Plugin test cases 0.85

Search cases

Test case name: UniProt_Ac 1

Operation:

Query box:

Q39009
Q9ZNV8

Search type: UniProt_Ac

Taxon id: Any

Iterations: 1

Create new view: no

Use canonical expansion: no

Expected Observation:

33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH). Checked node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute to Entrez/protein was correct. IRefIndex has correct i.taxid and i.geneID.

Checked node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute to UniProt/KB beta was correct. IRefIndex has correct i.taxid and i.geneID. UniProt record agreed with iRefIndex on iRefSeq_Ac_TOP, i.taxid, i.geneID.

Selected two edges between query nodes : EBI-1555390, EBI-1555417. Checked linkouts for both edges (i.src_intxn_id) to Interaction databases/Intact. Confirmed that i.PMID and i.method_name were correct. Viewed EBI-1555390 in MI-XML 2.5 format and confirmed that i.RefSeq_Ac_TOP, i.UniProt_Ac_TOP, i.type_cv, i.type_name were correct. Note that NP_188928.2 was listed by IntAct while i.RefSeq_Ac_TOP listed NP_188928.

Checked linkout to http://wodaklab.org/iRefWeb/interaction/show/102203 from both interactions above.

Last tested: June 15, 2010

Plugin Version: 0.85

Data Version: 7.0 public (iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry

Test case name: RefSeq_Ac 1

Operation:

Query box:

NP_188928.2

Search type: RefSeq_Ac

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Expected Observation:

11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned. Edges returned include two edges described in test UniProt_Ac 1.

The same results are returned if the query box is changed to NP_188928.

The same results are returned if the query box is changed to NP_188928.567.

The same results are returned if the query box is changed to 188928. No results OK

No results are returned if the query box is changed to NP 188928. Ok.

Change the search type to UniProt_Ac. The interface says no results and when user presses ok, shows a blank panel. Ok.

The search type can also be changed to UniProt_ID, geneID, geneSymbol, ipi,, mass or rog with no results returned.

No results are returned if the query box is changed to 0. Error message says : Error resolving query. Ok.

No results are returned if the query box is changed to abcde.

Last tested: June 15, 2010

Plugin Version: 0.85

Data Version: 7.0 public(iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry

Notes: :(SABRY) : The index file name was included the control tag _EXT_ (To perform only exact matches)

Test case name: UniProt_ID 1

Operation:

Query box:

AHP2_ARATH

Search type: UniProt_ID

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Expected Observation:

26 nodes, 67 edges.

The same results are returned if the query box is changed to AHP2. No results : PASS

AHP2 ARATH returns no results. Ok.

ARATH no results : OK (Now UniProt_ID is exact match only)

AH2_ARATH returns no results. Ok.

AHP2_ARATH.2 returns no results. OK.

Searching for AHP2_ARATH but with search type UniProt_Ac, geneID, geneSymbol, ipi or mass all return 0 results. The interface says no results and when user presses ok, shows a blank panel. Ok.

No results are returned if the query box is changed to 0. Error message says : Error resolving query. Ok.

No results are returned if the query box is changed to abcde.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: PASS

Tester: Ian

Notes: :(SABRY) : UniProt_ID is now EXACT match only. If the user failed to enter exactly matching query no results will be returned. Query helper will never be invoked.

Test case name: geneID 1

Operation:

Query box:

821860
822593

Search type: geneID

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Expected Observation:

Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8 (33 nodes and 94 edges). Ok.

0 returned "error resolving query. Ok.

00001 returned 0 results. Ok.

abcdes returned 0 results. Ok.

1234 returned 34 nodes and 70 edges. Ok. 1234 is CCR5.

