Thursday, November 24, 2016

The Semantic Web made fun: d3sparql

Screenshot 2016 11 24 10 08 22

Continuing my on-again off-again relationship with the Semantic Web, I stumbled across a cool approach to visualising the results of SPARQL queries. Toshiaki Katayama (@tktym) has put together d3sparql, a set of Javascript scripts that takes SPARQL queries and formats the results graphically using D3.

For example, give the SPARQL endpoint, the following query retrieves the NCBI classification for the tardigrade family Hypsibiidae:

PREFIX rdfs: PREFIX up: SELECT ?root_name ?parent_name ?child_name FROM WHERE { VALUES ?root_name { "Hypsibiidae" } ?root up:scientificName ?root_name . ?child rdfs:subClassOf+ ?root . ?child rdfs:subClassOf ?parent . ?child up:scientificName ?child_name . ?parent up:scientificName ?parent_name . }

By outputting the results as a list of parent-child pairs, it is straightforward to convert the output of this query into a form that D3 accepts, so we can get a tree like this:

HypsibiidaeHebesuncusHebesuncus conjugensHebesuncus ryaniHebesuncus sp. Hebe_06_218Hebesuncus sp. Hebe_06_221DiphasconDiphascon sp. CJS-2007aDiphascon sp. CJS-2007bDiphascon cf. scoticum MC-2011Diphascon (Adropion) sp. MC-2011Diphascon maucciDiphascon puniceumDiphascon sp. Diph_06_114Diphascon sp. Diph_06_147Diphascon sp. Diph_07_008Diphascon sp. Diph_07_168Diphascon sp. Diph_07_169Diphascon sp. Diph_07_176Diphascon alpinumDiphascon sp. F6456Diphascon sp. F6457Diphascon sp. F6458Diphascon sp. F6459Diphascon sp. F6460Diphascon pingueDiphascon belgicaeDiphascon scoticumDiphascon higginsiDiphascon nodulosumDiphascon pataneiDiphascon ramazzottiiDiphascon sp. F7485Diphascon sp. Diph06_146Diphascon sp. Diph07_25Diphascon sp. Diph07_28Diphascon sp. Diph07_29Diphascon sp. Diph07_61Diphascon sp. Diph07_64AcutuncusAcutuncus antarcticusAcutuncus sp. PC-2013HypsibiusHypsibius cf. convergens 1 EK-2007Hypsibius klebelsbergiHypsibius scabropygusHypsibius cf. convergens 2 EK-2007Hypsibius dujardiniHypsibius sp. CJS-2008Hypsibius sp. 'Moon 1997'Hypsibius sp. F7889Hypsibius convergensHypsibius pallidusHypsibius cf. convergens MD-2013BorealibiusBorealibius zetlandicusThuliniusThulinius stephaniaeThulinius sp. JCR-2003Thulinius sp. DVL-2010Thulinius augustiIsohypsibiusIsohypsibius granuliferIsohypsibius cambrensisIsohypsibius asperIsohypsibius prosostomusIsohypsibius papilliferIsohypsibius sp. Tardi_OakIsohypsibius elegansIsohypsibius sp. Tar179Isohypsibius sp. Tar194Isohypsibius sp. Tar195Isohypsibius dastychiHalobiotusHalobiotus crispaeHalobiotus stenostomusRamazzottiusRamazzottius oberhaeuseriRamazzottius cf. oberhaeuseriRamazzottius sp. Rama_07_123Ramazzottius sp. F10349Ramazzottius sp. F10350Ramazzottius sp. F10470Ramazzottius sp. F10471Ramazzottius sp. F10472Ramazzottius sp. F10473Ramazzottius sp. F3679Ramazzottius sp. F3680Ramazzottius sp. F3681Ramazzottius sp. F3682Ramazzottius sp. F3683Ramazzottius sp. F6917Ramazzottius sp. F6918Ramazzottius sp. F6919Ramazzottius sp. F6920Ramazzottius sp. F6921Ramazzottius sp. F6922Ramazzottius varieornatusPseudobiotusPseudobiotus sp. SHR-2005Pseudobiotus kathmanaePseudobiotus megalonyxAstatumenAstatumen trinacriaeEremobiotusEremobiotus alicataiDoryphoribiusDoryphoribius flavusDoryphoribius macrodonItaquasconItaquascon placophorumMixibiusMixibius cf. saracenus MC-2011Mixibius saracenusPlaticristaPlaticrista angustata

The ability to quickly generate trees, charts, and maps from SPARQL queries makes things a lot easier. We can play around a little and explore things. The strength (and challenge) of SPARQL is that it is very open-ended, you can more or less develop queries to do anything. Being able to visualise the results will help guide that exploration.

The code for d3sparql is on GitHub. One "gotcha" is that the cached examples and external Javascript libraries aren't included. I've forked the repository here and added the missing files, so that if you grab that version it works straight out of the box.