HCLSIG/SWANSIOC/Examples

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Examples of current approaches to the representation of scientific statements, hypotheses and relationships

This page will collect examples of current RDF/OWL - based approaches to the representation of scientific statements, hypotheses and relationships, as well as discourse representation.

SWAN

The SWAN ontology is representing the scientific discourse through 'Discourse Elements', these are typically 'Hypothesis', 'Claim', 'Research Question' and 'Comment'. The discourse elements can:

  • refer or be connected to other discourse elements through relationships like: consistent, inconsistent and alternative.
  • refer or be connected to other entities such as - supportive, discussing or refuting - evidence and life science entities - genes, proteins, organisms, antibodies, GO processes...
  • be annotated with controlled vocabularies - also SKOS based vocabularies
  • be organized to define a scientific discourse - for instance an hypothesis can be represented as a discourse made of claims, questions and/or other hypothesis
  • refer or be connected with experiments and experimental data (in progress)

for more details see the SWAN Ontology.

Example of Claim

The following claim has been extracted from the SWAN Alzheimer Knowledge Base. As the SWAN Alzheimer knowledge base is currently using LSIDs as unique identifiers - we are in the process of changing our naming strategy - for demonstrations purposes only I will use more readable unique identifiers.


<http://hypothesis.alzforum.org/researchstatement/100> a swan_discourse-elements:ResearchStatement ;
   swan_discourse-elements:title "Aside from its well-established role in promoting the stabilization of microtubules (MTs), tau may have additional functions as a result of its interactions with other structures and enzymes"@en;
   swan_discourse-elements:description "Poorly defined interactions and functions of tau contribute to the difficulty of understanding how pathologically altered tau mediates neurodegeneration. For example, tau interacts with the plasma membrane, the actin cytoskeleton and with src tyrosine kinases such as FYN."@en;
   swan_commons:citesAsSupportiveEvidence <http://hypothesis.alzforum.org/citation/321>,
       <http://hypothesis.alzforum.org/citation/322>,
       <http://hypothesis.alzforum.org/citation/323>,
       <http://hypothesis.alzforum.org/citation/324>,
       <http://hypothesis.alzforum.org/citation/325>;
   swan_commons:researchStatementQualifiedAs <http://swan.mindinformatics.org/ontologies/1.2/rsqualifiers/claim>;
   swan_qualifiers:qualifiedBy <http://swan.mindinformatics.org/ontologies/1.2/pathogenic-narrative/initial_condition>;
   swan_discourse-relationships:refersTo <http://hypothesis.alzforum.org/protein/201>;
   swan_pav:curatedBy <http://hypothesis.alzforum.org/people/gwen_wong>;
   swan_pav:createdBy <http://hypothesis.alzforum.org/people/elizabeth_wu>;
   swan_pav:createdOn "April 1, 2009".


Example of Hypothesis

The following hypothesis has been extracted from the SWAN Alzheimer Knowledge Base and contains the claim of the previous example. The number of contained statements has been reduced to increase readability.


<http://hypothesis.alzforum.org/researchstatement/99> a swan_discourse-elements:ResearchStatement ;
   swan_discourse-elements:title "Tau-linked disease processes drive the onset and progression of AD and related tauopathies"@en;
   swan_discourse-elements:description "This hypothesis suggests that tau mediates neurodegeneration. The authors provide analysis of the progress made towards a mechanistic  understanding of tau-mediated neurodegeneration, and a discussion of the therapeutic strategies that target the most severe toxic consequences of tau pathologies. This hypothesis summarizes the current understanding of normal tau functions and the pathogenic effects of tau aggregates in AD and related neurodegenerative tauopathies, in the onset and progression of these disorders."@en;
   swan_commons:researchStatementQualifiedAs <http://swan.mindinformatics.org/ontologies/1.2/rsqualifiers/hypothesis>;
   swan_discourse-elements:contains <http://hypothesis.alzforum.org/researchstatement/100>,
      <http://hypothesis.alzforum.org/researchstatement/101>,
      <http://hypothesis.alzforum.org/researchstatement/102>,
      <http://hypothesis.alzforum.org/researchstatement/103>;
   swan_citations:derivedFrom <http://hypothesis.alzforum.org/citation/320>;
   swan_pav:authoredBy <http://hypothesis.alzforum.org/personname/23>,
      <http://hypothesis.alzforum.org/personname/24>,
      <http://hypothesis.alzforum.org/personname/25>;
   swan_pav:curatedBy <http://hypothesis.alzforum.org/people/gwen_wong>;
   swan_pav:createdBy <http://hypothesis.alzforum.org/people/elizabeth_wu>;
   swan_pav:createdOn "April 1, 2009".

<http://hypothesis.alzforum.org/personname/23> a swan_agents:PersonName ;
   swan_agents:firstName "Carlo";
   swan_agents:lastName "Ballatore".

<http://hypothesis.alzforum.org/personname/24> a swan_agents:PersonName ;
   swan_agents:firstName "Virginia";
   swan_agents:lastName "Lee".

