Fwd: possible Catalysis meeting on names

[Robert Guralnick]

Resending this to all.  You also caught Arlin's post.  Maybe we can look to tomorrow or Wed. late in the day for Call #2 so we can have a bit more chatter via email first?

-r

---------- Forwarded message ----------
From: Robert Guralnick <Robert.G...@colorado.edu>
Date: Mon, Nov 19, 2012 at 1:20 PM
Subject: Re: possible Catalysis meeting on names
To: David Patterson <dpatt...@mbl.edu>
Cc: "Blum, Stan" <SB...@calacademy.org>, Richard Pyle <deep...@bishopmuseum.org>, David Patterson <dpatt...@eol.org>, Arlin Stoltzfus <ar...@umd.edu>, Dmitry Mozzherin <dmozz...@gmail.com>, "Shorthouse, David" <dshor...@mbl.edu>, Matt Yoder <diap...@gmail.com>, hinc...@umich.edu, Cynthia Parr <csp...@gmail.com>, Hilmar Lapp <hl...@nescent.org>, Naim Matasci <nmat...@iplantcollaborative.org>, Gaurav Vaidya <ggva...@gmail.com>

   Hi everyone --- A quick update on a meeting this morning that involved myself, Hilmar, Matt Yoder, Cody Hinchlif, Naim Matasci and, briefly, Arlin.  Here are some main points from that call:

1)  We all agreed its worth us aiming for a December 1 _working group_ proposal (not Catalysis meeting) that tackles the key issue of how we both represent taxon information in formal ontologies and how that can help in developing standardization and linking across multiple taxon name resolution services.  And finally, we absolutely need to link all of this to quality assurances aspects of key endeavors in our discipline, including Open Tree of Life, EO,  Map of Life, GBIF, etc.   Matt et al., feel free to add further content to this admittedly brief description.

2)  We have a REALLY short deadline and the opportunity to do this might not easily come again because this may be NESCent's last working group proposal call.  If we are going to do it, we need a game plan, like NOW.  This starts with PIs, and the sense on the call was that someone from GNA, along with Matt Yoder, maybe Naim, and one other "taxon name consumer" person would work.  If you want to be a PI, please speak up!

3)  In order to get this done, it would be great to get a one or two page "early draft" developed in the next couple days that covers:

• Introduction and Goals – A statement of the outstanding question in evolutionary science being addressed and a concise review of the concept and the literature to place the project in context.
• Proposed Activities-  This should include a clear statement of specific data (include citations or urls) and analytical tools that will be required for the project, along with a clear description of how synthesis will be achieved.

My guess is that much of the content needed to write up the above exists in grant proposals and papers on which many of you have worked.  The big challenge will be focusing on synthesis, but I think all of us have a pretty good idea about the next obvious steps forward.  

If I am forgetting anything, let me know.  I should say that I am really enthused about this idea -- think it is absolutely the right one -- but am much less sure how much capacity I have to really push it forward.  I am going to definitely _try_ very hard to devote myself to this but hope others can take the mantle here.  Tick tick tick.

Best, Rob

On Sun, Nov 18, 2012 at 2:19 PM, David Patterson <dpatt...@mbl.edu> wrote:

Rob

I agree with Stan.

I think the idea MUST be pursued if we expect to make progress on interconnecting distributed data in Biology.  I believe we now have the proof of concept applications that allow us to say that we have the right infrastructure in place, and will make good progress with further investment in bringing content together and in improving the customizability of serrvices.   That is, I think this is a very timely idea, and has the capacity to deliver good results in the near future. 

Global names has many dimensions, but overcoming the challenges associated with variation in names for the same taxon motivated much of the work at MBL.  

You can see and example of our work at http://demo.globalnames.org/reconciler?token=wN6HUIvWQuG1JdEVdaJ7cw.  This demonstrates name finding and resolution (pink highlights).  We are also in the final stages of finishing off a new indexing service for Biodiversity Heritage Library, a service that not only finds names, but reconciles what it finds and offers links to other sources  - i.e. has to option of 'resolving' the name (assuming resolution = provide me with the name that is preferred by an aiuthoritative source of your choosing).  You will see that the system can break the back of the problems, but we still have some issues to address.

I understand this space reasonably well, but our code has been build by David Mozzherin and Dave Shorthouse (copied here).   There is some very time-costly stuff in this area (collection of the taxonomic synonyms being one of them) that I do not believe it makes any sense to try to build reconciliation and resolution services de nova.  Rather, our best best is to have a common and open foundation that can be expanded by ohers to meet their needs.

We would be delighted to collaborate with enthusiastic users.  Depending on how many people might come together, I'd recommend at least Dima and myself attend.  Dima worked closely with the iPlant TNRS group.

In addition, I have recently send an email to some of the NESCENT guys about collaborating on a proposal to act as a taxonomic learing house for the OToL project.  Support for that would ensure we have the funds to collect a lot of taxonomic information.

I think it would be very valuable for all for me to add some text to the http://www.evoio.org/wiki/TNRS_Meeting_Proposal page as it makes no mention of the Global Names work and progress to date.  I have been reticent to promote GN  too much before we have some robust services out there, but it is important to ensure that we don't try to reinvent wheels.  I have tried to log in under various names but always end with an error.  I presume that I need to be assigned some rights to contribute.  Can you arrange this and I will put some information about GN onto that page.

As these issues have been central to our thinking for many years, we should be able to contribute a lot to a catalysis proposal.

