Difference between revisions of "iRefScape Test Cases 1.0"

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Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}
 
Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}
  
 +
All tests have been performed against iRefIndex 8.1 data.
  
 
==Search cases==
 
==Search cases==
 
All tests have been performed against iRefIndex 8.1 data.
 
  
 
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
 
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
Line 13: Line 12:
 
! align="center" style="background:#f0f0f0;" | Pass/Fail
 
! align="center" style="background:#f0f0f0;" | Pass/Fail
 
|-
 
|-
| rowspan="9" valign="top" | <pre>Q39009
+
| rowspan="10" valign="top" | <pre>Q39009
 
Q9ZNV8</pre>
 
Q9ZNV8</pre>
| rowspan="11" valign="top" | <pre>UniProt_Ac</pre>
+
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre>
| rowspan="11" valign="top" | <pre>Taxon id: Any
+
| rowspan="9" valign="top" | <pre>Taxon id: Any
 
Iterations: 1
 
Iterations: 1
 
Create new view: no
 
Create new view: no
Line 46: Line 45:
 
|-
 
|-
 
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB
 
| Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB
 +
| Pass
 +
|-
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: no
 +
Use canonical expansion: no
 +
Add edges between neighbours: no</pre>
 +
| 2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges
 
| Pass
 
| Pass
 
|-
 
|-
 
| valign="top" | <pre>Q39009-1
 
| valign="top" | <pre>Q39009-1
 
Q9ZNV8-2</pre>
 
Q9ZNV8-2</pre>
 +
| rowspan="2" valign="top" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: no
 +
Use canonical expansion: no
 +
Add edges between neighbours: no</pre>
 
| Return the same results as for UniProtKB: the isoform information is ignored when searching
 
| Return the same results as for UniProtKB: the isoform information is ignored when searching
 
| Pass
 
| Pass
Line 64: Line 76:
 
Create new view: yes
 
Create new view: yes
 
Use canonical expansion: no</pre>
 
Use canonical expansion: no</pre>
| 11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned.  Edges returned include two edges described in test ''UniProt_Ac 1''.
+
| 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
 
|-
 
|-
 
| <pre>NP_188928</pre>
 
| <pre>NP_188928</pre>
 
| The same results are returned
 
| The same results are returned
|
+
| Pass
 
|-
 
|-
 
| <pre>NP_188928.567</pre>
 
| <pre>NP_188928.567</pre>
 
| The same results are returned
 
| The same results are returned
|
+
| Pass
 
|-
 
|-
 
| <pre>188928</pre>
 
| <pre>188928</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| <pre>NP 188928</pre>
 
| <pre>NP 188928</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>UniProt_Ac</pre>
 
| valign="top" | <pre>UniProt_Ac</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>geneID</pre>
 
| valign="top" | <pre>geneID</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>geneSymbol</pre>
 
| valign="top" | <pre>geneSymbol</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>ipi</pre>
 
| valign="top" | <pre>ipi</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>mass</pre>
 
| valign="top" | <pre>mass</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>NP_188928.2</pre>
 
| valign="top" | <pre>rog</pre>
 
| valign="top" | <pre>rog</pre>
 
| No results are returned
 
| No results are returned
|
+
| Pass (''Modified to give a warning'')
 
|-
 
|-
 
| valign="top" | <pre>AHP2_ARATH</pre>
 
| valign="top" | <pre>AHP2_ARATH</pre>
Line 205: Line 217:
 
| Pass
 
| Pass
 
|-
 
|-
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers)
+
| valign="top" | All geneIds from a search for <pre>1234</pre> (45 values producing 44 unique gene identifiers - highlight values in i.geneID and use control-C to copy)
 
| valign="top" | <pre>geneID</pre>
 
| valign="top" | <pre>geneID</pre>
 
| valign="top" | <pre>Taxon id: Any
 
| valign="top" | <pre>Taxon id: Any
Line 212: Line 224:
 
