iRefScape Test Cases 1.0

From irefindex

Last edited: 2011-06-22

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 (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 (what Paul is talking about here is the Cytoscape export,not the iRefScape export). 
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 
11401546
SPTAN1
 No results are returned Pass 
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)
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 the query node having i.geneID = 2175 and 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
 Presumably similar results to the previous query Fail (iRefScape insists on an exact match and doesn't find anything)

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

Not currently tested

  • src_intxn_id search 1
  • omim search 1
  • digid search 1
  • audit against external database - Intact
  • audit against external database - MINT
  • audit against external database - BioGRID
  • iterations 1
  • use canonical expansion 1

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

List of GeneIDs to test the new canonical expansion

Available in data version 8.4:

All iRefIndex Pages

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