Saturday, March 30, 2019

What metabolites are found in which species? Nanopublications from Wikidata

In December I reported about Groovy code to create nanopublications. This has been running for some time now, extracting nanopubs that assert that some metabolite is found in some species. I send the resulting nanopubs to Tobias Kuhn, to populate his Growing Resource of Provenance-Centric Scientific Linked Data (doi:10.1109/eScience.2018.00024, PDF).

Each data set comes with an index pointing to the individual nanopubs, and that looks like this:

I wonder what options I have to to archive the full set up nanopublications on Figshare or Zenodo, and see that DOI show up here...

Tuesday, March 05, 2019

New paper: "Beyond Pathway Analysis: Identification of Active Subnetworks in Rett Syndrome"

Figure 4 of the article.
Ryan Miller and Friederike Ehrhart worked together in this paper on furthering our understanding of the Rett syndrome  (doi:10.3389/fgene.2019.00059). They looked at the following: our biological pathways are social constructs that help us think and talk about the biology in our body (and other animals, plants, etc, of course). What if we ignore the boundaries of those constructs, can we learn the pathways? Turns out, sort of.

Using PathVisio, WikiPathways, and Cytoscape's jActiveModules they developed new modules that capture a particular aspect of the biology, and, as usual, color the transcriptional change on top of that. The Methods is richly annotated and all stuff is open source.

The authors conclude with mostly bioinformatics conclusions. No new shocking new insights into Rett syndrome (yet, but unfortunately), but they indicate that by taking advantage of our interoperability approaches (e.g. the ELIXIR Recommended Interoperability Resource BridgeDb, using mappings from Ensembl, HMDB, ChEBI, and Wikidata) pathway resources can be integrated, allowing these approaches.

Mind you, each pathway, and regularly down to the gene, metabolite, and interaction level, the information is not just built in collaboration with research communities, curated, but also backed by literature: 22494 unique PubMed references of which almost 4000 unique to WikiPathways (i.e. not in Reactome).

Have fun!

Monday, March 04, 2019

New projects: RiskGONE and NanoSolveIT

This January two new Horizon 2020 projects started for me: RiskGone and NanoSolveIT. It kept me busy in the past few weeks, with the kick-off meeting of the latter task week in Athens. Both continue on previous work of the EU NanoSafety Cluster, and I'm excited to continue with research done during the eNanoMapper project.

NanoSolveIT "aspires to introduce a ground-breaking in silico Integrated Approach to Testing and Assessment (IATA) for the environmental health and safety of Nanomaterials (NM), implemented through a decision support system packaged as both a stand-alone open software and via a Cloud platform."

I will be involved here in the knowledge infrastructure. Plenty of research there to be done around the representation of chemical composition of the nanomaterials, the structuring and consistency of ontologies to capture and integrate everything, how to capture our knowledge around the adverse outcome pathways, and how to use this all in predictive computation.

"The focus of RiskGONE will be to produce nano-specific draft guidance documents for application to ENM RA; or, alternatively, to suggest ameliorations to OECD, ECHA, and ISO/CEN SOPs or guidelines. Rather than producing assays and methods ex novo, this will be achieved through Round Robin exercises and multimodal testing of OECD TGs and ECHA methods supporting the “Malta-project”, and on methods not yet considered by OECD." (from the CORDIS website)

Here our involvement will be around similar topics.

Oh, and like all new H2020 projects, FAIR and Open Data is central words.