STRING --> Your query returned no results

[Andrey Markov]

Dear colleagues,

Today I faced the problem with the STRING App. 

After switching on the Cytoscape, I pushed on the button "From Network Database..." into the "Welcome to Cytoscape" window. After that I chose Data source: "STRING: protein query" and Search Mode: Search by ID. Than I entered the name of proteins (official gene ID like, STAT1, TLR4, APP. etc.), installed confidence score 0.7 and max. numb. of interactors: 20 and pushed on Import. After that the window with text "No results. Your query returned no results". I tried to enter the names of proteins encoded by another ID (Entrez, Uniprot), but mentioned problem did not disappear. Some days ago I constructed PPI Network without any problems.

Please, could you tell me - what should I do?

Additional Information:

Cytoscape 3.5.1

Java version: 1.8.0_131

stringApp 1.1.1

Thanks a lot!

Sincerely yours,

Andrey Markov 

[Andrey Markov]

четверг, 16 ноября 2017 г., 15:34:52 UTC+7 пользователь Andrey Markov написал:

[Scooter Morris]

Hi Andrey,
   I just tested and things are working for me here.  Can you run Cytoscape from a shell and see if you get any errors?  There also might be some clues in the Task History (second button in the lower-left hand corner).

-- scooter

[Andrey Markov]

Dear Scooter,

Thanks a lot! I repeated my analysis and now Cytoscape and STRING App are working fine!

Sincerely,

Andrey

четверг, 16 ноября 2017 г., 23:50:41 UTC+7 пользователь Scooter Morris написал:

[Tejas Chirmade]

Dear Colleagues,

I am facing the same error with the STRING App. I have tried using TAIR IDs, official gene IDs. It used to work earlier and all of a sudden it is giving the same error "Your query returned no results". I have updated the Java version, the OS. Can anyone please help me with this?

Thanks and regards,

Tejas

[Tejas Chirmade]

Hi Scooter,

I am facing the same problem with STRING App for Arabidopsis thaliana IDs. Is there any update that I need to perform?

Thanks,

Tejas

On Thursday, 16 November 2017 14:04:52 UTC+5:30, Andrey Markov wrote:

[Andrey Markov]

Hey Tejas!

I tried to create a PPI network with random Arabidopsis thaliana IDs (information from https://www.arabidopsis.org/servlets/processor?type=genesymbol&update_action=view_symbol) and really the aforemantioned problem appeared again! Moreover, the error  "Your query returned no results" doesn't disappear when I worked with Homo sapiense protein identifiers (official gene name). Unfortunatelly I don't know how to run Cytoscape from a shell, but I did not find any problems in the Task History.

In the previous case, the problem was solved within about 1 day without my manipulations with updating the Cytoscape, Java, STRING App. I hope, that it will happen again this time.

Sincerely,

Andrey

четверг, 23 ноября 2017 г., 21:15:06 UTC+7 пользователь Tejas Chirmade написал:

[Scooter Morris]

Hi Andrey,
    Can you send me the gene symbols that are causing you problems?  I'm not having any problems here with Cytoscape 3.6.0 and StringApp 1.2.0 (which will be released tomorrow).

-- scooter

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[Andrey Markov]

