Hi Anton, We've already got folks from the Galaxy Project, Reactome, InterMine, and BioPython on board. And now several more folks are on the Gitter channel as well. I think we may end up with too many people involved. *(But that's the kind of problem I want to have! :-)* Also, the project isn't about biology per se. It's about finding papers that reference software projects often in indirect ways. The software can be from any domain. And I would argue that identifying where to search and what to search for is up to the people using the software (for example, me), rather than the person developing the software (Chris). Questions? I suggest continuing this conversation on gitter <https://gitter.im/references-tracking/Lobby>. Cheers, Dave C On Mon, May 15, 2017 at 6:00 AM, Anton Nekrutenko <anton@nekrut.org> wrote:
Krzysztof:
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?
a.
Anton Nekrutenko Professor of Biochemistry and Molecular Biology Penn State University http://nekrut.bx.psu.edu (814) 826-9628
On Mon, May 15, 2017 at 1:14 AM, Krzysztof Kutt <krzysztof.kutt@gmail.com> wrote:
Hi!
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
University 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 Computing field.
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 keep
here? 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 field.
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 irrelevant), 4) generates citation reports (e.g. list of papers that cite our project 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: https://github.com/kkutt/references-tracking/wiki/Tool-Description * discuss it on the Gitter channel: https://gitter.im/references-
tasks: tracking/Lobby or simply write me an e-mail
We already have interest from members of the Galaxy, Reactome, InterMine, and BioPython communities. I am waiting for your comments :)
If you are not interested in a project, maybe your colleagues are? :)
Best regards, Chris Kutt
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