UniProt

Types of data loaded

genes, proteins, GO annotation, protein domains, publications, UniProt features, comments, synonyms, cross references, EC numbers, components

How to download the data

This source loads data from the UniProt website here: ftp://ftp.uniprot.org/pub/databases/uniprot/current_release

The UniProt source expects the data files to be in a special format:

TAXONID_uniprot_sprot.xml

TAXONID_uniprot_trembl.xml

To download a single taxon, you can use this URL:

http://www.uniprot.org/uniprot/?format=xml&query=taxonomy%3A9606+AND+reviewed%3Ayes&compress=yes

parameter	value
taxonomy	e.g. 9606 for human
reviewed	yes for swiss prot, no for trembl
compress	if yes, zipped

How to load the data into your mine

Configuration

Gene identifier fields

You can specify which gene fields are assigned when UniProt data is loaded. An example entry:

10116.uniqueField = primaryIdentifier

10116.primaryIdentifier.dbref = RGD

10116.secondaryIdentifier.dbref = Ensembl

10116.symbol.name = primary

The format for the file is:

<TAXONID>.<IDENTIFIER_FIELD> = <VALUE>

An example

A rat uniprot entry: http://www.uniprot.org/uniprot/Q923K9.xml

The second line of that configuration would set the ID value as the gene.primaryIdentifier:

<dbReference type="RGD" id="619834" key="33">

<property type="gene designation" value="Acf"/>

</dbReference>

The third line would set this ID value as gene.secondaryIdentifier:

<dbReference type="Ensembl" id="ENSRNOG00000033195" key="30">

<property type="organism name" value="Rattus norvegicus"/>

</dbReference>

The last line would set the value between the <name/> tags as gene.symbol:

<gene>

<name type="primary">A1cf</name>

<name type="synonym">Acf</name>

<name type="synonym">Asp</name>

</gene>

The values for symbol.name can be primary, ORF or ordered locus.

Protein feature types

You can also configure which protein features to load.

To load specific feature types only, specify them like so:

# in uniprot_config.properties

feature.types = helix

To load NO feature types:

# in uniprot_config.properties

feature.types = NONE

To load ALL feature types, do not specify any feature types, remove that line from this config file. Loading all feature types is the default behaviour.

Project.xml

<source name="uniprot" type="uniprot" >

<property name="uniprot.organisms" value="7227 9606"/>

<property name="src.data.dir" location="/data/uniprot"/>

<property name="creatego" value="true"/>

<property name="creategenes" value="true"/>

<property name="allowduplicates" value="false"/>

<property name="loadfragments" value="false"/>

<property name="loadtrembl" value="true"/>

</source>

property	description	default
creategenes	if TRUE, process genes	true
creatego	if TRUE, process GO annotation	false
allowduplicates	if TRUE, allow proteins with duplicate sequences to be processed	false
loadfragments	if TRUE, load all proteins even if isFragment = true	false
loadtrembl	if FALSE, not load trembl data for given organisms, load sprot data only	true

FASTA

This source loads FASTA data for isoforms. The UniProt entry is does not contain the sequences for isoforms. ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/uniprot_sprot_varsplic.fasta.gz

<source name="uniprot-fasta" type="fasta">

<property name="fasta.taxonId" value="7227 9606"/>

<property name="fasta.className" value="org.intermine.model.bio.Protein"/>

<property name="fasta.classAttribute" value="primaryAccession"/>

<property name="fasta.dataSetTitle" value="UniProt data set"/>

<property name="fasta.dataSourceName" value="UniProt"/>

<property name="src.data.dir" location="/data/uniprot/current"/>

<property name="fasta.includes" value="uniprot_sprot_varsplic.fasta"/>

<property name="fasta.sequenceType" value="protein" />

<property name="fasta.loaderClassName" value="org.intermine.bio.dataconversion.UniProtFastaLoaderTask"/>

</source>

UniProt keywords

Loads the names for the UniProt keywords contained in the main UniProt converter. ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/docs

<source name="uniprot-keywords" type="uniprot-keywords">

<property name="src.data.dir" location="/data/uniprot/current"/>

<property name="src.data.dir.includes" value="keywlist.xml"/>

</source>