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Re: [beemonitoring] Comments on NAS-NRC Status of Pollinators study

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  • John S. Ascher
    I feel compelled to respond to the following comment by F. Christian ... My comments may or may not have been totally out-of-line but your particular and
    Message 1 of 28 , Aug 15, 2008
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      I feel compelled to respond to the following comment by F. Christian
      Thompson, Systematic Entomology Lab., ARS, USDA:

      > John Asher's comments on NAS-NRC are totally out-of-line and represent a
      > personal resentment that he was not selected for the panel.

      My comments may or may not have been "totally out-of-line" but your
      particular and highly personal accusation is patently untrue. At the time
      the committee was selected I had just finished graduate school, had few
      publications, and for many other reasons obviously did not have the
      relevant experience, credentials, or gravitas to even be considered for
      selection to such a prestigious committee of well-known scientists. My
      senior colleagues in the field of bee taxonomy didn't make the cut so why
      so how could I ever have expected to do so?

      Next time you slander me in a public forum please at least include the "c"
      in my last name.

      > Two museum-based taxonomists were included. So, to imply that a dipterist
      > and a lepidopterist some how resulted in the "deemphasizes museum-based
      > expeditions ..." is simply not true.

      Bees are the most important pollinator group and sampling of these entails
      unique challenges. The taxonomic impediment to bee research is one of the
      biggest problems we must overcome to document status of pollinators in the
      US. It is my "totally out-of-line" view that bee taxonomists should be
      directly involved as full partners when planning any solution.

      The report itself provides prima fascie evidence of the degree to which
      concerns particular to bee taxonomy have or have not received due
      consideration.

      > We pushed for and got recommendation to support basic taxonomic research
      > on pollinators.

      I never said or implied otherwise! We are all grateful for this.

      > However, for good defensible scientific monitoring, to document CHANGE,
      > etc., you must have "monitoring of fixed study sites with sampling regimes
      > chosen primarily to obtain "statistically verifiable measures." And that
      > does include and require basic taxonomy.

      The overemphasis on CHANGE is itself perhaps the most obvious problem with
      the NAS-NRC status report. First we need to establish a sufficient
      baseline and the report does not adequately specify how best to do so. To
      develop such a baseline it is highly inefficient to concentrate sampling
      only at fixed study sites and it is also highly inefficient to marginalize
      or even exclude data not collected under preferred sampling protocols.

      I take it for granted that any scientist, including taxonomists, would
      seek to generate data useful for statistical analyses. However, sampling
      protocols need not be ecologically-focused nor done at fixed study sights
      in order to yield data amenable to robust statistical analyses. I do
      concede that it is difficult to verify CHANGE from data gathered in
      disparate ways from disparate sites, but must note that it is difficult to
      VERIFY change from ANY bee data set, even if good defensibly scientific
      sampling methods are employed.

      Many people regard museum-based expeditions as scientifically dubious or
      even indefensible and if that is your position than our views are in
      serious conflict.

      Taxonomically-focused sampling can be good, defensible science even if
      certain museum-based scientists themselves fail to acknowledge this.

      > Yes, John is right about there being much to be discovered and the
      > traditional museum taxonomists and their collecting techniques are ALSO
      > needed.

      We all recognize that all partners and their viewpoints should be
      respected. The essential questions are to what degree and when ("slowly
      ..." I suppose?).

      It is damning with faint praise to acknowlwedge that the collecting
      techniques of museum taxonomists are needed but to also imply that these
      are not sufficiently good, defensible, or scientific to have been endorsed
      prominently in the NAS-NRC report.

