GO Content Meeting Proposals

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We have prepared a list of proposals for changes to the GO to be discussed prior to and at the GO Content Meeting, to be held November 15-16 at TIGR.

The proposals are uploaded as files attached to this SourceForge entry. Amelia and Jane prepared proposal A, and I (Alex) did the rest. Note that my proposals are, by and large, unfinished, preliminary, and subject to change based on my additional work and input from the community. I am putting them out there so that others can get an idea of what types of changes are proposed.

There are Microsoft Word documents describing the various proposals and pdf file for a few of them that graphically illustrate the proposed DAGs.

Anyone who can't either download or open the files can contact me directly for copies.

I will be updating the proposal documents on a weekly basis with up- to-date versions.

Discussion of these changes can be done here, by direct email to me, or on the pathogenesis mailing list. Please keep discussion off the GO and GOfriends lists for the time being. I will attempt to keep digests of all discussions related to these proposals.

Thanks,

Alex and the GO Content Meeting Organizing Committee (Michelle Gwinn, Linda Hannick, Candace Collmer, Jane Lomax, Amelia Ireland, Alexander Diehl)

Proposal List for GO Content Meeting

A. How to represent processes where one organism is manipulating and harnessing the processes in another organism.

B. Reorganization of cytokine function terms

C. Adding CD antigen binding terms

D. Improvements to T cell differentiation hierarchy

E. Reorganization of immune response terms in several ways Alex with help 1) Separating terms related to activation of the immune system from terms describing the effector mechanisms of the immune system. 2) Expansion of the innate immune response DAG to incorporate terms reflecting commons mechanisms in animals and plants. 3) Separating out immune cell differentiation terms from immune response since major portions of hemopoietic cell differentiation occur prior to an immune response per se. There are currently major true path violations here. 4) Improving the definition and DAG under GO:0006954 inflammatory response.

F. The problem of regulation terms under immune response.

G. The need to add tumor surveillance terms (Not yet written up separately). Tumor development may itself be considered an abnormal process by GO, but detection and elimination of tumors by the immune system is clearly a normal, evolutionarily selected, process, and worthy of notice in the GO.

Reported by: addiehl

Original Ticket: "geneontology/ontology-requests/2871":https://sourceforge.net/p/geneontology/ontology-requests/2871

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Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: addiehl

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Please note the in the pdf files in the DAG graphs green nodes represent new terms.

-- Alex

Original comment by: addiehl

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Original comment by: addiehl

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GO Content Meeting Update

I have prepared an updated document essentially amounting to a combined proposal covering points D, E, and F above, which will become the main focus for discussion of changes to how immunology is handled in the Gene Ontology. The document, "GCM_Proposal_Update.doc" has been uploaded to this SourceForge entry. Based on the document, I will prepare an agenda for the meeting, which will be posted here shortly.

Please note that in addition to the document, two zipped files have also been added to the SourceForge entry, "GCM_updated_PDFs.zip" and "GCM_updated_flatfiles.zip". The first is a collection of PDF files with graphical representations of the many DAGs involved in the proposal, showing new and old terms and how they are related to each other. The second is a collection of text files which present these DAGs in flat file format.

Please read the "GCM_Proposal_Update.doc" for additional information.

And note, while I am not deleting the earlier files for points D and E, these files are superceded by the information in the new files.

-- Alex

Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: addiehl

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Please note that I had to split the "GCM_updated_PDFs.zip" file into two separate files to accomodate SourceForge's size limitation on uploaded files.

-- Alex

Original comment by: addiehl

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Original comment by: addiehl

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I've uploaded the logical information and agenda for the meeting. -- Alex

Original comment by: addiehl

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I've uploaded some PDF and flatfiles with minor revisions and improvements from those of last week. Also I created some sub-DAGs from the immune response and cell activation in order to allow clearer representation of some of processes in these hierarchies.

-- Alex

Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: addiehl

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This entry is now closed with the implementation of the immunology revision.

-- Alex

Original comment by: addiehl

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Original comment by: addiehl

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Original comment by: mah11