Difference between revisions of "WormBase Models"

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{| border="1" class="wikitable"
 
{| border="1" class="wikitable"
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! No.
 
! No.
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! Comment/Brief Description
 
! Comment/Brief Description
 
! Curator(s)
 
! Curator(s)
 +
! Model copied
 
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| 1
 
| 1
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|Sanger
 
|Sanger
 
| ?
 
| ?
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| ?
 
| ?
 
| ?
 
| ?
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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|
 
|
 
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| ?
 
| ?
 
| This class is used along with ?Condition to store meta data about an experiment  
 
| This class is used along with ?Condition to store meta data about an experiment  
 +
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|
 
|
 
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| ?
 
| ?
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
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| ?
 
| ?
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
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| ?
 
| ?
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
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| Caltech
 
| Caltech
 
| ?
 
| ?
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| ?
 
| ?
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
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| 10
 
| 10
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| OICR
 
| OICR
 
| WORMBASE ATLAS (VIRTUAL WORM)
 
| WORMBASE ATLAS (VIRTUAL WORM)
 +
|
 
|
 
|
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
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| ?
 
| ?
 
| ?
 
| ?
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| ?
 
| ?
 
| [[User:Pdavis|Paul Davis]] + others
 
| [[User:Pdavis|Paul Davis]] + others
 +
| Done
 
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| 14
 
| 14
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| ?
 
| ?
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
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| ?
 
| ?
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
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| 16
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
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| 18
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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| Sanger
 
| Sanger
 
| ?
 
| ?
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
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| 22
 
| 22
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
|
 
|-
 
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| 23
 
| 23
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| ?
 
| ?
 
| [[User:Pdavis|Paul Davis]] Mary Anne
 
| [[User:Pdavis|Paul Davis]] Mary Anne
 +
|
 
|-
 
|-
 
| 25
 
| 25
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| Sanger
 
| Sanger
 
| ?Class of data used to mark up features on Transcript data
 
| ?Class of data used to mark up features on Transcript data
 +
|
 
|
 
|
 
|-
 
|-
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| Envelope for collecting/connecting data pertaining to a single gene
 
| Envelope for collecting/connecting data pertaining to a single gene
 
| Mary Ann
 
| Mary Ann
 +
|
 
|-
 
|-
 
| 27
 
| 27
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| Used for describing and grouping a family of genes
 
| Used for describing and grouping a family of genes
 
| Mary Ann
 
| Mary Ann
 +
|
 
|-
 
|-
 
| 28
 
| 28
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| Sanger
 
| Sanger
 
| Used to denote a cluster of genes of a specific type - not maintained?
 
| Used to denote a cluster of genes of a specific type - not maintained?
 +
|
 
|
 
|
 
|-
 
|-
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Sanger
 
| Sanger
 
| Allows for alternate genetic codes for Mitocondria and selenocysteine.
 
| Allows for alternate genetic codes for Mitocondria and selenocysteine.
 +
|
 
|
 
|
 
|-
 
|-
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
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|
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Sanger
 
| Sanger
 
| Used for storing alignment data
 
| Used for storing alignment data
 +
|
 
|
 
|
 
|-
 
|-
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
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| ?
 
| ?
 
| ?
 
| ?
 +
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| Acedb?
 
| Acedb?
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| Caltech  
 
| Caltech  
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Sanger
 
| Sanger
 
| libraries used for sequencing of nematode ESTs // Information to come from Mark Blaxters
 
| libraries used for sequencing of nematode ESTs // Information to come from Mark Blaxters
 +
|
 
|
 
|
 
|-
 
|-
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
|
 
|-
 
|-
 
| 46
 
| 46
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| Sanger
 
| Sanger
 
| This class is a reminent that should be cleaned up.
 
| This class is a reminent that should be cleaned up.
 +
|
 
|
 
|
 
|-
 
|-
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
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|-
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| ?
 
| ?
 
| Gary Williams
 
| Gary Williams
 +
|
 
|-
 
|-
 
| 53
 
| 53
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| ?
 
| ?
 
| Gary Williams
 
| Gary Williams
 +
|
 
|-
 
|-
 
| 54
 
| 54
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| ?
 
| ?
 
| AceDB class that details display etc. of objects in the other classes
 
| AceDB class that details display etc. of objects in the other classes
 +
|
 
|
 
|
 
|-
 
|-
Line 342: Line 398:
 
| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
|
 
|-
 
|-
 
| 56
 
| 56
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
|
 
|-
 
|-
 
| 57
 
| 57
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
|
 
|-
 
|-
 
| 58
 
| 58
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Used to capture molecules that influence gene activity and affect phenotypes.
 
