[OWW-SC] Fwd: Postgenomic + OWW

Mon Oct 30 10:09:07 EST 2006

We'll this is a step towards getting OWW citations/contributions more
into the mainstream:

http://www.postgenomic.com/papers.php?min_links=0&timeframe=100y&comment_sou
rce=openwetware

jason

---------- Forwarded message ----------
From: Adie, Euan <e.adie at nature.com>
Date: Oct 30, 2006 8:22 AM
Subject: Re: Postgenomic + OWW
To: Jason Kelly <jasonk at mit.edu>

Hi Jason,

Sorry, I meant to email you back sooner. Postgenomic is now collecting links
from OWW - for examples see:

http://www.postgenomic.com/papers.php?min_links=0&timeframe=100y&comment_sou
rce=openwetware

It'd be good to have an excerpt rather than just the basic "this paper has
been cited on OWW" message; I'll work on that.

Thanks for the test pages - that definitely helps.

Cheers,

Euan

On 30/10/06 13:10, "Jason Kelly" <jasonk at mit.edu> wrote:

> Hi Euan,
>
> How are things going?  Please let us know if there's anything that
> makes sense for us to do on our end.  I made a little test page in
> case that would help, it has some sample edits that are related to
> adding or modifying references.
>
> adding 3 references:
> http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8
> 3725
>
> removing 2 of them:
> http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8
> 3726
>
> adding one back:
> http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8
> 3727
>
> removing them all:
> http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8
> 3728
>
> modifying a pmid:
> http://openwetware.org/index.php?title=Postgenomic_test_page&diff=prev&oldid=8
> 3731
>
> Thanks,
> jason
>
>
> On 10/16/06, Adie, Euan <e.adie at nature.com> wrote:
>> Hi Jason,
>>
>> Yeah, the fulltext feed thing is mostly laziness on my part, to be honest -
>> that way I could just add OWW as a "blog" feed and only have to write a
>> small amount of code to look for the Biblio markup. My main worry was
>> recognizing when references have been removed or modified...
>>
>> Having thought about it some more, though, a better solution might be to
>> just watch the existing "changes" feed and if anything that looks like a
>> reference crops up then Postgenomic can retrieve the whole page itself,
>> parse out the paper links and delete / modify / add internally as
>> appropriate. That wouldn't require any coding on your part.
>>
>> I'll have a more in-depth look at it this afternoon and let you know if I
>> come across any problems.
>>
>> Cheers!
>>
>> Euan
>>
>>
>>
>>> That would be a pretty obvious thing for you to look for, so you'd
>>> know when someone added a reference to a paper and you'd know the URL
>>> of the page that references it.
>>>
>>> We thought a little about making the feed contain the whole page --
>>> the issue then will be that you will get the whole page (including the
>>> Bibliography tags) sent every time there is any edit to it. (e.g.
>>> correcting a typo)  So i guess it would look like multiple posts that
>>> are all the same?  Though I suppose you could just check and not allow
>>> repeated posts from the same URL?  We were wondering why you guys need
>>> the whole page through the feed --  is it just a technical issue in
>>> that it will be easier to post that on postgenomic without having to
>>> follow the link and scrape the page or something?
>>>
>>> OK, thanks again for working with us on this, seems like this would be
>>> a great thing to get working properly.
>>>
>>> best,
>>> jason
>>>
>>> On 10/4/06, Adie, Euan <e.adie at nature.com> wrote:
>>>> Hi Jason,
>>>>
>>>> The short answer is yes - I'm definitely interested. :)
>>>>
>>>> I think that at the very least it'd be cool to link papers already in the
>>>> Postgenomic database to the wiki pages that cite them - we do something
>>>> similar already with Faculty of 1000 reviews. As you say, this sort of
>>>> thing
>>>> is currently outside of the current paper-cites-paper referencing system.
>>>>
>>>> Technically speaking, ideally there'd be a feed of recently modified pages
>>>> that included the full text of the page (not just the edit): if you're
>>>> using
>>>> the MediaWiki citation plugin (?) then we could get everything else by
>>>> looking for that markup...
>>>>
