Difference between revisions of "WormMine"
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= Current status = | = Current status = | ||
− | ''' | + | '''ONLINE''' |
==Data contained in WormMine== | ==Data contained in WormMine== |
Revision as of 14:49, 3 May 2013
Contents
Current status
ONLINE
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 |
What is this data mapping?
A loading program plugin has been created for InterMine which extracts data embedded in XML files directly into an InterMine instance. Mapping files are used to configure this program and detail the AceDB XML dumps to InterMine translation. XPath is used to query the XML, and can be reviewed here.