      John

      >
      >
      >
      > So, slowly ...
      >
      >
      >
      > F. Christian Thompson
      >
      > Systematic Entomology Lab., ARS, USDA
      >
      > c/o Smithsonian Institution MRC-0169
      >
      > PO Box 37012
      >
      > Washington, D. C. 20013-7012
      >
      > (202) 382-1800 voice
      >
      > (202) 786-9422 fax
      >
      > www.diptera.org Diptera Website
      >
      > ________________________________
      >
      > From: beemonitoring@yahoogroups.com [mailto:beemonitoring@yahoogroups.com]
      > On Behalf Of John S. Ascher
      > Sent: Friday, August 15, 2008 12:27 PM
      > To: beemonitoring@yahoogroups.com
      > Subject: RE: [beemonitoring] Proposal to Hold a Meeting on The Development
      > of a North American Bee Inventory and Monitoring Network
      >
      >
      >
      >
      >
      > Like Terry, I am concerned that the initial "global and continental
      > foundation" for the proposed project does not cite ongoing, successful
      > efforts by the global bee taxonomic community. These include compilation
      > of relevant taxonomic data, including distributional records, and
      > databasing and mapping of bee specimen records.
      >
      > I'm all in favor of this proposed effort, but if it is to transcend the
      > limitations of previous efforts such as the ALARM project (highlighted in
      > the NAS-NRC status report as a premiere example of pollinator monitoring)
      > then it is imperative that the essential role of taxonomists and their
      > institutions be made clear from the outset. For example, the expertise of
      > taxonomists must be fully incorporated when designing sampling protocols.
      >
      > The 15-member NAS-NRC Committee on the Status of Pollinators in North
      > America did not include a single bee taxonomist, and perhaps as a result
      > their recommended monitoring program emphasizes ecologically-oriented
      > monitoring at fixed sites and deemphasizes museum-based expeditions and
      > other sampling protocols that more efficiently yield certain essential
      > discoveries. Results best obtained from a systematic/taxonomic,
      > museum-based approach rather than from an
      > ecological/experimental/statistical approach include discovery of new
      > species and and life stages, of biogeographically significant new
      > distributional records, and of host-parasite and bee-plant relationships.
      >
      > We are still in a discovery phase in terms of bee species distributions
      > and basic natural history, including floral associations, so we must find
      > a way to efficiently obtain fill gaps in these data. While the ecological
      > approach emphasizes unbiased samples, necessarily consisting for the most
      > part of common and widespread species, much essential information can
      > better be obtained by biasing samples in favor of specimens and
      > observations of systematic/taxonomic interest. To do so we must make full
      > use of existing taxonomic expertise, e.g. knowledge of areas of endemism,
      > and support maintenance and enhancement of this. We simply cannot
      > efficiently fill gaps in knowledge of our bee fauna solely through
      > monitoring of fixed study sites with sampling regimes chosen primarily to
      > obtain "statistically verifiable measures."
      >
      >
      >
      >
      >


      --
      John S. Ascher, Ph.D.
      Bee Database Project Manager
      Division of Invertebrate Zoology
      American Museum of Natural History
      Central Park West @ 79th St.
      New York, NY 10024-5192
      work phone: 212-496-3447
      mobile phone: 917-407-0378
    • Sam Droege
      Barb: This is a point that needs some discussion at some point. In my mind the purpose of the meeting would be to put science(reseachers) and
      Message 2 of 28 , Aug 15, 2008
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        Barb:
         
        This is a point that needs some discussion at some point.  In my mind the purpose of the meeting would be to put science(reseachers) and money(administrators) together to hopefully birth a sustainable as well as scientifically defensible program.  That is my narrow view of things.
         
        However, I can also see your point which is that there is hunger for more summarized information as well as a networking among workers on the topic. 
         
        So, while my selfish view would be that the number of people at the meeting be restricted to those with a direct role...there is no reason that there couldn't also be a preceeding meeting along the lines of which you spoke.  Having over-extended myself too many times, I am not ready to volunteer on that idea, but would love to work with a group that would like to focus on a larger public meeting.
         
        sam
         

        Bees are black, with Gilt Surcingles
        Buccaneers of Buzz.
        Ride abroad in ostentation
        And subsist on fuzz.  