>>>> I don't know how feasible that is on your end: I don't really know an awful
>>>> lot about the MediaWiki internals, unfortunately. :(
>>>>
>>>> Anyway, thanks for your mail,
>>>>
>>>> Cheers,
>>>>
>>>> Euan
>>>>
>>>>
>>>> On 28/9/06 05:26, "Jason Kelly" <jasonk at mit.edu> wrote:
>>>>
>>>>>
>>>>> (1) Commentary about a particular paper (e.g. a summary or critique) -
>>>>> this most closely resembles the blog-type content that postgenomic
>>>>> currently aggregates.
>>>>> http://openwetware.org/wiki/Stephanopoulos:Literature_Reviewed
>>>>>
>>>>> (2) Reference to a paper in a protocol, material description (e.g.
>>>>> media recipe), etc.
>>>>> http://openwetware.org/wiki/Bacterial_Transformation#References
>>>>>
>>>>> (3) Reference to a paper in a research project description (e.g.
>>>>> referencing it as prior work)
>>>>> http://openwetware.org/wiki/Reshma_Shetty/Thesis_research
>>>>>
>>>>> What's interesting about the last 2 types is that they are analogous
>>>>> to references in a typical peer-reviewed publication.  However, since
>>>>> OWW falls outside the normal referencing system, author's aren't
>>>>> receiving any real recognition for other scientists citing their work.
>>>>>   (e.g. it doesn't contribute to the "citation score" of the paper).
>>>>>
>>>>> So I'm not sure which of the above sort of content postgenomic would
>>>>> be interested in aggregating (if any), but would love to talk more
>>>>> about this if it's something you think is worthwhile.  it might
>>>>> require a bit more of a technical hack to set it up, since the only
>>>>> RSS feed off the site currently is the RecentChanges (e.g. every change
>>>>> made to the site).
>>>>>
>>>>> Let me know if you'd be interested in talking more.  We're available
>>>>> to talk by phone or email, whatever works best for you guys.
>>>>>
>>>>> Thanks,
>>>>> Jason
>>>>
>>>>
>>>> ***************************************************************************
>>>> **
>>>> ***
>>>> DISCLAIMER: This e-mail is confidential and should not be used by anyone
>>>> who
>>>> is
>>>> not the original intended recipient. If you have received this e-mail in
>>>> error
>>>> please inform the sender and delete it from your mailbox or any other
>>>> storage
>>>> mechanism. Neither Macmillan Publishers Limited nor any of its agents
>>>> accept
>>>> liability for any statements made which are clearly the sender's own and
>>>> not
>>>> expressly made on behalf of Macmillan Publishers Limited or one of its
>>>> agents.
>>>> Please note that neither Macmillan Publishers Limited nor any of its agents
>>>> accept any responsibility for viruses that may be contained in this e-mail
>>>> or
>>>> its attachments and it is your responsibility to scan the e-mail and
>>>> attachments (if any). No contracts may be concluded on behalf of Macmillan
>>>> Publishers Limited or its agents by means of e-mail communication.
>>>> Macmillan
>>>> Publishers Limited Registered in England and Wales with registered number
>>>> 785998
>>>> Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS
>>>> ***************************************************************************
>>>> **
>>>> ***
>>>>
>>

********************************************************************************
DISCLAIMER: This e-mail is confidential and should not be used by anyone who is
not the original intended recipient. If you have received this e-mail in error
please inform the sender and delete it from your mailbox or any other storage
mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
liability for any statements made which are clearly the sender's own and not
expressly made on behalf of Macmillan Publishers Limited or one of its agents.
Please note that neither Macmillan Publishers Limited nor any of its agents
accept any responsibility for viruses that may be contained in this e-mail or
its attachments and it is your responsibility to scan the e-mail and
attachments (if any). No contracts may be concluded on behalf of Macmillan
Publishers Limited or its agents by means of e-mail communication. Macmillan
Publishers Limited Registered in England and Wales with registered number 785998
Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS
********************************************************************************