Expected results by Ian-----------------------------

Retrieved all geneIds from above query and queried (iterations = 0). Should return same number of nodes as above (33 protein nodes). But 30 protein nodes are returned and there are differences. NOTE. Keep this example for further reference. Explanation. Two of the nodes from the first graph did not have a gene id. Two nodes had the same gene id 7852. If you search for 7852, a graph of 12 nodes, 21 edges is returned. But only one of the nodes has a gene id of 7852. This seems like the search does not continue past the first match found?! FAIL until this is resolved. Also check that all other searches that are exact match searches are "continue after first match found" and write in test cases to ensure that this happens. The gene in question is CXCR4 and has two isoforms (P61073-2 and P61073). A geneSymbol search for CXCR4 (iteration=0) returns two nodes as expected. A UniProt_Ac search for P61073-2 or P61073 each return only one node when use canonical expansion is turned off. Each search returns two nodes when canonical expansion is turned on. By default, canonical expansion should be turned on. A hidden advanced option should be made available to turn this off. This can be used as a test case for the Export function "on Target network Node ID type"= i.Canonical_ROGID_TOP Searched 821860 but by each other search type. No results returned in any case. Ok

Expected results by Ian END.------------------

Expected results by Sabry-----------------------------

1. Steep 1

Search for

821860
822593

• Search type: geneID
• Taxon id: Any
• Iterations: 1
• Create new view: no
• Use canonical expansion: no

Returns 33 nodes and 94 edges.

1. Steep 2

collect all GeneIds from the above search and search for ZERO order interactions.

• 814707|814714|814714|817659|818662|818730|819356|819583|820940|821860|822593|823965|824871|827076|827297|828230|829038|829322

831710|832208|833552|837587|838487|839621|842288|842783|842951|854659

• Search type: geneID
• Taxon id: Any
• Iterations: 1
• Create new view: yes
• Use canonical expansion: no

• Result: 29 nodes and 125 Edges returned. This is what was expected and works according to the implementation.
• Reason for having different node count than Step one: 4 of the nodes in Step one did not have GeneIds. Two nodes had the same GeneId (814714)
• Reason for having different Edge count than step one: The two searches are different. The step 1 search for interactions of the products of the 2 genes. The second step searches for interactions in between the list of genes. So we will get more interactions in second step. This is because in the second step we will get interactions between nodes which were first order neighbors in the step 1.

e.g. the interaction between 829322 and 814707 will not be shown in step one. because they are neighbors of the query proteins.

Other observation by Ian using GeneID=7852 can not be reproduced as this Geneid never returned in my search for 821860 and 822593.

Expected results by Sabry END.------------------

Last tested: June 15, 2010

Plugin Version: 0.85

Data Version: 7.0 public

Result: FAIL (Zero order search algorithm need to be totally changed to achieve what has requested)

Tester: Sabry

Notes: :(SABRY) :

Test case name: geneSymbol 1

Operation:

Query box:

CXCR4

Search type: geneSymbol

Taxon id: Any

Iterations: 0

Create new view: no

Use canonical expansion: no

Expected Observation:

Warning for user : "You have not limited your search to a specific organism. Proceed anyway? Yes No - Yes selected

Returns two nodes with i.UniProt_Ac_TOP of P61073 and P61073-2.

0 returns no results. Ok.

0000 returns no results. Ok.

12345 returns no results. Ok.

abcde returns no results. Ok.

cxcR4 returns identical results to CXCR4. Ok.

Link-outs to NCBI : removed, query Helper removed (Exact match search will not use query helper)

Search CXCR5 as a UniProt_ID : No results , UniProt_Id is now exact match only

Search CXCR5 against other query types returned no results. Ok.

Last tested: June 15, 2010

Plugin Version: 0.85

Data Version: 7.0 public (iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry

Notes: :(SABRY) :

1. hyperlink removed
2. The default batch file mode the user has to specify a taxonid, this was overridden as requested in an earlier release should this be reactivated as well?.

Test case name: geneSymbol 2

Operation:

Query box:

RPB1

Search type: geneSymbol

Taxon id: Any

Iterations: 0

Create new view: yes

Use canonical expansion: no

Warning for user : "You have not limited your search to a specific organism. Proceed anyway? Yes No - Yes selected

Expected Observation:

RPB1 for any taxon returns 1 node (RPB1_SCHPO). Ok.