Thanks

Paddy

On Sun, Nov 18, 2012 at 6:39 AM, Blum, Stan <SB...@calacademy.org> wrote:

Rob, this is relevant to the work all three of us are doing (or vice versa).  I'm sure everyone in GNA would like to be there.

I'm traveling for another 48 hours or so, and I'm sure I'm going to walk in under a huge mound of stuff that will fall on me.  If you guys schedule a conference call, please count me in.

-Stan 

From: Robert Guralnick <Robert.G...@colorado.edu>
Date: Sunday, November 18, 2012 4:11 AM
To: Richard Pyle <deep...@bishopmuseum.org>, David Patterson <dpatt...@eol.org>, Stan Blum <sb...@calacademy.org>
Cc: Arlin Stoltzfus <ar...@umd.edu>
Subject: possible Catalysis meeting on names

  Hey Stan, Paddy, Rich --- I wanted to touch base with you guys really quickly about the idea for a Catalysis meeting proposal to be held at NESCent on the topic of Taxonomic Name Resolution and how to build services across projects.  Arlin Stoltzfus has been trying to get a lot folks involved in such activities in the same place to discuss how to avoid duplication of effort both in terms of assembling resources and in terms of how these are compiled and used by other projects/consumers.   The proposal is due in just a couple weeks but I personally think its an exciting and timely topic and likely to yield significant value especially if we can leverage the time together and maybe have the meeting and outcomes also associated with help on key aspects of the project.  As it turns out, my student Gaurav Vaidya will be at NESCent on a graduate fellowship next semester, so the timing could work particularly well.  

 

I am not sure when we will next talk as a group, but hopefully Arlin can chime in and maybe we can pull this off?  Are you interested?  I absolutely am.  For more details on where we are, check here:  http://www.evoio.org/wiki/TNRS_Meeting_Proposal

Best, Rob

--
___________________________________
David J Patterson

Senior Scientist, Marine Biological Laboratory
7 MBL Street, Woods Hole, MASS 02543, USA.

Research Professor
School of Life Sciences, Arizona State University
Tempe, AZ 85287-4501

Professor (MBL) Ecology and Evolutionary Biology
Brown University, Providence, Rhode Island
 
Life Sciences Lead, Data Conservancy dataconservancy.org

globalnames.org

[Arlin Stoltzfus]

On Nov 19, 2012, at 3:43 PM, Hilmar Lapp wrote:

On Nov 19, 2012, at 3:20 PM, Robert Guralnick wrote:

My guess is that much of the content needed to write up the above exists in grant proposals and papers on which many of you have worked.  The big challenge will be focusing on synthesis, but I think all of us have a pretty good idea about the next obvious steps forward.

One note post-call here - I sensed some hesitation along the lines of "I'll put my stuff in once I see a skeleton and where this is going". My recommendation is that everyone who has a paragraph (or more) motivating and arguing what might turn into proposal objectives throw it up there on a Google Doc. It's much easier then to go through as a group to prioritize, and subsequently for a few people to edit into a more coherent whole. The earlier it's up there for everyone to look at even it it's a hodgepodge, the more time for everyone to stew over it and ideas / thoughts for streamlining to flow from that.

I agree with that in the sense that if we all decide on a vision, and a prioritized list of major goals, then a few of us can do the writing and produce a proposal.  We don't all have to agree on a detailed plan-- just like with any funding proposal, the details are subject to change.  The most important thing is that, *before* we commit to spending 100s of hours working together, we agree on our common goals.  

Arlin

-------
Arlin Stoltzfus (ar...@umd.edu)
Fellow, IBBR; Adj. Assoc. Prof., UMCP; Research Biologist, NIST
IBBR, 9600 Gudelsky Drive, Rockville, MD, 20850
tel: 240 314 6208; web: www.molevol.org

[Matt Yoder]

Who want's to take the lead on a google doc to throw ideas/draft text
down on? I can if need be- not sure if I missed earlier versions
somwhere here.

M

[Matt Yoder]

Meh- I see Arlin's start on the group - I'll post some text there
(though I do like documents as a way to more fluidly move bits of text
around).

M

[Cynthia Parr]

I think we may have overlapping but slightly different ideas about
where we want to go, it will help to see the goals all together before
we finalize the scope.

I don't see a document if Arlin started one. I also prefer a Google doc.

Cyndy

> --
>
>

[Arlin Stoltzfus]

No, please go ahead with your earlier plan-- some people were having trouble accessing the wiki, and we don't want to force them to learn a new language (wiki) too.  

So please go ahead and move all the content to a google doc, and leave a note on the wiki page pointing to the google doc. 

Arlin

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[Matt Yoder]

Document shared, please check the shared list. I'll port the wiki now.

M

[Cody Hinchliff]

I have written up some stuff and sent it out to the opentree group for comments/validation. I can copy and paste it into the relevant google doc for you folks as soon as that happens. Is there a doc yet? If so, could someone send the link? 

--
 
 

[Cody Hinchliff]

Nevermind! I got the link...

[David Patterson]

As the lead PI of the NSF funded Global Names project, I offer my services to be a voice of Global Names in your discussions.

Dec 1 is tight but doable.

I am djpmapleferryman on Skype.

Absent from your list of tasks is an assessment of what is already present and that this Catalysis meeting can build from.  

As I have not been involved in the leadup, perhaps it might be simplest for me to react to an early draft by embellishing with indications of where GN has got to.

The big challenges for the basic names services are funds for more development (but our code is open) and for content acquisition.  We can almost certainly make a shortlist of the areas where more software is needed, but perhaps that is better left for a first meeting.

I am available Tuesday and Wednesday for a call.

Paddy

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