7tm Receptor Demo

This document describes the 7tm Receptor Demo, including compiling and running the source. This work done by the BioRDF task force in HCLS. For a broader description, please see the A journey to Semantic Web query federation in the life sciences.

Integrating 7TM GPCR data

7TM GPCRs play a significant role in cell signal transduction.
This demo integrates tabular laboratory data about 7tm receptors:

+----+-----------------+--------------------+-----------+----------------------+-----------------+---------+----------------------------+-------------------------+----------------------+-----------------+-------------------+---------------+------------------------+--------------------------+-----------------------+--------------------+---------------+-----------------+-----------------+-----------------------------+----------------------------+-------------------------+----------------------+-----------------+-------------------+
| ID | Family          | Code               | Ligand    | Official_IUPHAR_name | Human_gene_name | HGNC_ID | Human_genetic_localisation | Human_nucleotide_RefSeq | Human_protein_RefSeq | Human_SwissProt | Human_Entrez_Gene | Rat_gene_name | Rat_Genome_Database_ID | Rat_genetic_localisation | Rat_nucleotide_RefSeq | Rat_protein_RefSeq | Rat_SwissProt | Rat_Entrez_Gene | Mouse_gene_name | Mouse_Genome_Informatics_ID | Mouse_genetic_localisation | Mouse_nucleotide_RefSeq | Mouse_protein_RefSeq | Mouse_SwissProt | Mouse_Entrez_Gene |
+----+-----------------+--------------------+-----------+----------------------+-----------------+---------+----------------------------+-------------------------+----------------------+-----------------+-------------------+---------------+------------------------+--------------------------+-----------------------+--------------------+---------------+-----------------+-----------------+-----------------------------+----------------------------+-------------------------+----------------------+-----------------+-------------------+
|  3 | GABAB receptors | 2.3:GABA:1:GABAB1: | GABA      | GABAB1               | GABBR1          |    4070 | 6p21.3                     | NM_001470               | NP_001461            | Q9UBS5          | 2550              | Gabbr1        |                 621537 | 20p12                    | NM_031028             | NP_112290          | Q920D8        | 81657           | Gabbr1          |                       46968 | 17B3                       | NM_019439               | NP_062312            | Q9WV18          | 54393             | 
+----+-----------------+--------------------+-----------+----------------------+-----------------+---------+----------------------------+-------------------------+----------------------+-----------------+-------------------+---------------+------------------------+--------------------------+-----------------------+--------------------+---------------+-----------------+-----------------+-----------------------------+----------------------------+-------------------------+----------------------+-----------------+-------------------+

against structured data in wikipedia:

Identifiers
Symbol GABBR1
Entrez 2550
HUGO 4070
OMIM 603540
RefSeq NM_021905
UniProt Q9UBS5
Other data
Locus Chr. 6 p21.3
Identifiers
Symbol GABBR2
Alt. Symbols GPR51
Entrez 9568
HUGO 4507
OMIM 607340
RefSeq NM_005458
UniProt O75899
Other data
Locus Chr. 9 q22.1-22.3

and assertions embedded in HTML embedded in HTML via ATAGs:

"Ethanol enhances GABA(B)-mediated inhibitory postsynaptic transmission on rat midbrain dopaminergic neurons by facilitating GIRK currents." aTags: Ethanol GABAB receptor Dopamine G protein-coupled inwardly-rectifying potassium channel (Source)

by executing a single SPARQL query with variables (?humanEntrez and ?label) shared between the sources:

… WHERE {
SERVICE <http://localhost:8888/7tm_receptors>
  {
    ?iuphar  iface:family      ?family .
    ?iuphar  iface:code	       ?code .
    ?iuphar  iface:iupharName  ?iupharNm .
    ?human   iface:iuphar      ?iuphar .
    ?human   iface:geneName    "GABBR1" .
    ?human   iface:entrezGene  ?humanEntrez .
  }
SERVICE <http://dbpedia.org/sparql?default-graph-uri=http%3A%2F%2Fdbpedia.org&should-sponge=&>
  {
     _:gene  dbp:entrezgene    ?humanEntrez ;
             rdfs:label        ?label ;
    FILTER (lang(?label) = "en")
  }
GRAPH <http://hcls.deri.org/atag/data/gabab_example.html>
  {
     ?topic  rdfs:label        ?label .
     ?post   sioc:topic        ?topic
  }
}

The 7tm_receptor data is stored in a single SQL table constructed from a CSV file, though could also be represented in a spreadsheet.

SWObjects

(sourceforge) ⁃ (wikipedia)

SWObjects is a library for general RDF storage, query and query manipulation. After compilation, running the 7tm demo looks like:

INCLUDES=-I../dlib-17.11 make -k tests/7tm_receptors-flat.results
( cd tests/7tm_receptors/flat/ && ../../../bin/SPARQL_server --once http://localhost:8888/7tm_receptors receptors.map > ../../../tests/7tm_receptors-flat.results )&
sleep 1
( cd tests/7tm_receptors/flat/ && ../../../bin/SWtransformer -x -q --sparql-pattern http://dbpedia.org/.\* --sparql-pattern http://localhost:8888/.\* q.rq )
┌─────────────────────┬───────────────────────────────────────────────────────────────────┬──────────────┬──────────────────────┬──────────────────────────────┬─────────────────────┐
│ ?label              │ ?post                                                             │ ?humanEntrez │ ?code                │ ?family                      │ ?iupharNm           │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49d3249aec0b0> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49d230abda515> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49cab494999c6> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49cab3f287c53> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49c22f5a6faa9> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
└─────────────────────┴───────────────────────────────────────────────────────────────────┴──────────────┴──────────────────────┴──────────────────────────────┴─────────────────────┘

