From ImageWeb

Data available through SPARQL endpoints

These pages have links to some SPARQL endpoints:

• http://esw.w3.org/topic/SparqlEndpoints - Data available through SPARQL endpoints
• http://sites.wiwiss.fu-berlin.de/suhl/bizer/d2r-server/ - a few endpoints published by the D2R server.

Some specific end points:

• http://www4.wiwiss.fu-berlin.de/dblp/ - bibliography server

Querying annotated images of Gene Expression in fruitfly embryogenesis

• Get the gene expression that is located in "pole cell":

PREFIX oborel: <http://www.obofoundry.org/ro/ro.owl#>
SELECT * WHERE {
?gp oborel:located_in <http://spade.lbl.gov:2021/resource/location/1>
}

or

PREFIX oborel: <http://www.obofoundry.org/ro/ro.owl#>
SELECT * WHERE {
?gp oborel:located_in ?location .
?location rdf:type <http://purl.org/obo/xref/FBbt:00000092>
}

In this dataset, the anatomical information about each gene expression is annotated using terms from the FlyBase Anatomy controlled vocabury. This ontology can be downloaded from http://www.berkeleybop.org/ontologies. Each term in the ontology is a numeric ID, (FBbt_nnnnnnnn) and it is described by the rdfs:label. Each term is mapped to a form of "db:location/nn" in this Sparql endpoint. That is, the <db:location/1> maps to the term <FBbt_00000092> for a polo cell.

• Get information about the above gene expression

PREFIX oborel: <http://www.obofoundry.org/ro/ro.owl#>
PREFIX xref: <http://purl.org/obo/xref/>
SELECT * WHERE {
?gp oborel:located_in ?location .
?location rdf:type <xref:FBbt:00000092> .
?gp ?predicate ?object
}

This gets information, for examle:

• the duration information about the expression, e.g. <db:duration/1>
• has participates from <db:gene_product/4492>,
• rdf:type <http://www.berkeleybop.org/ontology/oban/alpha#CoordinatedExpressionEvent>
• the image it depicts of: insitu:/img_dir_23/insitu23227.jpe

• Get the information about the gene product <db:gene_product/4492>

SELECT *
WHERE {
  { <http://spade.lbl.gov:2021/resource/gene_product/4492> ?predicate ?hasValue }
  UNION
  { ?isValueOf ?predicate <http://spade.lbl.gov:2021/resource/gene_product/4492> }
}

This gets the information about the gene product, including:

• its relationship with an anatomical term
• different identifiers for the gene, such as its cDNA identity(LD11379), its FlyBase name (CG4183), its FlyBase ID (FBgn0001225), etc.

The cDNA can be used to query the GO dataset. (http://spade.lbl.gov:2021/sparql)

Cross search with Gene Ontology Endpoint

Using results from previous queries over the Gene Expression Image endpoint, we can do a subsequent query over the Gene Ontology endpoint. For example, search for the information about the gene product "CG4138", which participates in the one of the gene expressions located in the "pole cell".

prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix skos: <http://www.w3.org/2004/02/skos/core#>
SELECT ?name ?p ?o WHERE {?s rdfs:label ?name .
?s skos:altLabel ?syn .
filter regex(?syn, "CG4183", "i") .
?s ?p ?o
}

This returns the following information about the gene:

• its alternative labels
• descriptions about the gene
• its role related to another GO term
• its type, as a <gene>
• its DNA sequence
• and the organism information about the gene, expressed using terms from the NCBI taxonomy (NCBITaxon_7227)

Cross search with UniProt Endpoint

The results from the above two endpoints cannot be used to do a subsequent search over the UniProt endpoint. This is because that the published UniProt Sparql endpoint is based on an older version of Sparql. We did not try to do the cross search programmatically. Instead a query is performed in the UniProt interface, to look for information about the gene (uniprot:P02517, i.e. flybase:FBgn0001225).

The query gives rich information about the protein held in UniProt, such as its citation, cross-references for many other databases, its taxonomical information, etc.