Re: [cytoscape-helpdesk] PSICQUIC ID

[Rafael Jimenez]

Dear Lei,

Unfortunately different PSICQUIC services use different type of identifiers for proteins. The PSICQUIC data distribution best practices guideline recommends to use UniProt and RefSeq accessions suggesting to use UniProt as primary identifiers. It is up to the PSICQUIC providers to follow this guideline.

In the PSICQUIC results (PSI-MITAB) you have different columns with identifiers (unique indentifier, alternative identifier and alias). Not sure how it is displayed by cytoscape. You will likely be able to query and find gene symbols in the alias column. To query all the identifier columns in PSICQUIC use the identifier MIQL field ...

indentifier:DAB2

After you query several PSIQCUI services, you might step into the problem of getting different type of identifiers in the primary identifier column. In most cases it would be possible to reorganize the identifiers looking at the three columns I mentioned before, but that is something I would not know how to do with cytoscape. In cytoscape 3 you could solve this problem by using the merging(cluster) functionality provided in the PSICQUIC import functionality.

Regards,
Rafael.

On 22 August 2012 10:50, 王磊 <wln...@126.com> wrote:

Dear Cytoscapers,

I am interested in PSICQUIC, but Many interaction databases are different IDs, for instance, GeneMANTA(Q00288 Q5XI41 Q9DBG1 Q91XQ6), BIND(NC_000016.4 NP_206830.1 NP_012855.1). My data ID is gene symbol(DAB2 DHCR24 DLK1 FCGR2A GMFG). I did not know how to accord PSICQUIC different IDs and my data ID.

Many thanks in advance

Lei

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