| Used to capture molecules that influence gene activity and affect phenotypes.
 
| [[User=kyook|Karen]]
 
| [[User=kyook|Karen]]
 +
|
 
|-
 
|-
 
| 60
 
| 60
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Sanger?
 
| Sanger?
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| ?
 
| ?
 
| Not used?
 
| Not used?
 +
|
 
|
 
|
 
|-
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| ?Not Used
 
| ?Not Used
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
 +
|
 
|-
 
|-
 
| 66
 
| 66
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| ? Not Used
 
| ? Not Used
 
|[[User:raymond|Raymond]]
 
|[[User:raymond|Raymond]]
 +
|
 
|-
 
|-
 
| 67
 
| 67
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| ?
 
| ?
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| ?
 
| ?
 
| ?
 
| ?
 +
|
 
|
 
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|-
 
|-
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| Stores genes that are in Operons
 
| Stores genes that are in Operons
 
| [[User:Pdavis|Paul Davis]]
 
| [[User:Pdavis|Paul Davis]]
 +
|
 
|-
 
|-
 
| 70
 
| 70
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| ?
 
| ?
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| ?
 
| ?
 
| Cecilia Nakamura
 
| Cecilia Nakamura
 +
|
 
|-
 
|-
 
| 73
 
| 73
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
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|-
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
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|-
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| Sanger
 
| Sanger
 
| Stores the Pseudogene models
 
| Stores the Pseudogene models
 +
|
 
|
 
|
 
|-
 
|-
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| OICR
 
| OICR
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| OICR
 
| OICR
 
| ?
 
| ?
 +
|
 
|
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
|
 
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|-
 
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| Stores information pertaining to RNAi experiments, including RNAi probe targets, resulting phenotypes, and associated papers.
 
| Stores information pertaining to RNAi experiments, including RNAi probe targets, resulting phenotypes, and associated papers.
 
| Gary Schindleman, [[User:Cgrove|Chris Grove]]
 
| Gary Schindleman, [[User:Cgrove|Chris Grove]]
 +
|
 
|-
 
|-
 
| 87
 
| 87
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
|
 
|-
 
|-
 
| 88
 
| 88
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| ?
 
| ?
 
| Wen Chen
 
| Wen Chen
 +
|
 
|-
 
|-
 
| 89
 
| 89
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| Sanger
 
| Sanger
 
| A broad class for storing genomic, Transcripts Sequence etc.  
 
| A broad class for storing genomic, Transcripts Sequence etc.  
 +
|
 
|
 
|
 
|-
 
|-
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
|
 
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| Caltech
 
| Caltech
 
| ?
 
| ?
 +
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
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| OICR
 
| OICR
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
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| OICR
 
| OICR
 
| ?
 
| ?
 +
|
 
|
 
|
 
|-
 
|-
Line 587: Line 684:
 
| Sanger
 
| Sanger
 
| Stores RNAgenes and the Full length Coding_transcripts
 
| Stores RNAgenes and the Full length Coding_transcripts
 +
|
 
|
 
|
 
|-
 
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| ?
 
| ?
 
|  
 
|  
 +
|
 
|-
 
|-
 
| 98
 
| 98
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| Stores the Transposon span and S_child info
 
| Stores the Transposon span and S_child info
 
| [[User:Pdavis|Paul Davis]]
 
| [[User:Pdavis|Paul Davis]]
 +
|
 
|-
 
|-
 
| 99
 
| 99
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| Used for grouping like ?Transposons
 
| Used for grouping like ?Transposons
 
| [[User:Pdavis|Paul Davis]]
 
| [[User:Pdavis|Paul Davis]]
 +
|
 
|-
 
|-
 
| 100
 
| 100
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| ?
 
| ?
 
| Mary Ann
 
| Mary Ann
 +
|
 
|-
 
|-
 
| 101
 
| 101
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| Sanger
 
| Sanger
 
| ?
 
