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
|
# ProbeSet Metadata
## 'dump-probeset'
## Generated Triples:
The following SQL query was executed:
```sql
SELECT IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name)) AS ProbeSetIdName, ProbeSet.Id, ProbeSet.Name, ProbeSet.alias, IFNULL(GeneChip.Name, '') AS GeneChipName, NULLIF(TRIM(ProbeSet.TargetId), '') AS TargetId, ProbeSet.Symbol, ProbeSet.description, NULLIF(TRIM(ProbeSet.Probe_set_target_region), '') AS Probe_set_target_region, ProbeSet.Chr, IFNULL(ProbeSet.Mb, '') AS Mb, IFNULL(ProbeSet.Mb_mm8, '') AS Mb_mm8, IFNULL(ProbeSet.Mb_2016, '') AS Mb_2016, IFNULL(ProbeSet.Probe_set_specificity, '') AS Probe_set_specificity, IFNULL(ProbeSet.Probe_set_BLAT_score, '') AS Probe_set_BLAT_score, IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '') AS Probe_set_Blat_Mb_start, IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '') AS Probe_set_Blat_Mb_start_2016, IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '') AS Probe_set_Blat_Mb_end, IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '') AS Probe_set_Blat_Mb_start_2016, ProbeSet.BlatSeq, ProbeSet.TargetSeq, IFNULL(ProbeSet.HomoloGeneID, '') AS HomoloGeneID, IFNULL(ProbeSet.UniProtID, '') AS UniProtID, IFNULL(ProbeSet.PubChem_ID, '') AS PubChem_ID, IFNULL(ProbeSet.KEGG_ID, '') AS KEGG_ID, IFNULL(ProbeSet.OMIM, '') AS OMIM, IFNULL(ProbeSet.ChEBI_ID, '') AS ChEBI_ID FROM ProbeSet LEFT JOIN GeneChip ON GeneChip.Id = ProbeSet.ChipId
```
The above query results to triples that have the form:
```text
gn:probeset_probesetidname -> rdf:type -> gnc:probeset
gn:probeset_probesetidname -> rdfs:label -> ProbeSet(Name)
gn:probeset_probesetidname -> skos:altLabel -> ProbeSet(alias)
gn:probeset_probesetidname -> gnt:hasChip -> gn:platform_genechipname
gn:probeset_probesetidname -> gnt:hasTargetId -> TargetId
gn:probeset_probesetidname -> gnt:symbol -> ProbeSet(Symbol)
gn:probeset_probesetidname -> dct:description -> ProbeSetdescription
gn:probeset_probesetidname -> gnt:targetsRegion -> Probe_set_target_region
gn:probeset_probesetidname -> gnt:chr -> ProbeSet(Chr)
gn:probeset_probesetidname -> gnt:mb -> "Mb"^^xsd:double
gn:probeset_probesetidname -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double
gn:probeset_probesetidname -> gnt:mb2016 -> "Mb_2016"^^xsd:double
gn:probeset_probesetidname -> gnt:hasSpecificity -> Probe_set_specificity
gn:probeset_probesetidname -> gnt:hasBlatScore -> Probe_set_BLAT_score
gn:probeset_probesetidname -> gnt:hasBlatMbStart -> "Probe_set_Blat_Mb_start"^^xsd:double
gn:probeset_probesetidname -> gnt:hasBlatMbStart2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double
gn:probeset_probesetidname -> gnt:hasBlatMbEnd -> "Probe_set_Blat_Mb_end"^^xsd:double
gn:probeset_probesetidname -> gnt:hasBlatMbEnd2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double
gn:probeset_probesetidname -> gnt:hasBlatSeq -> ProbeSetBlatSeq
gn:probeset_probesetidname -> gnt:hasTargetSeq -> ProbeSetTargetSeq
gn:probeset_probesetidname -> gnt:hasHomologeneId -> homologene:HomoloGeneID
gn:probeset_probesetidname -> gnt:hasUniprotId -> uniprot:UniProtID
gn:probeset_probesetidname -> gnt:hasPubChemId -> pubchem:PubChem_ID
gn:probeset_probesetidname -> gnt:hasKeggId -> kegg:KEGG_ID
gn:probeset_probesetidname -> gnt:hasOmimId ->
gn:probeset_probesetidname -> gnt:hasChebiId -> chebi:ChEBI_ID
```
Here's an example query:
```sparql
PREFIX gn: <http://genenetwork.org/id/>
PREFIX probeset: <http://genenetwork.org/probeset/>
PREFIX gnc: <http://genenetwork.org/category/>
PREFIX gnt: <http://genenetwork.org/term/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX kegg: <http://bio2rdf.org/ns/kegg#>
PREFIX pubchem: <https://pubchem.ncbi.nlm.nih.gov/>
PREFIX omim: <https://www.omim.org/entry/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX uniprot: <http://purl.uniprot.org/uniprot/>
PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX homologene: <https://bio2rdf.org/homologene:>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
SELECT * WHERE {
?s rdf:type gnc:probeset .
