Difference between revisions of "iRefScape Test Cases 1.0"

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Last edited: {{REVISIONYEAR}}-{{padleft:{{REVISIONMONTH}}|2}}-{{REVISIONDAY2}}
  
 +
All tests have been performed against iRefIndex 8.1 data.
  
 
==Search cases==
 
==Search cases==
  
−
===Test case name: UniProt_Ac 1 ===
+
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
−
 
+
! align="center" style="background:#f0f0f0;" | Query
−
'''Operation: '''
+
! align="center" style="background:#f0f0f0;" | Search Type
−
 
+
! align="center" style="background:#f0f0f0;" | Options
−
Query box:
+
! align="center" style="background:#f0f0f0;" | Expected Result
−
 
+
! align="center" style="background:#f0f0f0;" | Pass/Fail
−
  Q39009
+
|-
−
Q9ZNV8
+
| rowspan="10" valign="top" | <pre>Q39009
−
 
+
Q9ZNV8</pre>
−
Search type: UniProt_Ac
+
| rowspan="12" valign="top" | <pre>UniProt_Ac</pre>
−
 
+
| rowspan="9" valign="top" | <pre>Taxon id: Any
−
Taxon id: Any
+
Iterations: 1
−
 
+
Create new view: no
 +
Use canonical expansion: no
 +
Add edges between neighbours: no</pre>
 +
| 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
 +
|-
 +
| 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
 +
|-
 +
| valign="top" | <pre>Q39009-1
 +
Q9ZNV8-2</pre>
 +
| rowspan="2" valign="top" | <pre>Taxon id: Any
 
Iterations: 1
 
Iterations: 1
−
 
 
Create new view: no
 
Create new view: no
−
 
 
Use canonical expansion: no
 
Use canonical expansion: no
−
 
+
Add edges between neighbours: no</pre>
−
Add edges between neighbours: no
+
| Return the same results as for UniProtKB: the isoform information is ignored when searching
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>Q39009.1
−
33 nodes, 94 edges.  2 queried nodes are blue (DMC_ARATH and AHP2_ARATH).
+
Q9ZNV8.2</pre>
−
Checked node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute to Entrez/protein was correct. IRefIndex has correct i.taxid and i.geneID.  
+
| Returns no results. Version information is not a valid annotation for UniProtKB.
−
 
+
| Pass
−
Checked node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute to UniProt/KB beta was correct.  IRefIndex has correct i.taxid and i.geneID. UniProt record agreed with iRefIndex on iRefSeq_Ac_TOP, i.taxid, i.geneID.
+
|-
−
 
+
| valign="top" | <pre>NP_188928.2</pre>
−
Selected two edges between query nodes : EBI-1555390, EBI-1555417. Checked linkouts for both edges (i.src_intxn_id) to Interaction databases/Intact.  Confirmed that i.PMID and i.method_name were correct. The molecule names were DMC1 and ATHP1 in IntAct and these names were available under interactor_alias attribute
+
| rowspan="5" valign="top" | <pre>RefSeq_Ac</pre>
−
Checked linkout to http://wodaklab.org/iRefWeb/interaction/show/102203 from both interactions above.
+
| rowspan="11" valign="top" | <pre>Taxon id: Any
−
 
+
Iterations: 1
−
The query:
+
Create new view: yes
−
Q39009-1
+
Use canonical expansion: no</pre>
−
Q9ZNV8-2
+
| 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
−
Returns the same results as for UniProtKB the isoform information is ignored when searching.
+
|-
−
 
+
| <pre>NP_188928</pre>
−
The query:
+
| The same results are returned
−
Q39009.1
+
| Pass
−
Q9ZNV8.2
+
|-
−
 
+
| <pre>NP_188928.567</pre>
−
Do not return any results. Version information is not a valid annotation for UniProtKB.
+
| The same results are returned
−
 
+
| Pass
−
'''Last tested: April 18, 2011'''
+
|-
−
 
+
| <pre>188928</pre>
−
'''Plugin Version: '''1.00
+
| No results are returned
−
 
+
| Pass
−
'''Data Version: '''8.0
+
|-
−
 
+
| <pre>NP 188928</pre>
−
<span style="color:green">'''Result: '''PASS</span>
+
| No results are returned
−
 
