Difference between revisions of "WormMine"
Line 142: | Line 142: | ||
=== How to read it === | === How to read it === | ||
+ | Looking at the protein class: | ||
+ | <class name="Protein" extends="BioEntity" is-interface="true"> | ||
+ | <attribute name="molecularWeight" type="java.lang.Float"/> | ||
+ | <attribute name="md5checksum" type="java.lang.String"/> | ||
+ | <attribute name="length" type="java.lang.Integer"/> | ||
+ | <attribute name="geneName" type="java.lang.String"/> | ||
+ | <attribute name="primaryAccession" type="java.lang.String"/> | ||
+ | <reference name="sequence" referenced-type="Sequence"/> | ||
+ | <collection name="CDSs" referenced-type="CDS" reverse-reference="protein"/> | ||
+ | <collection name="genes" referenced-type="Gene" reverse-reference="proteins"/> | ||
+ | <collection name="transcripts" referenced-type="Transcript" reverse-reference="protein"/> | ||
+ | </class> | ||
+ | |||
+ | ==== Line by line: ==== | ||
+ | <code><class name="Protein" extends="BioEntity" is-interface="true"></code> | ||
+ | |||
+ | <code>extends="BioEntity"</code>: Protein is a child of BioEntity therefore it inherits BioEntity's data fields. | ||
+ | |||
+ | Looking at BioEntity: <small> | ||
+ | <class name="BioEntity" is-interface="true"> | ||
+ | <attribute name="secondaryIdentifier" type="java.lang.String"/> | ||
+ | <attribute name="symbol" type="java.lang.String"/> | ||
+ | <attribute name="primaryIdentifier" type="java.lang.String"/> | ||
+ | <attribute name="lastUpdated" type="java.util.Date"/> | ||
+ | <attribute name="name" type="java.lang.String"/> | ||
+ | <reference name="organism" referenced-type="Organism"/> | ||
+ | <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/> | ||
+ | <collection name="publications" referenced-type="Publication" reverse-reference="bioEntities"/> | ||
+ | <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/> | ||
+ | <collection name="phenotypesObserved" referenced-type="Phenotype" reverse-reference="observedIn"/> | ||
+ | <collection name="phenotypesNotObserved" referenced-type="Phenotype" reverse-reference="notObservedIn"/> | ||
+ | <collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject"/> | ||
+ | <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/> | ||
+ | <collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn"/> | ||
+ | <collection name="locations" referenced-type="Location" reverse-reference="feature"/> | ||
+ | </class> | ||
+ | </small> | ||
+ | |||
+ | Protein contains copies of all these attributes, references, and collections for itself. If BioEntity inherits any fields itself, those are included as well. | ||
==Account management== | ==Account management== |
Revision as of 20:46, 6 May 2013
Contents
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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.
This schema file contains all of the data types contained in WormMine, relationships between them, and each one's data fields.
How to read it
Looking at the protein class:
<class name="Protein" extends="BioEntity" is-interface="true"> <attribute name="molecularWeight" type="java.lang.Float"/> <attribute name="md5checksum" type="java.lang.String"/> <attribute name="length" type="java.lang.Integer"/> <attribute name="geneName" type="java.lang.String"/> <attribute name="primaryAccession" type="java.lang.String"/> <reference name="sequence" referenced-type="Sequence"/> <collection name="CDSs" referenced-type="CDS" reverse-reference="protein"/> <collection name="genes" referenced-type="Gene" reverse-reference="proteins"/> <collection name="transcripts" referenced-type="Transcript" reverse-reference="protein"/> </class>
Line by line:
<class name="Protein" extends="BioEntity" is-interface="true">
extends="BioEntity"
: Protein is a child of BioEntity therefore it inherits BioEntity's data fields.
Looking at BioEntity:
<class name="BioEntity" is-interface="true"> <attribute name="secondaryIdentifier" type="java.lang.String"/> <attribute name="symbol" type="java.lang.String"/> <attribute name="primaryIdentifier" type="java.lang.String"/> <attribute name="lastUpdated" type="java.util.Date"/> <attribute name="name" type="java.lang.String"/> <reference name="organism" referenced-type="Organism"/> <collection name="synonyms" referenced-type="Synonym" reverse-reference="subject"/> <collection name="publications" referenced-type="Publication" reverse-reference="bioEntities"/> <collection name="ontologyAnnotations" referenced-type="OntologyAnnotation" reverse-reference="subject"/> <collection name="phenotypesObserved" referenced-type="Phenotype" reverse-reference="observedIn"/> <collection name="phenotypesNotObserved" referenced-type="Phenotype" reverse-reference="notObservedIn"/> <collection name="crossReferences" referenced-type="CrossReference" reverse-reference="subject"/> <collection name="dataSets" referenced-type="DataSet" reverse-reference="bioEntities"/> <collection name="locatedFeatures" referenced-type="Location" reverse-reference="locatedOn"/> <collection name="locations" referenced-type="Location" reverse-reference="feature"/> </class>
Protein contains copies of all these attributes, references, and collections for itself. If BioEntity inherits any fields itself, those are included as well.