I’ve been doing some analysis in rice for a while. Here is a short post on some resources for the rice GO annotation. Many of them also contain GO info for other species.
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Rice Genome Annotation Project aka MSU7. You can download the GOSlim assignment from its FTP website.
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agriGO v2.0. It allows you to do GO analysis online. You can also download the GO annotaion files from its website.
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PLAZA. Similar with agriGO, PLAZA has many online analysis tools. The functional annotation files can be downloaded from PLAZA website, including GO and InterPro. The PLAZA 4.0 also has Mapman.
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Ensembl Plant. The GO, KEGG and some other annotaions can be accessed from online biomart. Or biomaRt and biomartr R packages. Ensembl Plant and Gramene uses RAPDB IDs only.
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Phytozome. Similar with Ensembl Plant. It uses MSU7 IDs only. It’s also possible to access GO from PhytzoMine online or through its API.
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g:Profiler. I use this for rice most of the time. The backend data is based on Ensembl Plant, so RAPDB IDs only. It has easy to use webiste and gprofiler2 pacakge.
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AnnotationHub. The AnnotationHub contains four databases related to Oryza Sativa. Three OrgDB and one Inparanoid8Db. Not sure what’s the difference among three OrgDB. They all uses ENTREZID and REFSEQ.
