-
Notifications
You must be signed in to change notification settings - Fork 7
Expand file tree
/
Copy path03_02_targetInfo_Batch.ttl
More file actions
162 lines (154 loc) · 7.4 KB
/
03_02_targetInfo_Batch.ttl
File metadata and controls
162 lines (154 loc) · 7.4 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
@base <http://www.openphacts.org/api> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dc: <http://purl.org/dc/elements/1.1/> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix dcterms: <http://purl.org/dc/terms/>.
@prefix api: <http://purl.org/linked-data/api/vocab#> .
@prefix rel: <http://vocab.org/relationship/> .
@prefix void: <http://rdfs.org/ns/void#> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .
@prefix drugbank: <http://bio2rdf.org/drugbank_vocabulary:> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix chembl: <http://rdf.ebi.ac.uk/terms/chembl#> .
@prefix ops: <http://www.openphacts.org/api#> .
@prefix uniprot: <http://purl.uniprot.org/core/> .
<#target> a api:API ;
rdfs:label "Target"@en ;
api:sparqlEndpoint <http://alpha.openphacts.org:8890/sparql/> ;
api:contentNegotiation api:parameterBased ;
api:variable <#input> ;
api:variable drugbank:drugType ;
api:dataset <http://www.conceptwiki.org> ;
api:dataset <http://www.ebi.ac.uk/chembl>;
api:dataset <http://www.openphacts.org/bio2rdf/drugbank> ;
api:vocabulary <http://semanticscience.org/resource/> ;
api:vocabulary <http://bio2rdf.org/drugbank_vocabulary:> ;
api:vocabulary <http://www.w3.org/2004/02/skos/core#> ;
api:description "An API configuration to return information about targets" ;
api:endpoint [
a api:BatchEndpoint ;
api:name "Target Information: Batch" ;
api:description "Information about a list of targets, separated by '|'.";
api:variable <http://bio2rdf.org/drugbank_resource:Approved> ;
api:variable <http://bio2rdf.org/drugbank_resource:Experimental> ;
api:variable <http://bio2rdf.org/drugbank_resource:Illicit> ;
api:variable <http://bio2rdf.org/drugbank_resource:Investigational> ;
api:variable <http://bio2rdf.org/drugbank_resource:Nutraceutical> ;
api:variable <http://bio2rdf.org/drugbank_resource:Withdrawn> ;
api:uriTemplate "/target/batch?uri_list={uri_list}" ;
api:exampleRequestPath "/target?uri_list=http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F00059958-a045-4581-9dc5-e5a08bb0c291|http%3A%2F%2Fwww.conceptwiki.org%2Fconcept%2F7b21c06f-0343-4fcc-ab0f-a74ffe871ade";
api:viewer <#targetBatchViewer> ;
api:defaultViewer <#targetBatchViewer> ] .
<http://www.conceptwiki.org> api:label "ConceptWiki" .
<http://www.ebi.ac.uk/chembl> api:label "ChEMBL - RDF" .
<http://www.openphacts.org/bio2rdf/drugbank> api:label "DrugBank" .
<http://semanticscience.org/resource/> api:label "sio" .
<http://bio2rdf.org/drugbank_vocabulary:> api:label "drugbank" .
<http://www.w3.org/2004/02/skos/core#> api:label "skos" .
<http://bio2rdf.org/drugbank_resource:Approved> api:name "approved" .
<http://bio2rdf.org/drugbank_resource:Experimental> api:name "experimental" .
<http://bio2rdf.org/drugbank_resource:Illicit> api:name "illicit" .
<http://bio2rdf.org/drugbank_resource:Investigational> api:name "investigational" .
<http://bio2rdf.org/drugbank_resource:Nutraceutical> api:name "nutraceutical" .
<http://bio2rdf.org/drugbank_resource:Withdrawn> api:name "withdrawn" .
<#input> api:name "uri_list" ;
api:label "uri_list";
api:value "A list of target URIs. e.g.: http://www.conceptwiki.org/concept/00059958-a045-4581-9dc5-e5a08bb0c291|http://www.conceptwiki.org/concept/7b21c06f-0343-4fcc-ab0f-a74ffe871ade" ;
rdfs:range rdfs:Resource .
drugbank:drugType api:name "drug_type" ;
api:label "drug_type" ;
api:value "One of: 'approved', 'biotech', 'experimental', 'illicit', 'investigational', 'nutraceutical', 'smallMolecule', 'withdrawn'";
api:filterVariable "?drugType_uri" ;
rdfs:subPropertyOf api:graphFilter ;
a rdf:Property .
