My answers, not only for biological molecules:
and of course the database of biological entities/molecules for which there are no biological databases...
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...
@Eric, Well... the authors could decide to flag their papers as obsolete :-)
@Neil, no, that's why I said "not only for biological molecules" :o)
Pierre, there is a semantic pubmed...
ok, let's say that I want an official semantic from the NCBI :-)
Another answer inspired by : Easiest Way To Obtain Chromosome Length?
The Chromosome Length Database
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Pierre Lindenbaum
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).
the paper is here: http://bioinformatics.oxfordjournals.org/content/20/16/2886
(I have also edited my post)
I suppose you could also say the gene + mutation + disease + pathway + drug semantic database.
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.
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/
There's a catalog at Broad: http://www.broadinstitute.org/genome_bio/human_lincrnas/
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The arsenic DNA database :^)