iRefScape Test Cases 1.0

Last edited: 2011-05-16

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
IPI00543858 IPI00517160	ipi	Taxon id: Any Iterations: 1 Create new view: no Use canonical expansion: no	33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)	Pass
IPI00543858.1 IPI00517160.1				Pass
00543858 00517160				Pass
00543858 0051716			33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper	Pass
Note: the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up).
IPI	ipi	Taxon id: Any Iterations: 1 Create new view: no Use canonical expansion: no	Initiates query helper	Pass
IPI00543858			26 nodes, 67 edges	Pass
72854<-->72866	mass	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no	The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.	Pass
Note: the nodes are not laid out in a nice way, probably because no edges connect them.
72854 kda	mass	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no	No results are returned	Pass
11401546	PMID	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no	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.
11401546.1			No results are returned
1140154			No results are returned
SPTAN1			No results are returned
11401546 SPTAN1			No results are returned
10551855 11401546			6 nodes and 27 edges
10551855|11401546			6 nodes and 27 edges
10551855| 11401546			6 nodes and 27 edges
10551855 | 11401546			6 nodes and 27 edges
10551855 [tab] 11401546			6 nodes and 27 edges
10551855, 11401546			6 nodes and 27 edges
10551855 11401546			No results are returned (since space-delimited queries are not supported)

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
0	mass		No results are returned
0	pmid		No results are returned
23	UniProt_ID		No results are returned	Pass
-1	mass		No results are returned
-1	pmid		No results are returned
0000	geneSymbol		No results are returned
00001	geneID		No results are returned
12345	geneSymbol		No results are returned
abcd	ipi		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
MW	mass		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.

The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.

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: 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:

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:

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

• Available in data version 8.4
• 945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577
• 947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704
• 2765365 http://www.ncbi.nlm.nih.gov/gene/?term=2765365
• 944797 http://www.ncbi.nlm.nih.gov/gene/?term=944797
• 29924 http://www.ncbi.nlm.nih.gov/gene/?term=29924
• 948517 http://www.ncbi.nlm.nih.gov/gene/?term=948517
• 3673 http://www.ncbi.nlm.nih.gov/gene/?term=3673
• 946848 http://www.ncbi.nlm.nih.gov/gene/?term=946848
• 653361 http://www.ncbi.nlm.nih.gov/gene/?term=653361
• 5657 http://www.ncbi.nlm.nih.gov/gene/?term=5657