+
| Pass
−
'''Tester: '''Sabry
+
|-
−
 
+
| valign="top" | <pre>NP_188928.2</pre>
−
'''Confirmed by: '''NA
+
| valign="top" | <pre>UniProt_Ac</pre>
−
 
+
| No results are returned
−
===Test case name: RefSeq_Ac 1 ===
+
| Pass
−
 
+
|-
−
'''Operation: '''
+
| valign="top" | <pre>NP_188928.2</pre>
−
 
+
| valign="top" | <pre>geneID</pre>
−
Query box:
+
| No results are returned
−
 
+
| Pass
−
NP_188928.2
+
|-
−
 
+
| valign="top" | <pre>NP_188928.2</pre>
−
Search type: RefSeq_Ac
+
| valign="top" | <pre>geneSymbol</pre>
−
 
+
| No results are returned
−
Taxon id: Any
+
| Pass
−
 
+
|-
 +
| valign="top" | <pre>NP_188928.2</pre>
 +
| valign="top" | <pre>ipi</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>NP_188928.2</pre>
 +
| valign="top" | <pre>mass</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| valign="top" | <pre>NP_188928.2</pre>
 +
| valign="top" | <pre>rog</pre>
 +
| No results are returned
 +
| Pass (''Modified to give a warning'')
 +
|-
 +
| valign="top" | <pre>AHP2_ARATH</pre>
 +
| valign="top" rowspan="6" | <pre>UniProt_ID</pre>
 +
| valign="top" rowspan="10" | <pre>Taxon id: Any
 
Iterations: 1
 
Iterations: 1
−
 
 
Create new view: yes
 
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
Use canonical expansion: no
+
| 26 nodes, 67 edges
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>AHP2</pre>
−
11 nodes, 29 edges.  i.RefSeq_Ac = NP_188928 was returned.  Edges returned include two edges described in test ''UniProt_Ac 1''.
+
| No results are returned
−
 
+
| Pass
−
The same results are returned if the query box is changed to '''NP_188928'''.
+
|-
−
 
+
| valign="top" | <pre>AHP2 ARATH</pre>
−
The same results are returned if the query box is changed to '''NP_188928.567'''.
+
| No results are returned
−
 
+
| Pass
−
No results if the query box is changed to '''188928'''.  (Expected behaviour-OK)
+
|-
−
 
+
| valign="top" | <pre>ARATH</pre>
−
No results are returned if the query box is changed to '''NP 188928'''.  (Expected behaviour-OK)
+
| No results are returned
−
 
+
| Pass
−
Change the search type to UniProt_Ac.  The interface says no results and when user presses ok.(Expected behaviour-OK)
+
|-
−
 
+
| valign="top" | <pre>AH2_ARATH</pre>
−
The search type can also be changed to UniProt_ID, geneID, geneSymbol, ipi,, mass or rog with no results returned.
+
| No results are returned
−
 
+
| Pass
−
No results are returned if the query box is changed to '''0'''.  
+
|-
−
No results are returned if the query box is changed to '''abcde'''.
+
| valign="top" | <pre>AHP2_ARATH.2</pre>
−
 
+
| No results are returned
−
 
+
| Pass
−
'''Last tested: April 20, 2011'''
+
|-
−
 
+
| valign="top" | <pre>AHP2_ARATH</pre>
−
'''Plugin Version: '''1.00
+
| valign="top" | <pre>UniProt_Ac</pre>
−
 
+
| No results are returned
−
'''Data Version: '''8.0
+
| Pass
−
 
+
|-
−
<span style="color:green">'''Result: '''PASS</span>
+
| valign="top" | <pre>AHP2_ARATH</pre>
−
 
+
| valign="top" | <pre>geneID</pre>
−
'''Tester: '''Sabry
+
| No results are returned
−
 
+
| Pass
−
'''Confirmed by: '''NA
+
|-
−
 
+
| valign="top" | <pre>AHP2_ARATH</pre>
−
===Test case name: UniProt_ID 1 ===
+
| valign="top" | <pre>geneSymbol</pre>
−
 
+
| No results are returned
−
'''Operation: '''
+
| Pass
−
 
+
|-
−
Query box:
+
| valign="top" | <pre>AHP2_ARATH</pre>
−
 
+
| valign="top" | <pre>ipi</pre>
−
AHP2_ARATH
+
| No results are returned
−
 
+
| Pass
−
Search type: UniProt_ID
+
|-
−
 
+
| valign="top" | <pre>821860
−
Taxon id: Any
+
822593</pre>
−
 
+
| valign="top" | <pre>geneID</pre>
 +
| valign="top" | <pre>Taxon id: Any
 
Iterations: 1
 
Iterations: 1
−
 
 
Create new view: yes
 
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
Use canonical expansion: no
+
| 33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.)
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>821860</pre>
−
26 nodes, 67 edges.
+
| valign="top" | <pre>geneID</pre>
−
 
