BSC Shorthouse ESC 2011


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Entomological Society of Canada, 2011, Halifax. Biological Survey of Canada Symposium.

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  • Clearly, anything the Biological Survey of Canada does MUST be online.
  • But, getting online does not mean what it did merely 5 years ago. It MUST have a purpose, a vision, a goal, a clearly understood tag line, direction, and more importantly, a distinct presence. It also means sharing its ware as widely as possible being clear about what you want to do, where you might need help, and being a good citizen in helping others realize their visions.
  • Getting online today means producing content that can be reused in ways that you did not imagine were possible and to showcase these efforts as a way to bolster enthusiasm. This message is equally important to the incumbent Editor in Chief for the Canadian Entomologist. Gone are the days of producing PDF reprints behind paywalls as a primary stream of revenue. The game is now all about Semanticizing the content, making it accessible via Application Programming Interfaces for 3 rd party access. Open the pipes as widely as you can using widely accepted techniques and let others use what you have.
  • Gone are the days of putting content online in flat HTML, having it indexed by Google and declaring it a success. That was last decade. Being online today means distributing your content, engaging your audience, taking advantage of social networking opportunities, encouraging others to help get the word out. Being online today means you are prepared to slough your web page presence with a new skin to re-present your core business under a new light to meet the needs of stakeholders.
  • Politically-charged question that only the BSC Board of Directors can answer as it weighs all its options. What we CAN say with certainty is that if it doesn’t make significant steps in this ‘Big New Biology’ of being online, being purposeful, producing re-usable content, engaging its audience, it will be exceptionally difficult to maintain any sustainability model.
  • The BSC CAN be a player in this space. It will not be without effort, but steps toward the light can be incremental and organized. What’s working to immense advantage are its wealth of publications. Key integrators in the information age for Biology are: Geography Time Scientific Names
  • GNI has 17.5M indexed namestrings
  • The BSC could jump headlong onto web and go like gangbusters, heads pulling in multiple directions, but the result will no doubt be a nasty beast that hides its true strengths behind teeth, spit, and knobby horns.
  • Or, the BSC can tentatively prance into this new world like a gentle unicorn; unseen by (most) taxonomist crumblies and revered by the kids that still have the purity of imagination.
  • A grand vision that we all share is a facile list of all taxa that can be browsed, navigated (by some means), extracted, pre-linked to relevant literature, linked to useful, rapidly accessible information such as host, prey, distribution, type specimens, type localities. In short, a Canadian Entomological Encyclopedia of Life. But the reality of such a vision kicks in. Your time is limited, you need to publish, you need to teach, you need to chase funds to maintain a vibrant lab. Your students also have limited time to contribute to such an Encyclopedia, especially if it is unclear what will be the rewards. And so, let’s stick with what we do, strip it down to an easily produced manuscript, but tweak it to ensure the publication has the flexibility to remain competitive and to be a leader in this new biology.
  • What emerged from these calls was a clear need to establish context or boundaries to a checklist. One idea was to encourage expression of taxon / biogeographic association.
  • Come from ArcView shapefiles I found on Government of Canada web site, ingested into PostGIS (spatially-aware) database
  • A proxy for the human capacity for submission to such a Journal
  • BSC Shorthouse ESC 2011

    1. 1. The way forward is… <ul><li>ONLINE </li></ul>
    2. 2. The way forward is… <ul><li>PURPOSEFUL </li></ul>
    3. 3. The way forward is… <ul><li>REUSABLE </li></ul>
    4. 4. The way forward is… <ul><li>ENGAGING </li></ul>
    5. 5. <ul><li>Does the BSC WANT to be a player in this space, and to what extent CAN it play? </li></ul>
    6. 6. NAMES ARE THE KEY TO THE BIG NEW BIOLOGY: A BOTTOM-UP SOLUTION TO CREATING A MACROSCOPE David P. Shorthouse ( Dmitry Mozzherin David J. Patterson The Marine Biological Laboratory Center for Library & Informatics
    7. 7. TREE 25(12): 686-691 doi:10.1016/j.tree.2010.09.004  
    8. 8. David J. Patterson Dmitry Mozzherin
    9. 9.
