AnnBuilder GO url question
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@tae-hoon-chung-783
Last seen 8.1 years ago
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Seth Falcon ★ 7.4k
@seth-falcon-992
Last seen 8.1 years ago
Tae-Hoon Chung <thchung at="" tgen.org=""> writes: > Hi, All; > > When I tried to build a custom annotation package with AnnBuilder, it > complained with a warning that it was not able to resolve > www.godatabase.org? It seems that either their server is down or the URL has changed. I haven't been able to reach their site from a web browser in a few days. > (But the process ended smoothly and the package was > built eventually.) I think this one is due to the global option set in the > AnnBuilder package for GO url which is > ?http://www.godatebase.org/dev/database/archive/latest?. Question 1. Does > the fact that R was not able to resolve the Url cause any damage on the > custom annotation package? Well, take a look at what was generated. But if AnnBuilder can't access the GO data, then yes this will have bad effect on the GO annotation! > Are the GO associations with probes still > correct? Question 2. What is the correct Url for GO repository in this case? > How can I reset the global option for GO Url? I'm not sure what the correct URL is, but we will look into it. As for updating/changing the URL that is used, I'm pretty sure there is documentation on how to do this in the AnnBuilder vignettes. Best, + seth -- Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center http://bioconductor.org
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Nianhua Li ▴ 870
@nianhua-li-1606
Last seen 8.1 years ago
Hi, Tae-Hoon, Even if accessing GO website is a problem, it won't affect your custom annotation package. There are only 3 objects in the custom package that are related to GO: <pkg>GO, <pkg>GO2PROBE and <pkg>GO2ALLPROBES. Here I use <pkg> to represent your package name. <pkg>GO and <pkg>GO2PROBE are created by using direct mapping relations between gene and GO obtained from Entrez Gene website. <pkg>GO2ALLPROBES is created by using <pkg>GO2PROBE and the GO package in bioconductor. So, you don't need access to GO website. But this is just based on my own understanding of AnnBuilder. You can check the quality control data of your package to make sure the GO annotation is OK. In R, load your package and type "<pkg>()" (replace <pkg> with your package name). If the numbers are reasonable, then everything is fine. Which GO package in bioconductor are you using now? We are updating the GO package in bioc 2.0 now. If you are using GO 1.15.12, you may want to wait a week until a more stable GO is available. hope this is helpful nianhua
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