        Fuzz ordained - not fuzz contingent -
        Marrows of the hill.
        Jugs - a Universe's fracture
        Could not jar or spill.
             - Dickinson  





        -----beemonitoring@yahoogroups.com wrote: -----

        To: <beemonitoring@yahoogroups.com>
        From: <barbara.abraham@...>
        Sent by: beemonitoring@yahoogroups.com
        Date: 08/15/2008 01:10PM
        Subject: RE: [beemonitoring] Proposal to Hold a Meeting on The Development of a North American Bee Inventory and Monitoring Network

        HTML

        All,

         

        I am a novice at bees, but my future research plans include studying native pollinators of native plants.  The proposed meeting seems like a great way to consolidate and review all of the information and misinformation that is out there on CCD and the status of pollinators in general for non-experts like me.  Not being familiar with the location of those who would want to attend, I can only selfishly suggest that the meeting NOT be held on the West Coast, but rather either on the East Coast (preferably) or Midwest.

         

        Barb

         

        Barbara J. Abraham, Ph.D.

        Associate Professor

        Department of Biological Sciences

        Hampton University

        Hampton , VA   23668

        757-727-5283

        barbara.abraham@ hamptonu. edu

         


        From: beemonitoring@ yahoogroups. com [mailto:beemonitori ng@yahoogroups. com] On Behalf Of Sam Droege
        Sent: Friday, August 15, 2008 9:55 AM
        To: beemonitoring@ yahoogroups. com
        Subject: [beemonitoring] Proposal to Hold a Meeting on The Development of a North American Bee Inventory and Monitoring Network

         

         

        All:

         

        I think the time is right to bring together scientists and administrators to talk about creating, expanding, and implementing a unified means of documenting the status of bees in North America .  As a start to that process I would like to enlist the ideas and ultimately the support of members of this listserv.

         

        The global and continental foundation for such an effort already exists:

        (corrections and additions to this list welcomed)

        • 1999 Sa˜o Paulo Declaration on Pollinators
        • 2007 Committee on the Status of Pollinators in North America
        • Colony Collapse Disorder and the vulnerability of the current North American honeybee pollination system
        • Bee Barcode of Life Project
        • North American Pollinator Protection Campaign
        • The Xerxes Society Pollinator Conservation Program
        • Individual efforts by all of the U.S. Federal Agencies with major biological programs
        • Numerous State and Provincial Efforts
        • High interest among park, refuge, and other protected areas managers and biologists
        • High interest among orchardists and other agriculturalists dependent upon bee pollination of crops
        • Recent Farm Bill and honeybee legislation

        (need to further document efforts in Mexico and Canada )

         

         

        Given the poor understanding of status, distributions, and even a complete list of species I would like to propose that a meeting take place in 2009 to design a statistically valid, interconnected system of North American inventories and surveys of bees.

         

        Proposed Title (not surprisingly) :  Design of an Interconnected System of North American Inventories and Surveys of Bees

         

        To start the conversation going regarding whether such a meeting is needed and how it might look I have an initial series of questions for the group to reflect upon and discuss.

         

        1. Are there any competing processes for the programmatic inventory and monitoring of bees currently planned in any of the countries?  If so, then can or how could they be integrated?
        2. What should the date of the meeting be?  I would like to propose that it in September of 2009 (note: that’s next September not this September) as that will give the community enough time to pull together and share analyses of survey techniques PRIOR to the meeting.
        3. Where should the location of the meeting be held?  Ralph Grundel has said that there is a nice new facility with meeting and sleeping quarters at Indiana Dunes National Lakeshore in Indiana (U.S.A.) (near Chicago ).  However, that is but one suggestion, others are welcome…but costs are a big consideration at this point.
        4. What should the geographic coverage be of such an effort?  Does it make sense to work across the U.S. , Canada , and Mexico or should such efforts simply inform each other?
        5. What should the meeting objectives be?  I would propose the following:
          1. Establishing a set of statistically verifiable measures of the current status of bees in North America .
          2. Establishment of appropriate taxonomic support.
          3. Establishment of a set of Agency responsibilities in each of the countries to implement these measures.
          4. Establishment of a plan for funding these measures and their programs.
        1. Who should attend this meeting?  I would propose that attendees consist largely of four groups:  researchers who have performed relevant research on survey methodologies, bee taxonomists, survey statisticians, and administrators with responsibility for the taxonomy, conservation, research, and conservation of bees.
        2. Who should pay for the meeting?  At this point I have no pot of money available for the meeting.  I think such money could be found, but, in general, my preference would be to keep costs and administration minimal.
        3. Should there be published proceedings?  I think it important to produce a report, but would like to keep all publications of methodologies and results within the existing scientific publication world where they will be more accessible worldwide. 

         

        I look forward to your thoughts, discussion, and ultimately your participation on the topics above.

         

        Background:  I would like to bring up some related background information to put things in perspective.

         

        My job at USGS Patuxent Wildlife Research Center is to develop large geographic monitoring programs for animals in the U.S. that are of high conservation interest, have few existing sources of status information, and for which development of surveys is feasible.  Native bees fit that description and my lab has been working on that group now for several years.  It’s been a longer process than some of our past projects due to the taxonomic impediments (i.e., not being able to determine the name of the specimens we collected) and the practical problem of near complete loss of general funding for such things.  While it has taken longer than normal, I want to thank the many people who have supported me financially, with data, with field work, through conversations, and while visiting their labs, as such I feel that there already been a great and generous community effort on this topic and hope to see it continue as such.

         

        This brings up my last topic…compilation and anlayses of data.  Our lab has already started the process of putting together a series of methodological papers on bee sampling.  I know that a number of you are sitting on papers and useful datasets that have pertinent information on sampling methodologies that would be useful to have published prior to any upcoming meetings on survey design.   So, you can expect me to periodically encourage you to publish your data or perhaps contribute some of your old used up odds and ends research datasets in exchange for co-authorship on one of our upcoming papers.   

         

        Many thanks.

         

        sam

         

        Sam Droege  Sam_Droege@USGS. GOV                      
        w 301-497-5840 h 301-390-7759 fax 301-497-5624
        USGS Patuxent Wildlife Research Center
        BARC-EAST, BLDG 308, RM 124 10300 Balt. Ave., Beltsville , MD   20705
        Http://www.pwrc. usgs.gov

         

        The murmuring of Bees, has ceased
        But murmuring of some
        Posterior, prophetic,
        Has simultaneous come.
        The lower metres of the Year
        When Nature's laugh is done
        The Revelations of the Book
        Whose Genesis was June.
        Appropriate Creatures to her change
        The Typic Mother sends
        As Accent fades to interval
        With separating Friends
        Till what we speculate, has been
        And thoughts we will not show
        More intimate with us become
        Than Persons, that we know.

         

             - Emily Dickinson

         

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      • Michael Wilson
        Just trying to understand, To determine change in the health of oligolectic species, wouldn t one need to follow plant communities that often move dynamically
        Message 3 of 28 , Aug 15, 2008
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          Just trying to understand,
          To determine change in the health of oligolectic species, wouldn't
          one need to follow plant communities that often move
          dynamically across the landscape? How would this
          be done with static locations?
          Thanks,
          Michael Wilson


