Dear all,
It has become a convention that each tool/wrapper in Galaxy includes citation instructions in their help text (although not all the tools do this - I think they should).
It occurred to me this could be formalised, with explicit markup in the tool XML file, embedding the citation (at very least with an identifier like the DOI or ISBN, there is probably a good existing XML standard that could be followed).
Then, Galaxy would be able to automatically pull out a list of citations the tool authors have requested be cited, removing duplicates (e.g. matching DOI), from a history or a workflow.
The aim of this is (a) to make it easier to write up your methods by supplying all the references, and (b) to help ensure tool authors get the acknowledgement they deserve.
Does this sound like a good idea?
Peter
On Thu, Dec 15, 2011 at 6:16 AM, Peter Cock p.j.a.cock@googlemail.comwrote:
Dear all,
It has become a convention that each tool/wrapper in Galaxy includes citation instructions in their help text (although not all the tools do this - I think they should).
It occurred to me this could be formalised, with explicit markup in the tool XML file, embedding the citation (at very least with an identifier like the DOI or ISBN, there is probably a good existing XML standard that could be followed).
Then, Galaxy would be able to automatically pull out a list of citations the tool authors have requested be cited, removing duplicates (e.g. matching DOI), from a history or a workflow.
The aim of this is (a) to make it easier to write up your methods by supplying all the references, and (b) to help ensure tool authors get the acknowledgement they deserve.
Does this sound like a good idea?
Hi, Peter.
I think this can be useful for tool authors, developers, and users. As for markup, bibtex has low barriers to entry, is a stable format, and could easily be included in a <citation> tag as text and used semantically when available.
Sean
Excellent idea, and the BibTeX comment makes sense too...
Dear all,
It has become a convention that each tool/wrapper in Galaxy includes citation instructions in their help text (although not all the tools do this - I think they should).
It occurred to me this could be formalised, with explicit markup in the tool XML file, embedding the citation (at very least with an identifier like the DOI or ISBN, there is probably a good existing XML standard that could be followed).
Then, Galaxy would be able to automatically pull out a list of citations the tool authors have requested be cited, removing duplicates (e.g. matching DOI), from a history or a workflow.
The aim of this is (a) to make it easier to write up your methods by supplying all the references, and (b) to help ensure tool authors get the acknowledgement they deserve.
Does this sound like a good idea?
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Paul, Sean,
On Thu, Dec 15, 2011 at 3:09 PM, Paul Gordon gordonp@ucalgary.ca wrote:
Excellent idea, and the BibTeX comment makes sense too...
I'm glad there is enthusiasm for the basic idea :)
However, while I am a LaTeX and BibTeX user and fan, I really don't think BibTex is an appropriate choice for embedding a citation within the Galaxy tool XML files. Let's face it, BibTeX is not mainstream and would be an additional hurdle for tool authors to add their citations. I think it has to be XML based.
Now this could be something incredibly simple, with just a DOI tag/attribute and a plain text citation string. But I suspect there is a suitable existing XML standard we should adopt. Maybe citations using RDFa? http://wiki.digitalclassicist.org/Citations_with_added_RDFa
Peter
Peter / Paul -
I propose to take this a step farther. How about developing a galaxy tool that uses a history/workflow to write a draft of your methods section using principles from Natural Language Generation [http://en.wikipedia.org/wiki/Natural_language_generation], with relevant citations pulled as you suggest, as well as automatically generating a .ps figure of your history/workflow.
Ever hopeful, Casey
Casey Bergman, Ph.D. Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road, M13 9PT Manchester, UK
Tel: +44-(0)161-275-1713 Lab: +44-(0)161-275-5980 Fax: +44-(0)161-275-5082 skype: caseymbergman
Email: casey.bergman@manchester.ac.uk Web: http://bergmanlab.smith.man.ac.uk/ Twitter: http://twitter.com/bergmanlab
On 15 Dec 2011, at 15:22, Peter Cock wrote:
Hi Paul, Sean,
On Thu, Dec 15, 2011 at 3:09 PM, Paul Gordon gordonp@ucalgary.ca wrote:
Excellent idea, and the BibTeX comment makes sense too...
I'm glad there is enthusiasm for the basic idea :)
However, while I am a LaTeX and BibTeX user and fan, I really don't think BibTex is an appropriate choice for embedding a citation within the Galaxy tool XML files. Let's face it, BibTeX is not mainstream and would be an additional hurdle for tool authors to add their citations. I think it has to be XML based.
Now this could be something incredibly simple, with just a DOI tag/attribute and a plain text citation string. But I suspect there is a suitable existing XML standard we should adopt. Maybe citations using RDFa? http://wiki.digitalclassicist.org/Citations_with_added_RDFa
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
+1 for me :-) Alex
________________________________________ Van: galaxy-dev-bounces@lists.bx.psu.edu [galaxy-dev-bounces@lists.bx.psu.edu] namens Casey Bergman [casey.bergman@manchester.ac.uk] Verzonden: donderdag 15 december 2011 20:10 Aan: Peter Cock; Sean Davis CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Automatic citation list from a tool, workflow, or history
Peter / Paul -
I propose to take this a step farther. How about developing a galaxy tool that uses a history/workflow to write a draft of your methods section using principles from Natural Language Generation [http://en.wikipedia.org/wiki/Natural_language_generation], with relevant citations pulled as you suggest, as well as automatically generating a .ps figure of your history/workflow.
Ever hopeful, Casey
Casey Bergman, Ph.D. Faculty of Life Sciences University of Manchester Michael Smith Building Oxford Road, M13 9PT Manchester, UK
Tel: +44-(0)161-275-1713 Lab: +44-(0)161-275-5980 Fax: +44-(0)161-275-5082 skype: caseymbergman
Email: casey.bergman@manchester.ac.uk Web: http://bergmanlab.smith.man.ac.uk/ Twitter: http://twitter.com/bergmanlab
On 15 Dec 2011, at 15:22, Peter Cock wrote:
Hi Paul, Sean,
On Thu, Dec 15, 2011 at 3:09 PM, Paul Gordon gordonp@ucalgary.ca wrote:
Excellent idea, and the BibTeX comment makes sense too...
I'm glad there is enthusiasm for the basic idea :)
However, while I am a LaTeX and BibTeX user and fan, I really don't think BibTex is an appropriate choice for embedding a citation within the Galaxy tool XML files. Let's face it, BibTeX is not mainstream and would be an additional hurdle for tool authors to add their citations. I think it has to be XML based.
Now this could be something incredibly simple, with just a DOI tag/attribute and a plain text citation string. But I suspect there is a suitable existing XML standard we should adopt. Maybe citations using RDFa? http://wiki.digitalclassicist.org/Citations_with_added_RDFa
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
galaxy-dev@lists.galaxyproject.org
-
Bossers, Alex -
Casey Bergman -
Paul Gordon -
Peter Cock -
Sean Davis