Hi Eric, I was sure there was a Trello card for this, but I can't find it right now... I've pushed this idea on the mailing list before, and in person at the Galaxy Community Conference too. See also these threads: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html Are you familiar enough with the area of semantic web/linked data to know what would be the best XML based markup to use for embedding the citations? i.e. We should not reinvent the wheel here ;) Peter On Tue, May 27, 2014 at 5:54 PM, James Taylor <james@jamestaylor.org> wrote:

Eric, I'm very much in favor of this feature, and particularly the idea of generating a list of citations from a history or workflow. I imagine the only thing to quibble about will be the syntax. There are already some efforts to represent bibtex in xml (e.g. https://github.com/Zearin/BibTeXML), however they have always struck me as overly verbose.

-- jt

On Tue, May 27, 2014 at 12:45 PM, Eric Rasche <rasche.eric@yandex.ru> wrote:

...

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1

I'd want to open up discussion on a feature I'd like to see. I'll try and implement it if I can find time this summer. I didn't see a trello card for anything like this yet, but please feel free to direct me there if I missed it.

I'd like to see citations as a part of every tool.

This would happen in the form of a <citation> block in the XML, which would contain sub-elements with text. These sub-elements could be based off of BibTeX, since they have existing specs for citing things: https://en.wikipedia.org/wiki/BibTeX

These citations would then be accessible in the HTML generated tool pages, or via a View/Download button somewhere on the tool page. By storing as an XML tree, we could render these citations as BibTeX entries for the LaTeX users, and I believe there are ways to convert BibTeX to EndNote XML and so on.

This could be extended for use in workflows so that when you run workflows, somehow a list of citations for all tools used could be generated.

Anyone have thoughts or opinions on this?

Using the example bibtex entry from the wikipedia page:

@Book{abramowitz+stegun, author = "Milton {Abramowitz} and Irene A. {Stegun}", title = "Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables", publisher = "Dover", year = 1964, address = "New York", edition = "ninth Dover printing, tenth GPO printing" }

I imagine it'd look like the following in a real-life tool:

<tool> ... <citation type="book"> <author>Milton Abramowitz and Irene A. Stegun"</author> <title>Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables</title> <publisher>Dover</publisher> <year>1964</year> <address>New York</address> <edition>ninth Dover printing, tenth GPO printing</edition> </citation> </tool>

Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux)

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As hinted at in the Trello card Greg posted, it could be much simpler if the citation tag just took a DOI. It appears that the DOI to bibtex conversion can be done by Crossref: http://tex.stackexchange.com/questions/6848/automatically-dereference-doi-to... -Will On Tue, May 27, 2014 at 10:16 AM, Greg Von Kuster <greg@bx.psu.edu> wrote:

Peter, this may be the Trello card you were thinking of.

https://trello.com/c/kY7RCnd0/95-tool-shed-citation-for-tools-dois

Greg Von Kuster

On May 27, 2014, at 1:09 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:

...

Hi Eric,

I was sure there was a Trello card for this, but I can't find it right now...

I've pushed this idea on the mailing list before, and in person at the Galaxy Community Conference too. See also these threads:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html

Are you familiar enough with the area of semantic web/linked data to know what would be the best XML based markup to use for embedding the citations?

i.e. We should not reinvent the wheel here ;)

Peter

...

Eric, I'm very much in favor of this feature, and particularly the idea of generating a list of citations from a history or workflow. I imagine the only thing to quibble about will be the syntax. There are already some efforts to represent bibtex in xml (e.g. https://github.com/Zearin/BibTeXML), however they have always struck me as overly verbose.

-- jt

On Tue, May 27, 2014 at 12:45 PM, Eric Rasche <rasche.eric@yandex.ru> wrote:

...

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1

I'd want to open up discussion on a feature I'd like to see. I'll try and implement it if I can find time this summer. I didn't see a trello card for anything like this yet, but please feel free to direct me

On Tue, May 27, 2014 at 5:54 PM, James Taylor <james@jamestaylor.org> wrote: there

...

...

if I missed it.

I'd like to see citations as a part of every tool.

This would happen in the form of a <citation> block in the XML, which would contain sub-elements with text. These sub-elements could be based off of BibTeX, since they have existing specs for citing things: https://en.wikipedia.org/wiki/BibTeX

These citations would then be accessible in the HTML generated tool pages, or via a View/Download button somewhere on the tool page. By storing as an XML tree, we could render these citations as BibTeX entries for the LaTeX users, and I believe there are ways to convert BibTeX to EndNote XML and so on.

This could be extended for use in workflows so that when you run workflows, somehow a list of citations for all tools used could be generated.

Anyone have thoughts or opinions on this?

