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Đorđe Grbić
I would like to announce the new version (v.3) of MetaPIGA software.
MetaPIGA is a robust implementation of several stochastic heuristics for large phylogeny inference (under maximum likelihood).

Official release note can be found here: http://www.scribd.com/doc/127358328/MetaPIGA-v3-release-note

Official website: www.metapiga.org
Carl Boettiger
I made a simple R package from the TreeBASE API, http://wp.me/p1ek2R-rs (examples & code). grab the trees from any study listed here. feedback welcome
Roderic Page and Joseph Hughes like this.
Roderic Page
Roderic Page @cboettig Kewl! I'm not a big R user but I'm sure those that live in R will get a lot out of this.
17th May
Joseph Hughes
I like the new wikified #mendeley tagging. http://www.mendeley.com/research/a-complete-phylogeny-of-the-whales-dolphins-and-eventoed-hoofed-mammals-cetartiodactyla/ is the most popular paper tagged #treebase with 40 readers.
Carl Boettiger likes this.
Joseph Hughes
And I should forget phylota (http://phylota.net/) as a source a valuable phylogenetic data.
Joseph Hughes
All these disparate sources of historical data (GenBank, Paleobiology database, TreeBASE) desperately need to be integrated: @rdmpage please help!
Carl Boettiger likes this.
Joseph Hughes
Will we ever have an almost complete tree of extinct and extant organisms? #TreeBASE
Sjúrður Hammer
Roderic Page
Added more DOIs and PMIDs to papers in this group.
Sjúrður Hammer
Sjúrður Hammer wish edits showed up like this
7th March
Steve Dennis
Steve Dennis Will make sure it gets added into the use-cases for some upcoming projects related to meta-data.
7th March
Joseph Hughes
My attempt at inviting researchers who have submitted trees to #TreeBASE to join this #mendeley group has so far failed :(
Roderic Page likes this.
Steve Dennis
Steve Dennis I think starting discussions with the members already in the group would generate unique content and that may be more of an incentive for them to join.
7th March
Roderic Page
Roderic Page I suspect that the real driver will be having something outside Mendeley that makes use of this group, such as way to visualise/search/interact with the trees in TreeBASE and the literature in Mendeley, and makes use of the aded value the Mendeley group brings (e.g., more DOIs and PMIDs so we can find original papers, get GenBank sequences, etc.). ...
7th March
Sjúrður Hammer
Sjúrður Hammer for people that are not even members of mendeley, even less of a topic specific group, might be convinced to join if there was a a well designed preview page showing member list and some literature examples (with corresponding metadata). Isn't the first thing they knock into the Mendeley login screen, when they may just be interested in giving the ...
27th April
Joseph Hughes
#TreeBASE #Mendeley group now has 50 members + I love Mendeley's twitter integration
Steve Dennis and Roderic Page like this.
Roderic Page
OK, that's enough Mendeley for one day. I've updated DOIs and PMIDs for Systematic Biology, and tidied up a few other things. Might be fun to explore ways to integrate Mendeley with a phylogeny database, such as including readership stats in search results, and display Mendeley profiles of authors.
Roderic Page
Quick look at readership stats. Mendeley's API won't let me easily get these for group papers, so I've had a quick manual look. Most read articles so far are

113 http://www.mendeley.com/research/broad-phylogenomic-sampling-improves-resolution-of-the-animal-tree-of-life/
108 http://www.mendeley.com/research/a-phylogenomic-study-of-birds-reveals-their-evolutionary-history/
88 http://www.mendeley.com/research/phylogenydriven-genomic-encyclopaedia-bacteria-archaea/

Members of this group do quite well.

Vince Smith has http://www.mendeley.com/profiles/vince-smith/ has 28 readers for
http://www.mendeley.com/research/genetic-analysis-of-lice-supports-direct-contact-between-modern-and-archaic-humans/

Kate Jones has 26 for http://www.mendeley.com/research/a-phylogenetic-supertree-of-the-bats-mammalia-chiroptera-1/

Both Vince and Kate have yet to claim authorship of these papers on their Mendeley profiles!
Roderic Page
Oh, we have readership stats...
Joseph Hughes
Joseph Hughes I think the most read is "A phylogenomic study of birds reveals their evolutionary history." with 108 'readers'
16th December
Joseph Hughes
Joseph Hughes It's weird, I can't open the PDFs I uploaded to the public TreeBASE group yesterday even though they are on my hard drive.
16th December
Roderic Page
Tags have now been updated, so if you've sync your Mendeley Desktop library you should have tags "treebase1" and "treebase2" with the study identifiers for TreeBASE. This is a good thing, because it means if you edit a reference by looking up a DOI or PMID we won't loose the TreeBASE identifiers.
Rutger Vos
Let's say this group is creating large amounts of annotations.

In an ideal world, these annotations would be (translatable into) triples such that the subject is the treebase data object's URI, and the predicate, its namespace, and its value are something we agree upon (presumably evolving from the tagging that evolves here).

For example like this:

<http://purl.org/phylo/treebase/phylows/study/TB2:S1787><mug:hasDOI><doi:blah/blah>

Where "mug:" binds to some sort of "Mendeley User Group" namespace that explains what "hasDOI" means, and where that definition also makes explicit what scheme/format is used for DOIs.

Then, conceivably, TreeBASE would be able to fetch them, understand them and fold them into its output in the appropriate places (web pages, NeXML files), while making it clear that this is non-curated, user-generated content.
Roderic Page likes this.
Roderic Page
Roderic Page I wasn't suggesting manual monitoring, ideally you'd use a cron job or pubsubhubbub to poll the RSS feed. Then you'd either add the additional information from Mendeley as annotations, or update the TreeBASE object, creating a new version of that object. Adding annotations is probably simpler given TreeBASE's architecture, but requires clients to k...
16th December
User Deleted
User Deleted +1 for versioning.
TreeBASE bib data is definitely dirty (why? there's not much there tbh ~2500 references aren't that much to clean), and because it's so non-visible (in it's entirety) it's hard to query accurately.

1.) case errors
Compare "Mycological Research"
http://treebase.org/treebase-web/search/studySearch.html?query=prism.publicationName=...
16th December
Roderic Page
Roderic Page Yep, the bibliographic data is messy. Much of it is provided by the authors of the studies, so it's a bit of a worry that it's so crappy. Of course, Mendeley's data comes from researchers as well, but the expectation is that it will be reasonably clean as it much of it comes from bibliographies people use when writing papers, plus "many eyes" means...
16th December
Roderic Page
If anybody is editing papers in this group it's important to keep the "treebase1:" and "treebase2:" labels intact, as that enables us to link the papers to the studies in TreeBASE. Originally I'd stored these labels in the "keywords" field, but if you lookup a DOI or PubMed identifier in Mendeley the keywords field can be overwritten! To get around this I've copied the TreeBASE labels to the "tags" field, so they shouldn't be affected by DOI/PMID lookup.
Joseph Hughes likes this.
Roderic Page
Roderic Page Bugger. Looks like the tags won't sync with Mendeley web unless the reference is edited in Mendeley Desktop. I need a "touch" for Mendeley which tells it that all the documents have been changed (in this case in the sqlite database). Could try and hack the sqlite database further, at the risk of breaking something...
15th December
Joseph Hughes
So are you automating the upload of open access articles to the Mendeley TreeBASE group? How?
Roderic Page likes this.
Joseph Hughes
Joseph Hughes Cool! I have attached the pdfs to the BMC articles but I have a nagging feeling that you can't actually see them
15th December
Roderic Page
Roderic Page I can see that you've added them, but I can't access them. Mendeley needs to exclude Open Access PDFs from its exclusion rules for downloading PDFs.
15th December
Steve Dennis
Steve Dennis Working on it ;)
15th December
Roderic Page
Eventually we'll have some readership statistics for the TreeBASE papers (these can take a few days to appear). Might be worth assessing whether having data available in TreeBASE is correlated with readership (Dryad folks, would this be of interest?)
Steve Dennis likes this.
Roderic Page
Roderic Page I guess we could also add links to Dryad datasets as well...
16th December
Todd Vision
Todd Vision No reason for us not to create a separate group for that, is there?
16th December
Roderic Page
Roderic Page Sure, makes sense given Dryad is broader than TreeBASE.
16th December
Roderic Page
I've added the tag "publishedelsewhere" to references in TreeBASE where the authors submitted a paper to one journal, but it ended up being published elsewhere. In these cases the citation information in TreeBASE is incorrect. See http://www.mendeley.com/groups/734351/treebase/papers/title/0/tag/publishedelsewhere/ for examples.
Roderic Page
What if TreeBASE looked like this? http://twitpic.com/3fx0ym
Roderic Page
Roderic Page Discussions happen in various places. I agree that one might get a more focussed discussion within a Mendeley group. But for people to think it is worth their while to do so I think they'd like some indication that people will read it. This, I suspect, is one reason hardly anybody comments on articles on journal web sites -- who is going to read th...
15th December
Steve Dennis
Steve Dennis Cross posting to twitter is under active development, as are improved discussion facilities.
15th December
Joseph Hughes
Joseph Hughes I'm a big fan of DISQUS as a community commenting platform. It is a shame that publishers haven't integrated it to their websites for commenting on journals. In the end, I suspect that various commenting platforms will be integrated as big companies buy out smaller ones.
15th December

About this group

TreeBASE http://www.treebase.org/ is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. This group includes all the publications in TreeBASE as of 2010-12-13, and the aim is to clean up and annotate these publications, including adding missing DOIs and PubMed identifers. TreeBASE study numbers (both TreeBASE I and II) are included as keywords and tags, with the prefix "treebase1:" and "treebase2:", respectively.

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