Use canonical expansion: no</pre>
 
Use canonical expansion: no</pre>
 
| 80 nodes and 733 edges (upon last attempt)
 
| 80 nodes and 733 edges (upon last attempt)
|
+
| Pass
 +
|-
 +
| colspan="5" | '''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).
 +
|-
 +
| valign="top" | <pre>CXCR4</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| 2 nodes
 +
| Pass
 +
|-
 +
| valign="top" | <pre>P61073-2</pre>
 +
| valign="top" | <pre>UniProt_Ac</pre>
 +
| valign="top" rowspan="2" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| 2 nodes (CXCR4 and CXCR4_HUMAN)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>P61073</pre>
 +
| valign="top" | <pre>UniProt_Ac</pre>
 +
| 1 node (CXCR4_HUMAN)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>P61073-2</pre>
 +
| valign="top" | <pre>UniProt_Ac</pre>
 +
| valign="top" rowspan="2" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: yes</pre>
 +
| 2 nodes (CXCR4 and CXCR4_HUMAN)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>P61073</pre>
 +
| valign="top" | <pre>UniProt_Ac</pre>
 +
| 2 nodes (CXCR4 and CXCR4_HUMAN)
 +
| Pass
 +
|-
 +
| colspan="5" | '''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.
 +
|-
 +
| valign="top" | <pre>CXCR</pre>
 +
| valign="top" rowspan="4" | <pre>geneSymbol</pre>
 +
| valign="top" rowspan="4" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| No results are returned
 +
| Pass
 
|-
 
|-
 
| valign="top" | <pre>CXCR4</pre>
 
| valign="top" | <pre>CXCR4</pre>
 +
| rowspan="3"| 2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2
 +
| Pass
 +
|-
 +
| valign="top" | <pre>cxcR4</pre>
 +
| Pass
 +
|-
 +
| valign="top" | <pre>CXC
 +
CXCR
 +
CXCR4</pre>
 +
| Pass
 +
|-
 +
| colspan="5" | '''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.
 +
|-
 +
| valign="top" | <pre>CXCR5</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 +
| valign="top" rowspan="3" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| 3 nodes
 +
| Pass
 +
|-
 +
| valign="top" | <pre>CXCR5</pre>
 +
| valign="top" | <pre>UniProt_ID</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>PTK2</pre>
 
| valign="top" | <pre>geneSymbol</pre>
 
| valign="top" | <pre>geneSymbol</pre>
 +
| 6 nodes (involving 5 taxons)
 +
| Pass
 +
|-
 +
| valign="top" rowspan="3" | <pre>RPB1</pre>
 +
| valign="top" rowspan="3" | <pre>geneSymbol</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| 1 node (RPB1_SCHPO)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>Taxon id: 4932
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| 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
 +
|-
 +
| valign="top" | <pre>Taxon id: 9606
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| No results returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>5366033</pre>
 +
| valign="top" | <pre>rog</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: no
 +
Use canonical expansion: no</pre>
 +
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>IPI00543858
 +
IPI00517160</pre>
 +
| valign="top" rowspan="4" | <pre>ipi</pre>
 +
| valign="top" rowspan="4" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: no
 +
Use canonical expansion: no</pre>
 +
| rowspan="3" | 33 nodes, 94 edges.  2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>IPI00543858.1
 +
IPI00517160.1</pre>
 +
| Pass
 +
|-
 +
| valign="top" | <pre>00543858
 +
00517160</pre>
 +
| Pass
 +
|-
 +
| valign="top" | <pre>00543858
 +
0051716</pre>
 +
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper
 +
| Pass
 +
|-
 +
| colspan="5" | '''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).
 +
|-
 +
| valign="top" | <pre>IPI</pre>
 +
| valign="top" rowspan="2" | <pre>ipi</pre>
 
| valign="top" rowspan="2" | <pre>Taxon id: Any
 
| valign="top" rowspan="2" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: no
 +
Use canonical expansion: no</pre>
 +
| Initiates query helper
 +
| Pass
 +
|-
 +
| valign="top" | <pre>IPI00543858</pre>
 +
| 26 nodes, 67 edges
 +
| Pass
 +
|-
 +
| valign="top" | <pre>72854<-->72866</pre>
 +
| valign="top" | <pre>mass</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved.
 +
| Pass
 +
|-
 +
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.
 +
|-
 +
| valign="top" | <pre>72854 kda</pre>
 +
| valign="top" | <pre>mass</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>72854<-->72856 kda</pre>
 +
| valign="top" | <pre>mass</pre>
 +
| valign="top" | <pre>Taxon id: Any
 
