iRefIndex Testing 7.0

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

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