Changes between Version 29 and Version 30 of PombasePlanningMeetingAgenda20110815


Ignore:
Timestamp:
Dec 16, 2011, 5:18:43 PM (10 years ago)
Author:
gomidori
Comment:

update URLs to current server

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  • PombasePlanningMeetingAgenda20110815

    v29 v30  
    1111 * Val and Midori Refine and describe annotation extensions (annotation extensions are now in use)
    1212 * Val EMBL resubmission. This will allow all of the new genes/ gene structure changes to propagate through to Uniprot
    13  * Val circulate “names ideas”  list
     13 * Val circulate "names ideas"  list
    1414 * Pombeclub 10 May Val presented
    1515 * Pombe 2011 June 27-30 Val, Midori, Mark Presented 3 posters. Mark presented Pombase in workshop. Val did an infomercial for community curation
     
    4343
    4444All GeneDB features loaded into Chado
    45  * See [http://sloth.sysbiol.cam.ac.uk/test/view/list/types_and_counts?numrows=50&page=1&model=chado Types and Counts]
     45 * See [http://oliver0.sysbiol.cam.ac.uk/test/view/list/types_and_counts?numrows=50&page=1&model=chado Types and Counts]
    4646 * All are annotated with Sequence Ontology (SO) terms
    4747 * Loaded 25650 sequence features for fission yeast (Large number of "gene" is due to human and cerevisiae orthologs)
    4848
    4949All functional annotations are mapped to controlled vocabularies
    50  * See [http://sloth.sysbiol.cam.ac.uk/test/view/list/cv?numrows=200&page=1&model=chado Types and Counts]
     50 * See [http://oliver0.sysbiol.cam.ac.uk/test/view/list/cv?numrows=200&page=1&model=chado List of Controlled Vocabularies]
    5151 * Loaded  51,380 manual annotation
    5252
    5353Annotation Extensions (NEW annotation type):
    54  * Post-composed terms used for  [http://sloth.sysbiol.cam.ac.uk/test/view/object/cv/PomBase%20annotation%20extension%20terms?model=chado annotation extensions]
     54 * Post-composed terms used for  [http://oliver0.sysbiol.cam.ac.uk/test/view/object/cv/PomBase%20annotation%20extension%20terms?model=chado annotation extensions]
    5555 * 340 annotations to 254 terms
    5656 * We are the first MOD to use and submit GO annotation with annotation extensions (we are also using annotation_extension for other CVs)
     
    9898 * mapping modifications to MOD
    9999 * mapping phenotypes to FYPO
    100  
     100
    101101=== iii. Curation Tool  ===
    102102
    103 http://sloth.sysbiol.cam.ac.uk/redmine/projects/pomcur/issues/new
     103[https://sourceforge.net/tracker/?group_id=65526&atid=2525791 SourceForge PomBase Curation Tool tracker]
     104
    104105
    105106 * BioGRID-style data imported and can be curated
    106107 * Now shows   existing annotations (GO and BIoGRID) (for partially curated papers)
    107   * e.g. http://sloth.sysbiol.cam.ac.uk/test/curs/5d0ce7b96de4883d
    108   * e.g. http://sloth.sysbiol.cam.ac.uk/test/curs/d4e73d1a93ec5860 (existing and new)
     108  * e.g. http://oliver0.sysbiol.cam.ac.uk/test/curs/5d0ce7b96de4883d
     109  * e.g. http://oliver0.sysbiol.cam.ac.uk/test/curs/d4e73d1a93ec5860 (existing and new)
    109110 * Phenotype curation possible using FYPO
    110111 * Temporary "hack" to allow us to add annotation extensions, alleles, residues, and other qualifiers