In September 2013 I became a Lecturer in Computer Science at Heriot-Watt University where I have joined the Intelligent Systems research group. Between 2009 and 2013 I held a postdoc research position in the Information Management Group at the University of Manchester. Prior to that I was in the Information Retrieval group at the University of Glasgow. I obtained my PhD on integrating streams of data in 2007 from Heriot-Watt University where I worked in the Database, Information and Knowledge-base Systems group.
I once again attended the European BioHackathon which took place in November outside of Paris. It was another intense week with 150 developers from across Europe (and beyond) working together on 34 topics.
Bioschemas was well represented in the topics and the hacking activities of the week. By the end of the week we had an approach for marking up Intrinsically Disordered Proteins and Rare Disease resources. We also had several resources with newly deployed or improved Bioschemas markup.
For a fuller overview of the event and outcomes, please see the ELIXIR news item.
During the summer, BridgeDb has had a Google Summer of Code student working on extending the system to work with secondary identifiers; these are alternative identifiers for a given resource.
The student Manas Awasthi has maintained a blog of his experiences. Below are some excerpts of his activity.
Google Summer of Code 2019: Dream to Reality Manas Awasthi May 28 · 3 min read Google Summer of Code, an annual Google program which encourages open source contribution from students. The term I was introduced to by my seniors in my freshman year. Having no clue about open source, I started gathering knowledge about ‘How to contribute to open source projects?’ Then I came across version control, being a freshman it was an unknown territory for me. I started using Github for my personal projects which gave me a better understanding of how to use it. Version Control Service was off the checklists. By the time all this was done Google Summer of Code 2018 was announced.
Google Summer of Code 2019: Dream to Reality Manas Awasthi Jun 12 · 3 min read The Coding Period: The First Two Weeks The coding period of Google Summer of Code started on 27th of May, at the time of publishing it’s been more than 2 weeks, here I am writing this blog to discuss what I have done over the past two weeks, and what a ride it has been already. Plenty of coding along with plenty of learning. From the code base to the test suite.
Google Summer of Code 2019: Dream to Reality Manas Awasthi Jun 22 · 3 min read The Coding Period: Week 3 — Week 4 Hola Amigos!!! Let’s discuss my progress through week 3 and 4 of GSoC’s coding period. So the major part of what I was doing this week was to add support for the secondary identifier (err!!! whats that) to BridgeDb.
You can read about these activities in this second FAIRplus newsletter. On top of that, we bring you an update on upcoming events, news from our partners and also a new section ‘Track our progress’ where you can check for yourself how we are progressing towards our goals and what Deliverables and reports we’ve recently submitted.
Last November I had the privilege to be one of 150 participants at the Biohackathon organised by ELIXIR. The hackathon was organised into 29 topics, many of which were related to Bioschemas and one directly focused on Bioschemas. For the Bioschemas topic we had up to 30 people working around three themes.
The first theme was to implement markup for the various life sciences resources present. Representatives from ELIXIR Core Data Resources and node resources from the UK and Switzerland were there to work on this thanks to the staff exchange and travel fund. By the end of the week we had new live deploys for 11 additional resources and examples for many more.
The second theme was to refine the types and profiles that Bioschemas has been developing based on the experiences of deploying the markup. Prior to the hackathon, Bioschemas had moved from a minimal Schema.org extension of a single BioChemEntity type to collection of types for the different life science resources, e.g. Gene, Protein, and Taxon. Just before the hackathon a revised set of types and profiles were released. This proved to be useful for discussion, but it very quickly became clear that there was need for further refinement. During the hackathon we started new profiles for DNA, Experimental Studies, and Phenotype, and the Chemical profile was split into MolecularEntity and ChemicalSubstance. Long discussions were held about the types and their structure with early drafts for 17 types being proposed. These are now getting to a state where they are ready for further experimentation.
The third theme was to develop tooling to support Bioschemas. Due to the intensity of the discussions on the types and profiles, there was no time to work on this topic. However, the prototype Bioschemas Generator was extensively tested during the first theme and improvements fed back to the developer. There were also refinements made to the GoWeb tool.
Overall, it was a very productive hackathon. The venue proved to be very conducive to fostering the right atmosphere. During the evenings there were opportunities to socialise or carry on the discussions. Below are two of the paintings that were produced during one of the social activities that capture the Bioschemas discussions.
And there was the food. Wow! Wonderful meals, three times a day.