RPB1 for taxon 4932 returns 0 nodes. Ok.

RPB1 for taxon 9606 returns 0 nodes. Ok.

Last tested: June 15, 2010

Plugin Version: 0.85

Data Version: 7.0 public (iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry ' Notes: ':(SABRY) :Changed to exact search. query helper will never pop-up.

Test case name: rog search 1

Operation:

Query box:

5366033

Search type: rog

Taxon id: Any

Iterations: 1

Create new view: no

Use canonical expansion: no

Expected Observation: 5366033 returns 7 interactions (5 self interactions + 2 interactions with 5366026) (When canonical expansion turned on, 338 interactions and 96 nodes NP_057849,NP_705926,NP_705927,NP_705928,NP_789739,NP_789740,P04585)

Last tested: June 14, 2010

Plugin Version: 0.85

Data Version: 7.0 public

Result: PASS

Tester: Sabry ' Notes: ':(SABRY) The bug coursing freeze when performing ROG searches now fixed

Test case name: Iterations 1

Operation:

Perform search described in test UniProt_Ac 1 with Iterations=1. Then again with Iterations = 0 and confirm that the number of edges between the query nodes is identical.

Expected Observation:

Same number of edges (2 edges, 1 loop) in both cases.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: PASS

Tester: Ian

Notes:

Test case name: ipi 1 #

Operation:

Query box:

IPI00543858
IPI00517160

Search type: ipi

Taxon id: Any

Iterations: 1

Create new view: no

Use canonical expansion: no

Expected Observation:

Returns results identical to test case UniProt_Ac 1. Ok

Changing the query to "IPI00543858.1 IPI00517160.1" produces identical results. Ok.

Changing the query to "00543858 00517160" produces identical results. Ok.

Changing the query to "00543858 0051716" produces identical results for first query term and initiates query helper to resolve second term. Ok.

Changing the query to "abcd" produces no results. Ok.

Changing the query to "IPI" initiates query helper. Ok.

Searching for IPI00543858 as any other search type returns no results. Ok

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: PASS

Tester: Ian

Notes:

Test case name: mass search #

Operation:

Query box:

72854<-->72866

Search type: mass

Taxon id: Any

Iterations: 0

Create new view: yes

Use canonical expansion: no

Expected Observation:

The user is presented with the query helper to refine the query. A prompting message reads:

The following message included, the message is very long and there is no new line in message pop-up

"One or more of your mass query terms corresponds to a range. You may select one or more of the masses on the right (shift-click and cntrl-click are supported). Press return to add the selected terms to a new query. Clear the "Create new view" tick-box if you want to add the results to the current view."

Message too long : FAIL

NCBI links removed.

The query returns 4 nodes with mass in the expected range. Ok.

0 returns no results. Ok.

-1 returns no results. Ok.

MW returns no results. Ok.

72854 kda returns no results . OK

Last tested: June 15, 2010

Plugin Version: 0.85

Data Version: 7.0 public (iRefDATA_06152010.irfz)

Result: FAIL

Tester: Sabry (Message can not be displayed in full)

Notes:

Test case name: PMIDsearch 1

Operation:

Query box:

11401546

Search type: pmid

Taxon id: Any

Iterations: 0

Create new view: yes

Use canonical expansion: no

Expected Observation:

4 nodes and 7 edges are returned. Three edges have PMID 11401546 and these involve the 4 nodes shown. All other edges (from different PMIDs) involve these proteins. Ok.

11401546.1 returns 0 results. Ok.

1140154 returns 0 results Ok.

SPTAN1 returns 0 results. Ok.

11401546 SPTAN1 returns 0 results. Ok.

0 returns 0 results. Ok.

-1 returns 0 results. Ok.

10551855 [return character] 11401546 returns 6 nodes and 27 edges. Ok.

10551855|11401546 returns 6 nodes and 27 edges. Ok.

10551855| 11401546 returns 6 nodes and 27 edges. Ok.

10551855 | 11401546 returns 6 nodes and 27 edges. Ok.

