Mapping database

[ipsapo...@gmail.com]

I have newly installed pathvisio and some of its plugins but everytime I try to search for gene product or metabolite it shows that no identifier mapping database loaded. Please tell me what is the problem. Thanks

[Martina Summer-Kutmon]

Hi,

If you check the instructions here: https://pathvisio.github.io/tutorials/getting-started.html, you find a section on "Select an Identifier Mapping Database". If you follow the instructions, you should be able to search for gene products and metabolites when you have the .bridge files loaded.

Let me know if that doesn't work.

Best, Tina

On Wed, Jul 8, 2020 at 8:56 PM <ipsapo...@gmail.com> wrote:

I have newly installed pathvisio and some of its plugins but everytime I try to search for gene product or metabolite it shows that no identifier mapping database loaded. Please tell me what is the problem. Thanks

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[ipsapo...@gmail.com]

Thank you so much..... Got the point

[ipsapo...@gmail.com]

Hello
I have downloaded the databases according to the tutorial but still I am not able to search the information for a RNA or a Gene. Everytime it shows No identifier mapping database loaded.
Can you tell me what are the essential databases which should be downloaded
I have already downloaded complexes_20200510.bridge
Hs_derby_ensemble_91.bridge
Interactions20190228.bridge
Metabolites_20200610.bridge
Publications_20200510.bridge

[Egon Willighagen]

For RNA/Gene ID mapping, you only need the Hs_derby_ensemble_91.bridge file.

I am not sure what you mean with "Everytime it shows No identifier mapping database loaded". Can you plz share a screenshot?

Egon

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Have you heard about Wikidata already? "Use Scholia and Wikidata to find scientific literature" is a new tutorial from my colleague Lauren Dupuis. https://laurendupuis.github.io/Scholia_tutorial/

-----

E.L. Willighagen
Department of Bioinformatics - BiGCaT
Maastricht University (http://www.bigcat.unimaas.nl/)
Homepage: http://egonw.github.com/
Blog: http://chem-bla-ics.blogspot.com/
PubList: https://www.zotero.org/egonw
ORCID: 0000-0001-7542-0286
ImpactStory: https://impactstory.org/u/egonwillighagen

[Ipsa Singh]

Here is the screenshot. 

I am not able to search for any RNA, metabolite or gene.

[Kristina Hanspers]

Hi Ipsa,

I'm not sure if this was resolved or not (hard to tell from time stamps on the email thread), but if you are still having trouble go to "Data>Identifier mapping setup...". If you can send a screenshot of this interface, that would be great.

Thanks,

Kristina

To view this discussion on the web visit https://groups.google.com/d/msgid/wikipathways-discuss/5ecb85ee-d651-49ab-aca2-d9186663972en%40googlegroups.com.

[Ipsa Singh]

Hello Kristina

My query has been resolved. Somehow the data was not loaded earlier but when I tried again,  it was a success. Pathvisio in my laptop is working smoothly now.

Thanks,

Ipsa