Hi Scooter,

H. sapiens gene list: 

ABCB7

ACACA

ACADM

ACLY

ACTA2

ACTB

ACTG1

ACTN4

ACTN1

ACVR1

ACYP2

ADAR

ADM

AGL

AHCY

ALB

ABCD1

ALDH2

ALDH1A3

AMD1

AMY1B

AMY1C

ANG

ANXA1

BIRC2

BIRC3

APP

ARF3

ARF4

ARF5

ARG2

RHOB

RND3 Arabidopsis thaliana IDs: AAA AAC AACT AAF AAH AAO AAP AAPT AAR AARL AAT AATL AATP ABA ABC ABC ABF ABH ABI ABL ABO ABP ABR ABR ABS ACA ACA ACBP ACC ACD ACE ACEX ACF ACG ACHT ACI ACL ACLA ACLB ACN ACO ACOS ACP ACR ACS ACS ACT ACT ACW ACX ADA ADA ADC ADD ADE ADF ADG ADH ADK ADL ADN ADO ADP ADR ADS ADTO AEL AEP AES AESP AFB AFC AFL AFO AFP AFP AFR AFS AFT AG AGA AGB AGD AGE AGG AGI AGK AGL AGM AGO AGP AGR AGS AGT AHA AHASS AHB AHD AHG AHL AHM AHP AHS AIA AIF AIG AIL AIM AIN AIN AIP AIRF AIRL AIS AITR AJH AJX AKH AKR AKT AKV ALA ALAAT ALAC ALB ALBI ALC ALD ALDH ALE ALF ALH ALI ALIS ALK ALLTW ALNS ALR ALS ALT ALX AMK AML AMN AMO AMP AMPL AMS AMSH AMT AMT AMY AN ANA ANG ANL ANP ANT ANU ANY AOAT AOC AOE AOP AOS AOX AP APA APD APE APG APG API APIH APK APL APL APM APMU APO APP APP APPR APR APRR APS APS APS APSE APT APU APUM APX APY AQI AQP AR ARA ARA ARAD ARC ARD AREB ARF ARF ARG ARGAH ARH ARI ARI ARID ARIX ARK ARM ARP ARP ARP ARR ARS ART ARTEMIS ARU ARX AS ASA ASA ASB ASB ASC ASF ASG ASH ASIL ASK ASP ASP ASPGA ASPGB ASR AST ASY ATA ATBI ATBS ATC ATD ATEM ATFC ATG ATGH ATH ATHB ATI ATK ATKC ATKT ATM ATM ATML ATN ATO ATPT ATR ATRR ATS ATSR ATSR ATST ATT ATX AUG AUN AUR AUX AVA AVB AVP AVPL AWE AWN AXE AXR AXY AYA AZA AZD AZF Confidence score = 0.7 Max. number of interactors = 20 Thanks in advance!!!

Sincerely yours,

Andrey

пятница, 24 ноября 2017 г., 12:05:24 UTC+7 пользователь Scooter Morris написал:

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[Scooter Morris]

Hi Andrey,

Both of those lists work for me.  I get 53 nodes and 209 edges for the H. sapiens and 122 nodes and 250 edges for the A. thaliana.  I would suggest upgrading to 3.6.0 and grabbing the new stringApp (1.2.0) when it's released (hopefully tomorrow).

-- scooter

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[Andrey Markov]

Dear Scooter,

I have upgraded Cytoscape to 3.6.0 version but the problem, unfortunatelly, did not solved. So, let's wait for the novel STRING App's release.

Thank you for your care!

Andrey

пятница, 24 ноября 2017 г., 14:33:16 UTC+7 пользователь Scooter Morris написал:

[Andrey Markov]

Dear Scooter,

I checked Task History and found some mistakes depicted by orange triangles. I added the copy of this information - the problems are colored by orange. Is it critical for fine working in STRING App?

•  couldn't find resource 'groupSettings.props' in jar.

  Load Image Library

•  Loading image library from local disk...

•  Custom Graphics Image property file loaded from: C:\Users\Марков Андрей\CytoscapeConfiguration\images3

•  Image loading process finished in 0.007 sec.

•  Currently, -1 images are available.

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  adding IO taskFactory

•  Image saving process finished in 0.598 sec.

•  The virtual key 'VK_?' does not exist.

•  couldn't find resource 'layout.grid.props' in jar.

