ToLWeb

ToLWeb 1.0

Vision

According to David Maddison "The original (1994) vision was several fold:

• to have a database serving the community-consensus of the phylogenetic tree of all of life (ideally with the capability of displaying alternatives, too)
• to "decorate" that tree with information about clades and individual species
• to link the nodes to other information available on the Internet (its original subtitle was "a phylogenetic navigator")
• to serve both the needs of the research community, as well as present a unified vision of the diversity of life and its history to the general public
• to present web pages for each species and significant clade and on Earth
• this information would be contributed by experts in each clade

I think all of those visions are still valuable, although today their would be much greater clarity of what they would entail than the primitive ideas I had in my head 15 years ago.

The biggest change that has happened over the last 15 years is the tremendous growth in the ecosystem of biodiversity databases One project in particular, the EOL, has basically duplicated a large part of the public goals of the ToL (the web pages goal, second from last).

As all of these other projects should be fully integrated as much as possible, including with the ToL, we need to rethink the core structure of the ToL to be take full access of all that was available now, and to integrate into the growing bioinformatics ecosystem."

Project statistics

• contributors:
• images: 30,000
• videos: 800
• nodes in tree: a bit over 110,000

Project profile

Questions:

• who links to ToLWeb?
• who are the scientific users? what do they do?
• who are the educational users? what do they do?

Links to stakeholder community

• Contributors
  • Phylogenetic contributors
  • image contributors
  • other contributors?
• Research users
• Educational users
  • TreeHouses
• Data providers linking to content
  • EoL?
  • others?

ToLWeb Technical Wiki

Technical information about ToLWeb, including server configuration, development environment, database tables, etc., is on ToLWebTechnicalDetails.

ToLWeb 2.0

We talked about renaming the group from tolweb2 to something that better reflects the broader vision. Here are the suggestions so far:

• OpenPhylo
• PhyloShare
• Trees On The Internet (TOTI)
• TreeLink
• EvoIO-ToL
• Trees-R-Us
• phylocity
• PhyloCommons
• RefPhylo / PhyloRef

Meeting Notes

Telecon, Sept 8, 2010 (9 am CDT)

Present: Nico Cellinese, Karen Cranston, Arlin Stoltzfus, Hilmar Lapp, Rutger Vos (9:13)

Agenda: proposal to present to PRF board at its meeting

Resources:

• new proposal
• old proposal

Notes:

1. Proposal to present to PRF board at its meeting
   • timing: PRF board meeting not scheduled
2. Alternative idea: submit an NSF workshop proposal this fall
   • get endorsement from PRF board
   • NSF mechanism allows workshops at any time
   • how open-ended?
   • how focused on ToLWeb?
   • business plan (ToLWeb really needs)
3. Next steps
   • Karen talks to NSF program officer about workshop proposal (DONE by Hilmar: see list thread)
   • Karen talks to Bill Piel about dates for PRF board meeting (DONE: dates are Dec 13-14, 2010)
   • everyone adds specific goals / targets to the existing document (the new proposal, not the old proposal)

Telecon, 4 March, 2010

action items

• Karen will start a new google doc for the whitepaper, and a spreadsheet for choosing a new name
• Arlin, Karen, Nico, Rutger and possibly others will start on revisions
• the group sets a target date of 25 March to finish the revised whitepaper
• as a separate issue, David will follow up with Hilmar, Arlin, and others regarding ToLWeb-specific issues of governance etc

present: Rutger Vos, Katja Schulz, David Maddison, Arlin Stoltzfus, Hilmar Lapp, Nico Cellinese, Karen Cranston (arriving late due to a conflict)

Issues:

• updates on the ToLWeb project
  • server migration in progress (see ToLWebServerDoc)
  • AToL proposal (4 yr, NSF) (not available)
• rethinking the "tolweb2 group" vision
• followup and action items

Notes The meeting started late due to some nasty audio interference problem. Those present at 11:05 hung up, and called in again, and then things were fine. The meeting started about 11:09 and ended at about 11:49.

After about 20 minutes discussion, there was a general consensus to move ahead with a broadened vision for this group and its initial project of seeking funding for, and organizing, a stakeholder meeting. This will require a substantial revision of the whitepaper. The broadened vision is not specific to ToLWeb, though in practice, its likely that ToLWeb and its stakeholders will be a big part of what happens, and that some follow-up projects will focus on ToLWeb.

We then decided on how to move ahead with revising the whitepaper and other things. We decided to start from scratch. Karen will start a new google doc & share it with us. Arlin, Karen and Nico agree to get started on the text.

In regard to a name, Karen will start a worksheet to share with us. It would be a good idea to decide on the name before we submit the whitepaper.

Telecon, 29 January, 2010

action items

• everyone will look forward to telcon with AToL-proposal group, delay on submitting whitepaper
• Karen will tell David M to go ahead with the telecon plan and to invite others to the google group

present: Karen Cranston (presiding), David Maddison, Arlin Stoltzfus, Hilmar Lapp, Nico Cellinese

Notes For most of the first hour, David told us about an NSF proposal being planned that involves ToLWeb and developing it further, and we discussed how this might coordinate with our own ToLWeb2 effort.

The proposal hasn't been written. Its going to involve key players in ToLWeb and AToL, and its being led by Doug & Pam Soltis. The current plan is that the proposal will have two main foci:

• human-supervised synthesis of available data to make a big tree, improving coverage for under-represented groups
• outreach (defined broadly to include, not just education, but other stuff like strategic partnerships with other data projects, and addressing how to map other resources to ToL)

This is in response to the NSF AToL RFP with a due date on March 22. The budget cap on individual proposals is only $3M.

There was some discussion about "putting the cart before the horse" in the sense that this upcoming NSF proposal would delineate a vision for the future of ToLWeb before the bottom-up stakeholder-driven process even started. It would create barriers to new people and new ideas by putting money and leadership in the hands of "the usual suspects". The resolution to this, suggested by David, is that the NSF proposal necessarily is going to be incremental due to the budget limitations: it points the way toward ToLWeb 1.2 or 1.5, not ToLWeb 2.0. According to this interpretation, which seemed agreeable to those present, we could partner with the AToL proposers to develop the ToLWeb 2.0 vision, pretty much just as we had planned, with the difference that the sub-projects would all coordinate with ToLWeb 1.5 instead of ToLWeb 1.0.

At about 3:05, David hung up to allow the rest of us a chance to sort through what we had heard, and to make some decisions about how to proceed with the whitepaper and how to coordinate with the AToL group. We decided to delay releasing the whitepaper until we had the chance to meet with the AToL proposal group. We will invite them to join the google group and to view and edit the whitepaper, and we will give David the go-ahead to set up a teleconference. Consistent with previous practice of the ToLWeb2 group, that conference call would be open to participate for anyone in group.

The telecon ended at about 3:20.

Telecon, 21 Janurary, 2010

Present: Sheldon, Rutger, Hana, Karen, Arlin, Bill (5 min late), Hilmar (10 min late)

Action items

• Hilmar: clarify goals & outcomes in whitepaper
• Arlin: get an explicit endorsement from Maddison
• Karen: add ideas (from our discussion) about how to get people involved
• Arlin: add ideas (from our discussion) about how we propose to facilitate the follow-up process
• Sheldon: add section to whitepaper on credentials of organizers
• Hana: share ideas about educators and communities to involve in the process
• Karen: doodle poll for meeting next Friday, Jan 29

Notes

1. Review whitepaper
   1. Questions / comments about existing text
      • could be shorter
      • most of the specifics are there already
      • maybe need a few examples of possible projects that might emerge? no
      • goals vs process
      • number: 50 is too many, 40 is ok
      • has Maddison read this?
        • Hilmar: no record of him editing; would like to get endorsement
        • Arlin: will get him to read and comment
      • need to describe how we will choose participants (Karen will do)
      • open call- how many? do we need it?
        • need to get "young blood"
        • std procedure is search literature on topic, contact post-docs
        • alternative search: open queries to evoldir (do you want to do research with big trees)
      • alternative process: start electronic forum, invite everyone, sort out who is contributing
        • google group exists, we decided (last year) not to "launch" until whitepaper is done
      • what does composition of meeting look like:
        • more "outside" than "inside"
        • mostly people ready to commit, not butterflies sipping the nectar
        • need to add digital library, datanet (NSF), stakeholder category
   2. Identify sections that need work, assign tasks
2. Meeting logistics
   1. Do we need info re: dates and participants at this point
   2. How will we select / solicit participants?
      • see above
   3. Budget
3. Followup
   1. help subgroups to organize in productive ways to develop proposals (Arlin)
   2. draw more people into process
   3. publicity - invite bloggers, science writer

Telecon, 16 December, 2009

present: Hana Kucera, Enrico Pontelli, Arlin Stoltzfus, Karen Cranston, Sheldon McKay, Rutger Vos, Nico Cellinese, Omar Rota Stabelli, Hilmar Lapp

Agenda

1. Structure and logistics of whitepaper.
   1. How to write proposal and divide up effort
   2. Scope of TolWeb 2.0. Tree + pages or just tree?
   3. location (google doc? wiki?)
2. Stakeholder meeting. When? Who? Funding?
3. AToL panel March 2010. Are we attempting this?
4. Evointerop (closed) vs TolWeb2.0 (open) groups

Possible sponsors

• NESCent interested, good target, not necessarily only target. accepts whitepapers continuously
• BioSync has March deadline
• other possibilities?