+
| valign="top" rowspan="4"| <pre>Taxon id: Any
−
The same results are returned if the query box is changed to '''AHP2'''.  '''FAIL'''.  This should not be allowed.  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.
+
Iterations: 0
−
Also, first few characters of UniProt_ID's may be shared by multiple proteins from different organisms.  If you want to allow for inexact matches, use the query helper.
+
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
AHP2 ARATH returns no results.  Ok.
+
| 1 node
−
 
+
| Pass
−
ARATH returns "1001 matches and only first 1000 are shown".  Ok.  Inexact matches trigger the query helper.
+
|-
−
 
+
| valign="top" | <pre>821860</pre>
−
AH2_ARATH returns CAH2_ARATH. It should return 0 results.  '''FAIL'''.  Imagine if the user accidently had such a query term imbedded in a long list.  They would never detect this search error!  This should be is an exact match search by default (or use the query helper to allow the user to decide.
+
| valign="top" | <pre>geneSymbol</pre>
−
 
+
| No results are returned
−
AHP2_ARATH.2 returns results. It should return 0 results.  '''FAIL'''.
+
| Pass
−
 
+
|-
−
23 returns query helper dialog for disambiguation.  Ok.  But not very useful in this artificial test case.
+
| valign="top" | <pre>821860</pre>
−
 
+
| valign="top" | <pre>UniProt_Ac</pre>
−
Searching for AHP2_ARATH but with search type UniProt_Ac, geneID, geneSymbol, ipi or mass all return 0 results.  The interface says no results and when user presses ok, shows a blank panel. Ok.
+
| No results are returned
−
 
+
| Pass
−
No results are returned if the query box is changed to '''0'''.  Error message says : Error resolving query. Ok.
+
|-
−
 
+
| valign="top" | <pre>821860</pre>
−
No results are returned if the query box is changed to '''abcde'''.
+
| valign="top" | <pre>UniProt_ID</pre>
−
 
+
| No results are returned
−
 
+
| Pass
−
'''Last tested: June 1, 2010'''
+
|-
−
 
+
| valign="top" | <pre>1234</pre>
−
'''Plugin Version: '''0.83
+
| valign="top" | <pre>geneID</pre>
−
 
+
| valign="top" | <pre>Taxon id: Any
−
'''Data Version: '''7.0 public
 
−
 
 
−
<span style="color:red">'''Result: '''NOT TESTED</span>
 
−
 
 
−
'''Tester: '''Ian
 
−
 
 
−
<span style="color:red">'''Notes: ''':(SABRY)</span> : UniProt_ID is now EXACT match only. If the user failed to enter exactly matching query no results will be returned. Query helper will never be invoked.
 
−
 
 
−
===Test case name: geneID 1 ===
 
−
 
 
−
'''Operation: '''
 
−
 
 
−
Query box:
 
−
 
 
−
821860
 
−
822593
 
−
 
 
−
Search type: geneID
 
−
 
 
−
Taxon id: Any
 
−
 
 
 
Iterations: 1
 
Iterations: 1
−
 
 
Create new view: yes
 
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
Use canonical expansion: no
+
| 47 nodes and 158 edges
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| 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)
−
Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8 (33 nodes and 94 edges).  Ok.
+
| valign="top" | <pre>geneID</pre>
−
 
+
| valign="top" | <pre>Taxon id: Any
−
0 returned "error resolving query.  Ok.
+
Iterations: 0
−
 
+
Create new view: yes
−
00001 returned 0 results. Ok.
+
Use canonical expansion: no</pre>
−
 
+
| 80 nodes and 733 edges (upon last attempt)
−
abcdes returned 0 results. Ok.
+
| Pass
−
 
+
|-
−
1234 returned 34 nodes and 70 edges.  Ok.  1234 is CCR5.
+
| 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).
−
 