10551855 [tab] 11401546 returns 6 nodes and 27 edges. Ok.

10551855, 11401546 returns 6 nodes and 27 edges. Ok.

10551855 11401546 returns 0 results. Ok. We dont say we support space delimited queries.

Last tested: June 16, 2010

Plugin Version: 0.85

Data Version: 7.0 public

Result: PASS

Tester: Sabry

Notes:

Test case name: digid search 1

Operation:

Query box: 4

Search type: digid

Taxon id: Any

Iterations: 0

Create new view: no

Use canonical expansion: no

Expected Observation:

This query returns no results. FAIL. Because queries for gene ids 56922 and 64087 return those nodes for those queries that have expected i.omim results (210210 and 210200) and both of these nodes have i.digid of 4.

A similar search for digid 449 returns 24 nodes and 252 edges that seem reasonable - each protein node has a list of digids where at least one is 449. - Ok

A similar search for digid 449 but with "use canonical expansion" returns 28 nodes. The four additional nodes seem reasonable - they are FANCL, FANCD2 FANCI and BRCA2. BRCA2 has a known role in FA. Ok.

Last tested: July 17th, 2010

Plugin Version: 0.85

Data Version: public 7.0

Result: FAIL

Tester: Ian

Notes:

Test case name: example search 1

Operation:

Test the example searches listed at http://irefindex.uio.no/wiki/README_Cytoscape_plugin_0.8x#Using_the_Search_Panel

Query box: see below

Search type: see below

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: yes

Expected Observation:

Search Type	Example	Results
UniProt_Ac	Q7KSF4	67 nodes, 146 edges. 1 blue node with i.order=0 directly from query. 3 with blue nodes i.order=10 by canonical expansion. All 4 blue nodes has the i.query attribute=Q7KSF4
RefSeq_Ac	NP_996224	NP_996224
UniProt_ID	Q7KSF4_DROME	NP_996224|Q7KSF4_DROME
geneID	42066	NP_996224|Q7KSF4_DROME|42066
geneSymbol	cher	NP_996224|Q7KSF4_DROME|42066|CHER
mass	72854<-->72866	NP_996224|Q7KSF4_DROME|42066|CHER and Q7KSF4|Q7KSF4_DROME|42066|CHER and they are blue. This is because the connectivity of properties between views of cytoscape (we have visted this problem before and agreed to live with the outcome).
rog	10121899	FAIL. This return interactions of Q7KSF4
PMID	14605208	929 nodes and 1605 edges returned all with PMID of 14605208. SAme results if iteration is set to 0. Ok. Same results if canonical expansion is de-selected. Ok.
src_intxn_id	47513	2 nodes and 1 edge returned.
src_intxn_id	EBI-212627	2 nodes and 4 edges returned (2 from intact, 1 from BIND and 1 from MINT). Ok
src_intxn_id	147805	Returns 4 nodes and three interactions because BIND and BioGRID interaction id space overlap.
omim	227650	74 nodes and 224 edges returned. Ok.
digid	449	498 nodes and 61033 edges returned.
dig_title	fanconi	No index available for dig_title

Last tested: June 16, 2010

Plugin Version: 0.85

Data Version: 7.0 public

Result: FAIL (Results are not 100% compatible with what is requested, dig_title can not be distributed due to license)

Tester: Sabry

Notes:

Preferences

Test case name: what is being tested #

Operation:

Expected Observation:

Last tested: July 8, 2010

Plugin Version: 0.83

Data Version: 7.0

Result: FAIL

Tester: Ian

Notes:

iRefScape menu cases

Show spoke-represented complexes

Test case name: ability to show complexes generated by R, using rogIDs

Operation:

Query box:

991650

Search type: rog

Taxon id: 9606

Iterations: 2

Create new view: no

Use canonical expansion: no

Search & load

Menu: iRefScape / View tools / Show spoke-represented complexes

Filter1:

Attribute: i.rog

Condition: EQUAL

Value: 991650

Selection: Show_as_selected

Set i.alive: Do_not_change

Press Set selected

Filter2:

Attribute: i.rog

Condition: EQUAL

Value: 991650

Selection: Append_neighbours

Set i.alive: Do_not_change

Press Set selected

Menu iRefScape / Hide/Un-hide / Hide nodes not selected

Menu Layout /

Expected Observation:

Last tested:

June 16, 2010

Plugin Version:

0.85

Data Version:

iRefIndex 5.1 in R, and iRefIndex 7.0 in the plugin

Result: F

Tester:

Antonio Mora

Notes:

Test in process...

