Production priorities
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Production Priorities. Genome protein sets User Support Production systems change Database changes On-the-fly species gene associations. Genome protein sets (gp2protein). FASTA files of all proteins believed to occur from a genome, not just what is curated Provide standard defline format

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Production Priorities

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Production priorities

Production Priorities


Production priorities

  • Genome protein sets

  • User Support

  • Production systems change

  • Database changes

  • On-the-fly species gene associations


Genome protein sets gp2protein

Genome protein sets (gp2protein)

  • FASTA files of all proteins believed to occur from a genome, not just what is curated

  • Provide standard defline format

  • These datasets would be the input for Inparanoid and likely many other analysis projects

  • [*Future*] Include ID mappings: UniProt, IPI, CCD, MOD IDs, GI, Protein_ID, RefSeq

  • [*Future*] Mapping from proteins to gene


Production priorities

Only annotations with IMP, IDA, IPI, IGI and IEP


User support email lists to report problems

User SupportEmail Lists to report problems

  • GO

  • GO-DATABASE

  • GO-WEBMASTER

  • GOFRIENDS

  • GO-IN

  • GO-TOP

To which list do we want users to send questions, bug reports, …


Proposal

Proposal

  • Define specific email addresses for support

  • Supported Annotation Staff would be in a rotation to monitor email queries.

    • Answer questions that can be done so immediately

    • Forward questions to appropriate person or group as necessary

    • Track resolution of the query


Production systems change

Currently GODB & AmiGO run on main SGD database server

Moving GO to cluster environment where there will be multiple GO DB servers and GO HTML servers

Last year started building GO Lite DB three times a week. This means AmiGO is always using 2-4 day old data.

More cluster nodes are on order that may allow us to do daily updates. (no need for GOTerm DB)

CVS via HTTP

Production systems change


Potential production db changes

Build updating script, currently can only rebuild from scratch

Switch to Chado

This would also allow the incorporation of new data types

GOID & Term history tracking

Need to consider what files need to be archived

For some file types that are just derivative we can just provide a script

Potential Production DB Changes


Survey of go file downloads 43 replying

Survey of GO File Downloads(43 replying)


On the fly species gene associations

On-the-fly species gene associations

  • Mainly useful for multi-species gene associations data sets, eg. GOA UniProt.


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