I have a little bit confused in using biomaRt. I would like to retrieve GO term definition and name for each GO ID. I have done following
mart <- useMart(biomart = "ENSEMBL_MART_ENSEMBL", dataset = "hsapiens_gene_ensembl", host = "asia.ensembl.org") go_list <- getBM(attributes=c("go_id", "name_1006", "namespace_1003"), filters = "go", values = c("GO:0045576"), mart=mart)
I had suspected that this would give me a small list for GO:0045576, but I had gotten following
head(go_list, 10) go_id name_1006 namespace_1003 1 GO:0007165 signal transduction biological_process 2 GO:0043547 positive regulation of GTPase activity biological_process 3 GO:0005096 GTPase activator activity molecular_function 4 GO:0005737 cytoplasm cellular_component 5 GO:0005829 cytosol cellular_component 6 GO:0051056 regulation of small GTPase mediated signal transduction biological_process 7 GO:0032956 regulation of actin cytoskeleton organization biological_process 8 GO:0030833 regulation of actin filament polymerization biological_process 9 GO:0051497 negative regulation of stress fiber assembly biological_process 10 GO:1904425 negative regulation of GTP binding biological_process dim(go_list)  848 3
Do you guys know why this much of different GO id data returned for only one GO id query. Any comment will be a big help.
As an example of what Mike is implying here:
How to convert the ensemble_gene_id or hgnc_id to go_id? As I am trying through biomart, but it's not giving me the output. Any suggestions would be highly appreciated.
Thanks in advance.
I think it would be best to start a new question with an example of what you've already tried, and an explanation of how whatever you've getting differs from what you ultimately want. I think you're more likely to get some useful help doing this.