•  Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5fc147b,flags=256,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Remove Style] with gravity: 4.0

•  Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5fc147b,flags=256,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Rename Style...] with gravity: 3.0

•  Inserted menu separator with gravity: 5.9999

•  Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5fc147b,flags=256,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create Legend...] with gravity: 6.0

•  Inserted menu separator with gravity: 4.9999

•  Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5fc147b,flags=256,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Make Current Styles Default] with gravity: 5.0

•  CyNetwork w/ private tables created: ID = 2

•  CyNetwork w/ private tables created: Base Graph ID = 18

•  Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5fc147b,flags=256,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Copy Style...] with gravity: 2.0

•  Inserted menu item: javax.swing.JMenuItem[,0,0,0x0,invalid,alignmentX=0.0,alignmentY=0.0,border=javax.swing.plaf.basic.BasicBorders$MarginBorder@5fc147b,flags=256,maximumSize=,minimumSize=,preferredSize=,defaultIcon=,disabledIcon=,disabledSelectedIcon=,margin=javax.swing.plaf.InsetsUIResource[top=0,left=0,bottom=0,right=0],paintBorder=false,paintFocus=false,pressedIcon=,rolloverEnabled=false,rolloverIcon=,rolloverSelectedIcon=,selectedIcon=,text=Create New Style...] with gravity: 1.0

•  couldn't find resource 'layout.stacked-node-layout.props' in jar.

•  couldn't find resource 'layout.hierarchical.props' in jar.

•  couldn't find resource 'layout.isom.props' in jar.

•  couldn't find resource 'layout.attributes-layout.props' in jar.

•  couldn't find resource 'layout.fruchterman-rheingold.props' in jar.

•  couldn't find resource 'layout.circular.props' in jar.

•  couldn't find resource 'layout.attribute-circle.props' in jar.

•  couldn't find resource 'layout.kamada-kawai.props' in jar.

•  couldn't find resource 'layout.cose.props' in jar.

•  couldn't find resource 'layout.degree-circle.props' in jar.

•  couldn't find resource 'layout.force-directed.props' in jar.

•  adding IO taskFactory

•  Server socket started on 127.0.0.1:2607

•  Silencing event source: org.cytoscape.equations.internal.EquationParserImpl@74b2d6f7

•  New Function Registered: DEGREE

•  New Function Registered: INDEGREE

•  New Function Registered: OUTDEGREE

•  New Function Registered: SOURCEID

•  New Function Registered: TARGETID

•  Unsilencing event source: org.cytoscape.equations.internal.EquationParserImpl@74b2d6f7

•  Loaded app PSI-MI Reader

•  Loaded app CyCL

•  Loaded app JSON Support

•  Loaded app PSICQUIC Web Service Client

•  Loaded app Biomart Web Service Client

•  Loaded app OpenCL Prefuse Layout

•  Loaded app Core Apps

•  Loaded app Network Merge

•  Loaded app NetworkAnalyzer

•  Loaded app SBML Reader

•  Loaded app BioPAX Reader

•  Loaded app Welcome Screen

•  Loaded app cyREST

•  Loaded app Command Line Implementation

•  adding IO taskFactory

•  adding IO taskFactory

•  Started app PSI-MI Reader

•  Started app CyCL

•  adding IO taskFactory

•  adding IO taskFactory

•  Specified factory is null or has wrong DataCategory (SESSION)

•  Specified factory is null or has wrong DataCategory (SESSION)

•  Specified factory is null or has wrong DataCategory (SESSION)

•  Started app JSON Support

•  New network import client registered: Universal Interaction Database Client

•  Started app PSICQUIC Web Service Client

•  New network import client registered: BioMart Client

•  Started app Biomart Web Service Client

•  Started app OpenCL Prefuse Layout

•  Started app Core Apps

•  Started app Network Merge

•  Started app NetworkAnalyzer

•  Started app SBML Reader

•  New visual Style registered to VMM: BioPAX

•  Total Number of VS in VMM = 2

•  New visual Style registered to VMM: BioPAX_SIF

•  Total Number of VS in VMM = 3

•  Started app BioPAX Reader

•  Started app Welcome Screen

•  Started app cyREST

•  couldn't find resource 'layout.force-directed-cl.props' in jar.

