treebase-devel — TreeBASE developer mailing list

[Treebase-devel] More taxa labeling issues

[Michael J. <mjo...@gm...>]

Hello again,



I have a few questions regarding taxa label issues. For the purposes of
this thread, I will be referring to submission 12821 (on treebase.org (not
dev)) as an example.



Firstly, I’m wondering what my procedure should be when I encounter studies
with a numerous taxa with multiple “an unsuccesful attempt has been made to
link this to the external taxonomy” errors (the misspelling in this error
message is addressed in another thread). Based on the TreeBASE introduction
videos, I’m guessing that I should make an attempt to resolve each of these
labeling issues, as enumerated below, but this could add on a GREAT deal of
labor.



If I do need to resolve these issues, I’m guessing that I’ll have to find
the genus for each species in order to validate?



Lastly, I’m not sure what to do in the case of taxa labels containing a
number. For example, in 12821, there is data for both cassinia and
cassinia2. I suppose that this nomenclature probably denotes different
strains of the same species and that I should just put a space between the
cassinia and the 2?



Thanks,



Michael

Re: [Treebase-devel] Misspelled error message

[Hilmar L. <hl...@ne...>]

Thanks Michael. I fixed it. It will go live whenever the code is redeployed.

	-hilmar

On Jun 11, 2012, at 1:54 PM, Michael Jones wrote:

> Hello again,
> 
> When reviewing some unresolved taxa label errors, I noticed that the error message: “an unsuccesful attempt has been made to link this to the external taxonomy” is misspelled. Specifically, “unsuccesful” is missing a second s at the end. 
> 
> Michael
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

[Treebase-devel] Misspelled error message

[Michael J. <mjo...@gm...>]

Hello again,

When reviewing some unresolved taxa label errors, I noticed that the error
message: “an unsuccesful attempt has been made to link this to the external
taxonomy” is misspelled. Specifically, “unsuccesful” is missing a second s
at the end.

Michael

Re: [Treebase-devel] Submission searches

[William P. <wil...@ya...>]

On May 23, 2012, at 10:14 AM, Michael Jones wrote:

> Hello again,
> 
> I've noticed that when preforming a study search on TreeBASE ( http://www.treebase.org/treebase-web/search/studySearch.html ), if you search for one term, for instance the title, "Molecular Phylogeny and Phylogeography of the Australian Freshwater Fish Genus Galaxiella, with an Emphasis on Dwarf Galaxias (G. pusilla)," and then search for something else, such as the title, "More than 1000 ultraconserved elements provide evidence that turtles are the sister group of archosaurs," the second search won't run until you discard your previous search terms. 
> 
> I'm not sure that this is a bug as much as a preference, but at least to me, having to discard your previous search results doesn't seem particularly intuitive.
> 
> Oddly enough, this problem seems to have been circumvented in the Dev version of TreeBASE ( http://treebase-dev.nescent.org/treebase-web/search/studySearch.html ), which doesn't have the same search term capabilities. 
> 
> Michael

Hi Michael,

So, in the first case it is, in fact, intentional. The idea is to allow AND searches. For example, to find all trees published by Michael Donoghue that have more than 100 taxa, do this:

- Do Author search for Donoghue
- Click the Trees tab
- Enter "100.." for a NTAX search

I had not noticed that this feature is broken following Rutger's recent changes to an "any field search" design.

Rutger: is there a way to do an AND search (within or between tabs)? 

bp

[Treebase-devel] Submission searches

[Michael J. <mjo...@gm...>]

Hello again,

I've noticed that when preforming a study search on TreeBASE (
http://www.treebase.org/treebase-web/search/studySearch.html ), if you
search for one term, for instance the title, "Molecular Phylogeny and
Phylogeography of the Australian Freshwater Fish Genus Galaxiella, with an
Emphasis on Dwarf Galaxias (G. pusilla)," and then search for something
else, such as the title, "More than 1000 ultraconserved elements provide
evidence that turtles are the sister group of archosaurs," the second
search won't run until you discard your previous search terms.

I'm not sure that this is a bug as much as a preference, but at least to
me, having to discard your previous search results doesn't seem
particularly intuitive.

