Thanks for the explanation. Is there a big change between BioMart 0.7 and 0.9? Is it planned to include reading from Biomart 0.9 instances in the R package?
On Tuesday, October 18, 2016 at 3:18:45 PM UTC+2, Arek Kasprzyk wrote:
Hi Julia,
As far as I know biomaRt only interfaces BioMart 0.7 instances. The Phantom resource is version 0.9. I don't think you will be able to use biomaRt to access it
a.
On 6 September 2016 at 08:36, Julia Romanowska
<<a href="javascript:" target="_blank" gdf-obfuscated-mailto="Kxz1fvgoBAAJ" rel="nofollow" onmousedown="this.href='javascript:';return true;" onclick="this.href='javascript:';return true;">romano...@...> wrote:
Hi,
I'm new in using biomaRt and an advanced R user. I have problems retrieving list of marts from any other host than the default.
> listMarts( host = "<a href="http://biomart.gsc.riken.jp" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fbiomart.gsc.riken.jp\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF19S1OKw7kyECBhTPFUXX-Re4BOA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fbiomart.gsc.riken.jp\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNF19S1OKw7kyECBhTPFUXX-Re4BOA';return true;">biomart.gsc.riken.jp", verbose = TRUE )
Attempting web service request:
http://<a href="http://biomart.gsc.riken.jp:80/biomart/martservice?type=registry&requestid=biomaRt" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fbiomart.gsc.riken.jp%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE6ph1-ScYMYnrqm-hS15swFI9Xgw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fbiomart.gsc.riken.jp%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNE6ph1-ScYMYnrqm-hS15swFI9Xgw';return true;">biomart.gsc.riken.jp:80/biomart/martservice?type=registry&requestid=biomaRt
[1] biomart version
<0 rows> (or 0-length row.names)
> listMarts( host = "<a href="http://hapmart.hapmap.org/BioMart/martview" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fhapmart.hapmap.org%2FBioMart%2Fmartview\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbEyq7_GpUZY9AeC5IJrWNpCRHfA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fhapmart.hapmap.org%2FBioMart%2Fmartview\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNHbEyq7_GpUZY9AeC5IJrWNpCRHfA';return true;">hapmart.hapmap.org/BioMart/martview", verbose = TRUE )
Attempting web service request:
http://<a href="http://hapmart.hapmap.org/BioMart/martview:80/biomart/martservice?type=registry&requestid=biomaRt" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fhapmart.hapmap.org%2FBioMart%2Fmartview%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH-gzCk2FnpxBOm5rrRZ86mFmSBnw';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fhapmart.hapmap.org%2FBioMart%2Fmartview%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNH-gzCk2FnpxBOm5rrRZ86mFmSBnw';return true;">hapmart.hapmap.org/BioMart/martview:80/biomart/martservice?type=registry&requestid=biomaRt
[1] biomart version
<0 rows> (or 0-length row.names)
> listMarts( host = "<a href="http://www.biomart.org" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.biomart.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.biomart.org\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGTycqpJiNkOBMw43z-5DeV4RRH3w';return true;">www.biomart.org", verbose = TRUE )
Attempting web service request:
http://<a href="http://www.biomart.org:80/biomart/martservice?type=registry&requestid=biomaRt" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.biomart.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGX61d_3x6VmUf19G7LBFqaip8icg';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Fwww.biomart.org%3A80%2Fbiomart%2Fmartservice%3Ftype%3Dregistry%26requestid%3DbiomaRt\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNGX61d_3x6VmUf19G7LBFqaip8icg';return true;">www.biomart.org:80/biomart/martservice?type=registry&requestid=biomaRt
Space required after the Public Identifier
SystemLiteral " or ' expected
SYSTEM or PUBLIC, the URI is missing
Opening and ending tag mismatch: hr line 7 and body
Opening and ending tag mismatch: body line 4 and html
Premature end of data in tag html line 2
> listMarts()
biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 85
2 ENSEMBL_MART_SNP Ensembl Variation 85
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 85
4 ENSEMBL_MART_VEGA Vega 65
I am specifically interested in the FANTOM5 database (<a href="http://fantom.gsc.riken.jp/" target="_blank" rel="nofollow" onmousedown="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ffantom.gsc.riken.jp%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEPZjVaQXeZd-CWvT-ujvLRaI0BIA';return true;" onclick="this.href='http://www.google.com/url?q\x3dhttp%3A%2F%2Ffantom.gsc.riken.jp%2F\x26sa\x3dD\x26sntz\x3d1\x26usg\x3dAFQjCNEPZjVaQXeZd-CWvT-ujvLRaI0BIA';return true;">http://fantom.gsc.riken.jp/).
I would be grateful for any help!
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