| ?
 +
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|
 
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|-
 
|-

Revision as of 15:50, 9 August 2010

The A - Z of WormBase Models

Document created from WS218 models

Sanger CVS models.wrm

No. Class Institute Comment/Brief Description Curator(s) Model copied
1 2_point_data Sanger ?
2 3d_data ? ?
3 Accession_number Sanger ?
4 Analysis ? This class is used along with ?Condition to store meta data about an experiment
5 Anatomy_function Caltech ? Raymond
6 Anatomy_name Caltech ? Raymond
7 Anatomy_term Caltech ? Raymond
8 Antibody Caltech ?
9 AO_code ? ? Raymond
10 Atlas OICR WORMBASE ATLAS (VIRTUAL WORM)
11 Author Caltech ?
12 Balancer ? ?
13 CDS Sanger ? Paul Davis + others Done
14 Cell Sanger/Caltech? ? Raymond
15 Cell_group Sanger/Caltech? ? Raymond
16 Clone Sanger ?
17 Condition ? ? Wen Chen
18 Contig Sanger ?
19 Database Sanger ?
20 Database_field Sanger ?
21 Expression_cluster Caltech ? Wen Chen
22 Expr_pattern Caltech ? Wen Chen
23 Expr_profile Caltech ?
24 Feature Sanger ? Paul Davis Mary Anne
25 Feature_data Sanger ?Class of data used to mark up features on Transcript data
26 Gene Sanger Envelope for collecting/connecting data pertaining to a single gene Mary Ann
27 Gene_class Sanger Used for describing and grouping a family of genes Mary Ann
28 Gene_cluster Sanger Used to denote a cluster of genes of a specific type - not maintained?
29 Gene_name Sanger ?
30 Gene_regulation Caltech ?
31 Genetic_code Sanger Allows for alternate genetic codes for Mitocondria and selenocysteine.
32 GO_code Caltech ?
33 GO_term Caltech ?
34 Grid Sanger ?
35 Grid_data Sanger ?
36 Grid_row Sanger ?
37 Homol_data Sanger Used for storing alignment data
38 Homology_group Caltech ?
39 Interaction Caltech ?
40 Interval_col_conf ? ?
41 Jade Acedb? ?
42 Lab_Location Caltech ?
43 Laboratory Caltech ?
44 Library Sanger libraries used for sequencing of nematode ESTs // Information to come from Mark Blaxters
45 Life_stage Caltech ? Wen Chen
46 Locus Sanger This class is a reminent that should be cleaned up.
47 ManyMap Sanger ?
48 Map Sanger ?
49 Map_error Sanger ?
50 Map_offset Sanger ?
51 Map_position Sanger ?
52 Mass_spec_experiment Sanger ? Gary Williams
53 Mass_spec_peptide Sanger ? Gary Williams
54 Method ? AceDB class that details display etc. of objects in the other classes
55 Microarray Caltech ? Wen Chen
56 Microarray_experiment Caltech ? Wen Chen
57 Microarray_results Caltech ? Wen Chen
58 Mixed_grid_row Sanger ?
59 Molecule Caltech Used to capture molecules that influence gene activity and affect phenotypes. Karen
60 Motif Sanger ?
61 Movie Caltech ?
62 Multi_counts Sanger? ?
63 MultiMap ? Not used?
64 Multi_pt_data Sanger ?
65 Neurodata ? ?Not Used Raymond
66 Neuro_location ? ? Not Used Raymond
67 Oligo ? ?
68 Oligo_set ? ?
69 Operon Sanger Stores genes that are in Operons Paul Davis
70 Paper Caltech ?
71 PCR_product ? ?
72 Person Caltech ? Cecilia Nakamura
73 Person_name Caltech ?
74 Phenotype Caltech ?
75 Phenotype_Assay Caltech ?
76 Phenotype_name Caltech ?
77 Picture Caltech ?
78 Position_Matrix Caltech ?
79 Pos_neg_data Sanger ?
80 Protein Sanger ?
81 Pseudogene Sanger Stores the Pseudogene models
82 Rearrangement Caltech ?
83 ReconCellInfo OICR ?
84 Reconstruction OICR ?
85 Reference Caltech ?
86 RNAi Caltech Stores information pertaining to RNAi experiments, including RNAi probe targets, resulting phenotypes, and associated papers. Gary Schindleman, Chris Grove
87 SAGE_experiment Sanger ? Wen Chen
88 SAGE_tag Sanger ? Wen Chen
89 Sequence Sanger A broad class for storing genomic, Transcripts Sequence etc.
90 SK_map Caltech ?
91 SO_term Caltech ?
92 Species Sanger ?
93 Strain Sanger ?
94 Structure_data OICR ?
95 Timepoint OICR ?
96 Transcript Sanger Stores RNAgenes and the Full length Coding_transcripts
97 Transgene Caltech ?
98 Transposon Sanger Stores the Transposon span and S_child info Paul Davis
99 Transposon_family Sanger Used for grouping like ?Transposons Paul Davis
100 Variation Sanger ? Mary Ann
101 Variation_name Sanger ?
102 YH Caltech ?