Using the example bibtex entry from the wikipedia page:

@Book{abramowitz+stegun, author = "Milton {Abramowitz} and Irene A. {Stegun}", title = "Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables", publisher = "Dover", year = 1964, address = "New York", edition = "ninth Dover printing, tenth GPO printing" }

I imagine it'd look like the following in a real-life tool:

<tool> ... <citation type="book"> <author>Milton Abramowitz and Irene A. Stegun"</author> <title>Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables</title> <publisher>Dover</publisher> <year>1964</year> <address>New York</address> <edition>ninth Dover printing, tenth GPO printing</edition> </citation> </tool>

Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux)

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___________________________________________________________ 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/

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I would suggest using as much as possible from PROV, especially since other workflow engines (Taverna and Pegasus come to mind) already support it. Rather than looking for bibtex mappings in XML, we should be looking for vocabularies that represent the elements we need to represent, and the relevant bibtex should be generated from that. PROV and Dublin Core Terms can get us most of the way there, I think. Jim On Tue, May 27, 2014 at 1:09 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:

Hi Eric,

I was sure there was a Trello card for this, but I can't find it right now...

I've pushed this idea on the mailing list before, and in person at the Galaxy Community Conference too. See also these threads:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html

Are you familiar enough with the area of semantic web/linked data to know what would be the best XML based markup to use for embedding the citations?

i.e. We should not reinvent the wheel here ;)

Peter

On Tue, May 27, 2014 at 5:54 PM, James Taylor <james@jamestaylor.org> wrote:

...

Eric, I'm very much in favor of this feature, and particularly the idea of generating a list of citations from a history or workflow. I imagine the only thing to quibble about will be the syntax. There are already some efforts to represent bibtex in xml (e.g. https://github.com/Zearin/BibTeXML), however they have always struck me as overly verbose.

-- jt

On Tue, May 27, 2014 at 12:45 PM, Eric Rasche <rasche.eric@yandex.ru> wrote:

...

-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1

I'd want to open up discussion on a feature I'd like to see. I'll try and implement it if I can find time this summer. I didn't see a trello card for anything like this yet, but please feel free to direct me there if I missed it.

I'd like to see citations as a part of every tool.

This would happen in the form of a <citation> block in the XML, which would contain sub-elements with text. These sub-elements could be based off of BibTeX, since they have existing specs for citing things: https://en.wikipedia.org/wiki/BibTeX

These citations would then be accessible in the HTML generated tool pages, or via a View/Download button somewhere on the tool page. By storing as an XML tree, we could render these citations as BibTeX entries for the LaTeX users, and I believe there are ways to convert BibTeX to EndNote XML and so on.

This could be extended for use in workflows so that when you run workflows, somehow a list of citations for all tools used could be generated.

Anyone have thoughts or opinions on this?

Using the example bibtex entry from the wikipedia page:

@Book{abramowitz+stegun, author = "Milton {Abramowitz} and Irene A. {Stegun}", title = "Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables", publisher = "Dover", year = 1964, address = "New York", edition = "ninth Dover printing, tenth GPO printing" }

I imagine it'd look like the following in a real-life tool:

<tool> ... <citation type="book"> <author>Milton Abramowitz and Irene A. Stegun"</author> <title>Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables</title> <publisher>Dover</publisher> <year>1964</year> <address>New York</address> <edition>ninth Dover printing, tenth GPO printing</edition> </citation> </tool>

Cheers, Eric - -- Eric Rasche Programmer II Center for Phage Technology Texas A&M University College Station, TX 77843 404-692-2048 esr@tamu.edu rasche.eric@yandex.ru -----BEGIN PGP SIGNATURE----- Version: GnuPG v2.0.17 (GNU/Linux)