+
|-
−
Retrieved all geneIds from above query and queried (iterations = 0).  Should return same number of nodes as above (33 protein nodes).  But 30 protein nodes are returned and there are differences.  NOTE.  Keep this example for further reference.
+
| valign="top" | <pre>CXCR4</pre>
−
Explanation.  Two of the nodes from the first graph did not have a gene id.  Two nodes had the same gene id 7852.
+
| valign="top" | <pre>geneSymbol</pre>
−
If you search for 7852, a graph of 12 nodes, 21 edges is returned.  But only one of the nodes has a gene id of 7852.  This seems like the search does not continue past the first match found?!  '''FAIL''' until this is resolved. Also check that all other searches that are exact match searches are "continue after first match found" and write in test cases to ensure that this happens.
+
| valign="top" | <pre>Taxon id: Any
−
 
+
Iterations: 0
−
The gene in question is CXCR4 and has two isoforms  (P61073-2 and P61073).
+
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
A geneSymbol search for CXCR4 (iteration=0) returns two nodes as expected. 
+
| 2 nodes
−
 
+
| Pass
−
A UniProt_Ac search for P61073-2 or P61073 each return only one node when use canonical expansion is turned off.  Each search returns two nodes when canonical expansion is turned on.  By default, canonical expansion should be turned on.  A hidden advanced option should be made available to turn this off.
+
|-
−
 
+
| valign="top" | <pre>P61073-2</pre>
−
This can be used as a test case for the Export function "on Target network Node ID type"= i.Canonical_ROGID_TOP
+
| valign="top" | <pre>UniProt_Ac</pre>
−
 
+
| valign="top" rowspan="2" | <pre>Taxon id: Any
−
 
+
Iterations: 0
−
 
+
Create new view: yes
−
Searched 821860 but by each other search type.  No results returned in any case.  Ok 
+
Use canonical expansion: no</pre>
−
 
+
| 2 nodes (CXCR4 and CXCR4_HUMAN)
−
'''Last tested: June 1, 2010'''
+
| Pass
−
 
+
|-
−
'''Plugin Version: '''0.83
+
| valign="top" | <pre>P61073</pre>
−
 
+
| valign="top" | <pre>UniProt_Ac</pre>
−
'''Data Version: '''7.0 public
+
| 1 node (CXCR4_HUMAN)
−
 
+
| Pass
−
<span style="color:red">'''Result: '''NOT TESTED</span>
+
|-
−
 
+
| valign="top" | <pre>P61073-2</pre>
−
'''Tester: '''Ian
+
| valign="top" | <pre>UniProt_Ac</pre>
−
 
+
| valign="top" rowspan="2" | <pre>Taxon id: Any
−
<span style="color:red">'''Notes: ''':(SABRY)</span> : The search results of a protein accession and a gene identifier (which could refer to more than one protein) will not be the same and it is OK as I see it (correct me if I am wrong). But as requested if canonical expansion is turned on the results will be the same. Although this is a very good suggestion for this search , I am sorry that I am  against the idea of default canonical expansion and hiding the stop expansion in advanced (which is now features under development) (but this does not mean I will not implement it).  
+
Iterations: 0
−
#When turned on canonical expansion affects many of the default behavior (abstract implementations) i.e I use the same network construction for ROG ,molecular mass and geneID and so on.
+
Create new view: yes
−
#The expansion uses a second phase index to index mapping and this slows down the query.
+
Use canonical expansion: yes</pre>
−
#Batch quires will take long time to complete and  will get more interactions (This seems to be a good thing, but the current network is already to much information), and the user has the option to expand if wanted
+
| 2 nodes (CXCR4 and CXCR4_HUMAN)
−
 
+
| Pass
−
*Let me know the final decision,
+
|-
−
 
+
| valign="top" | <pre>P61073</pre>
−
===Test case name: geneSymbol 1 ===
+
| valign="top" | <pre>UniProt_Ac</pre>
−
 
+
| 2 nodes (CXCR4 and CXCR4_HUMAN)
−
'''Operation: '''
+
| Pass
−
 
+
|-
−
Query box:  
+
| 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.
−
 
+
|-
−
CXCR4
+
| valign="top" | <pre>CXCR</pre>
−
 
+
| valign="top" rowspan="4" | <pre>geneSymbol</pre>
−
Search type: geneSymbol
+
| valign="top" rowspan="4" | <pre>Taxon id: Any
−
 
+
Iterations: 0
−
Taxon id: Any
+
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
 +
| No results are returned
 +
| Pass
 +
|-
 +
| 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>
 +
| 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
 
Iterations: 0
−
 
 
Create new view: yes
 
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
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
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>Taxon id: 9606
−
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
 
−
 
 
−
'''FAIL'''.  No warning is given.  With no taxon specifier present, the search (iteration=0) returns 6 nodes and 5 taxons.  This will create havoc if the user has searched using a list of identifiers. 
 