Iterations: 0
 
Iterations: 0
 
Create new view: yes
 
Create new view: yes
 
Use canonical expansion: no</pre>
 
Use canonical expansion: no</pre>
| 2 nodes
+
| Query helper with 3 possible results
 +
| Pass
 +
|-
 +
| valign="top" | <pre>11401546</pre>
 +
| valign="top" rowspan="12" | <pre>PMID</pre>
 +
| valign="top" rowspan="12" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| 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.
 +
|
 +
|-
 +
| valign="top" | <pre>11401546.1</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>1140154</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>SPTAN1</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>11401546
 +
SPTAN1</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>10551855
 +
11401546</pre>
 +
| 6 nodes and 27 edges
 +
| Pass
 +
|-
 +
| valign="top" | <pre>10551855|11401546</pre>
 +
| 6 nodes and 27 edges
 +
| Pass
 +
|-
 +
| valign="top" | <pre>10551855| 11401546</pre>
 +
| 6 nodes and 27 edges
 +
| Pass
 +
|-
 +
| valign="top" | <pre>10551855 | 11401546</pre>
 +
| 6 nodes and 27 edges
 +
| Pass
 +
|-
 +
| valign="top" | <pre>10551855 [tab] 11401546</pre>
 +
| 6 nodes and 27 edges
 +
| Pass
 +
|-
 +
| valign="top" | <pre>10551855, 11401546</pre>
 +
| 6 nodes and 27 edges
 +
| Pass
 +
|-
 +
| valign="top" | <pre>10551855 11401546</pre>
 +
| No results are returned (since space-delimited queries are not supported)
 +
| Pass
 +
|-
 +
| colspan="5" | The following example searches are listed in the [[README_Cytoscape_plugin_0.8x#Using_the_Search_Panel|Using the Search Panel]] documentation.
 +
|-
 +
| valign="top" | <pre>Q7KSF4</pre>
 +
| valign="top" | <pre>UniProt_Ac</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: yes
 +
Use canonical expansion: yes</pre>
 +
| 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
 +
|-
 +
| valign="top" | <pre>Q7KSF4</pre>
 +
| valign="top" | <pre>UniProt_Ac</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search
 +
| Pass
 +
|-
 +
| valign="top" | <pre>NP_996224</pre>
 +
| valign="top" | <pre>RefSeq_Ac</pre>
 +
| valign="top" rowspan="3" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: yes
 +
Use canonical expansion: yes</pre>
 +
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>Q7KSF4_DROME</pre>
 +
| valign="top" | <pre>UniProt_ID</pre>
 +
| Pass
 +
|-
 +
| valign="top" | <pre>42066</pre>
 +
| valign="top" | <pre>geneID</pre>
 +
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066
 +
| Pass
 +
|-
 +
| valign="top" | <pre>42066</pre>
 +
| valign="top" | <pre>geneID</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| Pass
 +
|-
 +
| valign="top" | <pre>cher</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 +
| valign="top" rowspan="4" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: yes
 +
Use canonical expansion: yes</pre>
 +
| Pass
 +
|-
 +
| valign="top" | <pre>72854<-->72866</pre>
 +
| valign="top" | <pre>mass</pre>
 +
| 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
 +
|-
 +
| valign="top" | <pre>10121899</pre>
 +
| valign="top" | <pre>rog</pre>
 +
| 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
 +
|-
 +
| valign="top" | <pre>14605208</pre>
 +
| valign="top" | <pre>PMID</pre>
 +
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208
 +
|
 +
|-
 +
| valign="top" | <pre>14605208</pre>
 +
| valign="top" | <pre>PMID</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: yes</pre>
 +
|
 +
|-
 +
| valign="top" | <pre>14605208</pre>
 +
| valign="top" | <pre>PMID</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
|
 +
|-
 +
| valign="top" | <pre>47513</pre>
 +
| valign="top" | <pre>src_intxn_id</pre>
 +
| valign="top" rowspan="6" | <pre>Taxon id: Any
 +
Iterations: 1
 +
Create new view: yes
 +
Use canonical expansion: yes</pre>
 +
| 2 nodes and 1 edge returned (one query node, Q7KSF4_DROME)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>EBI-212627</pre>
 +
| valign="top" | <pre>src_intxn_id</pre>
 +
| 2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME)
 +
| Pass
 +
|-
 +
| valign="top" | <pre>147805</pre>
 +
| valign="top" | <pre>src_intxn_id</pre>
 +
| 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
 +
|-
 +
| valign="top" | <pre>227650</pre>
 +
| valign="top" | <pre>omim</pre>
 +
| 96 nodes (including 18 complex nodes) and 498 edges returned, with 10 query nodes having i.digid = 460
 +
| Pass
 +
|-
 +
| valign="top" | <pre>449</pre>
 +
| valign="top" | <pre>digid</pre>
 +
| 321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219
 +
| Pass
 +
|-
 +
| valign="top" | <pre>460</pre>
 +
| valign="top" | <pre>digid</pre>
 +
| 668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460
 +
| Pass
 +
|-
 +
| valign="top" | <pre>fanconi</pre>
 +
| valign="top" | <pre>dig_title</pre>
 +
| valign="top" | <pre>Taxon id: Any
 +
Iterations: 0
 +
Create new view: yes
 +
Use canonical expansion: no</pre>
 +
| ''(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
 
