Body: <p>I know there are existing GO slims predefined. But does anyone know how I can create my own collection of GO terms for enrichment analysis?</p>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-29T08:04:35.220Z
Comments.Text: I have never created one, but a GO slims is just a list of GO associated with genes, so you just need to download the list of GO and associate them with your list of genes.  What have you tried/searched? What do you need that it is not covered in the [FAQ](http://www.geneontology.org/faq/how-do-i-create-user-defined-go-slim)?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-11-29T08:33:57.227Z
Comments.Text: GO slims are just a subset of the gene ontology graph. Just a group of terms, no genes. We can't help you create one if you don't explain what terms you want and what sort of analysis you want to do.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-03T08:34:01.037Z
Comments.Text: I have a list of genes enriched in kidney. So I want to get a list of kidney-related terms and see which of them are significantly enriched.
Comments.UserDisplayName: Code42
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-05T09:17:37.193Z
Comments.Text: @Dr_Hope Then what you really want is to test an enrichment in GO related to kidney  not create a GO slim. But if you only use a subset of genes and a subset of GOs the test would be biased (AFAIk) if you don't tell the suitable background population of genes and GO terms.
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-12-12T17:27:58.047Z
Comments.Text: I've already done a canonical GO to check the background. The enriched terms are mostly kidney-related because our sample is a kidney. That's why I need a GO slim to check kidney-only terms.
Comments.UserDisplayName: Code42
Tags: <gene><gene-ontology><ontology>
Title: How can I create my own GO slim?
ThreadText: # How can I create my own GO slim?
  
  (Asked by: username_0 on 2017-11-29)
  
  I know there are existing GO slims predefined. But does anyone know how I can create my own collection of GO terms for enrichment analysis?
  
  **Tags:** gene, gene-ontology, ontology
  
  > **Comments:**
  > **username_1**: I have never created one, but a GO slims is just a list of GO associated with genes, so you just need to download the list of GO and associate them with your list of genes.  What have you tried/searched? What do you need that it is not covered in the [FAQ](http://www.geneontology.org/faq/how-do-i-create-user-defined-go-slim)?  
  > **username_2**: GO slims are just a subset of the gene ontology graph. Just a group of terms, no genes. We can't help you create one if you don't explain what terms you want and what sort of analysis you want to do.  
  > **username_0**: I have a list of genes enriched in kidney. So I want to get a list of kidney-related terms and see which of them are significantly enriched.  
  > **username_1**: @Dr_Hope Then what you really want is to test an enrichment in GO related to kidney  not create a GO slim. But if you only use a subset of genes and a subset of GOs the test would be biased (AFAIk) if you don't tell the suitable background population of genes and GO terms.  
  > **username_0**: I've already done a canonical GO to check the background. The enriched terms are mostly kidney-related because our sample is a kidney. That's why I need a GO slim to check kidney-only terms.  
  
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  ## 0 answers
  
  