Oddly enough, this problem seems to have been circumvented in the Dev
version of TreeBASE (
http://treebase-dev.nescent.org/treebase-web/search/studySearch.html ),
which doesn't have the same search term capabilities.

Michael

Re: [Treebase-devel] Analysis errors following submission

[William P. <wil...@ya...>]

On May 16, 2012, at 1:06 PM, Michael Jones wrote:

> I've been playing around with some of the Phenoscape files onto the
> Dev version of TreeBASE. I was trying to diagnose a problem
> (apparently) with my second analysis. In an attempt to diagnose the
> problem, I deleted my 2nd analysis and attempted the submission with
> only the first analysis entered and the submission passed. When I went
> back to add in the 2nd analysis, however, I ran into a bug with this
> error message:
> 
> http://treebase-dev.nescent.org/treebase-web/user/analysisStepForm.html?analysis_id=9641

hmm… 

I went to treebase-dev, found your study (12733 ?), and added a new analysis. No error for me. 

(though curiously, the new analysis_id that was generated was 9208, which is significantly lower than your one 9641..)

bp

[Treebase-devel] Analysis errors following submission

[Michael J. <mjo...@gm...>]

I've been playing around with some of the Phenoscape files onto the
Dev version of TreeBASE. I was trying to diagnose a problem
(apparently) with my second analysis. In an attempt to diagnose the
problem, I deleted my 2nd analysis and attempted the submission with
only the first analysis entered and the submission passed. When I went
back to add in the 2nd analysis, however, I ran into a bug with this
error message:

http://treebase-dev.nescent.org/treebase-web/user/analysisStepForm.html?analysis_id=9641

Uncaught Exception Encountered
java.lang.IllegalArgumentException: Target must not be null at
org.springframework.util.Assert.notNull(Assert.java:112) at
org.springframework.validation.DataBinder.(DataBinder.java:145) at
org.springframework.web.bind.WebDataBinder.(WebDataBinder.java:83) at
org.springframework.web.bind.ServletRequestDataBinder.(ServletRequestDataBinder.java:80)
at org.springframework.web.servlet.mvc.BaseCommandController.createBinder(BaseCommandController.java:414)
at org.springframework.web.servlet.mvc.BaseCommandController.bindAndValidate(BaseCommandController.java:366)
at org.springframework.web.servlet.mvc.AbstractFormController.handleInvalidSubmit(AbstractFormController.java:669)
at org.springframework.web.servlet.mvc.AbstractFormController.handleRequestInternal(AbstractFormController.java:272)
at org.springframework.web.servlet.mvc.AbstractController.handleRequest(AbstractController.java:153)
at org.springframework.web.servlet.mvc.SimpleControllerHandlerAdapter.handle(SimpleControllerHandlerAdapter.java:48)
at org.springframework.web.servlet.DispatcherServlet.doDispatch(DispatcherServlet.java:858)
at org.springframework.web.servlet.DispatcherServlet.doService(DispatcherServlet.java:792)
at org.springframework.web.servlet.FrameworkServlet.processRequest(FrameworkServlet.java:476)
at org.springframework.web.servlet.FrameworkServlet.doPost(FrameworkServlet.java:441)
at javax.servlet.http.HttpServlet.service(HttpServlet.java:637) at
javax.servlet.http.HttpServlet.service(HttpServlet.java:717) at
org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.tuckey.web.filters.urlrewrite.RuleChain.handleRewrite(RuleChain.java:164)
at org.tuckey.web.filters.urlrewrite.RuleChain.doRules(RuleChain.java:141)
at org.tuckey.web.filters.urlrewrite.UrlRewriter.processRequest(UrlRewriter.java:90)
at org.tuckey.web.filters.urlrewrite.UrlRewriteFilter.doFilter(UrlRewriteFilter.java:406)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.displaytag.filter.ResponseOverrideFilter.doFilter(ResponseOverrideFilter.java:125)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:70)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.springframework.orm.hibernate3.support.OpenSessionInViewFilter.doFilterInternal(OpenSessionInViewFilter.java:198)
at org.springframework.web.filter.OncePerRequestFilter.doFilter(OncePerRequestFilter.java:75)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at com.opensymphony.module.sitemesh.filter.PageFilter.parsePage(PageFilter.java:119)
at com.opensymphony.module.sitemesh.filter.PageFilter.doFilter(PageFilter.java:55)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:264)
at org.acegisecurity.intercept.web.FilterSecurityInterceptor.invoke(FilterSecurityInterceptor.java:107)
at org.acegisecurity.intercept.web.FilterSecurityInterceptor.doFilter(FilterSecurityInterceptor.java:72)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.ui.ExceptionTranslationFilter.doFilter(ExceptionTranslationFilter.java:110)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.wrapper.SecurityContextHolderAwareRequestFilter.doFilter(SecurityContextHolderAwareRequestFilter.java:81)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.ui.AbstractProcessingFilter.doFilter(AbstractProcessingFilter.java:217)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.context.HttpSessionContextIntegrationFilter.doFilter(HttpSessionContextIntegrationFilter.java:191)
at org.acegisecurity.util.FilterChainProxy$VirtualFilterChain.doFilter(FilterChainProxy.java:274)
at org.acegisecurity.util.FilterChainProxy.doFilter(FilterChainProxy.java:148)
at org.acegisecurity.util.FilterToBeanProxy.doFilter(FilterToBeanProxy.java:90)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:185)
at net.bull.javamelody.MonitoringFilter.doFilter(MonitoringFilter.java:159)
at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:235)
at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)
at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:233)
at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)
at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)
at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)
at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)
at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)
at org.apache.coyote.http11.Http11Processor.process(Http11Processor.java:859)
at org.apache.coyote.http11.Http11Protocol$Http11ConnectionHandler.process(Http11Protocol.java:602)
at org.apache.tomcat.util.net.JIoEndpoint$Worker.run(JIoEndpoint.java:489)
at java.lang.Thread.run(Thread.java:679) Cookies:
itemToHighlight=[http%3A//treebase-dev.nescent.org/treebase-web/user/analyses.html]
JSESSIONID=[D42071E2AB620270FCEE2713FFBC9CC3]
__utma=[53240375.1917107800.1336651351.1336651351.1336746144.2]
__utmz=[53240375.1336746144.2.2.utmccn]
__utma=[5099126.425216376.1336584179.1337182469.1337186622.11]
__utmb=[5099126.37.9.1337186625148] __utmc=[5099126]
__utmz=[5099126.1336584179.1.1.utmcsr]