−
 
 
−
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 prompts the user to select from a set of possibilities.  Linkouts to NCBI are impossible to use.  '''FAIL'''.  Take this hyperlink feature out until a later release.  This should be an exact match search unless the user specifically asks for related terms.
 
−
 
 
−
A search for "CXC CXCR CXCR4" returns results identical for CXCR4.  Ok.  The provides a helper window and a chance to refine the query.  User can select one or more specific terms for each ambiguous term (using shift or cntrl keys and pressing return to add the selected items to a new search).  The user should be informed of their options.  '''FAIL'''.  Message should read:
 
−
 
 
−
"One or more of your query terms did not have an exact match.  For each term on the left, you may select one or more of the refined terms 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."
 
−
 
 
−
 
 
−
Search CXCR5 as a UniProt_ID, presented user with option for refining the query. Ok
 
−
 
 
−
Search CXCR5 against other query types returned 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
 
−
 
 
−
<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
 
−
 
 
 
Iterations: 0
 
Iterations: 0
−
 
 
Create new view: yes
 
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
Use canonical expansion: no
+
| No results returned
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>5366033</pre>
−
RPB1 for any taxon returns 1 node (RPB1_SCHPO).  Ok.
+
| valign="top" | <pre>rog</pre>
−
 
+
| valign="top" | <pre>Taxon id: Any
−
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.
+
Iterations: 1
−
 
+
Create new view: no
−
RPB1 for taxon 9606 returns 3 nodes one of which is SIRPB1.  FAIL.  This is an exact match search.
+
Use canonical expansion: no</pre>
−
 
+
| 2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it)
−
'''Last tested: June 7, 2010'''
+
| Pass
−
 
+
|-
−
'''Plugin Version: '''0.83
+
| valign="top" | <pre>IPI00543858
−
 
+
IPI00517160</pre>
−
'''Data Version: '''7.0 public
+
| valign="top" rowspan="4" | <pre>ipi</pre>
−
 
+
| valign="top" rowspan="4" | <pre>Taxon id: Any
−
<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
 
Iterations: 1
−
 
 
Create new view: no
 
Create new view: no
−
 
+
Use canonical expansion: no</pre>
−
Use canonical expansion: no
+
| rowspan="3" | 33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH)
−
 
+
| Pass
−
<span style="color:red">' ''Notes: ''':(SABRY)</span> The bug coursing freeze when performing ROG searches is fixed in 0.85
+
|-
−
 
+
| valign="top" | <pre>IPI00543858.1
−
===Test case name: Iterations 1===
+
IPI00517160.1</pre>
−
 
+
| Pass
−
'''Operation: '''
+
|-
−
 
+
| valign="top" | <pre>00543858
−
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.
+
00517160</pre>
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>00543858
−
Same number of edges (2 edges, 1 loop) in both cases.
+
0051716</pre>
−
 
+
| 33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper
−
'''Last tested: June 1, 2010'''
+
| Pass
−
 
+
|-
−
'''Plugin Version: '''0.83
+
| 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).
−
 
+
|-
−
'''Data Version: '''7.0 public
+
| valign="top" | <pre>IPI</pre>
−
 
+
| valign="top" rowspan="2" | <pre>ipi</pre>
−
<span style="color:red">'''Result: '''NOT TESTED</span>
+
| valign="top" rowspan="2" | <pre>Taxon id: Any
−
 
 
−
'''Tester: '''Ian
 
−
 
 
−
'''Notes: '''
 
−
 
 
−
 
 
−
===Test case name: ipi 1 #===
 
−
 
 
−
'''Operation: '''
 
−
 
 
−
Query box:
 
−
 
 
−
IPI00543858
 
−
IPI00517160
 
−
 
 
−
Search type: ipi
 
−
 
 
−
Taxon id: Any
 
−
 
 
 