          --- In beemonitoring@yahoogroups.com, "Thompson, Chris"
          <chris.thompson@...> wrote:
          >
          > John Asher's comments on NAS-NRC are totally out-of-line and
          represent a personal resentment that he was not selected for the panel.
          >
          >
          >
          > Two museum-based taxonomists were included. So, to imply that a
          dipterist and a lepidopterist some how resulted in the "deemphasizes
          museum-based expeditions ..." is simply not true.
          >
          >
          >
          > We pushed for and got recommendation to support basic taxonomic
          research on pollinators. What came out of Congress in the new Farm
          Bill is not exactly what we recommended but that is another issue.
          >
          >
          >
          > However, for good defensible scientific monitoring, to document
          CHANGE, etc., you must have "monitoring of fixed study sites with
          sampling regimes chosen primarily to obtain "statistically verifiable
          measures." And that does include and require basic taxonomy.
          >
          >
          >
          > Yes, John is right about there being much to be discovered and the
          traditional museum taxonomists and their collecting techniques are
          ALSO needed. Things are changing, for example, the Smithsonian has
          finally re-filled its Curator of Bees, in the Hymenoptera Unit, with
          Dr. Seán G. Brady, who starts on August 18th.
          >
          >
          >
          > So, slowly ...
          >
          >
          >
          > F. Christian Thompson
          >
          > Systematic Entomology Lab., ARS, USDA
          >
          > c/o Smithsonian Institution MRC-0169
          >
          > PO Box 37012
          >
          > Washington, D. C. 20013-7012
          >
          > (202) 382-1800 voice
          >
          > (202) 786-9422 fax
          >
          > www.diptera.org Diptera Website
          >
          > ________________________________
          >
          > From: beemonitoring@yahoogroups.com
          [mailto:beemonitoring@yahoogroups.com] On Behalf Of John S. Ascher
          > Sent: Friday, August 15, 2008 12:27 PM
          > To: beemonitoring@yahoogroups.com
          > Subject: RE: [beemonitoring] Proposal to Hold a Meeting on The
          Development of a North American Bee Inventory and Monitoring Network
          >
          >
          >
          >
          >
          > Like Terry, I am concerned that the initial "global and continental
          > foundation" for the proposed project does not cite ongoing, successful
          > efforts by the global bee taxonomic community. These include compilation
          > of relevant taxonomic data, including distributional records, and
          > databasing and mapping of bee specimen records.
          >
          > I'm all in favor of this proposed effort, but if it is to transcend the
          > limitations of previous efforts such as the ALARM project
          (highlighted in
          > the NAS-NRC status report as a premiere example of pollinator
          monitoring)
          > then it is imperative that the essential role of taxonomists and their
          > institutions be made clear from the outset. For example, the
          expertise of
          > taxonomists must be fully incorporated when designing sampling
          protocols.
          >
          > The 15-member NAS-NRC Committee on the Status of Pollinators in North
          > America did not include a single bee taxonomist, and perhaps as a result
          > their recommended monitoring program emphasizes ecologically-oriented
          > monitoring at fixed sites and deemphasizes museum-based expeditions and
          > other sampling protocols that more efficiently yield certain essential
          > discoveries. Results best obtained from a systematic/taxonomic,
          > museum-based approach rather than from an
          > ecological/experimental/statistical approach include discovery of new
          > species and and life stages, of biogeographically significant new
          > distributional records, and of host-parasite and bee-plant
          relationships.
          >
          > We are still in a discovery phase in terms of bee species distributions
          > and basic natural history, including floral associations, so we must
          find
          > a way to efficiently obtain fill gaps in these data. While the
          ecological
          > approach emphasizes unbiased samples, necessarily consisting for the
          most
          > part of common and widespread species, much essential information can
          > better be obtained by biasing samples in favor of specimens and
          > observations of systematic/taxonomic interest. To do so we must make
          full
          > use of existing taxonomic expertise, e.g. knowledge of areas of
          endemism,
          > and support maintenance and enhancement of this. We simply cannot
          > efficiently fill gaps in knowledge of our bee fauna solely through
          > monitoring of fixed study sites with sampling regimes chosen
          primarily to
          > obtain "statistically verifiable measures."
          >
        • Sam Droege
          OK, I can see Matt s original message if I look on the listserv s web site...it was somehow corrupted by my email browser originally... For future reference
          Message 4 of 28 , Aug 15, 2008
          • 0 Attachment
            OK, I can see Matt's original message if I look on the listserv's web
            site...it was somehow corrupted by my email browser originally...

            For future reference all these messages are archived at:

            http://tech.groups.yahoo.com/group/beemonitoring/

            I believe that anyone can see these.

            So, this will be another important set of topics at any meeting.

            1. Standardized vs. Opportunistic samples or surveys

            2. Databasing and datasharing.

            In regards to topic one...Both general approaches are very useful, in
            their places and there is no reason not to develope systems for both.

            A survey or set of surveys can be established (likely at several
            geographic scales) that is systematic, standardized, and repeatable
            that will provide the most statistically rigorous means of looking at
            change and another complementary system can be established that
            compiles unstandarized studies, data collections, museum information,
            general collecting etc.

