Difference between revisions of "Advanced iRefWeb searches"

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solr / lucene field description
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The general rule for linking to iRefWeb is
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act_id interactor id
 
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alias interactor alias
 
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db source database name
 
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exp_id id from interactour source db experiment
 
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gene_id
 
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genetic is genetic?
 
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hpr
 
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int_id interaction id
 
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int_rec_id source db's own record id
 
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int_tax taxonomy (full name)
 
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interaction_detection_desc
 
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interaction_detection_name
 
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interaction_detection_type_id
 
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interaction_type_desc
 
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interaction_type_id
 
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interaction_type_name
 
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isd_id id from interaction source db
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http://wodaklab.org/iRefWeb/search/index?q=xxx:yyy
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lpr
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where
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xxx = some field specifier
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np
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yyy = query string to find in that field
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pubmed_id
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You can also use this xxx:yyy format directly in the iRefWeb search interface for advanced searching or to test links to iRefWeb.
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rigid
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You can use this format to link to specific records in iRefWeb using the rigid
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rogid
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ttl_interactors
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http://wodaklab.org/iRefWeb/search/index?q=rigid:DYa8mY5yb99oBLOIut37lj70N3I
 +
 
 +
/ in the rigid is no problem in my browser
 +
 
 +
http://wodaklab.org/iRefWeb/search/index?q=rigid:DhjxQ/mY1WTUbsKggOA7TeD8gm8
 +
 
 +
+ in the does not seem to be a problem either
 +
 
 +
http://wodaklab.org/iRefWeb/search/index?q=rigid:+++rYMwOW+jyQAUvSOiAxurVy00
 +
 
 +
Linking to search terms without specifying a field delimiter
 +
 
 +
http://wodaklab.org/iRefWeb/search/index?q=P04050
 +
 
 +
We still have direct links for interactions and interactors, and a direct link to view a protein's interaction network:
 +
 
 +
http://wodaklab.org/iRefWeb/interaction/show/56
 +
 
 +
http://wodaklab.org/iRefWeb/interactor/show/1354791
 +
 
 +
http://wodaklab.org/netility/graph?type=PROTEIN&id=1354791
 +
 
 +
 
 +
 
 +
We also have some special patterns, like GENE_ID, and ALIAS, PUBMED_ID that are synoms of a sort to queries that can also be expressed using the standard pattern, but this has more to do with the input boxes on the search form. In these three case there's no "q=".  See table below.
 +
 
 +
 
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There are lots of other xxx field specifiers.  If you are interested, look at the table below.
 +
 
 +
{| {{table}}
 +
| align="center" style="background:#f0f0f0;"|'''field'''
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| align="center" style="background:#f0f0f0;"|'''description'''
 +
| align="center" style="background:#f0f0f0;"|'''standard pattern'''
 +
| align="center" style="background:#f0f0f0;"|'''special pattern'''
 +
|-
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| ACT_ID||intearctor.id||||
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|-
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| ALIAS||protein alias||alias:SOD2||alias=SOD2
 +
|-
 +
| DB||source database||db:bind||
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|-
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| ETYPE||internal use only||||
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|-
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| EXP_ID||interaction_source_db_experiment.id||||
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|-
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| GENE_ID||entrez gene id||gene_id:6944||gene_id=6944
 +
|-
 +
| GENETIC||0=false, 1=true, 2=both||genetic:0||
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|-
 +
| HASH||internal use only||||
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|-
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| HPR||||||
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|-
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| INT_ID||interaction.id||||
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|-
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| INT_REC_ID||source databse record id||int_rec_id:EBI-759874||
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|-
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| INT_TAX||latin name||int_tax:\"Mus musculus\"||
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|-
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| INT_TAX_CNT||distinct organisms in interaction||||
 +
|-
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| INT_TAX_ID||standard taxonomy id||||
 +
|-
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| INTERACTION_DETECTION_DESC||||interaction_detection_desc:\"interaction detection method - dihydrofolate reductase reconstruction\"||
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|-
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| INTERACTION_DETECTION_NAME||||||
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|-
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| INTERACTION_DETECTION_TYPE_ID||interaction_dection_type.id||||
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|-
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| INTERACTION_TYPE_DESC||||||
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|-
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| INTERACTION_TYPE_ID||interaction_type.id||||
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|-
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| INTERACTION_TYPE_NAME||||||
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|-
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| ISD_ID||interaction_source_db.id||||
 +
|-
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| LPR||||lpr:[0 TO 20]||
 +
|-
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| MAX_CARD||max cardinality of interactors||||
 +
|-
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| NP||||||
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|-
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| PREDICTED||0=false, 1=true, 2=both||||
 +
|-
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| PUBLIC||0=false, 1=true, 2=both||||
 +
|-
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| PUBMED_ID||||pubmed_id:18467557||pubmed_id=18467557
 +
|-
 +
| RIGID||||rigid:LH6e8bQ+rKDoOoGr+mHan7bGLnk||
 +
|-
 +
| ROGID||||rogid:Wgd0xHDx1jc9msL55PpTWFNL7cA4932||
 +
|-
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| TEXT||full text field combining everything||||
 +
|-
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| TTL_DISTINCT_DBS||||ttl_distinct_dbs:[2 TO 3]||
 +
|-
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| TTL_INTERACTORS||||||
 +
|-
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| TTL_SRC_RECORDS||||||
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|-
 +
|
 +
|}
 +
 