Re: [Treebase-devel] searches by doi

[Rutger V. <rut...@gm...>]

In an also ideal world we would have some automated way of getting
crowd-sourced corrections and additions (e.g. from Rod Page's TreeBASE
Mendeley group) back into the database.

On Saturday, May 12, 2012, Carl Boettiger wrote:

> Thanks for adding this.
>
> Yes, I guess it makes sense that kind of thing would be difficult to
> automate.  It's nice feature to have though, since it's usually the easiest
> way to grab the trees of the study when staring at the paper.
>
> -Carl
>
> On Sat, May 12, 2012 at 2:11 PM, William Piel <wil...@ya...<javascript:_e({}, 'cvml', 'wil...@ya...');>
> > wrote:
>
>>
>> On May 12, 2012, at 10:59 PM, Carl Boettiger wrote:
>>
>> Not sure why the search by DOI fails for this paper. I search for the
>> following doi (from the API or the web interface)
>>
>> 10.1111/j.1558-5646.2011.01374.x
>>
>> and I get no results.  But the DOI resolves correctly to the paper:
>> http://dx.doi.org/10.1111/j.1558-5646.2011.01374.x
>> and the study appears in treebase:
>> http://www.treebase.org/treebase-web/search/study/summary.html?id=11550
>> What did I miss?
>>
>> --
>> Carl Boettiger
>>
>>
>> In an ideal world, submitters would return to their submissions once they
>> know the more citation metadata, and then update their submissions
>> accordingly (submitters always retain privileges for updating citation
>> metadata). But that doesn't always happen. 't any rate, I've now added this
>> DOI -- you should be able to search using it now.
>>
>> bp
>>
>>
>>
>
>
> --
> Carl Boettiger
> UC Davis
> http://www.carlboettiger.info/
>
>