| Pass
 
|}
 
|}
Line 237: Line 605:
 
|
 
|
 
| No results are returned
 
| No results are returned
|
+
|Pass
 
|-
 
|-
 
| valign="top" | <pre>0</pre>
 
| valign="top" | <pre>0</pre>
Line 243: Line 611:
 
|
 
|
 
| No results are returned
 
| No results are returned
|
+
|Pass
 
|-
 
|-
 
| valign="top" | <pre>0</pre>
 
| valign="top" | <pre>0</pre>
Line 249: Line 617:
 
|
 
|
 
| No results are returned
 
| No results are returned
 +
|Pass
 +
|-
 +
| valign="top" | <pre>0</pre>
 +
| valign="top" | <pre>geneID</pre>
 
|
 
|
 +
| No results are returned
 +
|Pass
 
|-
 
|-
 
| valign="top" | <pre>0</pre>
 
| valign="top" | <pre>0</pre>
| valign="top" | <pre>geneID</pre>
+
| valign="top" | <pre>mass</pre>
 
|
 
|
 
| No results are returned
 
| No results are returned
 +
|Pass
 +
|-
 +
| valign="top" | <pre>0</pre>
 +
| valign="top" | <pre>pmid</pre>
 
|
 
|
 +
| No results are returned
 +
|Pass
 
|-
 
|-
 
| valign="top" | <pre>23</pre>
 
| valign="top" | <pre>23</pre>
Line 263: Line 643:
 
| Pass
 
| Pass
 
|-
 
|-
| valign="top" | <pre>abcde</pre>
+
| valign="top" | <pre>-1</pre>
| valign="top" | <pre>RefSeq_Ac</pre>
+
| valign="top" | <pre>mass</pre>
 
|
 
|
 
| No results are returned
 
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>-1</pre>
 +
| valign="top" | <pre>pmid</pre>
 
|
 
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
| valign="top" | <pre>abcde</pre>
+
| valign="top" | <pre>0000</pre>
| valign="top" | <pre>UniProt_ID</pre>
+
| valign="top" | <pre>geneSymbol</pre>
 
|
 
|
 
| No results are returned
 
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>00001</pre>
 +
| valign="top" | <pre>geneID</pre>
 
|
 
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
| valign="top" | <pre>abcde</pre>
+
| valign="top" | <pre>12345</pre>
 
| valign="top" | <pre>geneSymbol</pre>
 
| valign="top" | <pre>geneSymbol</pre>
 
|
 
|
 
| No results are returned
 
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>abcd</pre>
 +
| valign="top" | <pre>ipi</pre>
 
|
 
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
 
| valign="top" | <pre>abcde</pre>
 
| valign="top" | <pre>abcde</pre>
| valign="top" | <pre>geneID</pre>
+
| valign="top" | <pre>RefSeq_Ac</pre>
 +
|
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>abcde</pre>
 +
| valign="top" | <pre>UniProt_ID</pre>
 
|
 
|
 
| No results are returned
 
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>abcde</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 
|
 