<http://hypothesis.alzforum.org/personname/25> a swan_agents:PersonName ;
   swan_agents:firstName "John";
   swan_agents:lastName "Trojanowski".

<http://hypothesis.alzforum.org/citation/320> a swan_citations:JournalArticle ;
   swan_citations:title "Tau-mediated neurodegeneration in Alzheimer's disease and related disorders" ;
   swan_citations:journalName "Nature reviews. Neuroscience" ;
   swan_citations:contributionAuthor <http://hypothesis.alzforum.org/personname/23>,
       <http://hypothesis.alzforum.org/personname/24>,
       <http://hypothesis.alzforum.org/personname/25>;
   swan_citations:contributionPublishingDate "2007 Sep";
   swan_citations:volume "8";
   swan_citations:issue "9";
   swan_citations:pagination "663-72";
   swan_citations:doi "10.1038/nrn2194" .


Example of Relationships between Discourse Elements

The following discourse elements have been extracted from the SWAN Alzheimer Knowledge Base.


<http://hypothesis.alzforum.org/researchstatement/145> a swan_discourse-elements:ResearchStatement ;
   swan_discourse-elements:title "With its ability to modulate MT-dynamics, tau contributes directly or indirectly to key structural and regulatory cellular functions"@en;
   swan_discourse-elements:description "For example, the action of tau on the MT network has great importance in maintaining an appropriate morphology of neurons, the processes of which typically extend over relatively great distances, making neurons the most asymmetrical of all cells. Furthermore, because the MT network is key to the sophisticated transport machinery that allows signalling molecules, trophic factors and other essential cellular constituents, including organelles (for example mitochondria and vesicles), to travel along the axons (axonal transport), then tau clearly has profound effects on axonal transport and, hence, on the function and viability of neurons and their highly extended processes. Importantly, under normal physiological conditions, tau is in a constant dynamic equilibrium, on and off the MTs. This equilibrium is thought to be controlled primarily by the phosphorylation state of tau, which in turn is determined by the actions of kinases and phosphatases. Indeed, frequent cycles of binding and detachment of tau from the MTs (corresponding to phosphorylations and dephosphorylations, respectively) may be needed to allow effective axonal transport."@en;
   swan_commons:citesAsSupportiveEvidence <http://hypothesis.alzforum.org/citation/361>,
       <http://hypothesis.alzforum.org/citation/366>;
   swan_commons:researchStatementQualifiedAs <http://swan.mindinformatics.org/ontologies/1.2/rsqualifiers/claim>;
   swan_qualifiers:qualifiedBy <http://swan.mindinformatics.org/ontologies/1.2/pathogenic-narrative/initial_condition>;
   swan_discourse-relationships:refersTo <http://hypothesis.alzforum.org/protein/241>;
   swan_discourse-relationships:inconsistentWith <http://hypothesis.alzforum.org/researchstatement/198>;
   swan_pav:curatedBy <http://hypothesis.alzforum.org/people/gwen_wong>;
   swan_pav:createdBy <http://hypothesis.alzforum.org/people/elizabeth_wu>;
   swan_pav:createdOn "April 17, 2009".


Example of document annotation with the SWAN annotation module

The SWAN annotation module - part of the SWAN ontology ecosystem - allows to define the links in between the text inside online documents and entities such as discourse elements, life science entities and terms belonging to controlled vocabularies. Such annotation can be serialized and published in the RDFa syntax that can be embedded into HTML pages or in RDF files that can be delivered with the original document when we can't control the document publishing process.

(add example here)

SWAN Ontology, SWAN Alzheimer Knowledge Base at Alzforum, SWAN HCLSIG Notes (in progress), SWAN-SIOC integration HCLSIG Notes (in progress),
Ciccarese Paolo et Al. The SWAN biomedical discourse ontology. J Biomed Inform. 2008 Oct;41(5):739-51. Epub 2008 May 4.

aTags

RDF of an aTag, shown in Turtle syntax:

<http://hcls.deri.org/atag-data/pastebin.html#49ddfee65f7f4> a sioc:Item ;
   sioc:content "Huperzine A acts as a non-competitive antagonist of the NMDA receptors"@en ;
   sioc:topic <http://dbpedia.org/resource/Huperzine_A> ,
      <http://purl.org/obo/owl/GO#GO_0048019> ,
      <http://dbpedia.org/resource/NMDA_receptor> ;
   rdfs:seeAlso <http://www.ncbi.nlm.nih.gov/pubmed/11516831> .


aTags are typically serialized and published in the RDFa syntax that can be embedded into HTML pages. Entities used for 'tagging' are usually taken from DBpedia, OBO and Uniprot RDF.

aTags are only used for the representation of statements, but they do not offer specialized vocabulary for capturing details about evidence or discourse representation. Such information should be encoded with SWAN. Basic interoperability between aTags and SWAN is made possible by the SWAN-SIOC alignment.

Collection of public aTag datasets

SIOC ontology specification (aTags make use of the SIOC vocabulary)

SALT

(add SALT examples here)

SALT ontologies/schemas

Others

(add description of other approaches here)