Biological Molecules For Which There Are No Databases

Question

[shrees]

Hello,

Can you please give examples of biological entities/molecules for which there are no biological databases (includes integrative databases too) available yet?

Thank you, Sonal

[Casey Bergman]

The arsenic DNA database :^)

Answer 1

[Pierre Lindenbaum]

My answers, not only for biological molecules:

• the mutation + sample + pedigree + phenotype (semantic) database
• the semantic pubmed
• the semantic catalog of softwares (see also seqanswers)
• the database of obsolete softwares
• the database of obsolete papers
• the database of obsolete databases
• the unique author-id database

[Gareth Palidwor]

and of course the database of biological entities/molecules for which there are no biological databases...

[Eric Fournier]

A database of obsolete software/paper/databases would be absolutely awesome! Except that whoever decides what is "obsolete" would probably make a lot of ennemies...

[Pierre Lindenbaum]

@Eric, Well... the authors could decide to flag their papers as obsolete :-)

[Neilfws]

Are software, publications and databases "biological entities"?

[Pierre Lindenbaum]

@Neil, no, that's why I said "not only for biological molecules" :o)

[Egon Willighagen]

Pierre, there is a semantic pubmed...

[Pierre Lindenbaum]

ok, let's say that I want an official semantic from the NCBI :-)

Answer 2

[Pierre Lindenbaum]

Another answer inspired by : Easiest Way To Obtain Chromosome Length?

The Chromosome Length Database

Answer 3

[Manu Prestat]

What would be very useful is I think a peptide signature database. I found one paper (COPS), but the database is not accessible, and anyway I don't think they updated since we have more than 2K complete microbial genomes (around 50 in the paper).

[Raygozak]

what paper is that?

[Manu Prestat]

the paper is here: http://bioinformatics.oxfordjournals.org/content/20/16/2886

(I have also edited my post)

Answer 4

[Mark Fortner]

I suppose you could also say the gene + mutation + disease + pathway + drug semantic database.

Answer 5

[Gustavo]

I'm not aware of any database collecting, for each studied tissue(*) in (for example) a vertebrate organism, the relative proportions of different cell types as defined by their respective signatures of single-cell gene expression levels.

(*) "Tissue" here would presumably be a hierarchical, multi-level description of multicellular context, from whole organs down to cellular microenvironment.

Answer 6

[Mary]

Is there a LINC database yet? I was interested in a linc recently and wasn't sure where to turn.

LINC: long intergenic non-coding RNAs. Like this: http://www.rinnlab.com/

[Gustavo]

There's a catalog at Broad: http://www.broadinstitute.org/genome_bio/human_lincrnas/

[Mary]

Thanks, that's handy--and I have uploaded a track of them at UCSC, but it's not exactly what I was looking for as a database per se.