Select between nodes

Test case name: Select between nodes 1

Operation:

Query box: 449

Search type: digid

Taxon id: Any

Iterations: 0

Create new view: no

Use canonical expansion: no

Expected Observation:

This query returns 24 nodes (10 are pseudonodes) and 252 edges - ok.

Select all protein nodes and then select iRefScape menu/View tools/Select between nodes.

All pseudonodes are now selected as expected. Ok. Sorted these selected nodes based on i.alive_degree. Selected first node in list (i.alive_degree of 7) and then select first neighbours of this node 7 nodes are selected as expected - Ok. i.alive_degree was zero for three of the protein nodes (initially selected). These had either no neighbours or pseudonode neighbours - so i.alive_degree was recalculated properly. Ok.

Selected just one protein node and then Select between nodes. Error message says "select at least two nodes first". Good.

Selected just two protein nodes (FANCI_HUMAN and BRCA2_HUMAN) then Select between nodes. Only one node was correctly returned (FACD2_HUMAN) and view recentres on this. Good. This node has i.alive_degree of 2 as expected. Ok. All other nodes had either a i.alive_degree of 1 (they were adjacent to only one of the two nodes selected as expected) or zero as expected - so i.alive_degree was correctly recalculated. Ok.

Last tested: June 17th, 2010

Plugin Version: 0.85

Data Version: public 7.0

Result: PASS

Tester: Ian

Notes:

Test case name: Select between nodes 2

Operation:

Query box: 449

Search type: digid

Taxon id: Any

Iterations: 1 (note difference to above test)

Create new view: yes

Use canonical expansion: no

Expected Observation:

This query returns 498 nodes and 1033 edges - ok.

Select all nodes with i.query of 449 and then select iRefScape menu/View tools/Select between nodes.

43 nodes are selected (11 are pseudonodes).

Made a new integer feature i.isBetween and marked all 43 nodes as 1. CAUTION. There is no other way to retrieve these nodes if the user deselects them (except by redoing the search); i.alive_degree => 2 cannot be used to retrieve them because some nodes from the original query list now have (correctly) a i.alive_degre of => 2. Consider adding a feature for the user called i.isBetween for the user.

Now I want to create a graph of 1) the original query nodes and 2) the between nodes. This is difficult because I cant select the original query nodes using Cytoscape filters - this seems to be a bug in Cytoscape filters . I can filter on i.query =449 or i.isBetween = 1 BUT NOT ON BOTH! Try doing this with iRefScape filters too - I cant do this either. CAUTION.

In the end, I sort all nodes on i.isBetween and then on i.query using the node attribute browser and then select those nodes I want from the table. Then I create a new subgraph from the selected nodes and edges. 59 nodes and 443 edges.

CAUTION. This functionality needs to be made easier for the user. Maybe keep original selection plus between nodes as selected. Also mark between nodes with new feature called i.isBetween. Could make the new network for the user.

Consider more messaging to user. 1) Between nodes now have feature i.isBetween = 1. Ok. 2) i.alive_degree has been recalculated for all nodes. Ok. 3) Create new subgraph with between nodes and original selection. Yes. No.

Last tested: June 17th, 2010

Plugin Version: 0.85

Data Version: public 7.0

Result: PASS

Tester: Ian

Notes:

Test case template

Test case name: what is being tested #

Operation:

Expected Observation:

Last tested:

Plugin Version:

Data Version:

Result: FAIL

Tester:

Notes: