[Taxacom] New feature in BioStor - BHL timelines for Taxonomic names

Donat Agosti agosti at amnh.org
Sat Dec 24 04:20:20 CST 2016


Hi Paul
Why aren't you starting to help Plazi to upload all the pdfs you find to BLR? You make them accessible, get and DOI and thus citable and usable for everybody in the future, and you can add the link to your own database.
Cheers
Donat


-----Original Message-----
From: Taxacom [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Paul Kirk
Sent: Saturday, December 24, 2016 11:02 AM
To: Roderic Page <Roderic.Page at glasgow.ac.uk>; David Patterson <patterson.david.joseph at gmail.com>
Cc: Taxa com <taxacom at mailman.nhm.ku.edu>
Subject: Re: [Taxacom] New feature in BioStor - BHL timelines for Taxonomic names

I am currently name/journal chasing using Google (a 'wonderful world' resource) and often get hits on the 'infamous' Hathi Trust Digital Library (what a 'joy to the world' this is) but I am frustrated by the 'Limited (search only)' because of copyright ... for a German journal published 100 years ago! The reason for this is that the aforementioned Digital Library is in the USA and I am physically in the UK (my IP address reveals this). I am a long time Microsoft software user so I'm typing this in an IE tab but I could go next door, fire up Chrome with a free proxy server installed and hey presto, I'm digitally in the USA and I get access. This is great for me but what I want to do is add a link to Index Fungorum to where the name of a fungus is first published (like I can do for BHL and many other digital libraries in Europe) but I cannot.


Paddy will know I have some 'radical' views on copyright in the context of registration of names so I think you all know which side of the fence I'm on ;-)


Best wishes to for a happy holiday and a peaceful, prosperous and productive [and copyright free biodiversity data]2017,


Paul

________________________________

From: Taxacom <taxacom-bounces at mailman.nhm.ku.edu> on behalf of Roderic Page <Roderic.Page at glasgow.ac.uk>
Sent: 24 December 2016 09:37
To: David Patterson
Cc: Taxa com
Subject: Re: [Taxacom] New feature in BioStor - BHL timelines for Taxonomic names

Hi Paddy,

I wish I shared your optimism that copyright on images was an easy thing to get around, but the comments on the paper  https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiorxiv.org%2Fcontent%2Fearly%2F2016%2F11%2F11%2F087015&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=bCDEOKD501TpGkkLy3lzXh61Enk%2BTX3o%2BfPv2Z%2BLouQ%3D&reserved=0 and on Twitter    https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstorify.com%2Frdmpage%2Fconversation-with-charlesoppenh-myrmoteras-rdmpage&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=heARsXYOgo4Bu9FfPF8Y%2FBdr11yINvpGwiRIN1S9taI%3D&reserved=0 suggest otherwise, or that at the very least it's debatable. I suspect that if you extracted images from a large commercial publisher, and they noticed and felt this was a potential threat to their business model, then academic arguments about copyright would not be much protection. If that's a risk Plazi wants to take, fine. Others may be a little more wary.

[https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstorify.com%2Fpublic%2Fimg%2Fdefault-thumb.gif&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=HFg08oq%2FdR0rBYR%2B%2FYtAAz6YP54fi8GngaaGz5ORf0Y%3D&reserved=0]<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstorify.com%2Frdmpage%2Fconversation-with-charlesoppenh-myrmoteras-rdmpage&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=heARsXYOgo4Bu9FfPF8Y%2FBdr11yINvpGwiRIN1S9taI%3D&reserved=0>

Conversation with @CharlesOppenh, @myrmoteras, @rdmpage and @SK53onOSM (with tweets) · rdmpage<https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fstorify.com%2Frdmpage%2Fconversation-with-charlesoppenh-myrmoteras-rdmpage&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=heARsXYOgo4Bu9FfPF8Y%2FBdr11yINvpGwiRIN1S9taI%3D&reserved=0>
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A Social Media Story storified by Roderic Page



Copyright and the Use of Images as Biodiversity Data | bioRxiv<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiorxiv.org%2Fcontent%2Fearly%2F2016%2F11%2F11%2F087015&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=bCDEOKD501TpGkkLy3lzXh61Enk%2BTX3o%2BfPv2Z%2BLouQ%3D&reserved=0>
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Taxonomy is the discipline responsible for charting the world's organismic diversity, understanding ancestor/descendant relationships, and organizing all species ...




Regards,

Rod

Sent from my iPhone




On Sat, Dec 24, 2016 at 9:00 AM +0000, "David Patterson" <patterson.david.joseph at gmail.com<mailto:patterson.david.joseph at gmail.com>> wrote:

Hi guys

Copyright is for taxonomists approximately as big an issue as the sky falling on Henny Penny's head.

The Plazi group has the benefit of good copyright legal input and with that we were able to make a list of information that cannot be subject to copyright (Patterson, D. J., Egloff, W., Agosti, D., Eades, D., Franz, N., Hagedorn, G., Rees, J. A. and Remsen, D. P. 2014. Scientific names of organisms: attribution, rights, and licensing BMC Research Notes 7:79 doi:10.1186/1756-0500-7-79 9pp) Here > https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiorxiv.org%2Fcontent%2Fearly%2F2016%2F11%2F11%2F087015&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=bCDEOKD501TpGkkLy3lzXh61Enk%2BTX3o%2BfPv2Z%2BLouQ%3D&reserved=0, you will find the arguments extended to cover images.

Copyright and the Use of Images as Biodiversity Data | bioRxiv<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiorxiv.org%2Fcontent%2Fearly%2F2016%2F11%2F11%2F087015&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=bCDEOKD501TpGkkLy3lzXh61Enk%2BTX3o%2BfPv2Z%2BLouQ%3D&reserved=0>
biorxiv.org
Taxonomy is the discipline responsible for charting the world's organismic diversity, understanding ancestor/descendant relationships, and organizing all species ...



Plazi is now contendly extracting treatments and images from taxonomic publications - example here https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Ftb.plazi.org%2FGgServer%2Fhtml%2FDD0FB428FFD2FFEAFF0609E34A3A4AC6&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=AJn76PnyCCo9KyGyMcYtUlxkVVZG%2B2GcK5PXBz4pw%2F4%3D&reserved=0
The point is that when a description of images follow a convention, then they cannot meet the legal requirements for a copyrightable work. There is no conflict with copyright to extract those elements of text that provide details of widely used traits, nor to extract the taxonomic treatment (and it follows that the nomenclatural acts can also be extracted), as can the images The concern is not copyright, but the business models of publishers that rely on charging folk for access to the information that they created, of institutions that argue they own content in the hope it will create a cash flow, and of individuals who confound effort with artistic creativity.
I am pleased to say things are going in a good direction and 2017 should be better than 2016.
David Patterson

On Fri, Dec 23, 2016 at 11:13 PM, Roderic Page <Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>> wrote:
Hi Mike,

Yes, copyright is an issue, but BHL is negotiating with lots of museums, Herbaria, and societies to get post-1923 content into BHL (e.g., the journal Zoologica https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiostor.org%2Fissn%2F0044-507X%2Fyear%2F1973&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=89iPwPbKcXp56pNKDzgXDerSsLlLAEk3AgoS1zIvJBM%3D&reserved=0 )

Sadly Russia seems to be a black hole in terms of online availability of literature and specimens. I guess for BHL it would be a case of figuring out who could grant them permission to scan the relevant literature. The thing about "specialist interest" is that I think it's easy to underestimate the potential interest. Once content is online all sorts of things can happen, such as extracting images, exploring font styles, automatic translation training, etc.

BHL would be receptive to requests for scanning, especially if some of the initial work had been done figuring out who can give the OK to scan.

Regards ,

Rod

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_____________________________
From: Michael Wilson <wilsomichael at gmail.com<mailto:wilsomichael at gmail.com><mailto:wilsomichael at gmail.com<mailto:wilsomichael at gmail.com>>>
Sent: Friday, December 23, 2016 12:00 pm
Subject: Re: [Taxacom] New feature in BioStor - BHL timelines for Taxonomic names
To: Roderic Page <roderic.page at glasgow.ac.uk<mailto:roderic.page at glasgow.ac.uk><mailto:roderic.page at glasgow.ac.uk<mailto:roderic.page at glasgow.ac.uk>>>


Hi Rod

Thanks for the reply. I shall give your BioNames a try.

As for gaps in BHL, as you have said before it is the copyright gap that might be most significant. What appears to be happening though is that groups of taxonomists are scanning certain keys, and sometime rare literature, and making it available to each other in various ways. Examples are Russian works from the 60's which are barely available in the west. I may have the only copy in the UK of a Russian work on Auchenorrhyncha from 1966 of around 250 pages in which a lot of species are described (line drawings and Russian text). It would be good if such works can be more widely available- but would be of limited and specialist interest!

