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toxicity association

From: John Wilbanks <wilbanks@w3.org>
Date: Mon, 16 Aug 2004 15:49:10 -0400
Message-ID: <41210FB6.3090605@w3.org>
To: public-semweb-lifesci@w3.org

As promised, some code using EricP's RDF-SQL paper cited in previous mail.

# ToxicAssoc0 - federate a query over several independent clinical databases

# $Id: ToxicAssoc0.alg,v 1.5 2004/08/12 17:36:49 eric Exp $

ns db=<http://www.w3.org/2003/01/21-RDF-RDB-access/ns#>
ns ma=<http://med.example/ma#>
ns cs=<http://med.example/cs#>
ns up=<http://med.example/up#>
ns sa=<http://med.example/sa#>
ns mt=<http://med.example/mt#>
attach db:dbs ?ma (properties="../test/MicroArray.prop")
attach db:dbs ?up (properties="../test/Uniprot.prop")
attach db:dbs ?sa (properties="../test/ScreeningAssay.prop")
attach db:dbs ?cs (properties="../test/ChemStructure.prop")
attach db:dbs ?mt (properties="../test/MouseToxicity.prop")

ask ?ma (?g     ma:name                ?name .
         ?g        ma:expression        "up" .
         ?g        ma:experiment        ?kinase .
         ?kinase ma:against        ?agin .
         ?agin        cs:chemical        ?chemical )
ask ?up (?p     ma:name                ?name .                # bound to ?ma.ma:name
         ?p        up:motif        ?motif .
         ?p        up:pathway        "apoptosis" )
ask ?sa (?a     sa:name                "KinaseAssay" .
         ?a        cs:chemical        ?chemical .        # bound to ?ma.cs:chemical
         ?a        sa:upname        ?saProt .
         ?a        ma:kd50                ?kd50 {?kd50 >= .7 || ?kd50 < .2} )
ask ?cs (?c     cs:chemical        ?chemical .        # bound to ?ma.cs:chemical, ?sa.cs:chemical
         ?c        cs:structure        "asdfasdf" .
         ?c        cs:sidechain        ?side .
         ?c2        cs:sidechain        ?side .
         ?c2        cs:chemical        ?like )
ask ?mt (?t     cs:chemical        ?like .                # bound to ?cs.cs:sidechain
         ?t        mt:toxicity        ?ld {?ld > .50} )

collect (?name ?chemical ?motif ?saProt ?kd50 ?like ?ld)

# Table Output:
# +------+--------------+-----------+-------------+-----+--------------+-----+
# |  name|      chemical|      motif|       saProt| kd50|          like|   ld|
# |------|--------------|-----------|-------------|-----|--------------|-----|
# |"rq23"|"lhrh-agonist"|"@@motif@@"|"KinaseAssay"|"0.8"|"lhrh-agonist"|"0.6"|
# |"rq23"|"lhrh-agonist"|"@@motif@@"|"KinaseAssay"|"0.8"|       "like1"|"0.7"|
# +------+--------------+-----------+-------------+-----+--------------+-----+

