Biological pathways provide intuitive diagrams of the interactions underlying biological processes. For example, the SIDS Susceptibility Pathways show interactions between metabolites, genes and proteins, such as DDC catalyzing the conversion of L-DOPA to Dopamine (look for the items highlighted in yellow on the lower right). The site WikiPathways is an open, collaborative platform dedicated to drawing and sharing biological pathways.
A common challenge in biological research is dealing with an ever-growing number of terms, some of them synonyms and others almost synonyms but with important differences in meaning. For instance, WikiPathways uses the term “GeneProduct” in its annotation panels (to see an example, click the “TNF” box in the upper left corner of the SIDS pathway). A WikiPathways user might be unsure of the exact definition of the “GeneProduct”, so it would be useful to point the user to the definition of the term in the WikiPathways vocabulary. This could be done with a link or a mouse over display. Another example from the SIDS pathway is the Extracellular Space, which could display information from this IRI: href="http://identifiers.org/go/GO:0005615".
The first two examples are easy to display because each IRI has an HTML representation, but a more challenging example is Protein. This IRI returns RDF but does not have an HTML representation, so it would be necessary to extract information from the RDF, such as the definition, and display it in a small, easy-to-read panel.
Goal
Develop a browser-based display system for dereferenced IRIs. The system will use content-type negotiation to request an HTML representation of a resource, but it will be able to convert JSON-LD, RDF and OWL representations into an HTML representation for display in a small details panel or pop-over. Additionally, develop a plugin for the WikiPathways viewer/editor pvjs that integrates the display system. Optionally, if time allows, add functionality to allow pvjs users to switch vocabularies for the GUI display, mapping from the built-in vocabularies to the user-preferred vocabularies with SKOS files.
Background
Biological pathways provide intuitive diagrams of the interactions underlying biological processes. For example, the SIDS Susceptibility Pathways show interactions between metabolites, genes and proteins, such as DDC catalyzing the conversion of L-DOPA to Dopamine (look for the items highlighted in yellow on the lower right). The site WikiPathways is an open, collaborative platform dedicated to drawing and sharing biological pathways.
A common challenge in biological research is dealing with an ever-growing number of terms, some of them synonyms and others almost synonyms but with important differences in meaning. For instance, WikiPathways uses the term “GeneProduct” in its annotation panels (to see an example, click the “TNF” box in the upper left corner of the SIDS pathway). A WikiPathways user might be unsure of the exact definition of the “GeneProduct”, so it would be useful to point the user to the definition of the term in the WikiPathways vocabulary. This could be done with a link or a mouse over display. Another example from the SIDS pathway is the Extracellular Space, which could display information from this IRI: href="http://identifiers.org/go/GO:0005615".
The first two examples are easy to display because each IRI has an HTML representation, but a more challenging example is Protein. This IRI returns RDF but does not have an HTML representation, so it would be necessary to extract information from the RDF, such as the definition, and display it in a small, easy-to-read panel.
Goal
Develop a browser-based display system for dereferenced IRIs. The system will use content-type negotiation to request an HTML representation of a resource, but it will be able to convert JSON-LD, RDF and OWL representations into an HTML representation for display in a small details panel or pop-over. Additionally, develop a plugin for the WikiPathways viewer/editor pvjs that integrates the display system. Optionally, if time allows, add functionality to allow pvjs users to switch vocabularies for the GUI display, mapping from the built-in vocabularies to the user-preferred vocabularies with SKOS files.
Links
Difficulty Level: 3
Demonstrated experience with semantic data handling is preferred
Technology and Skills
Potential Mentors
Contact
Anders Riutta, Alex Pico, Kristina Hanspers