Scheduling factors

• anchored by summer-fall grant proposal deadlines: stakeholder meeting in April or May to allow time for proposal (Hilmar)
• what are proposal deadlines (Nico)
• talk to NSF program officers (Arlin, Hilmar, Enrico volunteer)

Whitepaper text

• Karen will create google doc
• Arlin and Hilmar (busy in Jan) will get the draft started; others can contribute at any time

NSF AToL program deadline March 22, 2010

• discussion: too soon, missed opportunity,
• this is the standard yearly AToL (Nico)

Appropriate collaborative technology

• evointerop private listen for private discussions (e.g., people to invite) that should not be world-readable
• tolweb2.0 google group for developing proposal
• what about evoio wiki-- wiki not a good tool for access control or concurrent editing (Hilmar)

Educational uses

• Hana: online ToL readable and accessible to children, translated into different languages
• Omar: focus on EC; idea is to teach about relationships (ToL not EoL)

Telecon, 8 December, 2009

present: Nico, Arlin, Enrico, Hilmar, Rutger

Agenda:

1. Decide on a brief statement of who we are, what are our goals, and what we expect from this process.
2. List stakeholders communities, decide on the subset of stakeholders to include right NOW in the process
3. Decide on main points of the White Paper
4. Decide on logistics of how we will get this done
   • who is going to contact whom about getting involved at this (early) stage?
   • who is going to set up the whitepaper doc and manage permissions and access?
   • who is going to talk to possible sponsors (NESCent, BioSynC, other) about how to proceed?
   • who is going to gather links and other useful info

Minutes:

• This is a creative process out of which leaders will emerge.
  • We expect a vision to emerge that is fundable.
  • The EvoIO group has certain goals, pertaining to interoperability and reusability, and may be involved in that vision in the end, but doesn't necessarily have to be.
• Need to find out more details about the Phyloinformatics Research Foundation
  • What is the purview of that foundation? Solely governance?
  • How is ToLWeb covered (governed) by this? What is the advisory board and who will be on it?
  • Hilmar should talk to Bill Piel to find out more.
• Who to include from the stakeholder community right away?
  • Curators: Lots of content contributed to ToLWeb by curators. Arlin will ask Katja Schulz who are the most active and would be best to include in a stakeholder meeting.
• What are the research uses of ToLWeb?
  • Information is sparse, incomplete, presented in the wrong form, difficult to access and reuse.
  • Some data is accessible programmatically but the APIs are undocumented and not known to anyone.
  • Many taxa and groups are missing.
  • How does ToLWeb overlap with Phylota, or TreeBASE.
  • We could use the TolWeb publication to look for who cites it: Maddison, D. R., K.-S. Schulz, and W. P. Maddison. 2007. The Tree of Life Web Project. Pages 19-40 in: Zhang, Z.-Q. & Shear, W.A., eds. Linnaeus Tercentenary: Progress in Invertebrate Taxonomy. Zootaxa 1668:1-766.
• We would need to include people who can represent future uses (or users) of a ToLWeb resource
  • For example, use in web-services and workflows (Mark Wilkinson?), or eco-phylogenetics (Cam Webb? Mark Schildhauer?)
  • Semantic Web aspect
  • ToLWeb right now seems to operate similar to EOL, except that it has clade pages, rather than species pages
• ToLWeb needs links to raw data (such as from TOLKIN), so that users can determine how the phylogenies were constructed.
  • ToLWeb needs to be integrated with data repositories for this purpose.
• Educational use: ToLWeb has a media use survey on each image page.
  • Can we obtain the data? Rutger will ask David Maddison.
• Main scope of the whitepaper is the stakeholder meeting, specifically to argue compellingly why 1) those who we want to attend should want to attend, and 2) those who can fund the meeting should fund it.
  • Give hints of what a future vision could look like, e.g., focus on phylogeny, comprehensiveness, integration with other resources, outreach/education.
  • ToLWeb could be a synthesis of the tree of life, with information harvested for each clade.
  • Emphasize standards-compliant programmatic access
  • Not sure how important and what features the visual (GUI) interface would need to satisfy.
• Need to clearly define the stakeholder meeting
  • Draft agenda. How will we get to decisions, follow-up, and actually doing something.
• There is a concern that the level of support for such an initiative within the systematics community.
  • But there is certainly enough support and supportive people in the community for moving forward.