WormMine

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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.

Understanding our model

The data contained in WormMine follows a central model schema. This model should be understood sufficiently to be able to query the data and create templates.

WormMine model file

This schema file contains all of the data types contained in WormMine, relationships between them, and each one's data fields.