Difference between revisions of "iRefScape Test Cases 1.0"
PaulBoddie (talk | contribs) (Added the dig_title test result. Started an export tests section.) |
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− | | colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function. | + | | colspan="5" | '''Note:''' This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export). |
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| valign="top" | <pre>CXCR4</pre> | | valign="top" | <pre>CXCR4</pre> |
Revision as of 11:52, 22 June 2011
Last edited: 2011-06-22
All tests have been performed against iRefIndex 8.1 data.
Contents
Search cases
Query | Search Type | Options | Expected Result | Pass/Fail |
---|---|---|---|---|
Q39009 Q9ZNV8 |
UniProt_Ac |
Taxon id: Any Iterations: 1 Create new view: no Use canonical expansion: no Add edges between neighbours: no |
33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) | Pass |
Node AHP2_ARATH linkout from i.RefSeq_Ac_TOP attribute (NP_189581) to Entrez Protein gives http://www.ncbi.nlm.nih.gov/protein/NP_189581?report=GenPept | Pass | |||
i.taxid is 3702 and i.geneID is 822593 | Pass | |||
Node AHP2_ARATH linkout from i.UniProt_Ac_TOP attribute (Q9ZNV8) to UniProt/KB beta gives http://www.uniprot.org/uniprot/Q9ZNV8 | Pass | |||
UniProt record agrees with iRefScape on iRefSeq_Ac_TOP (see "Sequence databases"), i.taxid, i.geneID (see "Genome annotation databases") | Pass | |||
Two edges between query nodes are EBI-1555390, EBI-1555417 | Pass | |||
Linkouts for query node edges (i.src_intxn_id) to Intact ("Interaction databases") provide PubMed #17937504 which should match i.PMID, and an interaction detection method of "anti tag coip" which should match i.method_name | Pass | |||
The molecule names are DMC1 and ATHP1 in IntAct and these names should be available under the i.interactor_alias node attribute | Pass | |||
Both interactions should have http://wodaklab.org/iRefWeb/interaction/show/102203 as i.iRefWEB | Pass | |||
Taxon id: Any Iterations: 0 Create new view: no Use canonical expansion: no Add edges between neighbours: no |
2 nodes, 3 edges; 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) and are connected by two edges | Pass | ||
Q39009-1 Q9ZNV8-2 |
Taxon id: Any Iterations: 1 Create new view: no Use canonical expansion: no Add edges between neighbours: no |
Return the same results as for UniProtKB: the isoform information is ignored when searching | Pass | |
Q39009.1 Q9ZNV8.2 |
Returns no results. Version information is not a valid annotation for UniProtKB. | Pass | ||
NP_188928.2 |
RefSeq_Ac |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no |
11 nodes, 29 edges. i.RefSeq_Ac = NP_188928 was returned; edges returned include EBI-1555390, EBI-1555417 between DMC1_ARATH and AHP2_ARATH | Pass |
NP_188928 |
The same results are returned | Pass | ||
NP_188928.567 |
The same results are returned | Pass | ||
188928 |
No results are returned | Pass | ||
NP 188928 |
No results are returned | Pass | ||
NP_188928.2 |
UniProt_Ac |
No results are returned | Pass | |
NP_188928.2 |
geneID |
No results are returned | Pass | |
NP_188928.2 |
geneSymbol |
No results are returned | Pass | |
NP_188928.2 |
ipi |
No results are returned | Pass | |
NP_188928.2 |
mass |
No results are returned | Pass | |
NP_188928.2 |
rog |
No results are returned | Pass (no error given, though) | |
AHP2_ARATH |
UniProt_ID |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no |
26 nodes, 67 edges | Pass |
AHP2 |
No results are returned | Pass | ||
AHP2 ARATH |
No results are returned | Pass | ||
ARATH |
No results are returned | Pass | ||
AH2_ARATH |
No results are returned | Pass | ||
AHP2_ARATH.2 |
No results are returned | Pass | ||
AHP2_ARATH |
UniProt_Ac |
No results are returned | Pass | |
AHP2_ARATH |
geneID |
No results are returned | Pass | |
AHP2_ARATH |
geneSymbol |
No results are returned | Pass | |
AHP2_ARATH |
ipi |
No results are returned | Pass | |
821860 822593 |
geneID |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no |
33 nodes and 94 edges. (Should return the same result as a UniProt_Ac query for Q39009 and Q9ZNV8.) | Pass |
821860 |
geneID |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
1 node | Pass |
821860 |
geneSymbol |
No results are returned | Pass | |
821860 |
UniProt_Ac |
No results are returned | Pass | |
821860 |
UniProt_ID |
No results are returned | Pass | |
1234 |
geneID |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no |
47 nodes and 158 edges | Pass |
All geneIds from a search for 1234(45 values producing 44 unique gene identifiers) |
geneID |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
80 nodes and 733 edges (upon last attempt) | |
Note: This test is made incredibly difficult by the apparently unreliability of the export function (what Paul is talking about here is the Cytoscape export,not the iRefScape export). | ||||
CXCR4 |
geneSymbol |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
2 nodes | Pass |
P61073-2 |
UniProt_Ac |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
2 nodes (CXCR4 and CXCR4_HUMAN) | Pass |
P61073 |
UniProt_Ac |
1 node (CXCR4_HUMAN) | Pass | |
P61073-2 |
UniProt_Ac |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: yes |
2 nodes (CXCR4 and CXCR4_HUMAN) | Pass |
P61073 |
UniProt_Ac |
2 nodes (CXCR4 and CXCR4_HUMAN) | Pass | |
Note: P61073-2 and P61073 are isoforms of CXCR4. Searching for P61073-2 actually results in the removal of the "-2" and a search for all isoforms, under the assumption that the user is unsure which isoform should be retrieved; as a result, all isoforms are returned, even though a specific isoform was requested. In contrast, the search without a "-" character results in just one protein with that exact name being returned. | ||||
CXCR |
geneSymbol |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
No results are returned | Pass |
CXCR4 |
2 nodes with i.UniProt_Ac_TOP set to P61073 and P61073-2 | Pass | ||
cxcR4 |
Pass | |||
CXC CXCR CXCR4 |
Pass | |||
Note: no indication is given that CXC and CXCR failed to provide matches when the successfully used CXCR4 term is present. Maybe some feedback could be given about this. | ||||
CXCR5 |
geneSymbol |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
3 nodes | Pass |
CXCR5 |
UniProt_ID |
No results are returned | Pass | |
PTK2 |
geneSymbol |
6 nodes (involving 5 taxons) | Pass | |
RPB1 |
geneSymbol |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
1 node (RPB1_SCHPO) | Pass |
Taxon id: 4932 Iterations: 0 Create new view: yes Use canonical expansion: no |
No results returned (even though an alias for yeast RPO21, gene identifier 851415, is RPB1, this search only searches on official gene symbols from Entrez | Pass | ||
Taxon id: 9606 Iterations: 0 Create new view: yes Use canonical expansion: no |
No results returned | Pass | ||
5366033 |
rog |
Taxon id: Any Iterations: 1 Create new view: no Use canonical expansion: no |
2 nodes (POL_HV1H2 and POL_HV1B1 interacting with it) | Pass |
IPI00543858 IPI00517160 |
ipi |
Taxon id: Any Iterations: 1 Create new view: no Use canonical expansion: no |
33 nodes, 94 edges. 2 queried nodes are blue (DMC_ARATH and AHP2_ARATH) | Pass |
IPI00543858.1 IPI00517160.1 |
Pass | |||
00543858 00517160 |
Pass | |||
00543858 0051716 |
33 nodes, 94 edges, but only after IPI00517160 has been chosen from the query helper | Pass | ||
Note: the transfer of the search term from the query helper and the augmentation of results from the term isn't particularly easy to accomplish, or it isn't obvious how to accomplish this successfully, because the iRefScape panel is hidden in the main window (a Cytoscape bug which appears to switch the visible panel all the time) and because a new search is required (without a new view being created, which is potentially how the original search might be set up). | ||||
IPI |
ipi |
Taxon id: Any Iterations: 1 Create new view: no Use canonical expansion: no |
Initiates query helper | Pass |
IPI00543858 |
26 nodes, 67 edges | Pass | ||
72854<-->72866 |
mass |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
The query helper is shown. Upon transferring the 4 suggestions into the query box and searching again, 5 nodes are retrieved. | Pass |
Note: the nodes are not laid out in a nice way, probably because no edges connect them. | ||||
72854 kda |
mass |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
No results are returned | Pass |
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 | |||
1140154 |
No results are returned | |||
SPTAN1 |
No results are returned | |||
11401546 SPTAN1 |
No results are returned | |||
10551855 11401546 |
6 nodes and 27 edges | |||
10551855|11401546 |
6 nodes and 27 edges | |||
10551855| 11401546 |
6 nodes and 27 edges | |||
10551855 | 11401546 |
6 nodes and 27 edges | |||
10551855 [tab] 11401546 |
6 nodes and 27 edges | |||
10551855, 11401546 |
6 nodes and 27 edges | |||
10551855 11401546 |
No results are returned (since space-delimited queries are not supported) | |||
The following example searches are listed in the Using the Search Panel documentation. | ||||
Q7KSF4 |
UniProt_Ac |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes |
69 nodes, 213 edges, with the 4 query nodes having i.query = Q7KSF4, one of the query nodes having i.order = 0 (Q7KSF4_DROME) and the others having i.order = 10 (as canonical group members) | Pass |
Q7KSF4 |
UniProt_Ac |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: no |
1 node (Q7KSF4_DROME) verifying the attributes in the previous search | Pass |
NP_996224 |
RefSeq_Ac |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes |
69 nodes, 213 edges (same as the above query for Q7KSF4) | Pass |
Q7KSF4_DROME |
UniProt_ID |
Pass | ||
42066 |
geneID |
69 nodes, 213 edges, with the 4 query nodes having i.order = 0 since all also have i.geneID = 42066 | Pass | |
42066 |
geneID |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no |
Pass | |
cher |
geneSymbol |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes |
Pass | |
72854<-->72866 |
mass |
44 nodes, 140 edges, with 8 query nodes, 5 of which with i.mass in (72854, 72855, 72856, 72861) having i.order = 0 and the remaining 3 query nodes with i.mass outside the given range having i.order = 10 | Pass | |
10121899 |
rog |
69 nodes, 213 edges (same as the above query for Q7KSF4), but with one of the query nodes having i.order = 0 and i.query = 10121899 and the remaining 3 query nodes having i.order = 10 | Pass | |
14605208 |
PMID |
929 nodes and 1605 edges returned all with PMID of 14605208 | ||
14605208 |
PMID |
Taxon id: Any Iterations: 0 Create new view: yes Use canonical expansion: yes |
||
14605208 |
PMID |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: no |
||
47513 |
src_intxn_id |
Taxon id: Any Iterations: 1 Create new view: yes Use canonical expansion: yes |
2 nodes and 1 edge returned (one query node, Q7KSF4_DROME) | Pass |
EBI-212627 |
src_intxn_id |
2 nodes and 5 edges returned (from bind, dip, intact, mint and BIND_Translation), with 2 query nodes (CRBN_DROME and Q9W279_DROME) | Pass | |
147805 |
src_intxn_id |
Returns 4 nodes and 4 interactions because the BIND/BIND_Translation and BioGRID interaction identifier spaces overlap (so 147805 refers to completely different interactions in different databases) | Pass | |
227650 |
omim |
96 nodes (including 18 complex nodes) and 498 edges returned, with the query node having i.geneID = 2175 and i.digid = 460 | Pass | |
449 |
digid |
321 nodes and 1010 edges returned, with the 3 query nodes having i.omim = 612219 | Pass | |
460 |
digid |
668 nodes and 17554 edges returned, with the 16 query nodes having i.digid = 460 | Pass | |
fanconi |
dig_title |
Presumably similar results to the previous query | Fail (iRefScape insists on an exact match and doesn't find anything) |
Invalid input tests
Query | Search Type | Options | Expected Result | Pass/Fail |
---|---|---|---|---|
0 |
RefSeq_Ac |
No results are returned | ||
0 |
UniProt_ID |
No results are returned | ||
0 |
geneSymbol |
No results are returned | ||
0 |
geneID |
