wrote:

About BIND:

Databases in peril

Nature Cell Biology 7, 639 (2005) doi:10.1038/ncb0705-639b http://www.nature.com/ncb/journal/v7/n7/full/ncb0705-639b.html

"The Canadian government, for example, insists that its funding be matched by independent sources, which has led to the cancellation of funding for a number of large-scale projects (see Science, 24 June). One such project is the BIND database (see August 2004 editorial), which is set to shift activities to Singapore as a result (Science 308, 1529; 2005). "

ADD COMMENTlink written 5.2 years ago by Pierre Lindenbaum91k
1

Is the problem here the funding needed to host the databases, or is it something else?

As a side-note, someone might want to let Thomson-Reuters know about this little doozy:

Warning: secure.unleashedinformatics.com uses an invalid security certificate.

The certificate expired on 22/12/2009 02:36. The current time is 29/01/2012 20:36.

ADD REPLYlink written 5.2 years ago by Mark Anthony Gibbins130

Thanks Pierre, especially the Science paper mentioned is very interesting as it describes the background of the problem for BIND. But what I really would like to know is how it ended up with Thomson-Reuters and what that means for the future.

ADD REPLYlink written 5.2 years ago by Chris Evelo9.8k
7
gravatar for Mary
5.2 years ago by
Mary11k
Boston MA area
Mary11k wrote:

If this is a more general question about support for database availability, when I raised this issue because of KEGG's changes nobody seemed to think there were any community solutions possible, and maybe not even desirable, for this problem. That if a resource can't support itself, meh....

I am not of that opinion--I was hoping for more creative ways to save these things, obtain the legacy data, or some sort of community action we might undertake (like the SOPA petitions, perhaps). But it didn't seem there was that much interest.

How to ensure long-term support for crucial resources? Or should we?

ADD COMMENTlink written 5.2 years ago by Mary11k
1

Now that I think about this more formally again, I wonder if there really is an "obituary" paper that is needed. To assess the reasons that resources have gone away, what happened to that data, and if there are ways to mitigate complete vanishing of these...hmmm.

ADD REPLYlink written 5.2 years ago by Mary11k

The question was really just about BIND and Thomson Reuters. But I agree the more general question, and what the community can do about it, is very relevant as well. Which is why I created the "sustainability" tag. I think larger combined not-for-profit and for-profit sustainability funds/foundations are not abad idea. After all we all benefit. But government constructions should be clear too. Which is something I wondered about for BIND.

ADD REPLYlink written 5.2 years ago by Chris Evelo9.8k

There was a great idea in a blog post once--an "obituary" section of the NAR database/webserver issues! http://www.labspaces.net/blog/1421/Jerm_Looks_at_the_Annual_NAR_Web_Server_Issue At least we'd know....

ADD REPLYlink written 5.2 years ago by Mary11k
6
gravatar for Arnaud Ceol
5.2 years ago by
Arnaud Ceol710
Milan, Italy
Arnaud Ceol710 wrote:

If you're interested in BIND data, you should have a look at this address : http://baderlab.org/BINDTranslation

A great job has been done by people at Bader's lab to standardize (to official Protein Standard Initiative - Molecular Interaction standards version 2.5) and made available all data from BIND. Those standards are far easier and safer to use than the ones in which BIND was originally released.

reference : Ruth Isserlin, Rashad A. El-Badrawi, and Gary D. Bader The Biomolecular Interaction Network Database in PSI-MI 2.5 Database (2011) Vol. 2011 published online January 12, 2011, doi:10.1093/database/baq037

ADD COMMENTlink written 5.2 years ago by Arnaud Ceol710
0
gravatar for bounlu
21 months ago by
bounlu90
European Union
bounlu90 wrote:

Similarly, what happened to MINT?

http://mint.bio.uniroma2.it/mint

ADD COMMENTlink written 21 months ago by bounlu90

As far as I know, MINT has been merged into IntAct: http://nar.oxfordjournals.org/content/early/2013/11/13/nar.gkt1115.long

ADD REPLYlink modified 21 months ago • written 21 months ago by Jean-Karim Heriche8.7k

yes you are right, I also found out that they merged into MIntAct by combining their dataset, more like integrating MINT into IntAct.

ADD REPLYlink written 21 months ago by bounlu90

MINT has been working within the IMEx consortium with Intact and other databases for a while now. This means that the articles curated by each database were unique to avoid data redundancy. It has also been using the Intact model (database and Java API) for many years. MINT eventually decided that it was not necessary to duplicate the work of maintaining a curation interface, and is now inserting the new interactions directly into IntAct.

After this decision has been taken, IntAct started importing all the older entries from MINT, first the IMEx ones, and then all those that have been created once the PSI standards have been implemented. Note that a few older entries from MINT may not have been imported into Intact, mostly because they had been also curated by Intact (before IMEx), or because they didn't comply with PSI-MI/IMEx standards.

An important aspect of this MINTAct group, is that MINT curators are still doing the same job of curation and still have the same duties regarding the IMEx consortium.

 

ADD REPLYlink written 21 months ago by Arnaud Ceol710
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