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
| valign="top" | <pre>00001</pre>
+
| valign="top" | <pre>abcde</pre>
 
| valign="top" | <pre>geneID</pre>
 
| valign="top" | <pre>geneID</pre>
 
|
 
|
 
| No results are returned
 
| No results are returned
|
+
| Pass
 
|-
 
|-
 
| valign="top" | <pre>abcdes</pre>
 
| valign="top" | <pre>abcdes</pre>
Line 297: Line 707:
 
|
 
|
 
| No results are returned
 
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>MW</pre>
 +
| valign="top" | <pre>mass</pre>
 
|
 
|
 +
| 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 ===
 
=== User interface notes ===
  
Line 306: Line 730:
 
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!
 
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!
  
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.
+
Where the taxonomy field is set to <tt>Any</tt>, 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.
  
=== Currently under review ===
+
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 gene in question is CXCR4 and has two isoforms  (P61073-2 and P61073).
+
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.
  
A UniProt_Ac search for P61073-2 returns CXCR4 and CXCR4_HUMAN, whereas P61073 returns only CXCR4_HUMAN when canonical expansion is turned off. Both searches return two nodes when canonical expansion is turned on. '''POSSIBLE FAIL''' <span style="color:red">'''Notes: ''' (Paul)</span> This is recognised (if somewhat counterintuitive) behaviour: the isoform-based search 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.
+
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.
  
This can be used as a test case for the Export function "on Target network Node ID type"= i.Canonical_ROGID_TOP
+
== Export cases ==
  
===Test case name: geneSymbol 1 ===
+
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
 
+
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options
'''Operation: '''
+
! align="center" style="background:#f0f0f0;" | Export Type
 
+
! align="center" style="background:#f0f0f0;" | Expected Result
Query box:
+
! align="center" style="background:#f0f0f0;" | Pass/Fail
 
+
|-
CXCR4
+
| valign="top" rowspan="2" | <pre>CXCR4
 
 
Search type: geneSymbol
 
 
 
Taxon id: Any
 
 
 
Iterations: 0
 
 
 
Create new view: yes
 
 
 
Use canonical expansion: no
 
 
 
'''Expected Observation: '''
 
 
 
Returns two nodes with i.UniProt_Ac_TOP of P61073 and P61073-2.
 
 
 
Change search to PTK2.  The user should be warned that they have not selected a taxon.  "You have not limited your search to a specific organism.  Proceed anyway? Yes No" This warning is given. With no taxon specifier present, the search (iteration=0) returns 6 nodes and 5 taxons. (This would have created havoc if the user had searched using a list of identifiers and no warning had been given.)
 
 
 
0 returns no results.  Ok.
 
 
 
0000 returns no results. Ok.
 
 
 
12345 returns no results. Ok.
 
 
 
abcde returns no results. Ok.
 
 
 
cxcR4 returns identical results to CXCR4.  Ok.
 
 
 
CXCR returns no results. Ok.
 
 
 
A search for "CXC CXCR CXCR4" (using newlines, not spaces, to separate the terms) returns results identical for CXCR4.  Ok.  However, no indication is given that CXC and CXCR failed to provide matches. <span style="color:red">'''Notes''' (PAUL):</span> maybe some feedback could be given about this.
 
 
 
Search CXCR5 as a UniProt_ID, returned no results.
 
 
 
Search CXCR5 against other query types returned no results.  Ok.
 
 
 
'''Last tested: May 9, 2011'''
 
 
 
'''Plugin Version:''' 1.0
 
 
 
'''Data Version:''' 8.1
 
  
<span style="color:green">'''Result:''' TESTED</span>
+
geneSymbol
 
 
'''Tester:''' Paul
 
 
 
<span style="color:red">'''Notes''' (SABRY):</span>
 
# hyperlink removed
 
# Do you want to check the taxonid only for geneSymbol ?
 
# The default batch file mode the user has to specify a taxonid, this was overridden as requested in an earlier release should this be reactivated?
 
