Plugin test cases 0.89

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

Load interaction between neighbours: 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.

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.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

Load interaction between neighbours: 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. No results. Ok.

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

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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. No result. Ok.

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

Last tested: June 25, 2010

Plugin Version: 0.83

Data Version: 7.0 public(iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry

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

Load interaction between neighbours: 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.

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: 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 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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

Load interaction between neighbours: no

Expected Observation: 5366033 returns 7 interactions (5 self interactions + 2 interactions with 5366026)

Last tested: June 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public(iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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

Load interaction between neighbours: 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 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public(iRefDATA_06222010.irfz)

Result: PASS

Tester: Sabry

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

Load interaction between neighbours: no

Expected Observation:

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

Please select query from list (double click from yellow area)

Result: PASS

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 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public (iRefDATA_06152010.irfz)

Result: PASS

Tester: Sabry

Notes: . The details in the sugested message ealier by Ian now included as a Tool-tip

Test case name: PMIDsearch 1

Operation:

Query box:

11401546

Search type: pmid

Taxon id: Any

Iterations: 1

Create new view: yes

Use canonical expansion: no

Load interaction between neighbours: 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.

i.query for all four node set to 11401546 : 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 25, 2010

Plugin Version: 0.89

Data Version: 7.0 public(iRefDATA_06222010.irfz)

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: 0.89

Data Version: public 7.0

Result: FAIL

Tester: Ian

Notes: :(SABRY) : Single digit matching was blocked in beta 0.89 and now I have enable it. Noe even if the user enters a 0 or a 1 as query the complete search operation will proceed.

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: 0.89

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: checking generated complexes belong to same pmid, db and method

Operation:

Query box:

17353931

Search type: PMID

Taxon id: 9606

Iterations: 1

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: QEwKzfSB6ZCaXBi6jSNiTCIeAtg

Selection: Show_as_selected

Set i.alive: Do_not_change

Press Set selected

Filter2:

Attribute: i.rog

Condition: EQUAL

Value: QEwKzfSB6ZCaXBi6jSNiTCIeAtg

Selection: Append_neighbours

Set i.alive: Do_not_change

Press Set selected

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

Menu Layout / Cytoscape Layouts / Degree Sorted Circle Layout

Expected Observation:

All interactions in the complex belong to same DB and same experimental method.

Last tested:

June 18, 2010

Plugin Version:

0.89

Data Version:

iRefIndex 7.0

Result: PASS

8 intact interactions and 1 grid interaction appeared, but grid's interaction is the same than one in intact.

Tester:

Antonio Mora

Test case name: comparing number of preys for a given bait, with the same method, pmid and sourcedb, between iRefScape and iRefIndex MITAB

Operation:

Query box:

17353931

Search type: PMID

Taxon id: 9606

Iterations: 1

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: 4761161

Selection: Show_as_selected

Set i.alive: Do_not_change

Press Set selected

Filter2:

Attribute: i.rog

Condition: EQUAL

Value: 4761161

Selection: Append_neighbours

Set i.alive: Do_not_change

Press Set selected

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

Menu Layout / Cytoscape Layouts / Degree Sorted Circle Layout

Expected Observation:

There are 97 preys in iRefIndex for bait=4761161, pmid=17353931, sourcedb=INTACT and method="MI:0006"

Last tested:

June 18, 2010

Plugin Version:

0.89

Data Version:

iRefIndex 7.0

Result: FAIL

Only 10 interactions reported in iRefScape. Besides that, iRefScape generates two complexes, one of which is a subset of the other. In R, we are removing the small one.

Tester:

Antonio Mora

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 / Cytoscape Layouts / Degree Sorted Circle Layout

Expected Observation:

7 complexes, all with a very high number of members (all >30, some >100).

Last tested:

June 18, 2010

Plugin Version:

0.89

Data Version:

iRefIndex 5.1 in R, and iRefIndex 7.0 in the plugin

Result: FAIL

7 complexes with small degree. 6 of them are heterodimers and not considered as complexes in R. The other one has only 3 components.

Tester:

Antonio Mora

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

Operation:

Query box:

17353931

Search type: PMID

Taxon id: 9606

Iterations: 1

Create new view: no

Use canonical expansion: no

Search & load

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

Filter1:

Attribute: i.order

Condition: EQUAL

Value: -4

Selection: Show_as_selected

Set i.alive: Do_not_change

Press Set selected

Filter2:

Attribute: i.order

Condition: EQUAL

Value: -4

Selection: Append_neighbours

Set i.alive: Do_not_change

Press Set selected

Expected Observation:

505 complexes expected.

Last tested:

June 18, 2010

Plugin Version:

0.89

Data Version:

iRefIndex 5.1 in R, and iRefIndex 7.0 in the plugin

Result: FAIL

95 complexes were generated.

Tester:

Antonio Mora

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: 0.89

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: 0.89

Data Version: public 7.0

Result: PASS

Tester: Ian

Notes: :(SABRY) : As we have removed the earlier feature calculate node degree related to selected nodes and replaced it between nodes the generalization is lost. I believe we could achieve what you wanted here very easily with iRefScape filters (may be I am wrong). discuss with Ian before making any changes. e.g use Cytoscape filter to select nodes interacting with at least two things in the query list for iteration =1 AND was not in the query list.

1. Filter-1 using following settings {i.order=0;condition=EQULA;Value=0; Selection=Show as selected; Set i.alive=True for this condition} *Use i.query instead of i.order if there were mutiple searches during same session.
2. Filter -2 using following settings {i.alive_degree=2;condition=GREATER_THAN_OR_EQULA;Value=2; Selection=Slect_not_in_current_selection; Set i.alive=do_not_change for this condition}

Test case template

Test case name: what is being tested #

Operation:

Expected Observation:

Last tested:

Plugin Version:

Data Version:

Result: FAIL

Tester:

Notes: