Difference between revisions of "iRefIndex Testing 7.0"

From irefindex
 
(7 intermediate revisions by the same user not shown)
Line 107: Line 107:
 
# to get Experiment attributes. First get the experimental uid from int_experiment table using sourceid of the int_source2object table. Then for attribute use the int_xref and int_name tables with the uid of the int_experiment table.
 
# to get Experiment attributes. First get the experimental uid from int_experiment table using sourceid of the int_source2object table. Then for attribute use the int_xref and int_name tables with the uid of the int_experiment table.
  
 +
==Check the legacy data-sources==
 +
These are data source where the source data has not change.
 +
* verify the the reasons for differences in numbers if any.
  
 +
==Check SQL tables==
 +
The following tables should be checked for:
 +
* The expected number of rows and columns
 +
* Null values (these included MySQL null, 0, -1, -8 and -10).(Some time the null values are allowed and the attempt here is to verify there is no systematic error)
 +
* Reserved characters in PSI-MI Tab and XML.
 +
* Problems in character encoding.
 +
{| {{table}} cellpadding="10" cellspacing="0" border="1"
 +
 +
 +
| align="center" style="background:#f0f0f0;"|'''Table name'''
 +
| align="center" style="background:#f0f0f0;"|'''Check'''
 +
| align="center" style="background:#f0f0f0;"|'''What to expect'''
 +
|-
 +
|  acc_multiples                      ||NO||
 +
|-
 +
|  addeds                              ||NO||
 +
|-
 +
|  arbitrary                          ||NO||
 +
|-
 +
|  colon_patch                        ||NO||
 +
|-
 +
|  colon_patch_bk                      ||NO||
 +
|-
 +
|  config                              ||NO||
 +
|-
 +
|  cy_edgeatrib                        ||YES||This table is a denormalized table with all interaction attributes. Used when making the RIGID centric TAB file. This is also used when making iRefScape data. Blank values are "-". No fileds should contain NULL.Chack for columns with only "-" as value.
 +
|-
 +
|  cy_nodeatrib                        ||YES||This table is a denormalized table with all interactor attributes. Used when making the ROGID centric TAB file. This is also used when making iRefScape data.Blank values are "-". No fileds should contain NULL.Chack for columns with only "-" as value. Oly ROGIDs used in interactions will apear here
 +
|-
 +
|  equa_score_multiple                ||NO||
 +
|-
 +
|  equa_score_multiple_reset          ||NO||
 +
|-
 +
|  eutils                              ||Yes||This table contains sequences for deprecated protein sequences.(removed from current RefSeq, UniProt or other databases archived by Entrez. Row count in this table should not be significantly different from the previous release. The SEGUID column should be checked and should make sure the Eutil web service client has performed as expected. This is also a good point to check the "E" scores in the int_xref_mod table. Also cross check with the SEGUID table (entries here should also appear in the SEGUID table if they have a valid SEGUID)
 +
|-
 +
|  gene_acc                            ||No||
 +
|-
 +
|  gene2refseq                        ||YES|| This table has information on the protein products of each gene. This is the primary table from RGG (Redundant Gene Group) assignment. Check 5 records against NCBI web site. Select 5 RGGs and check that the assignment is performed correctly. Check for entries that does not appear in SEGUID table. Check for consistent null or balnk values.
 +
|-
 +
|  geneinfo                            ||YES||This table provides information about entrez gene Gene records. Check for consistent null values in columns. Check 5 rows against NCBI web site.Labels for genes are extracted from this table.
 +
|-
 +
|  int_category                        ||YES||
 +
|-
 +
|  int_db                              ||YES||
 +
|-
 +
|  int_deleted                        ||YES||
 +
|-
 +
|  int_experiment                      ||YES||
 +
|-
 +
|  int_generation                      ||YES||
 +
|-
 +
|  int_name                            ||YES||
 +
|-
 +
|  int_object                          ||YES||
 +
|-
 +
|  int_objecttype                      ||YES||
 +
|-
 +
|  int_participants                    ||YES||
 +
|-
 +
|  int_proteinUIDs                    ||YES||
 +
|-
 +
|  int_recordtype                      ||YES||
 +
|-
 +
|  int_seguerror                      ||YES||
 +
|-
 +
|  int_sequence                        ||YES||
 +
|-
 +
|  int_source                          ||YES||
 +
|-
 +
|  int_source2object                  ||YES||
 +
|-
 +
|  int_xref                            ||YES||
 +
|-
 +
|  int_xref_mod                        ||YES||
 +
|-
 +
|  intacc2rig                          ||YES||
 +
|-
 +
|  ipi2seq                            ||YES||
 +
|-
 +
|  ipi2xref                            ||YES||
 +
|-
 +
|  maxvals                            ||YES||
 +
|-
 +
|  none_prots                          ||YES||
 +
|-
 +
|  pdb                                ||YES||
 +
|-
 +
|  pdb_mmdb                            ||YES||
 +
|-
 +
|  pluses                              ||YES||
 +
|-
 +
|  pmid2int                            ||YES||
 +
|-
 +
|  pmid2rig                            ||YES||
 +
|-
 +
|  PPI_sourceid                        ||YES||
 +
|-
 +
|  ref_main                            ||YES||
 +
|-
 +
|  ref_xref                            ||YES||
 +
|-
 +
|  refseq                              ||YES||
 +
|-
 +
|  rig2rigid                          ||YES||
 +
|-
 +
|  rig2rog                            ||YES||
 +
|-
 +
|  risg2risgid                        ||YES||
 +
|-
 +
|  rog_found                          ||YES||
 +
|-
 +
|  rog_mult                            ||YES||
 +
|-
 +
|  rog_multiple                        ||YES||
 +
|-
 +
|  rog_reset                          ||YES||
 +
|-
 +
|  rog2rig                            ||YES||
 +
|-
 +
|  rog2rogid                          ||YES||
 +
|-
 +
|  score_multiple                      ||YES||
 +
|-
 +
|  segu2seq                            ||YES||
 +
|-
 +
|  seguid                              ||YES||
 +
|-
 +
|  seguid_aded                        ||YES||
 +
|-
 +
|  seguid_complex                      ||YES||
 +
|-
 +
|  seguid_gbnk                        ||YES||
 +
|-
 +
|  seguid_pdbd                        ||YES||
 +
|-
 +
|  seguid_refs                        ||YES||
 +
|-
 +
|  seguid_remv                        ||YES||
 +
|-
 +
|  seguid_rest                        ||YES||
 +
|-
 +
|  seguid_unip                        ||YES||
 +
|-
 +
|  sha_seguid                          ||YES||
 +
|-
 +
|  sha_seguid_redund                  ||YES||
 +
|-
 +
|  summary_rig                        ||YES||
 +
|-
 +
|  summary_rog                        ||YES||
 +
|-
 +
|  summary_score                      ||YES||
 +
|-
 +
|  tmp_orphaned_interaction_experiment ||YES||
 +
|-
 +
|  tmp_orphaned_interaction_name      ||YES||
 +
|-
 +
|  tmp_orphaned_interaction_source    ||YES||
 +
|-
 +
|  tmp_orphaned_interaction_xref      ||YES||
 +
|-
 +
|  tmp_orphaned_interactions          ||YES||
 +
|-
 +
|  tmp_orphaned_interactor_name        ||YES||
 +
|-
 +
|  tmp_orphaned_interactor_object      ||YES||
 +
|-
 +
|  tmp_orphaned_interactor_xref        ||YES||
 +
|-
 +
|  tmp_orphaned_interactors            ||YES||
 +
|-
 +
|  uid2rig                            ||YES||
 +
|-
 +
|  uid2rog                            ||YES||
 +
|-
 +
|  uniprot_fly_acc                    ||YES||
 +
|-
 +
|  uniprot_isoforms                    ||YES||
 +
|-
 +
|  uniprot_main                        ||YES||
 +
|-
 +
|  uniprot_ref                        ||YES||
 +
|-
 +
|  uniprot_sequence                    ||YES||
 +
|-
 +
|  uniprot_yeast_acc                  ||YES||
 +
|-
 +
|  unique_rigids                      ||YES||
 +
|-
 +
|  unique_rogs                        ||YES||
 +
|-
 +
|  used_rogs                          ||YES||
 +
|-
 +
|
 +
|}
 +
 +
 +
==Categories==
 +
The int_category table defines the categories used in int_xref, int_name and int_participant tables
 +
{| {{table}} cellpadding="10" cellspacing="0" border="1"
 +
| align="center" style="background:#f0f0f0;"|'''Category reference number'''
 +
| align="center" style="background:#f0f0f0;"|'''Tag'''
 +
| align="center" style="background:#f0f0f0;"|'''Description'''
 +
|-
 +
| 0||interaction_primaryref||NA
 +
|-
 +
| 1||interaction_secondaryref||NA
 +
|-
 +
| 2||object_primaryref||NA
 +
|-
 +
| 3||object_secondaryref||NA
 +
|-
 +
| 4||bib_primaryref||NA
 +
|-
 +
| 5||bib_secondaryref||NA
 +
|-
 +
| 6||int_ditection_primaryref||NA
 +
|-
 +
| 7||int_ditection_secondaryref||NA
 +
|-
 +
| 8||parti_dentifi_primaryref||NA
 +
|-
 +
| 9||parti_dentifi_secondaryref||NA
 +
|-
 +
| 10||interaction_shortlbl||NA
 +
|-
 +
| 11||interaction_alias||NA
 +
|-
 +
| 12||interaction_full||NA
 +
|-
 +
| 13||object_shortlbl||NA
 +
|-
 +
| 14||object_alias||NA
 +
|-
 +
| 15||object_full||NA
 +
|-
 +
| 16||experim_primaryref||NA
 +
|-
 +
| 17||experim_secondaryref||NA
 +
|-
 +
| 18||experim_shortlbl||NA
 +
|-
 +
| 19||experim_alias||NA
 +
|-
 +
| 20||experim_full||NA
 +
|-
 +
| 21||parti_dentifi_shortlbl||NA
 +
|-
 +
| 22||parti_dentifi_alias||NA
 +
|-
 +
| 23||parti_dentifi_full||NA
 +
|-
 +
| 24||int_ditection_shortlbl||NA
 +
|-
 +
| 25||int_ditection_alias||NA
 +
|-
 +
| 26||int_ditection_fullnm||NA
 +
|-
 +
| 27||int_type_sh||NA
 +
|-
 +
| 28||int_type_al||NA
 +
|-
 +
| 29||int_type_fl||NA
 +
|-
 +
| 30||object_giref||NA
 +
|-
 +
| 31||object_revers_primary_using_primary||NA
 +
|-
 +
| 32||uniprot_secondary||NA
 +
|-
 +
| 33||object_revers_primary_using_secondary||NA
 +
|-
 +
| 34||primary_uniprimary_fetch_dif_taxon||NA
 +
|-
 +
| 36||Interactor_ref_biological_role||NA
 +
|-
 +
| 37||Interactor_ref_Experimental_role||NA
 +
|-
 +
| 38||Experiment_Host_organism||NA
 +
|-
 +
| 39||Depricated_1||NA
 +
|-
 +
| 40||int_type_primaryref||NA
 +
|-
 +
| 41||int_type_secondaryref||NA
 +
|}
 
Follow this link for a listing of all iRefIndex related pages (archived and current).
 
Follow this link for a listing of all iRefIndex related pages (archived and current).
 
[[Category:iRefIndex]]
 
[[Category:iRefIndex]]

Latest revision as of 10:21, 14 December 2010

The testing procedure for iRefIndex

Cross check with output of element counter

Program to use : biotek.uio.no.XML.Element_Counter (SaxValidator package)

  • For each interaction source </interactor> count should match the UID count int_object (select (select name from int_db where int_db.id=source) as intSource, count(uid) from int_object group by source; ).
  • For each interaction source </interactor> count should match the UID count int_source (select (select name from int_db where int_db.id=source) as intSource, count(uid) from int_source group by source;).
  • When </interactor> is not usable to count distinct objects (when this occurs as part of interaction and repeated in interactorList) some other suitable element has to be used (e.g </participant>)
  • Why count the closing elements in the above cases (e.g. </interactor> , instead of <interaction> or </interaction ). The reason is interaction elements may have attributes and elements starting with interaction may be ambiguous. This program uses text matching (to be independent of any XML parsing).


Check SEGUID. Check one record each to very the process worked

Test SEGUID updating process

*SQL query = select orid, count(distinct rog) as rog_C from seguid where orid<0 group by orid;
orid Record_count
-30 16983
-26 2
-24 78
-23 14
-22 1043258
-21 669761
-12 2679
-11 1665
-8 6525
-7 6547
-6 5235
-5 50305
-3 10853842
-2 11972291
  • All entries with orid<0 are altered during update. All interies with orid>=0 are original entries from seguid annotation file.
ORID Description
-30 This is a iRefIndex Complex (RIGID used as ROGID), included in a previous process
-26 Is a OLN dead yeast_acc mapped using UniProt cross reference
-25 Is a SGD acc dead yeast_acc mapped using UniProt cross reference
-24 Is a dead fly_acc mapped using UniProt cross reference
-23 Is a dead PDB
-22 Is a dead RefSeq
-21 Is a dead UniProtKB
-12 Added to SEGUID from original sequence record (N-Scores) in a previous process
-11 Added to SEGUID using Eutils in a previous process
-8 Is a live OLN acc yeast_acc mapped using UniProt cross reference
-7 Is a live SGD acc yeast_acc mapped using UniProt cross reference
-6 Is a live fly_acc mapped using UniProt cross reference
-5 Is a alive PDB
-3 Is a alive RefSeq
-2 Is a alive UniProtKB

UID overlap testing

After parsing it is important to make sure there is no overlap in the UID: The following queries should return empty set:

  • select * from int_object where int_object.uid in (select uid from int_source)
  • select * from int_object where int_object.uid in (select uid from int_experiment)
  • select * from int_source where int_source.uid in (select uid from int_experiment)

Check five records each from all data sources

  • Check with the file
  • Check with the website if available

The method is to find the UID range for the source from the int_surce2object table. e.g for IntAct

  1. Select max(sourceid) as max_id , min(sourceid) as min_id from int_source2object where source=5;
  2. List the first interaction (min_id) the last (max_id) and few from the middle
  3. To list node attribute use the int_xref and int_name tables with the objectid
  e.g select * from int_xref where int_xref.uid = <the objectid from int_source2object table>
  1. To get the the interaction attributes use the int_xref and int_name tables with the sourceid
  2. to get Experiment attributes. First get the experimental uid from int_experiment table using sourceid of the int_source2object table. Then for attribute use the int_xref and int_name tables with the uid of the int_experiment table.

Check the legacy data-sources

These are data source where the source data has not change.

  • verify the the reasons for differences in numbers if any.

Check SQL tables

The following tables should be checked for:

  • The expected number of rows and columns
  • Null values (these included MySQL null, 0, -1, -8 and -10).(Some time the null values are allowed and the attempt here is to verify there is no systematic error)
  • Reserved characters in PSI-MI Tab and XML.
  • Problems in character encoding.
Table name Check What to expect
acc_multiples NO
addeds NO
arbitrary NO
colon_patch NO
colon_patch_bk NO
config NO
cy_edgeatrib YES This table is a denormalized table with all interaction attributes. Used when making the RIGID centric TAB file. This is also used when making iRefScape data. Blank values are "-". No fileds should contain NULL.Chack for columns with only "-" as value.
cy_nodeatrib YES This table is a denormalized table with all interactor attributes. Used when making the ROGID centric TAB file. This is also used when making iRefScape data.Blank values are "-". No fileds should contain NULL.Chack for columns with only "-" as value. Oly ROGIDs used in interactions will apear here
equa_score_multiple NO
equa_score_multiple_reset NO
eutils Yes This table contains sequences for deprecated protein sequences.(removed from current RefSeq, UniProt or other databases archived by Entrez. Row count in this table should not be significantly different from the previous release. The SEGUID column should be checked and should make sure the Eutil web service client has performed as expected. This is also a good point to check the "E" scores in the int_xref_mod table. Also cross check with the SEGUID table (entries here should also appear in the SEGUID table if they have a valid SEGUID)
gene_acc No
gene2refseq YES This table has information on the protein products of each gene. This is the primary table from RGG (Redundant Gene Group) assignment. Check 5 records against NCBI web site. Select 5 RGGs and check that the assignment is performed correctly. Check for entries that does not appear in SEGUID table. Check for consistent null or balnk values.
geneinfo YES This table provides information about entrez gene Gene records. Check for consistent null values in columns. Check 5 rows against NCBI web site.Labels for genes are extracted from this table.
int_category YES
int_db YES
int_deleted YES
int_experiment YES
int_generation YES
int_name YES
int_object YES
int_objecttype YES
int_participants YES
int_proteinUIDs YES
int_recordtype YES
int_seguerror YES
int_sequence YES
int_source YES
int_source2object YES
int_xref YES
int_xref_mod YES
intacc2rig YES
ipi2seq YES
ipi2xref YES
maxvals YES
none_prots YES
pdb YES
pdb_mmdb YES
pluses YES
pmid2int YES
pmid2rig YES
PPI_sourceid YES
ref_main YES
ref_xref YES
refseq YES
rig2rigid YES
rig2rog YES
risg2risgid YES
rog_found YES
rog_mult YES
rog_multiple YES
rog_reset YES
rog2rig YES
rog2rogid YES
score_multiple YES
segu2seq YES
seguid YES
seguid_aded YES
seguid_complex YES
seguid_gbnk YES
seguid_pdbd YES
seguid_refs YES
seguid_remv YES
seguid_rest YES
seguid_unip YES
sha_seguid YES
sha_seguid_redund YES
summary_rig YES
summary_rog YES
summary_score YES
tmp_orphaned_interaction_experiment YES
tmp_orphaned_interaction_name YES
tmp_orphaned_interaction_source YES
tmp_orphaned_interaction_xref YES
tmp_orphaned_interactions YES
tmp_orphaned_interactor_name YES
tmp_orphaned_interactor_object YES
tmp_orphaned_interactor_xref YES
tmp_orphaned_interactors YES
uid2rig YES
uid2rog YES
uniprot_fly_acc YES
uniprot_isoforms YES
uniprot_main YES
uniprot_ref YES
uniprot_sequence YES
uniprot_yeast_acc YES
unique_rigids YES
unique_rogs YES
used_rogs YES


Categories

The int_category table defines the categories used in int_xref, int_name and int_participant tables

Category reference number Tag Description
0 interaction_primaryref NA
1 interaction_secondaryref NA
2 object_primaryref NA
3 object_secondaryref NA
4 bib_primaryref NA
5 bib_secondaryref NA
6 int_ditection_primaryref NA
7 int_ditection_secondaryref NA
8 parti_dentifi_primaryref NA
9 parti_dentifi_secondaryref NA
10 interaction_shortlbl NA
11 interaction_alias NA
12 interaction_full NA
13 object_shortlbl NA
14 object_alias NA
15 object_full NA
16 experim_primaryref NA
17 experim_secondaryref NA
18 experim_shortlbl NA
19 experim_alias NA
20 experim_full NA
21 parti_dentifi_shortlbl NA
22 parti_dentifi_alias NA
23 parti_dentifi_full NA
24 int_ditection_shortlbl NA
25 int_ditection_alias NA
26 int_ditection_fullnm NA
27 int_type_sh NA
28 int_type_al NA
29 int_type_fl NA
30 object_giref NA
31 object_revers_primary_using_primary NA
32 uniprot_secondary NA
33 object_revers_primary_using_secondary NA
34 primary_uniprimary_fetch_dif_taxon NA
36 Interactor_ref_biological_role NA
37 Interactor_ref_Experimental_role NA
38 Experiment_Host_organism NA
39 Depricated_1 NA
40 int_type_primaryref NA
41 int_type_secondaryref NA

Follow this link for a listing of all iRefIndex related pages (archived and current).

Retrieved from "http://irefindex.vib.be/wiki/index.php?title=iRefIndex_Testing_7.0&oldid=3147"