Difference between revisions of "WormMine"

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Page stubs:
 
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* <nowiki>[[Data contained in WormMine]]</nowiki>
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==[[Data contained in WormMine]]==
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* [[Understanding our model]]
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This lists all data sources contained in WormMine
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* [[Account management]]
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−
* [[Using query builder]]
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{| border="1"
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* [[Creating templates]]
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! Source !! Description !! Source !! Species !! Data mapping
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* [[Creating lists]]
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* [[Creating widgets]]
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|-
 +
|  GO
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|| Ontology terms and relationships comprising GO
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|| GO project website.
 +
|| N/A
 +
 
 +
|-
 +
|  GO Annotations
 +
|| Relationships between Genes and GO
 +
|| GO project website.
 +
|| Caenorhabditis elegans
 +
 
 +
|-
 +
|  Genomic sequences
 +
|| Fasta DNA sequences
 +
|| WormBase FTP
 +
|| Caenorhabditis elegans
 +
 
 +
|-
 +
|  Protein sequences
 +
|| Fasta peptide sequences
 +
|| WormBase FTP
 +
|| Caenorhabditis elegans
 +
 
 +
|-
 +
|  Gene locations
 +
|| Gene chromosomal coordinates
 +
|| WormBase FTP GFF3
 +
|| Caenorhabditis elegans
 +
 
 +
|-
 +
|  Transcript locations
 +
|| Transcript chromosomal coordinates
 +
|| WormBase FTP GFF3
 +
|| Caenorhabditis elegans
 +
 
 +
|-
 +
|  CDS locations
 +
|| CDS chromosomal coordinates
 +
|| WormBase FTP GFF3
 +
|| Caenorhabditis elegans
 +
 
 +
|-
 +
|  Gene metadata
 +
|| Select fields extracted from Ace
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|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Gene Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Transcript metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Transcript Ace mapping|LINK]]
 +
 
 +
|-
 +
|  CDS metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine CDS Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Variation metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Variation Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Protein metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Protein Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Phenotype metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Phenotype Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Expression Pattern metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Expr_pattern Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Anatomy Term metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Anatomy_term Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Expression Cluster metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Expr_cluster Ace mapping|LINK]]
 +
 
 +
|-
 +
|  Life Stage metadata
 +
|| Select fields extracted from Ace
 +
|| AceDB XML dump
 +
|| All in AceDB
 +
|| [[WormMine Life_stage Ace mapping|LINK]]
 +
 
 +
|}
 +
 
 +
==[[Understanding our model]]==
 +
==[[Account management]]==
 +
==[[Using query builder]]==
 +
==[[Creating templates]]==
 +
==[[Creating lists]]==
 +
==[[Creating widgets]]==

Revision as of 20:22, 2 May 2013

Page stubs:

Data contained in WormMine

This lists all data sources contained in WormMine

Source Description Source Species Data mapping
GO Ontology terms and relationships comprising GO GO project website. N/A
GO Annotations Relationships between Genes and GO GO project website. Caenorhabditis elegans
Genomic sequences Fasta DNA sequences WormBase FTP Caenorhabditis elegans
Protein sequences Fasta peptide sequences WormBase FTP Caenorhabditis elegans
Gene locations Gene chromosomal coordinates WormBase FTP GFF3 Caenorhabditis elegans
Transcript locations Transcript chromosomal coordinates WormBase FTP GFF3 Caenorhabditis elegans
CDS locations CDS chromosomal coordinates WormBase FTP GFF3 Caenorhabditis elegans
Gene metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Transcript metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
CDS metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Variation metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Protein metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Phenotype metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Expression Pattern metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Anatomy Term metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Expression Cluster metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK
Life Stage metadata Select fields extracted from Ace AceDB XML dump All in AceDB LINK

Understanding our model

Account management

Using query builder

Creating templates

Creating lists

Creating widgets

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