Forum: Bioinformatics Tools And Resources Obituary Section
8
gravatar for Mary
5.6 years ago by
Mary11k
Boston MA area
Mary11k wrote:

For convenience and easy reference we list all resource below. This list will consolidate information from later followups.

Unavailable Resources

Background

A couple of times we've laughed about how hard it is to know if a tool or dataset or some bioinformatics resource has perished. You don't know if the server is down temporarily, if it has relocated but still available, or if it has ceased to be.

Inspired by Jeremey Leipzig's post about how handy it would be to have an obituary section of the NAR database issue,

One solution could be a obituary section to the web server issue, where sites are deemed dead, stale, or merely irrelevant by a panel of experts. Then corresponding authors could then indicate if they abandoned ship because of laziness, guilt, or simply out of spite

I propose that we keep an area here that has information on these resources. At least that way there would be some record that someone tried to trace it, and might save others time.

My proposal is that each suspected/alleged death notice get its own answer, which can be commented/discussed in replies. Maybe we can find some of them still. Or we can get some postings on milk cartons for stuff that's really crucial.

Below there will be a sample entry like I envision. Add your own if you have some.

forum • 3.4k views
ADD COMMENTlink modified 5.5 years ago • written 5.6 years ago by Mary11k
1

Hi Mary,

yes, this is a good idea ... maybe Michelle Brazas and I should include some of these thoughts in our commentary in this year's web server issue?

ADD REPLYlink written 5.5 years ago by francis190

Wow, that would be great. I've spent days tracking data or tools that I wanted to examine again. It might also help us to understand what happens to cause this. Funding? Grad student who ran it left? Superseded by other tools?

ADD REPLYlink written 5.5 years ago by Mary11k

Great idea Mary, I missed this originally. Interesting concept.

ADD REPLYlink written 5.5 years ago by Istvan Albert ♦♦ 74k

I think it's necessary. I need a place to store this--it happens to us a lot that we go looking for something, or someone asks us about it. So it's possibly self-serving, but might as well save others time later if I have the info. It will at least be google-able this way.

ADD REPLYlink written 5.5 years ago by Mary11k
1

we should edit and add/update the new entries to the original post in a designated section so that one does not need to read the entire thread to find all the names.

ADD REPLYlink written 5.5 years ago by Istvan Albert ♦♦ 74k

Ranking by vote score won't be ideal, quite so. But I'm not sure I understand what you mean. Feel free to edit or add an entry or something to illustrate.

ADD REPLYlink written 5.5 years ago by Mary11k
1

Reorganized the main post a bit, the listing is now at the top.

ADD REPLYlink written 5.5 years ago by Istvan Albert ♦♦ 74k

Ah, I see. Ok--I'll try to curate it when I notice new entries, but others should also feel free to edit if they have something to add that I haven't got to yet.

ADD REPLYlink written 5.5 years ago by Mary11k

This is definitely a good thing and I hope it will become both widely used and well-known. So far we have two databases but I hope people will also post about software.

ADD REPLYlink written 5.5 years ago by jmhancock0
3
gravatar for Mary
5.6 years ago by
Mary11k
Boston MA area
Mary11k wrote:

GDB, human genome database.

Was found at: http://www.gdb.org

Paper about it: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC147203/

It went through a few relocations, and then finally vanished a few years ago. I'm looking for a blog post I did on it back then to find the details. I'll edit this when I find it, but I wanted to put up a sample post now to illustrate what I meant on the obituary thing.

Sackings leave gene database floundering.

Edit: I can't find the post on it, but now I remember that last think I knew was that GDB ended up at RTI International, and then vanished.

http://www.genomeweb.com/gdb-moves-north-carolina-s-rti-international

http://www.rti.org/news.cfm?nav=423&objectid=B3FE683E-4193-4EA1-A1FFD809784458C4

There's a wikipedia entry on GDB that says it was shut down June 1, 2008 http://en.wikipedia.org/wiki/GDB_Human_Genome_Database

ADD COMMENTlink modified 5.5 years ago • written 5.6 years ago by Mary11k
2
gravatar for Mary
5.5 years ago by
Mary11k
Boston MA area
Mary11k wrote:

GENSAT: "The Gene Expression Nervous System Atlas (GENSAT) is is one of the first large-scale efforts to look at where specific genes are expressed in the brain and spinal cord. The project is funded by the NIH's National Institute of Neurological Disorders and Stroke (NINDS). " was found at NCBI, this text from this link at this time: http://www.ncbi.nlm.nih.gov/projects/genome/probe/doc/ProjGensat.shtml

On the GENSAT page right now: http://www.ncbi.nlm.nih.gov/gensat

We are sorry, but the page you requested is no longer available.

Due to budgetary constraints, the National Center for Biotechnology Information (NCBI) has discontinued support for the NCBI GENSAT database, and it has been removed from the Entrez System.

The Gene Expression Nervous System Atlas (GENSAT) project involves the large-scale creation of transgenic mouse lines expressing green fluorescent protein (GFP) reporter or Cre recombinase under control of the BAC promoter in specific neural and glial cell populations. BAC expression data for all the lines generated (over 1300 lines) are available in online, searchable databases www.gensat.org and the Database of GENSAT BAC-Cre driver lines).

If you have any specific questions, please feel free to contact us at info@ncbi.nlm.nih.gov

If you want to contact anyone on GENSAT, this was recommended to us: http://www.gensat.org/index.html

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Mary11k
1
gravatar for Mary
5.5 years ago by
Mary11k
Boston MA area
Mary11k wrote:

BioHealthBase vanished. We had this in our database collection, and when testing links I got a parking page/link farm now.

The BioHealthBase Bioinformatics Resource Center (BRC) (http://www.biohealthbase.org ) is a public bioinformatics database and analysis resource for the study of specific biodefense and public health pathogens—Influenza virus, Francisella tularensis, Mycobacterium tuberculosis, Microsporidia species and ricin toxin.

And this was not an old resource.

PubMed Central paper from an NAR database issue: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238987/?tool=pubmed

Link provided by that paper (now a link farm offering me Chevy Trucks mostly): http://www.biohealthbase.org and they also talk about their data being in Reactome.

I wrote to the corresponding author in January asking if there were server issues or if the resource had been relocated, and did not receive a response. Does anyone know what's up with this project?

ADD COMMENTlink modified 5.5 years ago • written 5.5 years ago by Mary11k
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