[open-bibliography] Getting started with Spinal Muscular Atrophy

Thu Jan 27 10:45:10 UTC 2011

On Thu, Jan 27, 2011 at 10:34 AM, Fabiana Kubke <mf.kubke at gmail.com> wrote:

> Peter,
> I should have access on the weekend of Feb 11 to people more literate than
> me (not too hard since I am not a lawyer) in NZ copyright law.  So if there
> are specific questions/issues it might be useful to have them identified
> before then so I can try to get some responses. (e.g., court precedents or
> amendments I would not be aware of). Sure, we are still not solving the full
> article issue, but an abstract is better than just the title.
>

Absolutely agreed - if we can liberate abstracts then we should do it - and
do it as part of Open Bibliography. We can't take them from UKPMC as there
are contractual aspects (I think) but we can scrape them from the primary
literature.

My strong stance on BtPDF is for the benefit of some of the academics who
believe that everyone who needs it has free access to the literature
(because only universities matter). I hadn't realised how arrogant academia
generally is. It's part of the problem.

I'd be delighted to have this reside in NZ! I think we should develop the
software to collect and index this and make it available. Maybe it will help
to encourage OKF activity in NZ.

> Cheers
> Fabiana
>
>
> On Thu, Jan 27, 2011 at 11:15 PM, Peter Murray-Rust <pm286 at cam.ac.uk>wrote:
>
>> Fabiane,
>> Thanks very much for this. I think it's best to fork this discussion and
>> take it to the OKF - there is little point in my continuing to try to
>> contribute to semantic discussions on BtPDF as I am powerless. I'm therefore
>> copying this to open-bibliography.
>>
>> OB people:
>> Background. We've had a very exciting meeting at BtPDF where we have been
>> identifying how to add semantics to science and medicine. The discussions
>> are all Open and archived and worth following. Several projects arose of
>> which one, the semantic analysis of
>> http://en.wikipedia.org/wiki/Spinal_muscular_atrophy has been taken as an
>> exemplar. We are offering to help with bibliography and citations (a wider
>> OKF involvement (Rufus, David Shotton, Cameron Neylon, Leslie Chan and the
>> OpenBib hackforce) will emerge in a few days).
>>
>> In the OKF we are strictly limiting ourselves to open material. This is
>> because only people in rich universities can read the full medical
>> literature - 99.9... % of the world including patient groups is effectively
>> forbidden to read the literature (in case you are unaware it costs 30-40 USD
>> to rent (sic) a single non-Open medical paper for 2 days).
>>
>> What we are allowed to read is the Bibliography in (UK)PubMedCentral
>> because that is in the public domain by right. We had believed that the
>> abstract might be subject to copyright. Now Fabiane has shown that in some
>> jurisdictions the abstract is specifically copyable and re-publishable.
>>
>> So I am taking this to the OKF for discussion about the extent of this
>> permission. So - unless other BtPDFers wish to discuss this I suggest that
>> REPLY is only to OKF
>>
>> [This doesn't alter *my* position on our projects - access to an abstract
>> of closed content is almost worse than nothing - it perpetuates the
>> philosophy of preventing people reading the literature which they have
>> funded.]
>>
>>
>> On Thu, Jan 27, 2011 at 9:51 AM, Fabiana Kubke <mf.kubke at gmail.com>wrote:
>>
>>> Peter, the NZ copyright law (
>>> http://www.legislation.govt.nz/act/public/1994/0143/latest/DLM346213.html?search=ts_act_copyright+act_resel#DLM346213)
>>> reads:
>>> Abstracts of scientific or technical articles
>>>
>>>    -
>>>
>>>    Where an article on a scientific or technical subject is published in