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I'm a semantic web folk (I'm on the PROV Data Model), and I'm willing to advise as needed. PROV is very generalized, but workflow provenance was one of the primary use cases for its design (it descends from OPM, which was almost entirely workflow provenance-oriented). Workflow tools probably should be prov:Plan, a subclass of prov:Entity. PROV can cover attribution of things, agents (people and orgs) acting on behalf of other agents, and virtual and physical locations (prov:atLocation). Tool provenance is a little smaller-scoped than workflow invocation provenance, but obviously we want the two to mesh neatly. Below I'm going to use Turtle to write out an example, but the tool XML can obviously embed RDF-XML instead. We would need to supply a little bit of our own vocabulary: galaxy:Tool rdfs:subClassOf prov:Plan. Citing a book in a tool might look like this: :mytool a galaxy:Tool; prov:wasDerivedFrom <http://dx.doi.org/10.1119/1.15378> ; # For DOI-able references. [1] dc:creator <http://tw.rpi.edu/instances/JamesMcCusker>. [1] dx.doi.org will return RDF for the document if you ask for it. We can use their vocabulary within our own RDF if there is no DOI for it. @prefix doi: <http://dx.doi.org/>. @prefix prism: <http://prismstandard.org/namespaces/basic/2.1/>. @prefix xsd: <http://www.w3.org/2001/XMLSchema#>. @prefix foaf: <http://xmlns.com/foaf/0.1/>. @prefix dc: <http://purl.org/dc/terms/>. @prefix bibo: <http://purl.org/ontology/bibo/>. @prefix owl: <http://www.w3.org/2002/07/owl#>. <http://id.crossref.org/contributor/milton-abramowitz-1hbgxt653tpie> a foaf:Person> ; foaf:familyName "Abramowitz" ; foaf:givenName "Milton" ; foaf:name "Milton Abramowitz" . doi:10.1119/1.15378 prism:doi "10.1119/1.15378" ; prism:startingPage "958" ; prism:volume "56" ; dc:creator < http://id.crossref.org/contributor/milton-abramowitz-1hbgxt653tpie> ; dc:date "1988"^^<gYear> ; dc:identifier "10.1119/1.15378" ; dc:isPartOf <http://id.crossref.org/issn/0002-9505> ; dc:publisher "American Association of Physics Teachers (AAPT)" ; dc:title "Handbook of Mathematical Functions with Formulas, Graphs, and Mathematical Tables" ; bibo:doi "10.1119/1.15378" ; bibo:pageStart "958" ; bibo:volume "56" ; owl:sameAs <doi:10.1119/1.15378> , <info:doi/10.1119/1.15378> . <http://id.crossref.org/issn/0002-9505> a bibo:Journal ; prism:issn "0002-9505" ; dc:title "American Journal of Physics" ; bibo:issn "0002-9505" ; owl:sameAs <urn:issn:0002-9505> . Jim On Tue, May 27, 2014 at 2:17 PM, Peter Cock <p.j.a.cock@googlemail.com>wrote:

On Tue, May 27, 2014 at 6:21 PM, Jim McCusker <jmccusker@5amsolutions.com> wrote:

...

I would suggest using as much as possible from PROV, especially since other workflow engines (Taverna and Pegasus come to mind) already support it. Rather than looking for bibtex mappings in XML, we should be looking for vocabularies that represent the elements we need to represent, and the relevant bibtex should be generated from that. PROV and Dublin Core Terms can get us most of the way there, I think.

Jim

This PROV ontology? http://www.w3.org/TR/prov-o/ http://www.taverna.org.uk/documentation/taverna-2-x/provenance/ https://github.com/wf4ever/taverna-prov

It looks potentially relevant, but tackling a wider issue. Are you aware of specific examples covering tool citation within the context of workflow provenance? I think many people (myself included) would find that useful - a basic example for what might go into a Galaxy Tool's XML file?

Maybe we need to CC some semantic web folk to advise... or schedule a get together as a BoF at GCC2014? It seems once a format is agreed, there is willingness on the Galaxy side to start coding :)

Peter

Hi Shari Have a look at the last few lines of the e-mail: "... To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ " Hans-Rudolf On 05/28/2014 03:56 AM, Shari Javadiyan wrote:

Hi all, Is there any way to unsubscribes from mail lists? Cheers, Shari

On Wednesday, 28 May 2014 2:52 AM, Jim McCusker <jmccusker@5amsolutions.com> wrote:

I would suggest using as much as possible from PROV, especially since other workflow engines (Taverna and Pegasus come to mind) already support it. Rather than looking for bibtex mappings in XML, we should be looking for vocabularies that represent the elements we need to represent, and the relevant bibtex should be generated from that. PROV and Dublin Core Terms can get us most of the way there, I think.

Jim

On Tue, May 27, 2014 at 1:09 PM, Peter Cock <p.j.a.cock@googlemail.com <mailto:p.j.a.cock@googlemail.com>> wrote:

Hi Eric,

I was sure there was a Trello card for this, but I can't find it right now...

I've pushed this idea on the mailing list before, and in person at the Galaxy Community Conference too. See also these threads:

http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-December/007873.html

http://lists.bx.psu.edu/pipermail/galaxy-dev/2012-June/010178.html

Are you familiar enough with the area of semantic web/linked data to know what would be the best XML based markup to use for embedding the citations?

i.e. We should not reinvent the wheel here ;)

