This can be very interesting potentially. However, to be useful such a tool
needs to take into account how real-world researchers (biologists) perform
literature searches. Do you have someone who can guide in understanding
this "very non-linear" process?
Professor of Biochemistry
and Molecular Biology
Penn State University
On Mon, May 15, 2017 at 1:14 AM, Krzysztof Kutt <krzysztof.kutt(a)gmail.com>
We do not know each other yet, so I will briefly introduce myself.
I'm Chris, a Polish PhD candidate in Computer Science field at AGH
of Science and Technology in Krakow. In my work I deal with the
broad concept of artificial intelligence. In particular the semantic web
technologies (RDF, SPARQL, Linked Data) and the ability to support a group
of knowledge engineers who create knowledge inside (semantic) wiki systems
- in my PhD I propose some methods and prototypical tools for quality
management, change management and motivation. I have also finished the
Master's degree in Psychology and as a result I also deal with Affective
I know, I'm quite far away from bioinformatics :) so, what I am doing
As a part of Google Summer of Code program I will prepare a tool to
track of publications that reference a specific project (project's papers,
tools, etc). I think that at the end it will be a quite good tool that any
researcher can use for dealing with the task, regardless of the research
Specifically, it will be a set of Python scripts + GUI that will do four
1) performs database search for new projects (search terms),
2) handles alerts for updating the results later,
3) gives the user the possibility to manually annotate results (e.g. as
4) generates citation reports (e.g. list of papers that cite our
during last year).
If you are interested in such a tool, do not hesitate to:
* read the more detailed description placed in the project's github wiki:
* discuss it on the Gitter channel:
or simply write me an e-mail
We already have interest from members of the Galaxy, Reactome,
and BioPython communities.
I am waiting for your comments :)
If you are not interested in a project, maybe your colleagues are? :)
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