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nrnb / GoogleSummerOfCode

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Improved citation framework for PathVisio and WikiPathways #28

Closed mkutmon closed 5 years ago

mkutmon commented 8 years ago

Background

PathVisio is a commonly-used pathway editor, visualization and analysis tool implemented in Java and is linked with the collaborative pathway database WikiPathways. In the pathway models created by PathVisio, curators can add references to literature for every element in the pathway (including the complete pathway). Currently, only the search and annotation of PubMed identifiers is enabled but there are existing libraries that allow querying of DOIs etc.

Goal

The goal of this project is to extend the functionality to allow the reference of other identifiers like DOIs, export references in standard formats like Bibtex or EndNote and provide statistics about citations used on WikiPathways (total number of citations, avg. number of citations per pathway, top cited papers/journals, ...).

Difficulty Level 2

The student will need to adapt the user interface in the PathVisio core application, implement functionality to query other services besides PubMed, and adapt the WikiPathways pathway page to show those references and their linkouts correctly.

Skills

Java, PHP (essential) mediawiki (nice to have)

Public Repository

PathVisio: https://github.com/PathVisio/pathvisio WikiPathways: https://github.com/wikipathways/wikipathways.org

Potential Mentors

Martina Kutmon Egon Willighagen

Contact

Martina Kutmon

koppor commented 8 years ago

Possibly related: The recommender system of Docear. See http://www.docear.org/docear/blog/.

egonw commented 5 years ago

@mkutmon, I'm going to park this idea. I still think it's important, but until GPML 201(x>3) is out, I think I should focus on BridgeDb.

khanspers commented 5 years ago

Closing for GSoC 2019.