Why don't all GOIDs and all ENTEZIDs appear in db query?
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18 months ago

I want to get all GO terms for a particular organism. Additionally, I want to get all of the ENTREZIDs

My problem is that (for example) GOID GO:0032501 does not appear in the list from the query below:

go_list <- mapIds(org.Hs.eg.db, keys(org.Hs.eg.db, "GO"),
                  "ENTREZID", "GO", multiVals = "list")

Furthermore, using a different query (shown below), GOID GO:0032501 does appear in the list but there are no ENTREZIDs associated with it:

go_list <- as.list(org.Hs.egGO2ALLEGS)

Whereas when I run this query, GOID GO:0032501 does appear in the list and there are ENTREZIDs associated with it:

egGO2ALLEGS <- getFromNamespace("org.Hs.egGO2ALLEGS", "org.Hs.eg.db")
GeneID.PathID <- AnnotationDbi::toTable(egGO2ALLEGS)

Does anyone know why this is?

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GO:0032501 is a very high level GO term that encompasses Multi-cellular organismal processes. Here is a link to all human genes associated with that term. There are 8225.

You can search and download GO/Ontologies using AmiGO ontology browser.

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