•  Started app Command Line Implementation       

пятница, 24 ноября 2017 г., 14:33:16 UTC+7 пользователь Scooter Morris написал:

[Tejas Chirmade]

Dear Scooter,

I have updated both the cytoscape and STRING App. However the problem is still not solved. Is that problem with using Arabidopsis database or with some other databases too?

Regards,

Tejas

On Thursday, 16 November 2017 14:04:52 UTC+5:30, Andrey Markov wrote:

[Scooter Morris]

Hi Tejas,
    Are you entering those ids with commas or newlines?  They should be entered with newlines.  If I enter:
PHYB
FLC
FT
PHYA
NPR1
AG
ETR1
LFY
CO
PR1

and set the number of additional proteins to 20, I get a network with 30 nodes and 318 edges.

-- scooter

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[Andreas Wrona]

I have the exact same problem. Would love a solution to this issue!

[Andreas Wrona]

Issue was resolved when running the following versions of software: Cytoscape 3.6.0, StringApp 1.2.1 and Java Runtime environment 8.

[Scooter Morris]

On 12/12/2017 02:11 AM, Andreas Wrona wrote:

Issue was resolved when running the following versions of software: Cytoscape 3.6.0, StringApp 1.2.1 and Java Runtime environment 8.

Excellent!  StringApp 1.2.1 was just released yesterday, so I'm glad to hear that it fixed your problem.

-- scooter

  

Den tirsdag den 12. december 2017 kl. 10.49.16 UTC+1 skrev Andreas Wrona:

I have the exact same problem. Would love a solution to this issue!

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[imn....@gmail.com]

Dear Morris,
I still have problem with String app. Cytoscape freezes after I start the search with mouse Uniprot ids. It throws an error stating "Unexpected exception while handling listener:org.cytoscape.model.events.ColumnCreatedListener". I have used Cytoscape 3.6.0 and StringApp 1.2.1 versions.
My id's are
P56391
P50516
P50518
P12787
Q9CPQ1
P48771
P17665
P00397
P00405
P00158
P03899
P03911
P03921
Q9CQ75
Q62425
Q91YT0
Q61387
Q9CQ69
Q9CZ13
Q8K3J1
Q91WD5
Q91VD9
Q3UIU2
Q80SY3
P52503
Q9R1Q9
Q99LY9
Q9CQ91
Q9DC69
P56393
Q8R1I1
Q9CQJ8
Q7TMF3
Q9Z1P6
Q9CPX8
Q9CR68
Q9CR61
Q9DB77
Q9CQZ5
Q9ERS2
Q99LC3
Q9CQ54
Q9CPU2
Q9CPP6
Q9DCT2
Q9DCJ5
Q9D6J6
P57746
Q9DC70



Best regards,
Imran

[Scooter Morris]

Hi Imran,
    I'm not seeing a problem with that list of proteins.  Are you
running that in an empty session?

-- scooter

[Imran Mohammad]

Please find the screenshot. Thanks.

Best regards,

Imran

On Thu, Jan 4, 2018 at 5:58 PM, Scooter Morris <sco...@cgl.ucsf.edu> wrote:

Hi Imran,
    I'm not seeing a problem with that list of proteins.  Are you running that in an empty session?

-- scooter

On 01/04/2018 05:53 AM, imn....@gmail.com wrote:

On Tuesday, December 12, 2017 at 5:09:42 PM UTC+2, Scooter Morris wrote:

On 12/12/2017 02:11 AM, Andreas Wrona
       wrote:

                 Issue was resolved when running the following
         versions of software: Cytoscape 3.6.0, StringApp 1.2.1 and Java
         Runtime environment 8.

                 Excellent!  StringApp 1.2.1 was just released yesterday, so I'm glad
     to hear that it fixed your problem.

