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iRefScape Test Cases 1.0

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Last edited: 2011-11-24

All tests have been performed against iRefIndex 8.1 data.

Contents

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:

All iRefIndex Pages