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geneontology / panther-enrichment

One of the main uses of the GO is to perform enrichment analysis on gene sets. For example, given a set of genes that are up-regulated under certain conditions, an enrichment analysis will find which GO terms are over-represented (or under-represented) using annotations for that gene set.
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Proposed changes to panther/enrichment docs #12

Open cmungall opened 5 years ago

cmungall commented 5 years ago

These comments pertain to the panther site not GO, but the user ends up here when they do an enrichment so I think it's important to make some clarification from a GO point of view

"Please refer to our article in Nature Protocols for detailed instructions on how to use this page"

When I link to the nature protocols paper outside my institution network I get "Subscribe to Journal for $495.00"

I think the documentation should be on the site rather than in a closed-source article

http://www.pantherdb.org/about.jsp

This doesn't mention the version of GO used (although you do get this when you do an enrichment analysis)

http://www.pantherdb.org/panther/ontologies.jsp

The PANTHER Protein Class ontology was adapted from the PANTHER/X molecular function ontology, and includes commonly used classes of protein functions, many of which are not covered by GO molecular function

It would be useful to see more on why they are not covered. Is it a scope issue or a deficiency in GO (the way it is worded sounds like the latter)

There is a link to the panther ontology http://data.pantherdb.org/PANTHER14.0/ontology/Protein_Class_14.0 but there are no mappings to GO

"PANTHER uses only a subset of GO terms (“GO slim”) to facilitate browsing. Download the PANTHER GO slim." http://data.pantherdb.org/PANTHER14.0/ontology/PANTHERGOslim.obo

But it's not clear what the use case is for this, or any version info (looks like this is from mid-2018?). A user may think that this is the subset used for enrichment analysis in GO.

ValWood commented 5 years ago

Should also be made clear in the docs (or preferably up front) that the panther enrichment tool does not include regulates relationship. This negatively affects enrichment results (many regulation annotations are within pathway, or direct upstream signalling and you need the "regulation of" terms to see these in enrichments

huaiyumi commented 5 years ago

The Nature Protocol paper has been uploaded to the PMC, and should be freely available soon. The About page in PANTHER is an overview of the gene families. The details about the data, including GO version and GO-slim version can be found at http://www.pantherdb.org/data/. Also, since we update GO on monthly base, its version is described on each test page. Protein Class is not mapped to GO. It has commonly used terms such as zinc finger transcription factor or cytoskeletal protein, which are not in GO.

huaiyumi commented 5 years ago

We have updated the followings:

  1. Updates to Help Tips on the landing page.
    1. Updates to counts on About page
    2. Updated from "annotation" to "terms" for Full GO description in the PANTHER data page.
    3. Added page with description about PANTHER GO-slim Please double check and see if this is sufficient, and close the ticket.