Simplifying the mechanics toward building a Biodiversity

Knowledge Graph

David P. ShorthouseChristian Gendreau

Université de Montréal / Canadensys

@dpsSpiders, @christgendreau

Biodiversity Knowledge Graph

RESTful & Resourceful APIs

JSON (JavaScript Object Notation)

OpenURL

• Created by librarian at University of Ghent in 1990s

• Used by libraries to connect patrons to subscription content

• Assists with the resolution of a request for a web resource

• ANSI/NISO Z39.88 standard• Base URL + structured query string

OpenURL

• Version 0.1 http://resolver.example.edu/cgi?genre=book&isbn=0836218310&title=The+Far+Side+Gallery+3

• Version 1.0 http://resolver.example.edu/cgi?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:book&rft.isbn=0836218310&rft.btitle=The+Far+Side+Gallery+3

COinS (Content in Spans) in HTML

<span class="Z3988" title="ctx_ver=Z39.88-2004&amp;rfr_id=info%3Asid%2Fmendeley.com%2Fmendeley&amp;rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&amp;rft.genre=article&amp;rft.date=2014&amp;rft.pages=n%2Fa-n%2Fa&amp;rft.atitle=Three+decades+of+vegetation+changes+in+peatlands+isolated+in+an+agricultural+landscape&amp;rft.jtitle=Applied+Vegetation+Science&amp;rft.title=Applied+Vegetation+Science&amp;rft.aulast=Pasquet&amp;rft.aufirst=Salom%C3%A9&amp;rft.au=Pellerin%2C+St%C3%A9phanie&amp;rft.au=Poulin%2C+Monique&amp;rft_id=info%3Adoi%2F10.1111%2Favsc.12142&amp;rft.issn=14022001"><!--COinS--></span>

http://www.biodiversitylibrary.org/openurlhelp.aspx

Problems with OpenURL

• Never fully satisfied anyone– Search vs. find– Granularity of linking (journal? article? page?)– Lazy exposure of known holdings

• Output does not have a specified format

OpenURL

Well-specified query parametersVersioning is explicit

Are there Canadidate Query Parameters in Our Community?

What About the Response Structure?

Vascular Plants of Canada

http://data.canadensys.net/vascan/api

http://eol.org/api/pages/1.0/1045608.json

http://www.itis.gov/…/…/getFullRecordFromTSN?tsn=202384

JSON-LD

JSON-LD

• W3C Recommendation, January 2014• Allows specification of @contexts– What the terms mean & what are their

characteristics• Allows specification of @id• May not break existing API responses• Transformation tools to express as RDF

Example

Encyclopedia of Life TraitBank®

JSON-LD

Well-specified semantics and structure for the content

Take Home Messages

• We should express versioning in our APIs• We should reuse DwC terms as API query parameters• We should use JSON-LD for API responses• Consumers can use services with (greater)

confidence• Documentation can be shared• It may be possible to inch toward a simple, effective

biodiversity knowledge graph without breaking existing JSON-based APIs

How Do We Get There?

• Workflow and Services Interest Group• Develop a common set of requirements• Early adopters• Proofs-of-concept, client applications• Libraries of code to consume• A name and a web presence