Linking molecular data (RETT syndrome)

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General/Content organiser:

  • Egon Willighagen, Friederike Ehrhart

Logistics organiser:

  • DTL


Maastricht University UNS60

BYOD Dates

Hackathon: November 1-3

First teleconference followup: Friday 31 October

Second teleconference followup: will follow

BYOD Introduction/Motivation

Nanopublications have a lot to offer to WikiPathways, and the Maastricht WikiPathways team has two incentives. First, WikiPathways contains a lot of statements backed by literature (~12500 different PubMed papers [0]); we wish to expose these statements as nanopublications with provenance, so that they can be linked to other data sets. Second, in the future, we like to use external nanopublications as information sources to be cited, just like PubMed papers are now cited. Using this kind of integration we expect to be able to increase the amount of provenance available in WikiPathways and we want to use this to explore which types of external nanopublications can be considered as evidence for statements that are part of pathways.


The goal of this BYOD is aimed at the first motivation. We like to make nanopublications out of WikiPathways and link this up to other data source. For this we would bring our data, invite a nanopublication expert to help us get the details right, release the software that create these nanopublications, share these online for consumption, ideally via a nanopublication repository. The nanopublication to be created will be based on links between genes, metabolite, interactions, and reactions, and the PubMed literature. Focus will first be on those statements that can be linked to other data brought to the meeting (if any, given the short notice). As a possible specific BYOD workshop outcome, compatibility with the “AIDA Nanopubs extracted from GeneRIF” data set may be explored, which makes statements about genes and proteins. This would require normalizing gene identifiers in pathways to those used in this data set using BridgeDb.

List of the target datasets and their main characteristics

  • WikiPathways
  • Clinical data from the Rett Expertise Center Maastricht
  • NanoPublications


Data experts:

  • Michel Dumontier, Luiz Olavo Bonino (Dutch Techcentre for Life Sciences, NL), Mark Wilkinson (Centro de Biotecnología y Genómica de Plantas

UPM-INIA, Madrid/Spain) Dataset owners/experts:

Data expert trainees:

  • Egon Willighagen (Maastricht​ ​University,​ ​NL), Nuno​ ​Nunes (Maastricht​ ​University,​ ​NL),​ Jonathan​ ​Melius (Maastricht​ ​University,​ ​NL)​, Tobias Kuhn (Vrije Universiteit Amsterdam, NL)

Subject matter experts:

  • Freddie Ehrhart (Maastricht​ ​University,​ ​NL), Leopold Curfs, Eric Smeets, Henk van Kranen (Maastricht University Medical

Center+), Elisa Cirillo (Maastricht​ ​University,​ ​NL), Rajaram Kaliyaperumal (Leiden University Medical Center, NL)

See also

BYOD meetings