On Mon, 2008-03-31 at 09:14 +0100, William Spooner wrote: > So, in your example, the 'exturl|' prefix is ignored? I.e. the > following two are the same; > > exturl|http://www.ebi.ac.uk/msd-srv/atlas?id=%s > http://www.ebi.ac.uk/msd-srv/atlas?id=%s > > Which would be the same as (if exturl in settings.conf were > 'http://www.ebi.ac.uk > ');
yes its same. We need to keep full URL in XML for MSD because we can only use one base URL in settings.conf and that is www.ensembl.org > > exturl|/msd-srv/atlas?id=%s > > All of my URLs are of this latter type which I understand works with > martview, but not martservice. Is this correct? correct again. > > Will > > > On 29 Mar 2008, at 00:36, Syed Haider wrote: > > Will, > > if i understand your question correctly, then the answer is no. > > What I mean by this is if you supply full URL in XML like the one i > > quoted for MSD, then the exturl param from settings.conf is ignored. > > However, if in your XML you supply a relative URL which is expected to > > begin with a forward slash (/) instead of (http), then the exturl > > param > > from the settings.conf is prepended to this. Yes, the to prepend or > > not > > check is based on forward slash. > > and unfortunately we only support one entry for exturl from > > settings.conf. > > > > cheers > > syed > > > > > > On Fri, 2008-03-28 at 16:54 +0000, William Spooner wrote: > >> OK - So I assume that 'http://www.ebi.ac.uk' is substituted with > >> whatever is in 'exturl'? In which case I can work with this. Could > >> you > >> confirm and I will add this to the job list. > >> > >> Will > >> > >> On 28 Mar 2008, at 16:26, Syed Haider wrote: > >>> fair enough. I thought you can add it like we do for MSD and Uniprot > >>> e.g exturl|http://www.ebi.ac.uk/msd-srv/atlas?id=%s > >>> > >>> added this on the requirements list for 0.8 release. > >>> > >>> cheers > >>> syed > >>> > >>> > >>> On Fri, 2008-03-28 at 16:18 +0000, William Spooner wrote: > >>>> Hi Syed, > >>>> > >>>> The URLs are internal (relative) to www.wormbase.org, or > >>>> dev.wormbase.org, or one of the wormbase mirrors depending on the > >>>> httpd. I set this on a per-server basis using exturl setting in > >>>> settings.conf. I cannot really hard-code the path due to mirroring > >>>> issues. > >>>> > >>>> Will > >>>> > >>>> > >>>> On 28 Mar 2008, at 16:08, Syed Haider wrote: > >>>>> > >>>>> Will, who runs Wormbase, is cc'ed would be able to comment. > >>>>> > >>>>> Will, you need to edit your XMLs and prepend servername for > >>>>> attributes > >>>>> with external URL links as this is expected to have www.wormbase.org > >>>>> instead of www.ensembl.org. > >>>>> > >>>>> > >>>>> > >>>>> > >>>>> On Fri, 2008-03-28 at 17:02 +0100, Isabelle Phan wrote: > >>>>>> wow that's real service! > >>>>>> > >>>>>> now the results look good: > >>>>>> > >>>>>> Anatomy Term ID Anatomy Term > >>>>>> WBbt:0003679 neuron > >>>>>> > >>>>>> however when I click on the link > >>>>>> > >>>>>> http://www.ensembl.org/db/ontology/anatomy?name=WBbt:0003679;class=Anatomy_term > >>>>>> > >>>>>> the page returns: > >>>>>> > >>>>>> 404 not found. > >>>>>> > >>>>>> ? > >>>>>> > >>>>>> > >>>>>> Isabelle > >>>>>> > >>>>>> Syed