     
     -- scooter

               
         
         Den tirsdag den 12. december 2017 kl. 10.49.16 UTC+1 skrev
         Andreas Wrona:
                    I have the exact same problem. Would love a
             solution to this issue!

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[Scooter Morris]

Got it.  I suspect that one of your apps is causing problems.  The easiest way to figure out which one is to go to the App Manager, (Apps->App Manager) and then "disable" all of the extra apps you have loaded.  One of those apps is listening for a NetworkViewAdded and then trying to create a column that already exists.  You could also run Cytoscape from the shell and (hopefully) that backtrace will give us a clue which app.

-- scooter

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[imn....@gmail.com]

Thanks a lot. The issues is resolved now.

Best regards,
Imran

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>
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[Akshay]

Hi Imran!

I have also same problem. How did you solve your issue?

Thanks!

Akshay

[Scooter Morris]

Hi all,
    There was a recent change to the string web site that is causing
problems with the app.  We hope to have a new version out very soon that
will fix things.

-- scooter

[akbi...@gmail.com]

Thank you Scooter!

Please update here when the new version arrives!

Regards,
Akshay

[akbi...@gmail.com]

Hi Scooter,

Why does the Cytoscape show error messages on start up? Cytoscape is unable to detect its set up (.props) files. I have observed that its .props files are located in a different folder <C:\Users\user>. Is the address for these files corrupted in cytoscape settings and can I fix it?

Please help!

Akshay

On Sunday, January 21, 2018 at 12:10:59 AM UTC-5, Scooter Morris wrote:

[ksivap...@tgen.org]

Can I know when the update will happen? is there any other way to get the network created? I have around 3000 genes and the website is not able to handle this.

On Thursday, November 16, 2017 at 1:34:52 AM UTC-7, Andrey Markov wrote:
> Dear colleagues,
>
>
> Today I faced the problem with the STRING App. 
> After switching on the Cytoscape, I pushed on the button "From Network Database..." into the "Welcome to Cytoscape" window. After that I chose Data source: "STRING: protein query" and Search Mode: Search by ID. Than I entered the name of proteins (official gene ID like, STAT1, TLR4, APP. etc.), installed confidence score 0.7 and max. numb. of interactors: 20 and pushed on Import. After that the window with text "No results. Your query returned no results". I tried to enter the names of proteins encoded by another ID (Entrez, Uniprot), but mentioned problem did not disappear. Some days ago I constructed PPI Network without any problems.
>
>
> Please, could you tell me - what should I do?
>
>
> Additional Information:
>
> Cytoscape 3.5.1
> Java version: 1.8.0_131
> stringApp 1.1.1
>
>
> Thanks a lot!
>
>
> Sincerely yours,
> Andrey Markov 


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[Scooter Morris]

The update has already happened.  It required Cytoscape 3.6, however,
which is why you weren't offered an update.  There is a remaining
problem with protein queries with over 2000 terms that will be fixed in
the next release.

-- scooter

[ksivap...@tgen.org]

Thank you for the quick response. I really appreciate.
So, with respect to handling 3000 proteins, what would your suggestion be other than waiting for the next release, since I am on a serious time crunch.

[Scooter Morris]

On 02/08/2018 01:56 PM, ksivap...@tgen.org wrote:
> Thank you for the quick response. I really appreciate.
> So, with respect to handling 3000 proteins, what would your suggestion be other than waiting for the next release, since I am on a serious time crunch.

No, there is a workaround.  Break you list up into two lists of 1500
proteins each.  Then query String for each group, but set the confidence
cutoff to 1.0.  This will retrieve only the nodes. Merge the two
resulting networks (or copy-paste from one network into the other).  Now
you have all 3000 nodes into a single network, but no edges.  Then
change the confidence cutoff from 1.0 to 0.8 or whatever you want.  This
will fetch all of the edges.

-- scooter

[ksivap...@tgen.org]

Thanks a lot. I am going to try this right away.

[ksivap...@tgen.org]

It worked like charm. Thank you once again for the timely help.