Pathway Talk:WP2258
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Start a new discussionWhat is the data source for IDs like FGSG 10629? (1)
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Currently, they are marked with Ensemble, but the link out leads to a 'not found' page.
Hello Egon,
FGSG IDs like FGSG10629 and FGSG_03537 are gene IDs for the fungal organism Gibberella zeae stored at ENSEMBL FUNGI (http://fungi.ensembl.org/index.html).
Currently the outlink is not correct between Wikipathways and Ensembl due to database issues. I contacted Alex Pico (Wikipathways) yesterday and he started a discussion with Ensembl to get this issue solved. He thinks a workaround in Wikipathways will be available by end of Dec 2013.
I am quite keen to have gene IDs such as FGSG_03537 in the pathway annotation and not use a work-a-round such as Uniprot IDs. The reason for this is that there is a recently funded project called PhytoPath (http://www.phytopathdb.org). The PhytoPath project links phenotypic information from gene deletion studies taken from the peer-reviewed literature (collected in the database project http://www.phibase.org) and links them to genes in Ensembl Fungi. Ensembl Fungi displays genes together with their knockout phenotypes directly in a chromosome browser. An example is the TRI5 gene (http://fungi.ensembl.org/Gibberella_zeae/Gene/Summary?g=FGSG_03537;r=2:6647925-6649292;t=FGSG_03537T0).
In the PhytoPath project ~100 agriculturally relevent pathogens will be included over the next years.
Best regards
--Martin Urban 09:25, 24 October 2013 (UTC)