-- 
Dr. Rutger A. Vos
Bioinformaticist
NCB Naturalis
Visiting address: Office A109, Einsteinweg 2, 2333 CC, Leiden, the
Netherlands
Mailing address: Postbus 9517, 2300 RA, Leiden, the Netherlands
http://rutgervos.blogspot.com

Re: [Treebase-devel] Uploading interpretations of published data sets

[William P. <wil...@ya...>]

On May 14, 2012, at 11:18 AM, Michael Jones wrote:

> (Reposted from treebase-Bugs)
> I'm interested in uploading data from the repository available
> http://www.graemetlloyd.com/matr.html. According to the sites curator,
> Dr. Graeme Lloyd, however: "1. The vast majority of the datasets are
> based on my interpretation of published datasets (usually matrices
> printed as tables in PDFs), and not the original files used by the
> author. (In theory these should be the same, but in practice...) 2.
> Similarly, all trees are from my own (parsimony) searches in TNT and
> don't necessarily reflect the settings used by the authors. 3. This
> list is a dynamic one and I am adding to it all the time." Since these
> files are interpretations of published data, I was wondering wether or
> not to upload them onto TreeBASE.


Hi Michael,

- For me, the biggest disappointment of the Graeme Lloyd data is the lack of character labels and state labels, which would be pretty critical for data reuse. But characters without character labels is still better than none. In the past, we have captured character label data using OCR from the hard-copy or copy/paste from the PDF. But turning free text into NEXUS can be tricky and requires some skill with TextWrangler and regular expressions. If you'd like to take a jab at acquiring these data, I'd be happy to Skype with you about how to do this with TextWrangler, MacClade, Mesquite, etc. 

- While mistakes may be present in Graeme Lloyd's data, I wouldn't worry about that too much it unless you find that the rate of it is quite high. 

- When I look at the page, I see that Graeme provides both MPTs and a consensus tree (in Phylip/Newick format). If possible, the tree submitted to TreeBASE should look like the one published in the original paper, so I would suggest the following: (1) Open the data matrix in Mesquite, (2) Do "include File" to import the consensus tree (selecting "philip" format type), (3) look at the original PDF and use the tools in Mesquite (move branch, collapse clade, swap branch, etc) to make any minor changes needed for the consensus tree to match the published tree, (4) do "Store Tree" from the Tree menu in Mesquite to commit these changes (this is a very important step), (5) use the List Tree tab to change the name of the tree to match its name in the publication (e.g. "Fig. 3" etc). (6) Save the nexus. (7) If there is no opportunity to match the consensus tree with what was published, I think it is okay to upload this anyway, but name the analysis and tree something like "Unpublished result; TreeBASE Fecit" or "Unpublished result; Graeme Lloyd Fecit". 

- Most important, it would be good form to contact Graeme Lloyd to praise him for his valuable efforts in assembling dino phylogenetic data, and then explain your plans to "mirror" these data in TreeBASE, again emphasizing the great value they will add to TreeBASE (on account of Dinos being very rare in TreeBASE). TreeBASE submissions have an "URL" field, and you can offer to put his web site in there as a way to credit the source of the data.

regards,

Bill

[Treebase-devel] Uploading interpretations of published data sets

[Michael J. <mjo...@gm...>]

(Reposted from treebase-Bugs)
I'm interested in uploading data from the repository available
http://www.graemetlloyd.com/matr.html. According to the sites curator,
Dr. Graeme Lloyd, however: "1. The vast majority of the datasets are
based on my interpretation of published datasets (usually matrices
printed as tables in PDFs), and not the original files used by the
author. (In theory these should be the same, but in practice...) 2.
Similarly, all trees are from my own (parsimony) searches in TNT and
don't necessarily reflect the settings used by the authors. 3. This
list is a dynamic one and I am adding to it all the time." Since these
files are interpretations of published data, I was wondering wether or
not to upload them onto TreeBASE.