    10. 10. <ul><li>Central plot: a macroscopic crystal that can focus on any location in space with exceptional clarity </li></ul>
    11. 11. Outline <ul><li>Setting the Stage </li></ul><ul><ul><li>Global Context </li></ul></ul><ul><li>The Vision </li></ul><ul><li>The Ball is Rolling </li></ul><ul><li>Who’s Got the Money? </li></ul>
    12. 12. eTaxonomy Will Happen <ul><li>ICZN Amendment </li></ul><ul><ul><li>New Article 8.5 electronic-only publication is an acceptable medium provided: </li></ul></ul><ul><ul><ul><li>Issued after 2011 & states date of publication on the work itself </li></ul></ul></ul><ul><ul><ul><li>Archived within one year with an organization other than the publisher, compliant with Open Archive Information System </li></ul></ul></ul><ul><ul><ul><ul><li>Permanent and irrevocable license to make work accessible should publisher no longer do so </li></ul></ul></ul></ul><ul><ul><ul><li>Recommendation 8C : electronic works should be structured to allow automated indexing and data extraction </li></ul></ul></ul><ul><ul><li>New Article 10.9 Registration of names and nomenclatural acts required in ZooBank when published in electronic-only work </li></ul></ul>
    13. 13. <ul><li>ZooBank for name registration IS Happening </li></ul><ul><li>Publishers, Institutions ARE jockeying for a poll position ( e.g. ZooKeys, SI) </li></ul><ul><li>Names aggregators ARE building machines and protocols ( e.g. Global Names Architecture, iD4Life) </li></ul><ul><li>Specimen data aggregation is a hot ticket BUT names management continues to be an embarrassing impediment </li></ul>
    14. 14. A Call to Arms <ul><li> </li></ul><ul><ul><li>“ The Biological Survey of Canada: The way forward!” </li></ul></ul><ul><ul><li>23 public responses: Kevin Floate, Rose DeClerck-Floate, Andy Hamilton, Martin Damus, Greg Pohl, Felix Sperling, Derek Sikes </li></ul></ul><ul><li>February 5, 2011: </li></ul><ul><ul><li>“… the BSC products to date have been top-down, unstructured narratives that are not conducive to broad-brushed compilations or re-use ( i.e. where are the upload and download buttons and how does one extract all the names within?). …there are not yet opportunities for bottom-up participation to enhance these products. There is currently no incentivized, scalable way to hone Hugh [Danks]’s estimate of the number of arthropod species in Canada.” </li></ul></ul>
    15. 17. My Gift: Hope for a Distinct Presence <ul><li> </li></ul><ul><ul><li>Registered with GoDaddy </li></ul></ul><ul><ul><li>Expires March 21, 2013 </li></ul></ul><ul><ul><li>Renewal $27 for additional 2 years </li></ul></ul><ul><li> </li></ul>
    16. 18. The Vision: A Unicorn <ul><li>A Checklist Journal </li></ul><ul><ul><li>Traditional, stable, human-consumable manuscripts with DOI </li></ul></ul><ul><ul><li>WITH a required, (Public Domain) standards-based Darwin Core Archive supplemental </li></ul></ul><ul><ul><li>Lightweight, generous peer review procedure </li></ul></ul><ul><ul><li>Public comments, post-publication, perpetual review </li></ul></ul>
    17. 19. PURPOSEFUL <ul><li>A bottom-up, comfortable mechanism to build an “all taxa” list </li></ul><ul><ul><li>It will be messy, but neatness is boring </li></ul></ul><ul><ul><li>It will require someone to compile whenever and however they see fit </li></ul></ul>
    18. 20.
    19. 21. Relationship With CJAI or Other <ul><li>Has been cursorily explored, but should be revisited </li></ul><ul><li>Cohesion/crosswalks entirely possible if visions are flexible and can align </li></ul><ul><li>Pairing of contextualized, extractable names lists with aides for their identification </li></ul>
    20. 22. What is a Checklist? <ul><li>Taxonomic Checklist </li></ul><ul><ul><li>explicit assertions of taxonomic status </li></ul></ul><ul><ul><li>references taxonomic usage and definition of the taxon concept. [ e.g. the Catalogue of Life] </li></ul></ul><ul><li>Nomenclatural Checklist </li></ul><ul><ul><li>details about the original publication but little information about taxonomic status [ e.g. Index Fugorum, International Plant Name Index] </li></ul></ul><ul><li>General Checklist </li></ul><ul><ul><li>distinct list of taxa with no explicit information concerning the taxonomic or nomenclatural status of taxa </li></ul></ul>