Compilation is easiest on a system with unix development tools:

# Check out version 781 of SWObjects into a director called SWObjects.
svn co -r 781  https://swobjects.svn.sourceforge.net/svnroot/swobjects/trunk SWObjects
# Install boost, expat and dlib-17.11 on your system.
# Install gcc, bison and flex on your system.
# Edit SWObjects/CONFIG
#   set HTTP_SERVER= DLIB
#   set XML_PARSER= EXPAT1
#   make sure INCLUDES points to your dlib installation, e.g. INCLUDES += -I/usr/local/dlib-17.11 .
# Install MySQL on your system.
# Create the 7tm_receptor database.
cd SWObjects/tests/7tm_receptors/flat/
emacs createDB.sh # and change "CREDS='-u root '" to whatever your MySQL requires.
./createDB.sh
# Build and run the test.
cd ../../..
make tests/7tm_receptors-flat.results

SWObjects should compile without warnings:

…
touch lib/SWObjects.d
makedepend -y -f lib/SWObjects.d lib/SWObjects.cpp config.h -DYYTEXT_POINTER=1 -I../dlib-17.11 -I/usr/local/dlib-17.11 -I/home/eric/checkouts/sparul -I/home/eric/checkouts/sparul/lib   -I/home/eric/checkouts/sparul/MapSetParser -I/home/eric/checkouts/sparul/SPARQLfedParser -I/home/eric/checkouts/sparul/TrigSParser -I/home/eric/checkouts/sparul/TurtleSParser -I/home/eric/checkouts/sparul/lib 2>/dev/null
…
g++ -DYYTEXT_POINTER=1 -fPIC -g -O0 -W -Wall -Wextra -Wnon-virtual-dtor -ansi -std=c++98 -I../dlib-17.11 -I/usr/local/dlib-17.11 -I/home/eric/checkouts/sparul -I/home/eric/checkouts/sparul/lib   -I/home/eric/checkouts/sparul/MapSetParser -I/home/eric/checkouts/sparul/SPARQLfedParser -I/home/eric/checkouts/sparul/TrigSParser -I/home/eric/checkouts/sparul/TurtleSParser -I/home/eric/checkouts/sparul/lib -pipe    -c -o lib/SWObjects.o lib/SWObjects.cpp
…
g++ -o bin/SWtransformer bin/SWtransformer.o -L/home/eric/checkouts/sparul/lib -lSWObjects -lboost_regex-mt -lboost_system-mt  -lexpat -lmysqlclient

and finish with the test output shown above. The output of the test is displayed. Additional process information is stored in tests/7tm_receptors-flat.results.

Debugging flags can make it easier to see which pieces are connecting. SWtransformer will take a -d flag and generate a narrative describing connections to remote services:

# start server in background
../../../bin/SPARQL_server --once http://localhost:8888/7tm_receptors receptors.map > /dev/null &

# start client with -d flag
../../../bin/SWtransformer -x -q --sparql-pattern http://dbpedia.org/.\* --sparql-pattern http://localhost:8888/.\* -d q.rq
reading web resource http://hcls.deri.org/atag/data/gabab_example.html
Querying <http://localhost:8888/7tm_receptors> for
SELECT ?human ?humanEntrez ?code ?family ?iupharNm ?iuphar {  ?iuphar <http://neuro.example/receptors#family> ?family .
  ?iuphar <http://neuro.example/receptors#code> ?code .
  ?iuphar <http://neuro.example/receptors#iupharName> ?iupharNm .
  ?human <http://neuro.example/receptors#iuphar> ?iuphar .
  ?human <http://neuro.example/receptors#geneName> "GABBR1"  .
  ?human <http://neuro.example/receptors#entrezGene> ?humanEntrez .
} yielded
┌──────────────────────┬──────────────────────────────┬────────┬──────────────┬─────────┬─────────────────────┐
│ ?code                │ ?family                      │ ?human │ ?humanEntrez │ ?iuphar │ ?iupharNm           │
│ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │     -- │       "2550" │      -- │ "GABA<sub>B1</sub>" │
└──────────────────────┴──────────────────────────────┴────────┴──────────────┴─────────┴─────────────────────┘
Querying <http://dbpedia.org/sparql?default-graph-uri=http%3A%2F%2Fdbpedia.org&should-sponge=&> for
SELECT ?label ?humanEntrez {  _:gene <http://dbpedia.org/ontology/entrezgene> ?humanEntrez .
  _:gene <http://www.w3.org/2000/01/rdf-schema#label> ?label .
  FILTER ( lang(?label) = "en" )
FILTER ((?humanEntrez="2550"))
} yielded
┌──────────────┬─────────────────────┐
│ ?humanEntrez │ ?label              │
│       "2550" │ "GABAB receptor"@en │
└──────────────┴─────────────────────┘
┌─────────────────────┬───────────────────────────────────────────────────────────────────┬──────────────┬──────────────────────┬──────────────────────────────┬─────────────────────┐
│ ?label              │ ?post                                                             │ ?humanEntrez │ ?code                │ ?family                      │ ?iupharNm           │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49d3249aec0b0> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49d230abda515> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49cab494999c6> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49cab3f287c53> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
│ "GABAB receptor"@en │ <http://hcls.deri.org/atag/data/gabab_example.html#49c22f5a6faa9> │       "2550" │ "2.3:GABA:1:GABAB1:" │ "GABA<sub>B</sub> receptors" │ "GABA<sub>B1</sub>" │
└─────────────────────┴───────────────────────────────────────────────────────────────────┴──────────────┴──────────────────────┴──────────────────────────────┴─────────────────────┘

Feel free to contact eric+7tm@w3.org with questions or comments.

$Id: 7tmdemo.html,v 1.12 2010/03/26 02:02:04 eric Exp $