Iterations: 1
 
Iterations: 1
−
 
 
Create new view: no
 
Create new view: no
−
 
+
Use canonical expansion: no</pre>
−
Use canonical expansion: no
+
| Initiates query helper
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>IPI00543858</pre>
−
Returns results identical to test case UniProt_Ac 1.  Ok
+
| 26 nodes, 67 edges
−
 
+
| Pass
−
Changing the query to "IPI00543858.1 IPI00517160.1" produces identical results. Ok.
+
|-
−
 
+
| valign="top" | <pre>72854<-->72866</pre>
−
Changing the query to "00543858 00517160" produces identical results. Ok.
+
| valign="top" | <pre>mass</pre>
−
 
+
| valign="top" | <pre>Taxon id: Any
−
Changing the query to "00543858 0051716" produces identical results for first query term and initiates query helper to resolve second term. Ok.
+
Iterations: 0
−
 
+
Create new view: yes
−
Changing the query to "abcd" produces no results. Ok.
+
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.
−
Changing the query to "IPI" initiates query helper. Ok.
+
| Pass
−
 
+
|-
−
Searching for IPI00543858 as any other search type returns no results.  Ok
+
| colspan="5" | '''Note:''' the nodes are not laid out in a nice way, probably because no edges connect them.
−
 
+
|-
−
'''Last tested: June 1, 2010'''
+
| valign="top" | <pre>72854 kda</pre>
−
 
+
| valign="top" | <pre>mass</pre>
−
'''Plugin Version: '''0.83
+
| valign="top" | <pre>Taxon id: Any
−
 
+
Iterations: 0
−
'''Data Version: '''7.0 public
+
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
<span style="color:red">'''Result: '''NOT TESTED</span>
+
| No results are returned
−
 
+
| Pass
−
'''Tester: '''Ian
+
|-
−
 
+
| valign="top" | <pre>72854<-->72856 kda</pre>
−
'''Notes: '''
+
| valign="top" | <pre>mass</pre>
−
 
+
| valign="top" | <pre>Taxon id: Any
−
 
+
Iterations: 0
−
===Test case name: mass search #===
+
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
'''Operation: '''
+
| Query helper with 3 possible results
−
 
+
| Pass
−
Query box:
+
|-
−
 
+
| valign="top" | <pre>11401546</pre>
−
72854<-->72866
+
| valign="top" rowspan="12" | <pre>PMID</pre>
−
 
+
| valign="top" rowspan="12" | <pre>Taxon id: Any
−
Search type: ipi
+
Iterations: 0
−
 
+
Create new view: yes
−
Taxon id: Any
+
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
 
Iterations: 0
−
 
 
Create new view: yes
 
Create new view: yes
−
 
+
Use canonical expansion: no</pre>
−
Use canonical expansion: no
+
| 1 node (Q7KSF4_DROME) verifying the attributes in the previous search
−
 
+
| Pass
−
'''Expected Observation: '''
+
|-
−
 
+
| valign="top" | <pre>NP_996224</pre>
−
The user is presented with the query helper to refine the query.  A prompting message reads:
+
| valign="top" | <pre>RefSeq_Ac</pre>
−
 
+
| valign="top" rowspan="3" | <pre>Taxon id: Any
−
"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."
+
Iterations: 1
−
 
+
Create new view: yes
−
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.
+
Use canonical expansion: yes</pre>
−
 
+
| rowspan="2" | 69 nodes, 213 edges (same as the above query for Q7KSF4)
−
The query returns 4 nodes with mass in the expected range. Ok.
+
| Pass
−
 
+
|-
−
0 returns no results. Ok.
+
| valign="top" | <pre>Q7KSF4_DROME</pre>
−
 
+
| valign="top" | <pre>UniProt_ID</pre>
−
-1 returns no results. Ok.
+
| Pass
−
 
+
|-
−
MW returns no results. Ok.
+
| valign="top" | <pre>42066</pre>
−
 
+
| valign="top" | <pre>geneID</pre>
−
72854 kda returns no results but hangs the interface.  FAIL.
+
| rowspan="3" | 69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066
−
 
+
| Pass
−
'''Last tested: June 1, 2010'''
+
|-
−
 
+
| valign="top" | <pre>42066</pre>
−
'''Plugin Version: '''0.83
+
| valign="top" | <pre>geneID</pre>
−
 
+
| valign="top" | <pre>Taxon id: Any
−
'''Data Version: '''7.0 public
+
Iterations: 1
−
 
