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BEL Statements: BioCreative BEL Track

 

The data for one BEL statement consists of two parts: The BEL statement itself and a corresponding evidence sentence. Additionally we provide a conversion of the BEL statements in BioC format, and also provide equivalent graphical representations. Check the examples provided in the next sections in order to better understand these formats. 

All Files can be downloaded here:

 

 

Format Examples

 

BEL statement
SEN:10000104 	cat(p(HGNC:FAS)) increases cat(p(HGNC:CASP9)) 	BEL:20000164

 

 

BEL sentence
SEN:10000104        10786680        we demonstrate that two of the early events after Fas ligation are the release of cytochrome c from the mitochondria and activation of caspase-9.        A

 

 

Equivalent BioC statement
<document>
    <id>20000164</id>
    <passage>
      <infon key="Sentence id">10000104</infon>
      <infon key="PMID">10786680</infon>
      <offset/>
      <text>we demonstrate that two of the early events after Fas ligation are the release of cytochrome c from the mitochondria and activation of caspase-9</text>
      <annotation id="a386">
        <infon key="HGNC">FAS</infon>
        <infon key="type">proteinAbundance</infon>
        <location offset="" length=""/>
        <text/>
      </annotation>
      <annotation id="a387">
        <infon key="HGNC">CASP9</infon>
        <infon key="type">proteinAbundance</infon>
        <location offset="" length=""/>
        <text/>
      </annotation>
      <annotation id="a388">
        <infon key="relationship">increases</infon>
        <infon key="type">relationship</infon>
        <text/>
      </annotation>
      <relation id="r274">
        <infon key="type">increases</infon>
        <node refid="r275" role="cause"/>
        <node refid="r276" role="theme"/>
        <node refid="a388" role="relationship"/>
      </relation>
      <relation id="r275">
        <infon key="type">catalyticActivity</infon>
        <node refid="a386" role="self"/>
      </relation>
      <relation id="r276">
        <infon key="type">catalyticActivity</infon>
        <node refid="a387" role="self"/>
      </relation>
    </passage>
  </document>
 

Graphical representation of the BioC version of the BEL statement:


 
The same BEL statement automatically expanded into RDF
<http://www.openbel.org/bel/cat_p_HGNC_FAS> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/Term> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/AbundanceActivity> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS> <http://www.openbel.org/vocabulary/hasActivityType> <http://www.openbel.org/vocabulary/Catalytic> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS> <http://www.w3.org/2000/01/rdf-schema#label> "cat(p(HGNC:FAS))" .
<http://www.openbel.org/bel/cat_p_HGNC_FAS> <http://www.openbel.org/vocabulary/hasChild> <http://www.openbel.org/bel/p_HGNC_FAS> .
<http://www.openbel.org/bel/p_HGNC_FAS> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/Term> .
<http://www.openbel.org/bel/p_HGNC_FAS> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/ProteinAbundance> .
<http://www.openbel.org/bel/p_HGNC_FAS> <http://www.w3.org/2000/01/rdf-schema#label> "p(HGNC:FAS)" .
<http://www.openbel.org/bel/p_HGNC_FAS> <http://www.openbel.org/vocabulary/hasConcept> <http://www.openbel.org/bel/namespace/FAS> .
<http://www.openbel.org/bel/cat_p_HGNC_CASP9> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/Term> .
<http://www.openbel.org/bel/cat_p_HGNC_CASP9> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/AbundanceActivity> .
<http://www.openbel.org/bel/cat_p_HGNC_CASP9> <http://www.openbel.org/vocabulary/hasActivityType> <http://www.openbel.org/vocabulary/Catalytic> .
<http://www.openbel.org/bel/cat_p_HGNC_CASP9> <http://www.w3.org/2000/01/rdf-schema#label> "cat(p(HGNC:CASP9))" .
<http://www.openbel.org/bel/cat_p_HGNC_CASP9> <http://www.openbel.org/vocabulary/hasChild> <http://www.openbel.org/bel/p_HGNC_CASP9> .
<http://www.openbel.org/bel/p_HGNC_CASP9> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/Term> .
<http://www.openbel.org/bel/p_HGNC_CASP9> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/ProteinAbundance> .
<http://www.openbel.org/bel/p_HGNC_CASP9> <http://www.w3.org/2000/01/rdf-schema#label> "p(HGNC:CASP9)" .
<http://www.openbel.org/bel/p_HGNC_CASP9> <http://www.openbel.org/vocabulary/hasConcept> <http://www.openbel.org/bel/namespace/CASP9> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS_Increases_cat_p_HGNC_CASP9> <http://www.openbel.org/vocabulary/hasSubject> <http://www.openbel.org/bel/cat_p_HGNC_FAS> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS_Increases_cat_p_HGNC_CASP9> <http://www.openbel.org/vocabulary/hasObject> <http://www.openbel.org/bel/cat_p_HGNC_CASP9> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS_Increases_cat_p_HGNC_CASP9> <http://www.openbel.org/vocabulary/hasRelationship> <http://www.openbel.org/vocabulary/Increases> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS_Increases_cat_p_HGNC_CASP9> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/Statement> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS_Increases_cat_p_HGNC_CASP9> <http://www.w3.org/2000/01/rdf-schema#label> "cat(p(HGNC:FAS)) increases cat(p(HGNC:CASP9))" .
_:7629ad00-a638-0132-68b0-0021cc689191 <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.openbel.org/vocabulary/Evidence> .
<http://www.openbel.org/bel/cat_p_HGNC_FAS_Increases_cat_p_HGNC_CASP9> <http://www.openbel.org/vocabulary/hasEvidence> _:7629ad00-a638-0132-68b0-0021cc689191 .
_:7629ad00-a638-0132-68b0-0021cc689191 <http://www.openbel.org/vocabulary/hasStatement> <http://www.openbel.org/bel/cat_p_HGNC_FAS_Increases_cat_p_HGNC_CASP9> .

Other

Additional supporting material will be releasead in the course of the challenge. For example, during the Biomedical Linked Annotation Hackathon (Kashiwa, Japan, Feb 2015) we converted some of the annotations in JSON format and uploaded them in PubAnnotation, which makes them viewable with the TextAE editor. See below an example for the statement discussed above:

 

 

Additional material will be provided in due course. 

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