FASTA

Types of data loaded

Features and their sequences. Will create a feature for each entry in a fasta file and set the sequence, the class of the feature to create is set for the whole file.

How to download the data

N/A - will parse any file in FASTA format

How to load the data into your mine

Project XML example

<source name="flybase-dmel-gene-fasta" type="flybase-dmel-gene-fasta">

<property name="flybase-dmel-gene-fasta.taxonId" value="7227"/>

<property name="flybase-dmel-gene-fasta.dataSetTitle" value="FlyBase fasta data set for Drosophila melanogaster"/>

<property name="flybase-dmel-gene-fasta.dataSourceName" value="FlyBase"/>

<property name="flybase-dmel-gene-fasta.className" value="org.intermine.model.bio.Gene"/>

<property name="flybase-dmel-gene-fasta.classAttribute" value="primaryIdentifier"/>

<property name="flybase-dmel-gene-fasta.includes" value="dmel-all-gene-*.fasta"/>

<property name="src.data.dir" location="/DATA/flybase/fasta"/>

<!-- add licence here -->

<property name="flybase-dmel-gene-fasta.licence" value="https://creativecommons.org/licenses/by/4.0/"/>

</source>

attribute	content	purpose
taxonId	space-delimited list of taxonIds	only features with the listed taxonIds will be loaded
className	fully-qualified class name	determines which feature will be loaded
classAttribute	identifier field from className	determines which field from the feature will be set
dataSetTitle	name of dataset	determines name of dataset object
dataSourceName	name of datasource	determines name of datasource object
src.data.dir	location of the fasta data file	these data will be loaded into the database
includes	name of data file	this data file will be loaded into the database
sequenceType	class name	type of sequence to be loaded
loaderClassName	name of Java file that will process the fasta files	only use if you have created a custom fasta loader
licence	URL pointing to standard data licence for data	updates DataSet.licence with value