+
Create new view: yes
−
<span style="color:red">'''Result: '''NOT TESTED</span>
+
Use canonical expansion: no</pre>
−
 
+
| Pass
−
'''Tester: '''Ian
+
|-
−
 
+
| valign="top" | <pre>cher</pre>
−
'''Notes: '''
+
| valign="top" | <pre>geneSymbol</pre>
−
 
+
| valign="top" rowspan="4" | <pre>Taxon id: Any
−
 
+
Iterations: 1
−
 
+
Create new view: yes
−
===Test case name: rog search 1===
+
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
−
===Test case name: PMIDsearch 1===
+
| Pass
−
 
+
|-
−
'''Operation: '''
+
| valign="top" | <pre>10121899</pre>
−
 
+
| valign="top" | <pre>rog</pre>
−
Query box:
+
| 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
−
11401546
+
|-
−
 
+
| valign="top" | <pre>14605208</pre>
−
Search type: pmid
+
| valign="top" | <pre>PMID</pre>
−
 
+
| rowspan="3" | 929 nodes and 1605 edges returned all with PMID of 14605208
−
Taxon id: Any
+
|
−
 
+
|-
 +
| valign="top" | <pre>14605208</pre>
 +
| valign="top" | <pre>PMID</pre>
 +
| valign="top" | <pre>Taxon id: Any
 
Iterations: 0
 
Iterations: 0
−
 
 
Create new view: yes
 
Create new view: yes
−
 
+
Use canonical expansion: yes</pre>
−
Use canonical expansion: no
+
|
−
 
+
|-
−
'''Expected Observation: '''
+
| valign="top" | <pre>14605208</pre>
−
 
+
| valign="top" | <pre>PMID</pre>
−
4 nodes and 7 edges are returned.  Three edges have PMID 11401546 and these involve the 4 nodes shown.
+
| valign="top" | <pre>Taxon id: Any
−
All other edges (from different PMIDs) involve these proteins.  Ok.
+
Iterations: 1
−
 
+
Create new view: yes
−
11401546.1 returns 0 results.  Ok.
+
Use canonical expansion: no</pre>
−
 
+
|
−
1140154 returns 0 results and starts query helper.  FAIL.  This should be an exact match search. 
+
|-
−
 
+
| valign="top" | <pre>47513</pre>
−
SPTAN1 returns 0 results.  Ok.
+
| valign="top" | <pre>src_intxn_id</pre>
−
 
+
| valign="top" rowspan="6" | <pre>Taxon id: Any
−
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
 
Iterations: 1
−
 
 
Create new view: yes
 
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
 +
|}
  
−
Use canonical expansion: yes
+
=== Invalid input tests ===
  
−
'''Expected Observation: '''
+
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
−
 
+
! align="center" style="background:#f0f0f0;" | Query
−
{|class="wikitable" style="text-align:left" border="1" cellpadding="5"
+
! align="center" style="background:#f0f0f0;" | Search Type
−
!width="50" align="center" style="background:#f0f0f0;"|Search Type
+
! align="center" style="background:#f0f0f0;" | Options
−
!width="50" align="center" style="background:#f0f0f0;"|Example
+
! align="center" style="background:#f0f0f0;" | Expected Result
−
!width="500" align="center" style="background:#f0f0f0;"|Results
+
! align="center" style="background:#f0f0f0;" | Pass/Fail
 +
|-
 +
| valign="top" | <pre>0</pre>
 +
| valign="top" | <pre>RefSeq_Ac</pre>
 +
|
 +
| No results are returned
 +
|Pass
 +
|-
 +
| valign="top" | <pre>0</pre>
 +
| valign="top" | <pre>UniProt_ID</pre>
 +
|
 +
| No results are returned
 +
|Pass
 +
|-
 +
| valign="top" | <pre>0</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 +
|
 +
| 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>mass</pre>
 +
|
 +
| No results are returned
 +
|Pass
 
|-
 
|-
−
| 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.
+
| valign="top" | <pre>0</pre>
 +
| valign="top" | <pre>pmid</pre>
 +
|
 +
| No results are returned
 +
|Pass
 