No results are returned | ||
0 |
mass |
No results are returned | ||
0 |
pmid |
No results are returned | ||
23 |
UniProt_ID |
No results are returned | Pass | |
-1 |
mass |
No results are returned | ||
-1 |
pmid |
No results are returned | ||
0000 |
geneSymbol |
No results are returned | ||
00001 |
geneID |
No results are returned | ||
12345 |
geneSymbol |
No results are returned | ||
abcd |
ipi |
No results are returned | ||
abcde |
RefSeq_Ac |
No results are returned | ||
abcde |
UniProt_ID |
No results are returned | ||
abcde |
geneSymbol |
No results are returned | ||
abcde |
geneID |
No results are returned | ||
abcdes |
geneID |
No results are returned | ||
MW |
mass |
No results are returned |
Not currently tested
- src_intxn_id search 1
- omim search 1
- digid search 1
- audit against external database - Intact
- audit against external database - MINT
- audit against external database - BioGRID
- iterations 1
- use canonical expansion 1
User interface notes
Many search types such as UniProt_ID now lead to exact-only searches. The production of results should not be allowed for imprecise protein names, for example, since the user might have entered gene names, selected UniProt_ID by mistake and would not be aware of their mistake because their search returned results. Also, since the first few characters of UniProt_ID search terms may be shared by multiple proteins from different organisms, an inexact match would need to trigger the query helper.
Generally, searches should provide predictable outcomes without resorting to the attribute browsers to discover which search terms produced which results. For example, AH2_ARATH which returns no results from an exact match search, should not encourage similar terms to be used for searching. Previously AH2_ARATH returned CAH2_ARATH. Imagine if the user accidentally had such a query term embedded in a long list. They would never detect this search error!
Where the taxonomy field is set to Any, a warning will be given. It is envisaged that the user will most frequently be working with a single organism's proteins or would at least tolerate being reminded that potentially irrelevant proteins might be searched for due to naming coincidences.
The iterations setting resets to 1 after a query, even one which led to the query helper being shown, where the query will be completed by trying the search again.
The i.query attribute on nodes will collect queries as they are performed. Thus, nodes will appear blue in a graph even if the current query had no direct relationship with the node.
Exporting lists of attribute values should be as simple as selecting the values in the attribute browser and opening a context menu and copying the selection. However, it is also possible (when the context menus don't work) to use the "File" -> "Export" -> "Node Attributes" menu entry and to choose "i.geneID", then saving and processing the saved file to get a list. This seems to be rather unreliable, however.
Export cases
Query/Search Type/Options | Export Type | Expected Result | Pass/Fail |
---|---|---|---|
CXCR4 geneSymbol Taxon id: Any Iterations: 0 Create new view: no Use canonical expansion: no |
i.UniProt_Ac_TOP |
1 node showing P61073 | Pass |
i.canonical_rog_TOP |
1 node showing 107322 | Pass |
Currently untested areas
- Preferences
- iRefScape menu
- Right-click menu
- Node attributes
- Edge attributes
- Wizard
- Installation
- Help system
- Windows and sessions
- Loading from file
To be corrected
- Remove the non-proprietary flag/check for current data
- Handle the neighbourhood completion when expanding network (do not use all the nodes)
- show_inxc dynamic index behaviour change not working
- Scaling GUI at low resolution, maximise button may get hidden
- Path finding cancelling time
- focus progress when path finding
- Ending with collapsed node error
- unselect all nodes before edge filtering
List of GeneIDs to test the new canonical expansion
Available in data version 8.4:
- 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