Question

makeTxDbFromBiomart Error: 1: Space required after the Public Identifier

4

Entering edit mode

luigi.cerulo ▴ 40

@luigicerulo-9132

Last seen 8.5 years ago

European Union

In the last two days I got the following error with a call to makeTxDbFromBiomart also by reproducing the function help examples.

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
Error: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2

software error maketxdbfrombiomart • 12k views

ADD COMMENT • link updated 8.4 years ago by Maciej Jończyk • 0 • written 8.5 years ago by luigi.cerulo ▴ 40

1

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that looks like the same problem I posted in Problem with biomart's listMarts function . We'll see, somebody for sure will find out what's going on.

cheers, jo

ADD REPLY • link 8.5 years ago Johannes Rainer ★ 2.0k

score 5 · Answer 1 · 2015-11-09

5

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Johannes Rainer ★ 2.0k

@johannes-rainer-6987

Last seen 23 days ago

Italy

Alternatively (as stated on the biomart.org News page), change the host to "www.ensembl.org".

> listMarts(host="www.ensembl.org")
               biomart               version
1 ENSEMBL_MART_ENSEMBL      Ensembl Genes 82
2     ENSEMBL_MART_SNP  Ensembl Variation 82
3 ENSEMBL_MART_FUNCGEN Ensembl Regulation 82
4    ENSEMBL_MART_VEGA               Vega 62
5                pride        PRIDE (EBI UK)

cheers, jo

ADD COMMENT • link 8.5 years ago Johannes Rainer ★ 2.0k

0

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Or for plants:

>listMarts(host="www.gramene.org")

ADD REPLY • link 8.4 years ago Maciej Jończyk • 0

0

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For plants, this works for me:

listMarts(host="plants.ensembl.org")
ensembl <- useMart(biomart="plants_mart", host="plants.ensembl.org")
listDatasets(ensembl)
...

ADD REPLY • link 8.0 years ago TimothéeFlutre ▴ 80

score 2 · Answer 2 · 2015-11-09

as the main portal is not available, you need to specify one their other serers.

this is working (mouse mart, but changeable):

ensembl = useMart(biomart = "ENSEMBL_MART_ENSEMBL",dataset="mmusculus_gene_ensembl", host = "jul2015.archive.ensembl.org")

this uses the latest archived version, Ensembl 81 (http://jul2015.archive.ensembl.org/index.html)

Assa

score 0 · Answer 3 · 2015-12-06

I have the same problem.

I have used biomaRt to access gramene data in the past using the default server. Now I'm not able to use it, here is the code:

> listMarts()
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
BŁĄD: 1: Space required after the Public Identifier
2: SystemLiteral " or ' expected
3: SYSTEM or PUBLIC, the URI is missing
4: Opening and ending tag mismatch: hr line 7 and body
5: Opening and ending tag mismatch: body line 4 and html
6: Premature end of data in tag html line 2
> listMarts(host="ensembl.gramene.org")
biomart version
1 ENSEMBL_MART_PLANT Plant Genes 48
2 ENSEMBL_MART_PLANT_SNP Plant Variation Mart 48
> useMart(biomart="ENSEMBL_MART_PLANT", dataset="zmays_eg_gene", host="ensembl.gramene.org")
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available.
Błąd w poleceniu 'if (BioMartVersion == "\n" | BioMartVersion == "") {':
argument jest długości zero
> gramene=useMart("ENSEMBL_MART_PLANT", host="ensembl.gramene.org")
Request to BioMart web service failed. Verify if you are still connected to the internet. Alternatively the BioMart web service is temporarily down. Check http://www.biomart.org and verify if this website is available.
Błąd w poleceniu 'if (BioMartVersion == "\n" | BioMartVersion == "") {':

As 'listMarts' using ensembl.gramene.org as host listed correct databases I supposed other commands would work with it but it is not the case.

The error messages don't show instantly but after few minutes.

How could I use gramene in biomaRt?