# Sql Queries:
# 040812  4:56:25           312 Connect     root@localhost on MicroArray
#                   313 Connect     root@localhost on Uniprot
#                   314 Connect     root@localhost on ScreeningAssay
#                   315 Connect     root@localhost on ChemStructure
#                   316 Connect     root@localhost on MouseToxicity
#                   312 Query       SELECT STRAIGHT_JOIN
#        MicroArray_0.id AS g_id,
#        MicroArray_0.name AS name_name,
# Kinase_0.id AS kinase_id,
#        Chemicals_0.id AS agin_id,
#        Chemicals_0.chemical AS chemical_chemical
# 
# FROM MicroArray AS MicroArray_0
#      INNER JOIN Kinase AS Kinase_0 ON MicroArray_0.experiment=Kinase_0.id
#      INNER JOIN Chemicals AS Chemicals_0 ON Kinase_0.against=Chemicals_0.id
# WHERE MicroArray_0.expression="up"
# GROUP BY g_id,name_name,kinase_id,agin_id,chemical_chemical
#                   313 Query       SELECT STRAIGHT_JOIN
#        Uniprot_0.id AS p_id,
#        Uniprot_0.name AS name_name,
# Uniprot_0.motif AS motif_motif
# 
# FROM Uniprot AS Uniprot_0
# WHERE Uniprot_0.pathway="apoptosis" 
#   AND  Uniprot_0.name="rq23"
# GROUP BY p_id,name_name,motif_motif
#                   314 Query       SELECT STRAIGHT_JOIN
#        ScreeningAssay_0.id AS a_id,
#        ScreeningAssay_0.chemical AS chemical_chemical,
# ScreeningAssay_0.name AS saProt_name,
# ScreeningAssay_0.kd50 AS kd50_kd50
# 
# FROM ScreeningAssay AS ScreeningAssay_0
# WHERE ScreeningAssay_0.name="KinaseAssay" 
#   AND  ((ScreeningAssay_0.kd50>=".7") OR (ScreeningAssay_0.kd50<".2")) 
#   AND  ScreeningAssay_0.chemical="lhrh-agonist"
# GROUP BY a_id,chemical_chemical,saProt_name,kd50_kd50
#                   315 Query       SELECT STRAIGHT_JOIN
#        ChemStructure_0.id AS c_id,
#        ChemStructure_0.chemical AS chemical_chemical,
# ChemStructure_0.sidechain AS side_sidechain,
# ChemStructure_1.id AS c2_id,
#        ChemStructure_1.chemical AS like_chemical
# 
# FROM ChemStructure AS ChemStructure_0
#      INNER JOIN ChemStructure AS ChemStructure_1 ON ChemStructure_1.sidechain=ChemStructure_0.sidechain
# WHERE ChemStructure_0.structure="asdfasdf" 
#   AND  ChemStructure_0.chemical="lhrh-agonist"
# GROUP BY c_id,chemical_chemical,side_sidechain,c2_id,like_chemical
#                   316 Query       SELECT STRAIGHT_JOIN
#        MouseToxicity_0.id AS t_id,
#        MouseToxicity_0.chemical AS like_chemical,
# MouseToxicity_0.toxicity AS ld_toxicity
# 
# FROM MouseToxicity AS MouseToxicity_0
# WHERE MouseToxicity_0.toxicity>".50" 
#   AND  MouseToxicity_0.chemical="lhrh-agonist"
# GROUP BY t_id,like_chemical,ld_toxicity
#                   316 Query       SELECT STRAIGHT_JOIN
#        MouseToxicity_0.id AS t_id,
#        MouseToxicity_0.chemical AS like_chemical,
# MouseToxicity_0.toxicity AS ld_toxicity
# 
# FROM MouseToxicity AS MouseToxicity_0
# WHERE MouseToxicity_0.toxicity>".50" 
#   AND  MouseToxicity_0.chemical="like1"
# GROUP BY t_id,like_chemical,ld_toxicity
#                   316 Query       SELECT STRAIGHT_JOIN
#        MouseToxicity_0.id AS t_id,
#        MouseToxicity_0.chemical AS like_chemical,
# MouseToxicity_0.toxicity AS ld_toxicity
# 
# FROM MouseToxicity AS MouseToxicity_0
# WHERE MouseToxicity_0.toxicity>".50" 
#   AND  MouseToxicity_0.chemical="like2"
# GROUP BY t_id,like_chemical,ld_toxicity
#                   316 Quit       
#                   315 Quit       
#                   314 Quit       
#                   313 Quit       
#                   312 Quit       


-- 
John Wilbanks
W3C Fellow
Semantic Web - Life Sciences
http://www.w3.org/People/all#wilbanks
wilbanks@w3.org
617-253-5845 (direct)
617-838-6333 (mobile; best voicemail #)
--
Received on Monday, 16 August 2004 19:48:42 GMT

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