 
 
===Test case name: geneSymbol 2 ===
 
 
 
'''Operation: '''
 
 
 
Query box:
 
 
 
RPB1
 
 
 
Search type: geneSymbol
 
  
 
Taxon id: Any
 
Taxon id: Any
 
 
Iterations: 0
 
Iterations: 0
 
Create new view: yes
 
 
Use canonical expansion: no
 
 
'''Expected Observation: '''
 
 
RPB1 for any taxon returns 1 node (RPB1_SCHPO).  Ok.
 
 
RPB1 for taxon 4932 returns 0 nodes.  Ok.  Even though an alias for yeast RPO21 (Gene Id 851415) is RPB1, this search only searches on official gene symbols from Entrez.
 
 
RPB1 for taxon 9606 returns 3 nodes one of which is SIRPB1.  FAIL.  This is an exact match search.
 
 
'''Last tested: June 7, 2010'''
 
 
'''Plugin Version: '''0.83
 
 
'''Data Version: '''7.0 public
 
 
<span style="color:red">'''Result: '''NOT TESTED</span>
 
 
'''Tester: '''Ian
 
<span style="color:red">'  ''Notes: ''':(SABRY)</span> :Changed to  exact search.
 
#There is a conflict between Test case name: geneID 1  and Test case name: geneID 2. When the search is now made a exact search, the query helper will never pop-up.
 
 
===Test case name: rog search 1===
 
 
'''Operation: '''
 
 
Query box:
 
 
5366033
 
 
Search type: rog
 
 
Taxon id: Any
 
 
Iterations: 1
 
 
 
Create new view: no
 
Create new view: no
 
+
Use canonical expansion: no</pre>
Use canonical expansion: no
+
| valign="top" | <pre>i.UniProt_Ac_TOP</pre>
 
+
| 1 node showing P61073
<span style="color:red">'  ''Notes: ''':(SABRY)</span> The bug coursing freeze when performing ROG searches is fixed in 0.85
+
| Pass
 
 
===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
 
 
 
<span style="color:red">'''Result: '''NOT TESTED</span>
 
 
 
'''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
 
 
 
<span style="color:red">'''Result: '''NOT TESTED</span>
 
 
 
'''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
 
 
 
<span style="color:red">'''Result: '''NOT TESTED</span>
 
 
 
'''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
 
 
 
<span style="color:red">'''Result: '''NOT TESTED</span>
 
 
 
'''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: '''
 
 
 
{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
 
!width="50" align="center" style="background:#f0f0f0;"|Search Type
 
!width="50" align="center" style="background:#f0f0f0;"|Example
 
!width="500" align="center" style="background:#f0f0f0;"|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. 
 
 
|-
 
|-
 +
| valign="top" | <pre>i.canonical_rog_TOP</pre>
 +
| 1 node showing 107322
 +
| Pass
 
|}
 
|}
  
 +
== Currently untested areas ==
  
 
+
* Preferences
'''Last tested: June 7, 2010'''
+
* iRefScape menu
 
+
* Right-click menu
'''Plugin Version: '''0.83
+
* Node attributes
 
+
* Edge attributes
'''Data Version: '''7.0 public
+
* Wizard
 
+
* Installation
<span style="color:red">'''Result: '''NOT TESTED</span>
+
* Help system
 
+
* Windows and sessions
'''Tester: '''Ian
+
* Loading from file
 
 
'''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'''
 
 
 
<span style="color:red">'''Result: '''NOT TESTED</span>
 
 
 
'''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: '''
 
 
 
<span style="color:red">'''Result: '''NOT TESTED</span>
 
 
 
'''Tester: '''
 
 
 
'''Notes: '''
 
  
 
==To be corrected==
 
==To be corrected==
Line 776: Line 782:
 
*Scaling GUI at low resolution, maximise button may get hidden
 
*Scaling GUI at low resolution, maximise button may get hidden
 
*Path finding cancelling time
 
*Path finding cancelling time
*focus progress when path finding
+
*Focus progress when path finding
 
*Ending with collapsed node error
 
*Ending with collapsed node error
*unselect all nodes before edge filtering
+
*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:
  
==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
 
*945577 http://www.ncbi.nlm.nih.gov/gene/?term=945577
 
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704
 
*947704 http://www.ncbi.nlm.nih.gov/gene/?term=947704

Latest revision as of 17:32, 24 November 2011

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:

All iRefIndex Pages