|-
 
|-
−
| RefSeq_Ac||NP_996224||67 nodes, 146 edges. See above. i.query feature fails to update to reflect the most recent search.  FAIL.
+
| valign="top" | <pre>23</pre>
 +
| valign="top" | <pre>UniProt_ID</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| UniProt_ID||Q7KSF4_DROME||67 nodes, 146 edges. 
+
| valign="top" | <pre>-1</pre>
 +
| valign="top" | <pre>mass</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| 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.
+
| valign="top" | <pre>-1</pre>
 +
| valign="top" | <pre>pmid</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| geneSymbol||cher||67 nodes, 146 edges. Now i.query says Q7KS4 for all four nodes returned by the search.  FAIL.
+
| valign="top" | <pre>0000</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| 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.
+
| valign="top" | <pre>00001</pre>
 +
| valign="top" | <pre>geneID</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| 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
+
| valign="top" | <pre>12345</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| 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. 
+
| valign="top" | <pre>abcd</pre>
 +
| valign="top" | <pre>ipi</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| src_intxn_id||47513|| 2 nodes and 1 edge returned.
+
| valign="top" | <pre>abcde</pre>
 +
| valign="top" | <pre>RefSeq_Ac</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| src_intxn_id||EBI-212627|| 2 nodes and 4 edges returned (2 from intact, 1 from BIND and 1 from MINT).  Ok
+
| valign="top" | <pre>abcde</pre>
 +
| valign="top" | <pre>UniProt_ID</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| src_intxn_id||147805||Returns 4 nodes and three interactions because BIND and BioGRID interaction id space overlap.
+
| valign="top" | <pre>abcde</pre>
 +
| valign="top" | <pre>geneSymbol</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| omim||227650||74 nodes and 224 edges returned.  Ok.
+
| valign="top" | <pre>abcde</pre>
 +
| valign="top" | <pre>geneID</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| 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
+
| valign="top" | <pre>abcdes</pre>
 +
| valign="top" | <pre>geneID</pre>
 +
|
 +
| No results are returned
 +
| Pass
 
|-
 
|-
−
| dig_title||fanconi|| FAIL - do not fix until next release. 
+
| 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
  
−
'''Last tested: June 7, 2010'''
+
=== User interface notes ===
  
−
'''Plugin Version: '''0.83
+
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.
  
−
'''Data Version: '''7.0 public
+
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!
  
−
<span style="color:red">'''Result: '''NOT TESTED</span>
+
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.
  
−
'''Tester: '''Ian
+
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.
  
−
'''Notes: '''
+
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.
  
−
===Test case name: audit against external database - Intact===
+
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.
  
−
===Test case name: audit against external database - MINT===
+
== Export cases ==
  
−
===Test case name: audit against external database - BioGRID===
+
{| border="1" cellspacing="0" cellpadding="5" style="margin: 2em"
 +
! align="center" style="background:#f0f0f0;" | Query/Search Type/Options
 +
! align="center" style="background:#f0f0f0;" | Export Type
 +
! align="center" style="background:#f0f0f0;" | Expected Result
 +
! align="center" style="background:#f0f0f0;" | Pass/Fail
 +
|-
 +
| valign="top" rowspan="2" | <pre>CXCR4
  
−
===Test case name: iterations 1===
+
geneSymbol
  
−
===Test case name: use canonical expansion 1===
+
Taxon id: Any
 +
Iterations: 0
 +
Create new view: no
 +
Use canonical expansion: no</pre>
 +
| valign="top" | <pre>i.UniProt_Ac_TOP</pre>
 +
| 1 node showing P61073
 +
| Pass
 +
|-
 +
| valign="top" | <pre>i.canonical_rog_TOP</pre>
 +
| 1 node showing 107322
 +
| Pass
 +
|}
  
 +
== Currently untested areas ==
  
−
==Advanced options cases==
+
* 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
  
−
==Preferences==
+
==List of GeneIDs to test the new canonical expansion==
−
 
 
−
===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: '''
+
Available in data version 8.4:
−
 
 
−
'''Plugin Version: '''
 
−
 
 
−
'''Data Version: '''
 
−
 
 
−
<span style="color:red">'''Result: '''NOT TESTED</span>
 
−
 
 
−
'''Tester: '''
 
−
 
 
−
'''Notes: '''
 
−
 
 
−
==to be corrected==
 
−
*Remove the non-proprietary flag/check for current data
 
−
*Handle the neighbourhood completion when expanding network (do not use all the nodes)
 
  
 +
*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
  
 
== All iRefIndex Pages ==
 
== All iRefIndex Pages ==
  
 
[[Category:iRefIndex]]
 
[[Category:iRefIndex]]

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

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