<#targetBatchViewer> a api:Viewer ;
api:name "targetBatchViewer" ;
api:template
"?ims_cw_target_uri skos:prefLabel ?target_name ;
void:inDataset <http://www.conceptwiki.org> .
?ims_uniprot_target_uri uniprot:existence ?existence ;
uniprot:organism ?organism ;
uniprot:sequence ?sequence ;
uniprot:Function_Annotation ?function ;
ops:interactsWith ?inter_prot ;
uniprot:classifiedWith ?class ;
uniprot:alternativeName ?alt_name ;
uniprot:mass ?mass ;
ops:molecularWeight ?mass ;
rdfs:seeAlso ?target_pdb ;
rdfs:seeAlso ?ppi ;
void:inDataset <http://purl.uniprot.org> .
?inter_prot rdfs:label ?inter_label .
?ims_chembl_target_uri chembl:hasTargetComponent ?target_component ;
a ?target_type ;
rdfs:label ?synonym ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?target_component dcterms:description ?description ;
skos:exactMatch ?cw_target ;
void:inDataset <http://www.ebi.ac.uk/chembl> .
?ims_db_target_uri drugbank:cellularLocation ?cellularLocation ;
drugbank:molecularWeight ?molecularWeight ;
drugbank:numberOfResidues ?numberOfResidues ;
drugbank:theoreticalPi ?theoreticalPi ;
ops:targetForDrug ?db_compound ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
?db_compound drugbank:genericName ?drug_name ;
drugbank:drugType ?drugType ;
void:inDataset <http://www.openphacts.org/bio2rdf/drugbank> .
" ;
api:where "
{
GRAPH <http://www.conceptwiki.org> {
?ims_cw_target_uri skos:prefLabel ?target_name
}
GRAPH <http://purl.uniprot.org> {
{?ims_uniprot_target_uri uniprot:existence ?existence .
?ims_uniprot_target_uri uniprot:organism ?organism .
?ims_uniprot_target_uri uniprot:alternativeName/uniprot:fullName ?alt_name .}
UNION { ?ims_uniprot_target_uri uniprot:annotation ?fun_uri .
?fun_uri a uniprot:Function_Annotation ;
rdfs:comment ?function . }
UNION { ?ims_uniprot_target_uri uniprot:sequence ?seq_uri .
?seq_uri rdf:value ?sequence ;
uniprot:mass ?mass .
{ [] uniprot:sequenceFor ?ims_uniprot_target_uri,
?seq_uri}
UNION {
[] uniprot:sequenceFor ?ims_uniprot_target_uri,
?seq_dot_uri
FILTER(STRSTARTS(STR(?seq_dot_uri), STR(?ims_uniprot_target_uri)))
}
}
UNION { ?intact1 owl:sameAs ?ims_uniprot_target_uri .
[] uniprot:participant ?intact1, ?intact2 .
FILTER(?intact1!=?intact2)
?intact2 owl:sameAs ?inter_prot .
?inter_prot rdfs:label ?inter_label . }
UNION { ?ims_uniprot_target_uri uniprot:classifiedWith ?class . }
UNION { ?ims_uniprot_target_uri rdfs:seeAlso ?target_pdb .
?target_pdb uniprot:database <http://purl.uniprot.org/database/PDB> . }
UNION { ?ims_uniprot_target_uri rdfs:seeAlso ?ppi .
?ppi uniprot:database <http://purl.uniprot.org/database/IntAct> . }
} }
UNION {
GRAPH <http://www.openphacts.org/bio2rdf/drugbank> {
{ ?ims_db_target_uri drugbank:numberOfResidues ?numberOfResidues }
UNION { ?ims_db_target_uri drugbank:cellular-location ?cellularLocation }
UNION { ?ims_db_target_uri drugbank:theoretical-pi ?theoreticalPi }
UNION { ?db_compound drugbank:target ?ims_db_target_uri ;
dcterms:title ?drug_name ;
drugbank:drug-group ?drugType_uri .
?drugType_uri rdfs:label ?drugType }
}
}
UNION {
GRAPH <http://www.ebi.ac.uk/chembl> {
?ims_chembl_target_uri a ?target_type .
?ims_chembl_target_uri rdfs:label ?synonym .
?ims_chembl_target_uri chembl:hasTargetComponent ?target_component .
?target_component dcterms:description ?description .
}
}
".