?s rdfs:label "100001_at" .
?s skos:altLabel "T3g; Ctg3; Ctg-3" .
?s gnt:hasChip gn:platform_mg_u74av2 .
?s ?p ?o .
}
```
Expected Result:
```rdf
gn:probeset_100001_at rdf:type gnc:probeset .
gn:probeset_100001_at rdfs:label "100001_at" .
gn:probeset_100001_at skos:altLabel "T3g; Ctg3; Ctg-3" .
gn:probeset_100001_at gnt:hasChip gn:platform_mg_u74av2 .
gn:probeset_100001_at gnt:symbol "Cd3g" .
gn:probeset_100001_at dct:description "CD3d antigen, gamma polypeptide" .
gn:probeset_100001_at gnt:chr "9" .
gn:probeset_100001_at gnt:mb "44.970689"^^xsd:double .
gn:probeset_100001_at gnt:mbMm8 "44.721684"^^xsd:double .
gn:probeset_100001_at gnt:mb2016 "44.778772"^^xsd:double .
gn:probeset_100001_at gnt:hasSpecificity "9.3" .
gn:probeset_100001_at gnt:hasBlatScore "186" .
gn:probeset_100001_at gnt:hasBlatMbStart "44.970689"^^xsd:double .
gn:probeset_100001_at gnt:hasBlatMbStart2016 "44.778772"^^xsd:double .
gn:probeset_100001_at gnt:hasBlatMbEnd "44.971291"^^xsd:double .
gn:probeset_100001_at gnt:hasBlatMbEnd2016 "44.778772"^^xsd:double .
gn:probeset_100001_at gnt:hasBlatSeq "CTCTGTTGCAAAATGAACAGCTGTACAGCCCCTCAAGGACCGGGAATATGACCAGTACAGCCATCTCCAAGGAAACCAACTGAGGAAGAAGTGAACTCAGCAGGACTCAGGGTGTCCCCACAATGCATTTTGGAGAGAGCCCAGACTGCAAGCAGAGAGGAAGAACTGAGGAAAACAAGCACAGCGTGGTGTT" .
gn:probeset_100001_at gnt:hasTargetSeq "ctctgttgcaaaatgaacagctgtaccagcccctcaaggaccgggaatatgaccagtacagccatctccaaggaaaccaactgaggaagaagtgaactcagcaggactcagggtgtccccccttntatccagcacccagaatcaaaacaatgcattttggagagagcccagtagagagattttcaaccctacaggtagactgcaagcagagaggaagaactgtcaaagaaattttggtcttttttttttttttnncaaaataaaataaaagcttggaggagccagtggtatgantnnnnnntgnancanttgtcaaccttgtttggggttnncagcaccccacccccagaccccccaaaaaaattcagtgaaggaaaacaagcacagcgtggtgtt" .
gn:probeset_100001_at gnt:hasHomologeneId homologene:55 .
gn:probeset_100001_at gnt:hasOmimId omim:186740 .
```
|
