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iRefScape Test Cases 1.0

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Last edited: 2011-05-13


Contents

Search cases

All tests have been performed against iRefIndex 8.1 data.

Query Search Type Options Expected Result Pass/Fail
Q39009
Q9ZNV8
UniProt_Ac
Taxon id: Any
Iterations: 1
Create new view: no
Use canonical expansion: no
Add edges between neighbours: no
33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) Pass
Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept Pass
i.taxid is 3702 and i.geneID is 822593 Pass
Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8 Pass
UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases") Pass
Two edges between query nodes are EBI-1555390, EBI-1555417 Pass
Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name Pass
The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute Pass
Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB Pass
Taxon id: Any
Iterations: 0
Create new view: no
Use canonical expansion: no
Add edges between neighbours: no
2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges Pass
Q39009-1
Q9ZNV8-2
Taxon id: Any
Iterations: 1
Create new view: no
Use canonical expansion: no
Add edges between neighbours: no
Return the same results as for UniProtKB: the isoform information is ignored when searching Pass
Q39009.1
Q9ZNV8.2
Returns no results. Version information is not a valid annotation for UniProtKB. Pass
NP_188928.2
RefSeq_Ac
Taxon id: Any
Iterations: 1
Create new view: yes
Use canonical expansion: no
11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH Pass
NP_188928
The same results are returned Pass
NP_188928.567
The same results are returned Pass
188928
No results are returned Pass
NP 188928
No results are returned Pass
NP_188928.2
UniProt_Ac
No results are returned Pass
NP_188928.2
geneID
No results are returned Pass
NP_188928.2
geneSymbol
No results are returned Pass
NP_188928.2
ipi
No results are returned Pass
NP_188928.2
mass
No results are returned Pass
NP_188928.2
rog
No results are returned Pass (no error given, though)
AHP2_ARATH
UniProt_ID
Taxon id: Any
Iterations: 1
Create new view: yes
Use canonical expansion: no
26 nodes, 67 edges Pass
AHP2
No results are returned Pass
AHP2 ARATH
No results are returned Pass
ARATH
No results are returned Pass
AH2_ARATH
No results are returned Pass
AHP2_ARATH.2
No results are returned Pass
AHP2_ARATH
UniProt_Ac
No results are returned Pass
AHP2_ARATH
geneID
No results are returned Pass
AHP2_ARATH
geneSymbol
No results are returned Pass
AHP2_ARATH
ipi
No results are returned Pass
821860
822593
geneID
Taxon id: Any
Iterations: 1
Create new view: yes
Use canonical expansion: no
33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.) Pass
821860
geneID
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: no
1 node Pass
821860
geneSymbol
No results are returned Pass
821860
UniProt_Ac
No results are returned Pass
821860
UniProt_ID
No results are returned Pass
1234
geneID
Taxon id: Any
Iterations: 1
Create new view: yes
Use canonical expansion: no
47 nodes and 158 edges Pass
All geneIds from a search for
1234
(45 values producing 44 unique gene identifiers)
geneID
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: no
80 nodes and 733 edges (upon last attempt)
Note: This test is made incredibly difficult by the apparently unreliability of the export function.
CXCR4
geneSymbol
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: no
2 nodes Pass
P61073-2
UniProt_Ac
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: no
2 nodes (CXCR4 and CXCR4_HUMAN) Pass
P61073
UniProt_Ac
1 node (CXCR4_HUMAN) Pass
P61073-2
UniProt_Ac
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: yes
2 nodes (CXCR4 and CXCR4_HUMAN) Pass
P61073
UniProt_Ac
2 nodes (CXCR4 and CXCR4_HUMAN) Pass
Note: P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned.
CXCR
geneSymbol
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: no
No results are returned Pass
CXCR4
2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2 Pass
cxcR4
Pass
CXC
CXCR
CXCR4
Pass
Note: no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this.
CXCR5
geneSymbol
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: no
3 nodes Pass
CXCR5
UniProt_ID
No results are returned Pass
PTK2
geneSymbol
6 nodes (involving 5 taxons) Pass
RPB1
geneSymbol
Taxon id: Any
Iterations: 0
Create new view: yes
Use canonical expansion: no
1 node (RPB1_SCHPO) Pass
Taxon id: 4932
Iterations: 0
Create new view: yes
Use canonical expansion: no
No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez Pass
Taxon id: 9606
Iterations: 0
Create new view: yes
Use canonical expansion: no
No results returned Pass
5366033
rog
Taxon id: Any
Iterations: 1
Create new view: no
Use canonical expansion: no
2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it) Pass

Invalid input tests

Query Search Type Options Expected Result Pass/Fail
0
RefSeq_Ac
No results are returned
0
UniProt_ID
No results are returned
0
geneSymbol
No results are returned
0
geneID
No results are returned
23
UniProt_ID
No results are returned Pass
0000
geneSymbol
No results are returned
00001
geneID
No results are returned
12345
geneSymbol
No results are returned
abcde
RefSeq_Ac
No results are returned
abcde
UniProt_ID
No results are returned
abcde
geneSymbol
No results are returned
abcde
geneID
No results are returned
abcdes
geneID
No results are returned

User interface notes

Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.

Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!

Where the taxonomy field is set to Any, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.

Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.

Currently under review

The CXCR4 isoforms test can be used as a test case for the Export function "on Target network Node ID type"= i.Canonical_ROGID_TOP

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: NOT TESTED

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: NOT TESTED

Tester: Ian

Notes:


Test case name: mass search #

Operation:

Query box:

72854<-->72866

Search type: ipi

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:

"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."

FAIL. The message given should be replaced with the above text. Also, there are inappropriate and unusable links to NCBI given in the query helper. Also, interface changes my selected iterations from 0 to 1 without asking. Annoying.

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 but hangs the interface. FAIL.

Last tested: June 1, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: NOT TESTED

Tester: Ian

Notes:


Test case name: rog search 1

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 and starts query helper. FAIL. This should be an exact match search.

SPTAN1 returns 0 results. Ok.

11401546 SPTAN1 returns 0 results. Ok.

0 finds 21493 matches and then says there are no results and open the query helper. FAIL. This is an exact match search.

-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 day we support space delimited queries.

Last tested: June 7, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: NOT TESTED

Tester: Ian

Notes:

Test case name: src_intxn_id search 1

Test case name: omim search 1

Test case name: digid search 1

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. 4 nodes are returned directly by the query, but only one is marked with i.query = Q7KSF4. FAIL nodes returned by a query (even with canonical expansion) should have an i.query value. i.order is 0 for Q7KSF4 but 10 for the other three nodes from the same canonical group. CAUTION. This is not what the documentation says for these attributes. With canonical expansion off, this search returns 43 nodes, 43 edges all from BioGRID.
RefSeq_Ac NP_996224 67 nodes, 146 edges. See above. i.query feature fails to update to reflect the most recent search. FAIL.
UniProt_ID Q7KSF4_DROME 67 nodes, 146 edges.
geneID 42066 67 nodes, 146 edges. See above. Now two nodes are marked as Q7KSF4 under i.query. FAIL. 42066 should be listed for the recently returned node.
geneSymbol cher 67 nodes, 146 edges. Now i.query says Q7KS4 for all four nodes returned by the search. FAIL.
mass 72854<-->72866 40 nodes, 94 edges. Four molecular mass values are returned by the query helper. Selecting all of these and doing the search returns 8 hi-lited nodes and their interactors. The 72855 mass node returns 1 node with that mass and two other members of the same canonical group. Two of the nodes are returned with i.query of Q7KSF4. FAIL.
rog 10121899 FAIL. This should return the Q7KSF4 node. Instead got "Sorry, please wait until current operations finish or stop the proces and restart Cytoscape." Subsequent searches do not work. Have to restart Cytoscape
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 58 nodes and 60 edges returned. FAIL. This should return the same results as omim 227650 plus more nodes that have the same digid. digid search is like searching for multiple omims. Problem with file name _EXT__ROG_digid.irft
dig_title fanconi FAIL - do not fix until next release.


Last tested: June 7, 2010

Plugin Version: 0.83

Data Version: 7.0 public

Result: NOT TESTED

Tester: Ian

Notes:

Test case name: audit against external database - Intact

Test case name: audit against external database - MINT

Test case name: audit against external database - BioGRID

Test case name: iterations 1

Test case name: use canonical expansion 1

Advanced options cases

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: NOT TESTED

Tester: Ian

Notes:

iRefScape menu cases

Right-click menu cases

Node attribute cases

Edge attribute cases

Wizard cases

Installations cases

Help cases

Windows and sessions cases

Test case name: Load from file search 1 #

Test case template

Test case name: what is being tested #

Operation:

Expected Observation:

Last tested:

Plugin Version:

Data Version:

Result: NOT TESTED

Tester:

Notes:

To be corrected

  • Remove the non-proprietary flag/check for current data
  • Handle the neighbourhood completion when expanding network (do not use all the nodes)
  • show_inxc dynamic index behaviour change not working
  • Scaling GUI at low resolution, maximise button may get hidden
  • Path finding cancelling time
  • focus progress when path finding
  • Ending with collapsed node error
  • unselect all nodes before edge filtering


List of GeneIDs to test the new caonical expansion

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