>>>    a periodical accompanied by an abstract indicating the contents of the
>>>    article, it is not an infringement of copyright in the abstract, or in the
>>>    article, to copy the abstract or issue copies of the abstract to the public.
>>>
>>> Would doing some of your work under a NZ jurisdiction help you bypass
>>> your title/abstract issue? If you are willing to consider this option I
>>> could do some asking around as to whether this could be a viable solution.
>>>
>>> The UK 1988 act reads the same (except for a provision I do not
>>> understand) (http://www.legislation.gov.uk/ukpga/1988/48/section/60) (I
>>> also don't know whether this is the current legislation in the UK). But it
>>> sounds like a publisher would actually have to apply to the secretary of
>>> state to not have this copyright waiver.
>>>
>>> 60 Abstracts of scientific or technical articles.E+W+S+N.I.
>>>
>>> (1)Where an article on a scientific or technical subject is published in
>>> a periodical accompanied by an abstract indicating the contents of the
>>> article, it is not an infringement of copyright in the abstract, or in the
>>> article, to copy the abstract or issue copies of it to the public.
>>>
>>> (2)This section does not apply if or to the extent that there is a
>>> licensing scheme certified for the purposes of this section under section
>>> 143 providing for the grant of licences.
>>>
>>>
>>> On Thu, Jan 27, 2011 at 9:50 PM, Peter Murray-Rust <pm286 at cam.ac.uk>wrote:
>>>
>>>>
>>>> [....]
>>>>
>>>> We have to work only from the titles as we cannot use the information in
>>>> abstracts since that is often by default the copyright of the journal ("our
>>>> content"). The attractive thing about diseases is that their name often
>>>> ensures high precision and recall. However in this case It wiuld be useful
>>>> to have any synonyms that might occur in the title.
>>>>
>>>>>
>>>>>
>>>>> --
>>>>> M Fabiana Kubke
>>>>>
>>>>> Department of Anatomy | University of Auckland | New Zealand
>>>>> (+64) 9 373-7599 Ext 86002 | (+64)9 923 6002 (direct) | Mobile: (+64)
>>>>> 210 437 121
>>>>>
>>>>> Skype: superfabs | http://twitter.com/Kubke | http://identi.ca/kubke |
>>>>> http://buildingblogsofscience.wordpress.com |
>>>>> http://sciblogs.co.nz/building-blogs-of-science |
>>>>> http://popscinz.wordpress.com | http://talkingteaching.wordpress.com
>>>>>
>>>>
>>>>
>>>>
>>>> --
>>>> Peter Murray-Rust
>>>> Reader in Molecular Informatics
>>>> Unilever Centre, Dep. Of Chemistry
>>>> University of Cambridge
>>>> CB2 1EW, UK
>>>> +44-1223-763069
>>>>
>>>
>>>
>>>
>>> --
>>> M Fabiana Kubke
>>>
>>> Department of Anatomy | University of Auckland | New Zealand
>>> (+64) 9 373-7599 Ext 86002 | (+64)9 923 6002 (direct) | Mobile: (+64) 210
>>> 437 121
>>>
>>> Skype: superfabs | http://twitter.com/Kubke | http://identi.ca/kubke |
>>> http://buildingblogsofscience.wordpress.com |
>>> http://sciblogs.co.nz/building-blogs-of-science |
>>> http://popscinz.wordpress.com | http://talkingteaching.wordpress.com
>>>
>>
>>
>>
>> --
>> Peter Murray-Rust
>> Reader in Molecular Informatics
>> Unilever Centre, Dep. Of Chemistry
>> University of Cambridge
>> CB2 1EW, UK
>> +44-1223-763069
>>
>
>
>
> --
> M Fabiana Kubke
>
> Department of Anatomy | University of Auckland | New Zealand
> (+64) 9 373-7599 Ext 86002 | (+64)9 923 6002 (direct) | Mobile: (+64) 210
> 437 121
>
> Skype: superfabs | http://twitter.com/Kubke | http://identi.ca/kubke |
> http://buildingblogsofscience.wordpress.com |
> http://sciblogs.co.nz/building-blogs-of-science |
> http://popscinz.wordpress.com | http://talkingteaching.wordpress.com
>

-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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