iRefScape Test Cases 1.0

Last edited: 2011-11-24

All tests have been performed against iRefIndex 8.1 data.

Search cases

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 (Modified to give a warning)
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 - highlight values in i.geneID and use control-C to copy)	geneID	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no	80 nodes and 733 edges (upon last attempt)	Pass
Note: This test is made incredibly difficult current bug in 2.8.1 attribute browser- right-click and copy of multiple values does not work).
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
72854<-->72856 kda	mass	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no	Query helper with 3 possible results	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	Pass
1140154			No results are returned	Pass
SPTAN1			No results are returned	Pass
11401546 SPTAN1			No results are returned	Pass
10551855 11401546			6 nodes and 27 edges	Pass
10551855|11401546			6 nodes and 27 edges	Pass
10551855| 11401546			6 nodes and 27 edges	Pass
10551855 | 11401546			6 nodes and 27 edges	Pass
10551855 [tab] 11401546			6 nodes and 27 edges	Pass
10551855, 11401546			6 nodes and 27 edges	Pass
10551855 11401546			No results are returned (since space-delimited queries are not supported)	Pass
The following example searches are listed in the Using the Search Panel documentation.
Q7KSF4	UniProt_Ac	Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes	69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members)	Pass
Q7KSF4	UniProt_Ac	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no	1 node (Q7KSF4_DROME) verifying the attributes in the previous search	Pass
NP_996224	RefSeq_Ac	Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes	69 nodes, 213 edges (same as the above query for Q7KSF4)	Pass
Q7KSF4_DROME	UniProt_ID			Pass
42066	geneID		69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066	Pass
42066	geneID	Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no		Pass
cher	geneSymbol	Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes		Pass
72854<-->72866	mass		44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10	Pass
10121899	rog		69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10	Pass
14605208	PMID		929 nodes and 1605 edges returned all with PMID of 14605208
14605208	PMID	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: yes
14605208	PMID	Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no
47513	src_intxn_id	Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes	2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)	Pass
EBI-212627	src_intxn_id		2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)	Pass
147805	src_intxn_id		Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases)	Pass
227650	omim		96 nodes (including 18 complex nodes) and 498 edges returned, with 10 query nodes having i.digid = 460	Pass
449	digid		321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219	Pass
460	digid		668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460	Pass
fanconi	dig_title	Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no	(Query helper invoked as the dig_title is a non-exact match, all choices selected) 44 nodes and 473 edges returned, 14 nodes have a digid of 460	Pass

Invalid input tests

Query	Search Type	Options	Expected Result	Pass/Fail
0	RefSeq_Ac		No results are returned	Pass
0	UniProt_ID		No results are returned	Pass
0	geneSymbol		No results are returned	Pass
0	geneID		No results are returned	Pass
0	mass		No results are returned	Pass
0	pmid		No results are returned	Pass
23	UniProt_ID		No results are returned	Pass
-1	mass		No results are returned	Pass
-1	pmid		No results are returned	Pass
0000	geneSymbol		No results are returned	Pass
00001	geneID		No results are returned	Pass
12345	geneSymbol		No results are returned	Pass
abcd	ipi		No results are returned	Pass
abcde	RefSeq_Ac		No results are returned	Pass
abcde	UniProt_ID		No results are returned	Pass
abcde	geneSymbol		No results are returned	Pass
abcde	geneID		No results are returned	Pass
abcdes	geneID		No results are returned	Pass
MW	mass		No results are returned	Pass

Not currently tested

• src_intxn_id search 1
• audit against external database - Intact
• audit against external database - MINT
• audit against external database - BioGRID

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.

The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.

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.

Export cases

Query/Search Type/Options	Export Type	Expected Result	Pass/Fail
CXCR4 geneSymbol Taxon id: Any Iterations: 0 Create new view: no Use canonical expansion: no	i.UniProt_Ac_TOP	1 node showing P61073	Pass
	i.canonical_rog_TOP	1 node showing 107322	Pass

Currently untested areas

• Preferences
• iRefScape menu
• Right-click menu
• Node attributes
• Edge attributes
• Wizard
• Installation
• Help system
• Windows and sessions
• Loading from file

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
• Repeated errors when importing networks not providing the chosen attribute for import

List of GeneIDs to test the new canonical 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