Peter

On Tue, May 27, 2014 at 5:54 PM, James Taylor <james@jamestaylor.org <mailto:james@jamestaylor.org>> wrote: > Eric, I'm very much in favor of this feature, and particularly the > idea of generating a list of citations from a history or workflow. I > imagine the only thing to quibble about will be the syntax. There are > already some efforts to represent bibtex in xml (e.g. > https://github.com/Zearin/BibTeXML), however they have always struck > me as overly verbose. > > -- jt > > > On Tue, May 27, 2014 at 12:45 PM, Eric Rasche <rasche.eric@yandex.ru <mailto:rasche.eric@yandex.ru>> wrote: >> -----BEGIN PGP SIGNED MESSAGE----- >> Hash: SHA1 >> >> I'd want to open up discussion on a feature I'd like to see. I'll try >> and implement it if I can find time this summer. I didn't see a trello >> card for anything like this yet, but please feel free to direct me there >> if I missed it. >> >> >> I'd like to see citations as a part of every tool. >> >> This would happen in the form of a <citation> block in the XML, which >> would contain sub-elements with text. These sub-elements could be based >> off of BibTeX, since they have existing specs for citing things: >> https://en.wikipedia.org/wiki/BibTeX >> >> These citations would then be accessible in the HTML generated tool >> pages, or via a View/Download button somewhere on the tool page. By >> storing as an XML tree, we could render these citations as BibTeX >> entries for the LaTeX users, and I believe there are ways to convert >> BibTeX to EndNote XML and so on. >> >> This could be extended for use in workflows so that when you run >> workflows, somehow a list of citations for all tools used could be >> generated. >> >> Anyone have thoughts or opinions on this? >> >> >> >> >> Using the example bibtex entry from the wikipedia page: >> >> @Book{abramowitz+stegun, >> author = "Milton {Abramowitz} and Irene A. {Stegun}", >> title = "Handbook of Mathematical Functions with >> Formulas, Graphs, and Mathematical Tables", >> publisher = "Dover", >> year = 1964, >> address = "New York", >> edition = "ninth Dover printing, tenth GPO printing" >> } >> >> I imagine it'd look like the following in a real-life tool: >> >> <tool> >> ... >> <citation type="book"> >> <author>Milton Abramowitz and Irene A. Stegun"</author> >> <title>Handbook of Mathematical Functions with Formulas, Graphs, and >> Mathematical Tables</title> >> <publisher>Dover</publisher> >> <year>1964</year> >> <address>New York</address> >> <edition>ninth Dover printing, tenth GPO printing</edition> >> </citation> >> </tool> >> >> >> Cheers, >> Eric >> - -- >> Eric Rasche >> Programmer II >> Center for Phage Technology >> Texas A&M University >> College Station, TX 77843 >> 404-692-2048 >> esr@tamu.edu <mailto:esr@tamu.edu> >> rasche.eric@yandex.ru <mailto:rasche.eric@yandex.ru> >> -----BEGIN PGP SIGNATURE----- >> Version: GnuPG v2.0.17 (GNU/Linux) >> >> iQIcBAEBAgAGBQJThMEUAAoJEMqDXdrsMcpVe9AP/1BjPbP5JdK6KDybOeV2ElvC >> jvmUGetAjdQzkKO1Ikeuxb46yp0j4abAGGG92AccxlBYALsT3jsPv5dYjm505vcU >> IwlfTBE7gc5y19x3zx1CuAd7PB11tryODz2LwXNKI75f39bNdX6Qe5aA74Vn/k8a >> FBeFL/EvkZwI8Z6CvuTGtZrEHvDXVvTFoxMX875f59g2vNy7W8Fh5wQCQ8qgiogi >> 0SWGIGZ6OJdqX60h2hOjJ06NhzBcTsjQea+AwTo5wAkyGPFJy4DV78jKOvsd5PMG >> qkk4U6gBcmcFolCeItlLPa/C4uiyOK2wVWHyTnEeKjdpD6dwLuemRmwtZrModbQu >> PPPFkKzQhUnh5Wgq8TIP4kSc2t1/jSpdV8MHqM0piqOFnR52fExPrwLn82WEFcp8 >> tXfHHTaZj+6gL+IGswdAgqvxk1V+6QTjH57igWmYtcENpIDbhZVBh+HOD8SS2qdv >> ohwFg/Vn8VrCeTGGehNSBvkam0HXjXXq7mZ8W4xrOS8vxv8HPAFZHze2sPlUG/Ob >> WeOdiLgD2HCH95SXYDDBNFG6HwFkLETA3DjpfvgHqPdaLmEfIZW+ks1WF9RG+Pmo >> jhbWH8OmtTk5A/Zh63uRowMaDe7QSCruPIfIwlrgqLozOj8htMyJPBIW9oZGGkqC >> 7Vu5UFeL8gcigRmQv5NA >> =ceAo >> -----END PGP SIGNATURE----- >> ___________________________________________________________ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >> http://galaxyproject.org/search/mailinglists/ > ___________________________________________________________ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ 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/

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