Re: [Treebase-devel] searches by doi

[William P. <wil...@ya...>]

On May 13, 2012, at 7:52 AM, Roderic Page wrote:

> This was one of the motivations behind setting up the TreeBASE group in Mendeley http://www.mendeley.com/groups/734351/treebase/ .
> 
> The idea was to consume TreeBASE papers, then edit the metadata (adding DOIs, PMIDs, etc.). I cleaned up a lot of papers from 2010 and earlier (there were some pretty spectacular examples of references differing wildly from what authors submitted (e.g., if paper ended up in different journal).
> 
> Ideally this group would be automatically populated by consuming a feed from TreeBASE, and any edits made in Mendeley could be harvested by TreeBASE. Wouldn't take long to set this up. Limiting factor is people taking time to clean up references, I think I'm the only one of the 140 members of the group to do this :(
> 
> Regards
> 
> Rod

Indeed, we need to harvest the edited files back into TreeBASE. And Mendeley's API should rich enough to perform all these tasks: i.e. both auto-creation of new Mendeley records from TreeBASE and capturing new edits back into TreeBASE. This was in our last grant proposal, I think.

Currently, TreeBASE allows the submitter to edit the citation at any future time, but nobody else. With an open Mendeley group, are there concerns about mischievous edits?

bp

Re: [Treebase-devel] searches by doi

[Roderic P. <r....@bi...>]

This was one of the motivations behind setting up the TreeBASE group in Mendeley http://www.mendeley.com/groups/734351/treebase/ .

The idea was to consume TreeBASE papers, then edit the metadata (adding DOIs, PMIDs, etc.). I cleaned up a lot of papers from 2010 and earlier (there were some pretty spectacular examples of references differing wildly from what authors submitted (e.g., if paper ended up in different journal).

Ideally this group would be automatically populated by consuming a feed from TreeBASE, and any edits made in Mendeley could be harvested by TreeBASE. Wouldn't take long to set this up. Limiting factor is people taking time to clean up references, I think I'm the only one of the 140 members of the group to do this :(


Regards

Rod

On 12 May 2012, at 22:25, Carl Boettiger wrote:

> Thanks for adding this.  
> 
> Yes, I guess it makes sense that kind of thing would be difficult to automate.  It's nice feature to have though, since it's usually the easiest way to grab the trees of the study when staring at the paper.  
> 
> -Carl
> 
> On Sat, May 12, 2012 at 2:11 PM, William Piel <wil...@ya...> wrote:
> 
> On May 12, 2012, at 10:59 PM, Carl Boettiger wrote:
> 
>> Not sure why the search by DOI fails for this paper. I search for the following doi (from the API or the web interface)
>> 
>> 10.1111/j.1558-5646.2011.01374.x
>> 
>> and I get no results.  But the DOI resolves correctly to the paper: http://dx.doi.org/10.1111/j.1558-5646.2011.01374.x
>> and the study appears in treebase: http://www.treebase.org/treebase-web/search/study/summary.html?id=11550
>> What did I miss?
>> 
>> -- 
>> Carl Boettiger
> 
> In an ideal world, submitters would return to their submissions once they know the more citation metadata, and then update their submissions accordingly (submitters always retain privileges for updating citation metadata). But that doesn't always happen. 't any rate, I've now added this DOI -- you should be able to search using it now. 
> 
> bp
> 
> 
> 
> 
> 
> -- 
> Carl Boettiger
> UC Davis
> http://www.carlboettiger.info/
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
Graham Kerr Building
University of Glasgow
Glasgow G12 8QQ, UK

Email: r....@bi...
Tel: +44 141 330 4778
Fax: +44 141 330 2792
Skype: rdmpage
AIM: rod...@ai...
Facebook: http://www.facebook.com/profile.php?id=1112517192
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html

Re: [Treebase-devel] searches by doi

[Carl B. <cbo...@gm...>]

Thanks for adding this.

Yes, I guess it makes sense that kind of thing would be difficult to
automate.  It's nice feature to have though, since it's usually the easiest
way to grab the trees of the study when staring at the paper.

-Carl

On Sat, May 12, 2012 at 2:11 PM, William Piel <wil...@ya...> wrote:

>
> On May 12, 2012, at 10:59 PM, Carl Boettiger wrote:
>
> Not sure why the search by DOI fails for this paper. I search for the
> following doi (from the API or the web interface)
>
> 10.1111/j.1558-5646.2011.01374.x
>
> and I get no results.  But the DOI resolves correctly to the paper:
> http://dx.doi.org/10.1111/j.1558-5646.2011.01374.x
> and the study appears in treebase:
> http://www.treebase.org/treebase-web/search/study/summary.html?id=11550
> What did I miss?
>
> --
> Carl Boettiger
>
>
> In an ideal world, submitters would return to their submissions once they
> know the more citation metadata, and then update their submissions
> accordingly (submitters always retain privileges for updating citation
> metadata). But that doesn't always happen. 't any rate, I've now added this
> DOI -- you should be able to search using it now.
>
> bp
>
>
>


-- 
Carl Boettiger
UC Davis
http://www.carlboettiger.info/

Re: [Treebase-devel] searches by doi

[William P. <wil...@ya...>]

On May 12, 2012, at 10:59 PM, Carl Boettiger wrote:

> Not sure why the search by DOI fails for this paper. I search for the following doi (from the API or the web interface)
> 
> 10.1111/j.1558-5646.2011.01374.x
> 
> and I get no results.  But the DOI resolves correctly to the paper: http://dx.doi.org/10.1111/j.1558-5646.2011.01374.x
> and the study appears in treebase: http://www.treebase.org/treebase-web/search/study/summary.html?id=11550
> What did I miss?
> 
> -- 
> Carl Boettiger

In an ideal world, submitters would return to their submissions once they know the more citation metadata, and then update their submissions accordingly (submitters always retain privileges for updating citation metadata). But that doesn't always happen. 't any rate, I've now added this DOI -- you should be able to search using it now. 

bp

[Treebase-devel] searches by doi

[Carl B. <cbo...@gm...>]

Not sure why the search by DOI fails for this paper. I search for the
following doi (from the API or the web interface)

10.1111/j.1558-5646.2011.01374.x

and I get no results.  But the DOI resolves correctly to the paper:
http://dx.doi.org/10.1111/j.1558-5646.2011.01374.x
and the study appears in treebase:
http://www.treebase.org/treebase-web/search/study/summary.html?id=11550
What did I miss?

-- 
Carl Boettiger
UC Davis
http://www.carlboettiger.info/

Re: [Treebase-devel] plugging the tree into a NEXUS file

[William P. <wil...@ya...>]

On May 11, 2012, at 10:46 PM, Hilmar Lapp wrote:

> Here's one that we've now encountered for two online sources: How to the tree, which is in a separate file (in Newick format) into the NEXUS file, which only holds the data matrix [1]. Are there recommended practices (e.g., using Mesquite) that submitters in this situation should follow?
> 
> 	-hilmar
> 
> [1] One example is this source: http://www.graemetlloyd.com/matr.html 

That site is quite a treasure-trove, especially seeing as TreeBASE is really weak on dinos. Pity that the character names and states are not coded -- by themselves, 0s and 1s are not terribly meaningful -- but better than nothing.

But yes, submitters are asked to mate their trees with their matrices, as shown in the instructional video:

http://www.treebase.org/treebase-web/submitTutorial.html

bp

[Treebase-devel] plugging the tree into a NEXUS file

[Hilmar L. <hl...@ne...>]

As I think (?) has been introduced before, Michael Jones is a student at UNC Chapel Hill who is working with us this summer to curate data into TreeBASE that's available online but not archived in TreeBASE. Aside from increasing the data content in TreeBASE, the more important aspect this is actually to surface and document the various issues associated with that.

Here's one that we've now encountered for two online sources: How to the tree, which is in a separate file (in Newick format) into the NEXUS file, which only holds the data matrix [1]. Are there recommended practices (e.g., using Mesquite) that submitters in this situation should follow?

	-hilmar

[1] One example is this source: http://www.graemetlloyd.com/matr.html 

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

Re: [Treebase-devel] corrections/versions

[William P. <wil...@ya...>]

Yes, this is correct. No versioning system in place, but we allow submitters to correct errors. In at least one case I recall a submitter adding a new dataset while retaining the older one as well. 

bp

On May 11, 2012, at 12:52 AM, Hilmar Lapp wrote:

> Hi Carl - 
> 
> It doesn't, AFAIAA. Though supposedly you could edit the data, say to correct mistakes. But that does't leave the original submission, and if the record was previously made public, it requires that the TreeBASE editor returns the submission to "in progress."
> 
> 	-hilmar
> 
> On May 10, 2012, at 5:35 PM, Carl Boettiger wrote:
> 
>> Hi,
>> 
>> Does treebase support the ability to add revisions / newer versions of submissions?  If so, can someone point me to the documentation for this, any perhaps any statistics on whether this feature is used?
>> 
>> Thanks!
>> 
>> Carl
>> 
>> -- 
>> Carl Boettiger
>> UC Davis
>> http://www.carlboettiger.info/
>> 
>> ------------------------------------------------------------------------------
>> Live Security Virtual Conference
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>> threat landscape has changed and how IT managers can respond. Discussions 
>> will include endpoint security, mobile security and the latest in malware 
>> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
>> Treebase-devel mailing list
>> Tre...@li...
>> https://lists.sourceforge.net/lists/listinfo/treebase-devel
> 
> -- 
> ===========================================================
> : Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
> ===========================================================
> 
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

Re: [Treebase-devel] corrections/versions

[Hilmar L. <hl...@ne...>]

Hi Carl - 

It doesn't, AFAIAA. Though supposedly you could edit the data, say to correct mistakes. But that does't leave the original submission, and if the record was previously made public, it requires that the TreeBASE editor returns the submission to "in progress."

	-hilmar

On May 10, 2012, at 5:35 PM, Carl Boettiger wrote:

> Hi,
> 
> Does treebase support the ability to add revisions / newer versions of submissions?  If so, can someone point me to the documentation for this, any perhaps any statistics on whether this feature is used?
> 
> Thanks!
> 
> Carl
> 
> -- 
> Carl Boettiger
> UC Davis
> http://www.carlboettiger.info/
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================

[Treebase-devel] corrections/versions

[Carl B. <cbo...@gm...>]

Hi,

Does treebase support the ability to add revisions / newer versions of
submissions?  If so, can someone point me to the documentation for this,
any perhaps any statistics on whether this feature is used?

Thanks!

Carl

-- 
Carl Boettiger
UC Davis
http://www.carlboettiger.info/

Re: [Treebase-devel] Treebase data license?

[Hilmar L. <hl...@ne...>]

The folks over at Creative Commons would be the ones to contact for such legal questions and assessments. +1 though from me on Ryan's response.

	-hilmar

On Apr 26, 2012, at 7:53 AM, William Piel wrote:

> 
> On Apr 26, 2012, at 1:16 AM, Hilmar Lapp wrote:
> 
>> such laws are quite different internationally
> 
> True…  This seems to indicate that under European law, databases acquire rights irrespective of the copyrights of the contributors to the database: 
> 
> http://en.wikipedia.org/wiki/Database_rights
> 
> TreeBASE could easily volunteer to waive its own rights in this respect. 
> 
> But with respect to the ownership rights of contributors, does anyone know any country where ideas (e.g. "Napoleon was born in 1769" or, in our case, "chimps are the sister group to humans") are owned or protected with respect to communication of said ideas? (as opposed to implementation or exploitation, such as patent protection on inventions). 
> 
> bp
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
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: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
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Re: [Treebase-devel] Treebase data license?

[Ryan S. <ry...@sc...>]

On Apr 26, 2012, at 7:53 AM, William Piel wrote:

> But with respect to the ownership rights of contributors, does anyone know any country where ideas (e.g. "Napoleon was born in 1769" or, in our case, "chimps are the sister group to humans") are owned or protected with respect to communication of said ideas? (as opposed to implementation or exploitation, such as patent protection on inventions). 

I'm not aware of countries that allow "ownership" of a single idea. But even a single Nexus file can qualify for protection under the database right, if it collects together a sufficient amount of information.

Regardless of the data's actual legal status, it would be useful to create an explicit statement about the rights and terms of use, so third parties like Carl aren't forced to make assumptions about their rights. Even better, TreeBase could require depositors to accept a particular rights statement at deposit time. This way, third parties would know that all deposits after date X fell under particular terms, even if the rights are unclear for earlier deposits.

