Querying & accessing Treefam using any identifier type

Jim Hutchins's Avatar

Jim Hutchins

21 May, 2013 09:26 AM

What would be fantastic from a data-mining point of view would be to be able to access Treefam using virtually any type of gene or sequence identifier (gene symbol, Ensembl, UniProt, RefSeq) and to be able to append that ID onto a URL 'stem', to jump directly to a TreeFam 'Summary' page.

I guess most standard nucleotide/protein identifiers would normally correspond to just one distinct Treefam family. So on that basis Treefam could theoretically jump straight to the Summary page for the corresponding family. This used to be possible in the previous version, when using Ensembl gene IDs, e.g.
http://www.treefam.org/cgi-bin/TFseq.pl?id=ENSG00000158402 (this link doesn't work any more)
- but I'm not sure whether this is doable at all now. Is there a workaround that allows this?

An example of a database that works really well for accessing the 'summary page' from virtually any ID type is the EBI's Gene Expression Atlas.

Here are some examples:

direct link via Ensembl gene ID:
http://www.ebi.ac.uk/gxa/gene/ENSG00000156970
direct link via mouse (MGI) gene ID:
http://www.ebi.ac.uk/gxa/gene/MGI:88351
direct link via C. elegans gene code:
http://www.ebi.ac.uk/gxa/gene/K08E3.6
direct link via FlyBase ID:
http://www.ebi.ac.uk/gxa/gene/FBgn0000147
direct link via Ensembl transcript ID:
http://www.ebi.ac.uk/gxa/gene/ENST00000509894
direct link via RefSeq nucleotide ID:
http://www.ebi.ac.uk/gxa/gene/NM_000546
direct link via RefSeq protein ID:
http://www.ebi.ac.uk/gxa/gene/NP_009125
direct link via UniProt ID:
http://www.ebi.ac.uk/gxa/gene/Q9H410
query via gene symbol:
http://www.ebi.ac.uk/gxa/gene/RAD21
query via organism name plus gene symbol:
http://www.ebi.ac.uk/gxa/qrs?specie_0=Drosophila+melanogaster&gprop_0=&gval_0=aur

I don't know how the Expression Atlas manages to do this so efficiently- maybe it uses some kind of lookup table? If so- would such a table be a common EBI resource that could be accessed and utilised by Treefam as well? Maybe the Expression Atlas developers/curators are in the same building! ;-)

  1. 1 Posted by Fabian on 21 May, 2013 12:30 PM

    Fabian's Avatar

    Hi Jim,
    thanks for your good suggestion.
    I agree Expression Atlas has done a terrific job at implementing this feature.
    We have something similar - although not as sophisticated yet - in place.

    You can find a short description on how you can link to e.g. TreeFam family summary pages here: http://treefam.tenderapp.com/kb/how-to/how-can-i-link-to-treefam

    For the moment, Ensembl IDs, FlyBase IDs, GeneSymbols, and UniProt IDs should work. We are planning to add more databases to this mapping (e.g. the one you mentioned) to make it even easier to find information in TreeFam.

    Does that help?

    Cheers,
    Fabian

  2. Matthieu Muffato closed this discussion on 16 Jun, 2020 04:09 PM.

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