    21. 23. Characteristics of a Checklist <ul><li>May include: </li></ul><ul><ul><li>Hierarchical classification </li></ul></ul><ul><ul><li>Synonymy </li></ul></ul><ul><ul><li>Vernacular names </li></ul></ul><ul><ul><li>Distribution </li></ul></ul><ul><ul><li>Specimen/type information </li></ul></ul><ul><ul><li>References </li></ul></ul>
    22. 24. Checklist Scope <ul><li>Taxonomic scope </li></ul><ul><ul><li>Highest common taxon group to which all members are ascribed </li></ul></ul><ul><li>Regional scope </li></ul><ul><ul><li>Geographic boundaries [ e.g. fauna or floral list] </li></ul></ul><ul><li>Thematic scope </li></ul><ul><ul><li>Common semantic qualifier to all members [ e.g. regulated, threatened species, ecological characteristics] </li></ul></ul>
    23. 25. REUSABLE
    24. 26. Second Tentative Steps: UI/UX <ul><li>Open Journal Systems </li></ul><ul><ul><li> </li></ul></ul><ul><ul><li>PostGIS </li></ul></ul><ul><li>PostBox </li></ul><ul><ul><li>Massage Excel, Open Office files into Darwin Core Archives </li></ul></ul><ul><ul><li>Horizontally scalable </li></ul></ul><ul><ul><li>Recognizes columns that belong to known controlled vocabularies & provides feedback </li></ul></ul>
    25. 27. <ul><ul><li> </li></ul></ul>
    26. 28. More Tentative Steps <ul><li>Several productive conference calls with BSC Board of Directors since February, 2011 </li></ul><ul><li>Greg Pohl instrumental in expressing needs as a potential author </li></ul><ul><li>Felix Sperling secured access to servers at UofA for DPS to play, building the human network </li></ul><ul><li>Donna Giberson searching for and building synergies </li></ul>
    27. 29. Stockpiled Terms & Vocabularies <ul><li>Terrestrial Ecozones: 9 </li></ul><ul><li>All US States and Canadian Provinces </li></ul><ul><li>Canadian Ecozones: 15 </li></ul><ul><li>Canadian Ecoprovinces: 52 </li></ul><ul><li>Canadian Ecoregions: 194 </li></ul><ul><li>Canadian Ecodistricts: 1020 </li></ul><ul><li>Taxonomic ranks: 124 (English) </li></ul><ul><li>Others… </li></ul>
    28. 30. Could this Have Legs (or Wings)? <ul><li>AES-ESC JAM 2011: </li></ul><ul><ul><li>201 papers & posters (includes plenary talks and this session) </li></ul></ul><ul><ul><li>99 likely candidates for submission </li></ul></ul><ul><ul><li>>50 extremely good fit </li></ul></ul>
    29. 31. Brainstorming the Potential <ul><li>Species introductions, species at risk </li></ul><ul><li>Species described by Canadians </li></ul><ul><li>Bioinventories </li></ul><ul><ul><li>Graduate student work/collections </li></ul></ul><ul><ul><li>Regional, thematic collections </li></ul></ul><ul><ul><li>BioBlitz lists BEFORE the event </li></ul></ul>
    30. 32. An Opportunity for a Champion <ul><li>An individual or a lab to raise the torch </li></ul><ul><ul><li>Ready to mold it into their vision </li></ul></ul><ul><ul><li>Interface between author and geek </li></ul></ul><ul><ul><li>Willing to take risks and push in new directions </li></ul></ul><ul><ul><li>Network with national, global initiatives </li></ul></ul><ul><ul><li>Collaborate with exploration of new funds </li></ul></ul>
    31. 33. ENGAGING
    32. 34. ENGAGING
    33. 35. WHO’S GOT THE MONEY? <ul><li>Heritage Links (National, Provincial, Regional) </li></ul><ul><ul><li> </li></ul></ul><ul><li>Fundsnet Services </li></ul><ul><ul><li> </li></ul></ul>
    34. 36. Suitable Foundations <ul><li>The McLean Foundation </li></ul><ul><li>Royal Bank of Canada </li></ul><ul><li>Salamander Foundation </li></ul><ul><li>J. W. McConnell Family </li></ul><ul><li>Wilburforce Foundation </li></ul>
    35. 37. Who Might Give Their Money? ( if they knew how ) <ul><li>Left Field Idea: </li></ul><ul><ul><li>Attractive bulletin board-like tool for authors to announce intentions, solicit co-authors and assistance </li></ul></ul><ul><ul><li>Donors Choose </li></ul></ul>
    36. 38. PULLING IT ALL TOGETHER <ul><li>“ Being” online means: PURPOSEFUL, REUSABLE, ENGAGING </li></ul><ul><li>BSC can be a key player if it </li></ul><ul><ul><li>energizes its greatest asset: humans </li></ul></ul><ul><ul><li>Executes a “product”, not a “project” </li></ul></ul><ul><li>Checklist Journal </li></ul><ul><ul><li>Submissions comfortably fit within author expectations </li></ul></ul><ul><ul><li>Human & machine-consumable </li></ul></ul><ul><ul><li>Standards-based yet flexible for future explorations </li></ul></ul>