CytoscapeNetworkDisplayer don't work

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CytoscapeNetworkDisplayer don't work

Pengcheng Yang

Dear InterMiners,

I have implemented FAWMine (http://www.insectmine.org:8080/fawmine/begin.do). The project and data model has been commit to github at https://github.com/pengchy/fawmine and https://github.com/pengchy/fawmine-bio-sources. I am sure that the Interaction network data has been successfully loaded and could be queried through the following [1] query command for the specific gene "SFR01273". However, the Network was not displayed on the report page of SFR01273 (http://159.226.67.243:8080/fawmine/gene:SFR01273). Could anyone help me out?

Best,

Pengcheng Yang



[1] query command for one gene
<query name="" model="genomic" view="InteractionDetail.interaction.participant1.primaryIdentifier InteractionDetail.interaction.participant2.primaryIdentifier InteractionDetail.type" longDescription="" sortOrder="InteractionDetail.interaction.participant1.primaryIdentifier asc">
  <constraint path="InteractionDetail.interaction.participant2.primaryIdentifier" op="=" value="SFR01273"/>
</query>



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Re: CytoscapeNetworkDisplayer don't work

Yo Yehudi-2
Hey Pengcheng!

I think the reason it returns no results is that the data are modelled slightly differently, and we're asking for columns that don't exist in your InterMine - this is the gene query: https://github.com/intermine/cytoscape-intermine/blob/master/js/query/query.json - specifically, we're asking for "interactions.details.role1" and "interactions.details.role2". (If I recall correctly these tend to be "prey" or "bait" most of the time).

If my suspicions above are correct, the answer is either to modify your data structure to add roles (is that likely to be easy for you?), or I suspect I could get around this issue by modifying the query to produce a left join and releasing a more up-to-date version of the visualiser.

Yo

On Thu, 6 Feb 2020 at 10:36, Pengcheng Yang <[hidden email]> wrote:

Dear InterMiners,

I have implemented FAWMine (http://www.insectmine.org:8080/fawmine/begin.do). The project and data model has been commit to github at https://github.com/pengchy/fawmine and https://github.com/pengchy/fawmine-bio-sources. I am sure that the Interaction network data has been successfully loaded and could be queried through the following [1] query command for the specific gene "SFR01273". However, the Network was not displayed on the report page of SFR01273 (http://159.226.67.243:8080/fawmine/gene:SFR01273). Could anyone help me out?

Best,

Pengcheng Yang



[1] query command for one gene
<query name="" model="genomic" view="InteractionDetail.interaction.participant1.primaryIdentifier InteractionDetail.interaction.participant2.primaryIdentifier InteractionDetail.type" longDescription="" sortOrder="InteractionDetail.interaction.participant1.primaryIdentifier asc">
  <constraint path="InteractionDetail.interaction.participant2.primaryIdentifier" op="=" value="SFR01273"/>
</query>


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Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs

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Re: CytoscapeNetworkDisplayer don't work

Pengcheng Yang

Hi Yo,

Through adding "role1", "role2", "daaSets", the cytoscape has been successfully displayed. Thank you.

Best,

Pengcheng Yang


On 2020-2-7 0:43, Yo Yehudi wrote:
Hey Pengcheng!

I think the reason it returns no results is that the data are modelled slightly differently, and we're asking for columns that don't exist in your InterMine - this is the gene query: https://github.com/intermine/cytoscape-intermine/blob/master/js/query/query.json - specifically, we're asking for "interactions.details.role1" and "interactions.details.role2". (If I recall correctly these tend to be "prey" or "bait" most of the time).

If my suspicions above are correct, the answer is either to modify your data structure to add roles (is that likely to be easy for you?), or I suspect I could get around this issue by modifying the query to produce a left join and releasing a more up-to-date version of the visualiser.

Yo

On Thu, 6 Feb 2020 at 10:36, Pengcheng Yang <[hidden email]> wrote:

Dear InterMiners,

I have implemented FAWMine (http://www.insectmine.org:8080/fawmine/begin.do). The project and data model has been commit to github at https://github.com/pengchy/fawmine and https://github.com/pengchy/fawmine-bio-sources. I am sure that the Interaction network data has been successfully loaded and could be queried through the following [1] query command for the specific gene "SFR01273". However, the Network was not displayed on the report page of SFR01273 (http://159.226.67.243:8080/fawmine/gene:SFR01273). Could anyone help me out?

Best,

Pengcheng Yang



[1] query command for one gene
<query name="" model="genomic" view="InteractionDetail.interaction.participant1.primaryIdentifier InteractionDetail.interaction.participant2.primaryIdentifier InteractionDetail.type" longDescription="" sortOrder="InteractionDetail.interaction.participant1.primaryIdentifier asc">
  <constraint path="InteractionDetail.interaction.participant2.primaryIdentifier" op="=" value="SFR01273"/>
</query>


_______________________________________________
dev mailing list
[hidden email]
https://lists.intermine.org/mailman/listinfo/dev


--
Please note I am ‘working to contract’ as part of the UCU industrial action to defend our pensions and fight for fair pay and equality. This may mean it takes longer for me to respond to emails. You can find out more about the dispute at: www.ucu.cam.ac.uk/faqs

_______________________________________________
dev mailing list
[hidden email]
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