Best wishes

Mike

On Fri, Dec 23, 2016 at 11:33 AM, Roderic Page <Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk><mailto:Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>>> wrote:
Hi Mike,

The results are entirely based on what has been scanned by BHL https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiodiversitylibrary.org&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=yQBAyLMq4ppjVXGWKi8flM2Tle3BPcJ6IWruYboRRAc%3D&reserved=0  and processed by BioStor. BHL has lots of gaps, hence the results will, be incomplete. Another limitations that the OCR used to extract text from the page images may fail to correctly interpret the words in a page, missing some taxonomic names. It's a tool for discovery.

Biodiversity Heritage Library<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiodiversitylibrary.org%2F&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=cI236JZm4VPmPlG%2BapYfjYsyiojBADy0%2BtNdZ7AAQ68%3D&reserved=0>
biodiversitylibrary.org
The Biodiversity Heritage Library works collaboratively to make biodiversity literature openly available to the world as part of a global biodiversity community.




If you want more coverage, especially more recent papers, then my other literature project BioNames may help, e.g.http://bionames.org/timeline/Animalia/Arthropoda/Insecta/Hemiptera/Homoptera/Auchenorrhyncha/Cicadelloidea

If anyone working at a museum or involved in a scientific society is interested in helping fill in the gaps in BHL then agreeing to have your in-house journal, society publication, etc. scanned would be a very useful, contribution.

Sorry if I'm didn't make the limitations of the timeline tool clear.

Regards,

Rod

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_____________________________
From: Michael Wilson <wilsomichael at gmail.com<mailto:wilsomichael at gmail.com><mailto:wilsomichael at gmail.com<mailto:wilsomichael at gmail.com>>>
Sent: Friday, December 23, 2016 8:47 am
Subject: Re: [Taxacom] New feature in BioStor - BHL timelines for Taxonomic names
To: Roderic Page <roderic.page at glasgow.ac.uk<mailto:roderic.page at glasgow.ac.uk><mailto:roderic.page at glasgow.ac.uk<mailto:roderic.page at glasgow.ac.uk>>>



Hi Rod

That looks interesting. I just tried Cicadellinae and the results were variable- but far from complete and nothing after 2010- yet at least 20 papers on new species of this leafhopper subfamily have been published.

Best wishes

Mike Wilson
National Museum of Wales

On Fri, Dec 23, 2016 at 7:24 AM, Roderic Page <Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk><mailto:Roderic.Page at glasgow.ac.uk<mailto:Roderic.Page at glasgow.ac.uk>>> wrote:
Dear All,

I've added a feature to BioStor that readers of this list might find useful. If you go tohttp://biostor.org/timeline.php<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiostor.org%2Ftimeline.php&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=G1%2BvUO7O760svwgP0FVndX9uEBXN5LwsAOVII7x3eYM%3D&reserved=0><https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiostor.org%2Ftimeline.php%3Fq%3DRoncus&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=Yuo535xQ3rDovb%2BUnUXIkNuEAoAReRsnHvVlgTNlNSI%3D&reserved=0> and enter a taxonomic name, BioStor will search BHL for that and and return a list of BHL pages and BioStor articles containing that name, and a chart showing the occurrence of the name overtime. For example seehttp://biostor.org/timeline.php?q=Roncus<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbiostor.org%2Ftimeline.php%3Fq%3DRoncus&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=Yuo535xQ3rDovb%2BUnUXIkNuEAoAReRsnHvVlgTNlNSI%3D&reserved=0>

For some background see https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fiphylo.blogspot.co.uk%2F2016%2F12%2Ftaxonomic-name-timelines-for-bhl.html&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=rkYS1eUA5aJfLtHX3l4SnK0BCTpvbHqCBM1blI0JCQg%3D&reserved=0

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Taxonomic name timelines for BHL<https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fiphylo.blogspot.co.uk%2F2016%2F12%2Ftaxonomic-name-timelines-for-bhl.html&data=01%7C01%7Cagosti%40amnh.org%7C51e8dd0b3432404216f108d42be3f380%7Cbe0003e8c6b9496883aeb34586974b76%7C1&sdata=rkYS1eUA5aJfLtHX3l4SnK0BCTpvbHqCBM1blI0JCQg%3D&reserved=0>
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Given a big corpus of literature one of the fun things to do is look at how the use of a term has changed over time. When did people first u...




Regards,

Rod


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Injecting Intellectual Liquidity for 29 years.






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Injecting Intellectual Liquidity for 29 years.



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Injecting Intellectual Liquidity for 29 years.
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Injecting Intellectual Liquidity for 29 years.


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