[biomart-users] GO terms wrong in biological process

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[biomart-users] GO terms wrong in biological process

haris.babacic
Hi!

When I want to check the GO terms related to my favourite proteins using the getBM function, I get the wrong GO terms related to biological processes.
For example, I get the GO term "membrane" related to a biological process, whereas it should be "cellular component".
Here is the code:

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
results <- getBM(attributes = c("hgnc_symbol","entrezgene", "go_id", "name_1006", "namespace_1003", "definition_1006"), filters = "hgnc_symbol", values=c("ACTR3", "ADA", "AHNAK", "C9", "CCL3"), quote="", mart = mart)

Would someone be so kind to help me?

Best regards,
Haris

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Re: [biomart-users] GO terms wrong in biological process

Syed Haider-5
Hi Haris,

Thomas Maurel (cc'ed here) manages Ensembl BioMarts and may be able to help on this one.

Best wishes,
Syed


---------- Forwarded message ---------
From: <[hidden email]>
Date: Wed, 17 Apr 2019 at 16:56
Subject: [biomart-users] GO terms wrong in biological process
To: biomart-users <[hidden email]>


Hi!

When I want to check the GO terms related to my favourite proteins using the getBM function, I get the wrong GO terms related to biological processes.
For example, I get the GO term "membrane" related to a biological process, whereas it should be "cellular component".
Here is the code:

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
results <- getBM(attributes = c("hgnc_symbol","entrezgene", "go_id", "name_1006", "namespace_1003", "definition_1006"), filters = "hgnc_symbol", values=c("ACTR3", "ADA", "AHNAK", "C9", "CCL3"), quote="", mart = mart)

Would someone be so kind to help me?

Best regards,
Haris

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Re: [biomart-users] GO terms wrong in biological process

Thomas Maurel
Dear Haris,

Thanks a lot for reporting this issue. I am afraid that the data is indeed wrong in our database. 
We are working on a fix at the moment and I will let you know as soon as the database is fixed.

Apologies for any inconvenience caused,
Kind Regards,
Thomas

On 17 Apr 2019, at 17:36, Syed Haider <[hidden email]> wrote:

Hi Haris,

Thomas Maurel (cc'ed here) manages Ensembl BioMarts and may be able to help on this one.

Best wishes,
Syed


---------- Forwarded message ---------
From: <[hidden email]>
Date: Wed, 17 Apr 2019 at 16:56
Subject: [biomart-users] GO terms wrong in biological process
To: biomart-users <[hidden email]>


Hi!

When I want to check the GO terms related to my favourite proteins using the getBM function, I get the wrong GO terms related to biological processes.
For example, I get the GO term "membrane" related to a biological process, whereas it should be "cellular component".
Here is the code:

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
results <- getBM(attributes = c("hgnc_symbol","entrezgene", "go_id", "name_1006", "namespace_1003", "definition_1006"), filters = "hgnc_symbol", values=c("ACTR3", "ADA", "AHNAK", "C9", "CCL3"), quote="", mart = mart)

Would someone be so kind to help me?

Best regards,
Haris

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Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom

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Re: [biomart-users] GO terms wrong in biological process

haris.babacic
Hi Thomas,

Splendid. Thank you very much for the prompt feedback.
Looking forward to hearing from you.

Best regards,
Haris


/ Haris Babačić, PhD student

Marie-Curie ESR Fellow, AiPBAND |
Lehtiö Lab, SciLifeLab | Department of Oncology and Pathology, Karolinska Institutet |
Tomtebodavägen 23A
171 65 Solna,
Sweden

[hidden email];  [hidden email];
Tel:      +46735663304;

On 24 Apr 2019, at 10:28, Thomas Maurel <[hidden email]> wrote:

Dear Haris,

Thanks a lot for reporting this issue. I am afraid that the data is indeed wrong in our database. 
We are working on a fix at the moment and I will let you know as soon as the database is fixed.

Apologies for any inconvenience caused,
Kind Regards,
Thomas

On 17 Apr 2019, at 17:36, Syed Haider <[hidden email]> wrote:

Hi Haris,

Thomas Maurel (cc'ed here) manages Ensembl BioMarts and may be able to help on this one.

Best wishes,
Syed


---------- Forwarded message ---------
From: <[hidden email]>
Date: Wed, 17 Apr 2019 at 16:56
Subject: [biomart-users] GO terms wrong in biological process
To: biomart-users <[hidden email]>


Hi!

When I want to check the GO terms related to my favourite proteins using the getBM function, I get the wrong GO terms related to biological processes.
For example, I get the GO term "membrane" related to a biological process, whereas it should be "cellular component".
Here is the code:

mart <- useMart(biomart = "ensembl", dataset = "hsapiens_gene_ensembl")
results <- getBM(attributes = c("hgnc_symbol","entrezgene", "go_id", "name_1006", "namespace_1003", "definition_1006"), filters = "hgnc_symbol", values=c("ACTR3", "ADA", "AHNAK", "C9", "CCL3"), quote="", mart = mart)

Would someone be so kind to help me?

Best regards,
Haris

--
You received this message because you are subscribed to the Google Groups "biomart-users" group.
To unsubscribe from this group and stop receiving emails from it, send an email to [hidden email].
Visit this group at https://groups.google.com/group/biomart-users.
For more options, visit https://groups.google.com/d/optout.


--
<font color="green">Please consider environment before you print this!</font>

--
Thomas Maurel
Bioinformatician - Ensembl Production Team
European Bioinformatics Institute (EMBL-EBI)
European Molecular Biology Laboratory
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
United Kingdom


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