Haider wrote: > >>>>>>> Hi Isabelle, > >>>>>>> > >>>>>>> www.biomart.org has the patch now. thanks for your patience. > >>>>>>> > >>>>>>> cheers > >>>>>>> syed > >>>>>>> > >>>>>>> On Fri, 2008-03-28 at 11:32 -0400, Arek Kasprzyk wrote: > >>>>>>>> On 28-Mar-08, at 11:09 AM, Isabelle Phan wrote: > >>>>>>>> > >>>>>>>>> I have now found some queries that work great! > >>>>>>>>> However I will have a hard time explaining why some data > >>>>>>>>> seem to > >>>>>>>>> be > >>>>>>>>> missing from the results table.... > >>>>>>>>> > >>>>>>>>> MartView query: > >>>>>>>>> > >>>>>>>>> Dataset: MSD > >>>>>>>>> Filters: R < 2A, single crystal X-ray diffraction > >>>>>>>>> Attributes: Molecule name, Organism Name, PDB ID(s) > >>>>>>>>> > >>>>>>>>> combined with > >>>>>>>>> > >>>>>>>>> Dataset: Uniprot proteomes > >>>>>>>>> Filters: none > >>>>>>>>> Attributes: UniProt AC > >>>>>>>>> > >>>>>>>>> Filter for unique rows: selected > >>>>>>>>> View: 200 rows > >>>>>>>>> > >>>>>>>>> I am getting entries with no organism data, e.g.: > >>>>>>>>> CYCLOPHILIN 3 1e3b P52011 > >>>>>>>>> > >>>>>>>>> both the PDB and UniProt data seem to contain the correct > >>>>>>>>> organism > >>>>>>>>> (C.elegans) with the correct taxID. > >>>>>>>>> > >>>>>>>> Hi Isabelle, > >>>>>>>> > >>>>>>>>> Why is the query not returning the organism data? Is this a > >>>>>>>>> synchronization issue? > >>>>>>>>> > >>>>>>>> most likely, MSD as well as UNIPROT are just prototype data > >>>>>>>> sources so > >>>>>>>> not really kept up to date. > >>>>>>>> You would be probably better off using something which is > >>>>>>>> regularly > >>>>>>>> updated e.g. Ensembl > >>>>>>>> > >>>>>>>> a. > >>>>>>>> > >>>>>>>> PS. We are investigating the Wormbase issue that you reported. > >>>>>>>> we'll > >>>>>>>> get back to you on this shortly > >>>>>>>> thanks for spotting it > >>>>>>>> > >>>>>>>>> thanks for any hints you may provide! > >>>>>>>> > >>>>>>>> > >>>>>>>>> I. > >>>>>>>>> -- > >>>>>>>>> Isabelle Phan, D.Phil. > >>>>>>>>> Swiss Institute of Bioinformatics Tel: (+41 22) 379 51 > >>>>>>>>> 89 > >>>>>>>>> CMU - 1, rue Michel Servet Fax: (+41 22) 379 58 > >>>>>>>>> 58 > >>>>>>>>> CH - 1211 Geneva 4 Switzerland email: [EMAIL PROTECTED] > >>>>>> > >>>>>> > >>>>> -- > >>>>> ====================================== > >>>>> Syed Haider. > >>>>> EMBL-European Bioinformatics Institute > >>>>> Wellcome Trust Genome Campus, Hinxton, > >>>>> Cambridge CB10 1SD, UK. > >>>>> ====================================== > >>>> > >>>> --- > >>>> William Spooner > >>>> Visiting Scientist > >>>> [EMAIL PROTECTED] > >>>> > >>>> > >>> -- > >>> ====================================== > >>> Syed Haider. > >>> EMBL-European Bioinformatics Institute > >>> Wellcome Trust Genome Campus, Hinxton, > >>> Cambridge CB10 1SD, UK. > >>> ====================================== > >> > >> --- > >> William Spooner > >> Visiting Scientist > >> [EMAIL PROTECTED] > >> > >> > > --- > William Spooner > Visiting Scientist > [EMAIL PROTECTED] > > -- ====================================== Syed Haider. EMBL-European Bioinformatics Institute Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. ======================================
