Automatic citation list from a tool, workflow, or history

classic Classic list List threaded Threaded
6 messages Options
Reply | Threaded
Open this post in threaded view
|

Automatic citation list from a tool, workflow, or history

Peter Cock
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:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Automatic citation list from a tool, workflow, or history

Sean Davis


On Thu, Dec 15, 2011 at 6:16 AM, Peter Cock <[hidden email]> wrote:
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
 

___________________________________________________________
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:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Automatic citation list from a tool, workflow, or history

Paul Gordon
In reply to this post by Peter Cock
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:
>
>    http://lists.bx.psu.edu/
>
>

___________________________________________________________
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:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Automatic citation list from a tool, workflow, or history

Peter Cock
Hi Paul, Sean,

On Thu, Dec 15, 2011 at 3:09 PM, Paul Gordon <[hidden email]> 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:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Automatic citation list from a tool, workflow, or history

Casey Bergman
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: [hidden email]
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 <[hidden email]> 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:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
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:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: Automatic citation list from a tool, workflow, or history

Bossers, Alex
+1 for me :-)
Alex

________________________________________
Van: [hidden email] [[hidden email]] namens Casey Bergman [[hidden email]]
Verzonden: donderdag 15 december 2011 20:10
Aan: Peter Cock; Sean Davis
CC: [hidden email]
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: [hidden email]
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 <[hidden email]> 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:
>
>  http://lists.bx.psu.edu/


___________________________________________________________
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:

  http://lists.bx.psu.edu/

___________________________________________________________
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:

  http://lists.bx.psu.edu/