 +
 
 +
 
 +
 
 +
== All iRefIndex Pages ==
 +
 
 +
Follow this link for a listing of all iRefIndex related pages (archived and current).
 +
[[Category:iRefIndex]]

Latest revision as of 01:14, 5 August 2010

The general rule for linking to iRefWeb is

http://wodaklab.org/iRefWeb/search/index?q=xxx:yyy

where xxx = some field specifier yyy = query string to find in that field

You can also use this xxx:yyy format directly in the iRefWeb search interface for advanced searching or to test links to iRefWeb.


You can use this format to link to specific records in iRefWeb using the rigid


http://wodaklab.org/iRefWeb/search/index?q=rigid:DYa8mY5yb99oBLOIut37lj70N3I

/ in the rigid is no problem in my browser

http://wodaklab.org/iRefWeb/search/index?q=rigid:DhjxQ/mY1WTUbsKggOA7TeD8gm8

+ in the does not seem to be a problem either

http://wodaklab.org/iRefWeb/search/index?q=rigid:+++rYMwOW+jyQAUvSOiAxurVy00

Linking to search terms without specifying a field delimiter

http://wodaklab.org/iRefWeb/search/index?q=P04050

We still have direct links for interactions and interactors, and a direct link to view a protein's interaction network:

http://wodaklab.org/iRefWeb/interaction/show/56

http://wodaklab.org/iRefWeb/interactor/show/1354791

http://wodaklab.org/netility/graph?type=PROTEIN&id=1354791


We also have some special patterns, like GENE_ID, and ALIAS, PUBMED_ID that are synoms of a sort to queries that can also be expressed using the standard pattern, but this has more to do with the input boxes on the search form. In these three case there's no "q=". See table below.


There are lots of other xxx field specifiers. If you are interested, look at the table below.

field description standard pattern special pattern
ACT_ID intearctor.id
ALIAS protein alias alias:SOD2 alias=SOD2
DB source database db:bind
ETYPE internal use only
EXP_ID interaction_source_db_experiment.id
GENE_ID entrez gene id gene_id:6944 gene_id=6944
GENETIC 0=false, 1=true, 2=both genetic:0
HASH internal use only
HPR
INT_ID interaction.id
INT_REC_ID source databse record id int_rec_id:EBI-759874
INT_TAX latin name int_tax:\"Mus musculus\"
INT_TAX_CNT distinct organisms in interaction
INT_TAX_ID standard taxonomy id
INTERACTION_DETECTION_DESC interaction_detection_desc:\"interaction detection method - dihydrofolate reductase reconstruction\"
INTERACTION_DETECTION_NAME
INTERACTION_DETECTION_TYPE_ID interaction_dection_type.id
INTERACTION_TYPE_DESC
INTERACTION_TYPE_ID interaction_type.id
INTERACTION_TYPE_NAME
ISD_ID interaction_source_db.id
LPR lpr:[0 TO 20]
MAX_CARD max cardinality of interactors
NP
PREDICTED 0=false, 1=true, 2=both
PUBLIC 0=false, 1=true, 2=both
PUBMED_ID pubmed_id:18467557 pubmed_id=18467557
RIGID rigid:LH6e8bQ+rKDoOoGr+mHan7bGLnk
ROGID rogid:Wgd0xHDx1jc9msL55PpTWFNL7cA4932
TEXT full text field combining everything
TTL_DISTINCT_DBS ttl_distinct_dbs:[2 TO 3]
TTL_INTERACTORS
TTL_SRC_RECORDS



All iRefIndex Pages

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

Retrieved from "http://irefindex.vib.be/wiki/index.php?title=Advanced_iRefWeb_searches&oldid=2852"