If you don't want to make a particularly strong statement, you could use the same sort of weasel-language that GenBank uses. See the "GenBank Data Usage" section here: http://www.ncbi.nlm.nih.gov/genbank/. This isn't a great solution, but at least it clearly states the repository's opinion on reuse.

--- Ryan

Re: [Treebase-devel] Treebase data license?

[William P. <wil...@ya...>]

On Apr 26, 2012, at 1:16 AM, Hilmar Lapp wrote:

> such laws are quite different internationally

True…  This seems to indicate that under European law, databases acquire rights irrespective of the copyrights of the contributors to the database: 

http://en.wikipedia.org/wiki/Database_rights

TreeBASE could easily volunteer to waive its own rights in this respect. 

But with respect to the ownership rights of contributors, does anyone know any country where ideas (e.g. "Napoleon was born in 1769" or, in our case, "chimps are the sister group to humans") are owned or protected with respect to communication of said ideas? (as opposed to implementation or exploitation, such as patent protection on inventions). 

bp

Re: [Treebase-devel] Treebase data license?

[Val T. <va...@ci...>]

>> I'm curious what license, if any, covers the treebase data? Dryad is very clear about all their data being public domain / CC0, but it's not obvious to me from the treebase website.  
> 
> Our "story" so far is that in the spectrum of Art vs. Ideas, TreeBASE stores ideas. Even if the original published tree was an "artwork" with respect to the journal, in TreeBASE the nodes and edges are decomposed into tables, and when re-serialized you can't be sure that it will look like the original artwork. So in that sense we are storing the concepts or ideas, not the art -- and therefore while some of these objects may be patented, we don't think they should be copyrightable. Hence copyright simply does not apply to the data, only to the codebase. 
> 
> While citations and abstracts are often considered art (and we also store those), I think our redistribution of them is considered "fair use". 

The attached is not exactly on data ownership but it has some interesting thoughts which are related.
Val

Re: [Treebase-devel] Treebase data license?

[Hilmar L. <hl...@ne...>]

Carl - 

Bill's analysis is about the legal standing someone could have who asserted copyright on their TreeBASE deposition. I'll note that TreeBASE is an international repository. While I would concur with Bill's conclusions (and the implication that TreeBASE records are in the public domain) for people governed by US copyright laws, such laws are quite different internationally. The matter of fact is that TreeBASE is, as far as I understand, not asking depositors to release the data under certain terms, or to expressly waive copyright, and so even for US depositors simply assuming public domain is a tricky proposition, I would say.

	-hilmar

On Apr 25, 2012, at 2:16 AM, William Piel wrote:

> 
> On Apr 24, 2012, at 9:17 PM, Carl Boettiger wrote:
> 
>> Hi list,
>> 
>> I'm curious what license, if any, covers the treebase data? Dryad is very clear about all their data being public domain / CC0, but it's not obvious to me from the treebase website.  
>> 
>> Thanks
>> 
>> Carl
> 
> Our "story" so far is that in the spectrum of Art vs. Ideas, TreeBASE stores ideas. Even if the original published tree was an "artwork" with respect to the journal, in TreeBASE the nodes and edges are decomposed into tables, and when re-serialized you can't be sure that it will look like the original artwork. So in that sense we are storing the concepts or ideas, not the art -- and therefore while some of these objects may be patented, we don't think they should be copyrightable. Hence copyright simply does not apply to the data, only to the codebase. 
> 
> While citations and abstracts are often considered art (and we also store those), I think our redistribution of them is considered "fair use". 
> 
> bp
> 
> 
> ------------------------------------------------------------------------------
> Live Security Virtual Conference
> Exclusive live event will cover all the ways today's security and 
> threat landscape has changed and how IT managers can respond. Discussions 
> will include endpoint security, mobile security and the latest in malware 
> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/_______________________________________________
> Treebase-devel mailing list
> Tre...@li...
> https://lists.sourceforge.net/lists/listinfo/treebase-devel

-- 
===========================================================
: Hilmar Lapp  -:- Durham, NC -:- informatics.nescent.org :
===========================================================