            In regards to topic number 2. Sharing data and databasing are often
            big bottlenecks in collaborative projects. I have seen a number of
            ways for the NOT to work in the past, but only 3 that seem to work
            well.

            1. One agency or group pays for, collects, analyzes, databases ALL
            the data (relatively unrealistic in this case). North American
            Waterfowl Surveys or the Breeding Bird Survey are good examples of
            these.

            2. One group maintains a data entry web site in which everyone
            shares and produces reports and dataset of equal value to the
            stakeholders. The North American Amphibian Monitoring program and
            FrogwatchUSA are good examples.

            3. Everyone does their own thing and keeps data in whatever
            database/spreadsheet they like and periodically contributes a text
            file with column headers to a central repository. Each database is
            owned by the contributor and is maintained (and included or excluded)
            by that group. Another body provides a service for extraction or
            display of these datasets...Discoverlife is a good example of this.

            sam






            --- In beemonitoring@yahoogroups.com, "Matthew Sarver" <mjsarver@...>
            wrote:
            >
            > All -
            >
            > Clearly, we each have different opinions on this topic, biased by
            our own
            > interests and specializations. Such is the challenge of
            collaborative work
            > in the age of academic globalization! The common ground, as I read
            it, is
            > threefold:
            >
            > (1) A desire for some level of standardization in methods of
            inventorying
            > bees for the specific purpose of monitoring long-term population and
            > distributional trends (Sam's original point, and the goal of his
            work, if I
            > understand it correctly)
            >
            > (2) A way to incorporate and make available the massive amount of
            > non-standardized data already available in museums, and that will
            continue
            > to be generated by taxonomists and ecological field workers. This
            data, as
            > John points out, is of tremendous importance in natural history,
            taxonomy,
            > and biogeography, and can add to the standardized data in (1), and
            may
            > supersede it in many cases of rare or infrequently collected
            species.
            >
            > (3) Following from the first two points, and as has been alluded to
            by John
            > and others, the need for a collaborative and
            accessible "clearinghouse" for
            > the resultant data from both standardized and non-standardized
            origins.
            >
            > As a bit of an outsider (I often find myself walking a tightrope
            between
            > academia, government, non-profits, etc) perhaps I can offer a start.
            >
            > It seems to me that the standardization of protocols is only useful
            if that
            > data ends up in a common database for analysis and sharing. If we
            are to
            > build a common database for bee records, it would be foolish not to
            include
            > all of the records from non-standardized methodology, including
            museum
            > specimens, expert-identified photographs, etc.
            >
            > While the georeferenced specimen mapping tools in the Discover Life
            guides
            > are a good start, I would argue that an expanded version of that
            database,
            > with a much fuller feature set and search functions, and including
            more
            > fields, would be highly desirable. This North American Bee
            Database (or
            > whatever it might be called) could become the standard location for
            storage
            > of all bee specimen and photo records for the continent, and could
            be made
            > accessible on the web.
            >
            > Issues of standardization could be dealt with by populating, for
            each import
            > of records, a selection of fields indicating the type of record, the
            > collection methods used, etc. This would hopefully not be as hard
            as it
            > might seem. Most bee specimens could be assigned to one of the
            following
            > collection methods: malaise, net/hand, bowl, vane trap, photograph
            only, or
            > unknown method (for museum specimens). Another field could ask for
            the
            > specific protocol used. Still more linked fields would hold floral
            > association, habitat data, etc
            >
            > In this way, all relevant data could be compiled in a centralized
            clearing
            > house. Researchers interested in monitoring trends could simply
            filter the
            > database and view only specimens from standardized methods, while
            those
            > interested in floral associations or distributions could make use
            of the
            > complete data set.
            >
            > Several challenges come to mind here:
            >
            > (1) Funding / Personnel - such a project would require full time
            attention
            > from at least a few people building and managing the database, in
            addition
            > to much time from taxonomists (who, as John points out, are already
            > overextended).
            > (2) Academic intellectual property - Regrettably, this is a major
            issue when
            > dealing with such an endeavor, but that is the nature of our field,
            and
            > everyone should get due credit for their contributions. Perhaps
            this could
            > be overcome by a lock that contributors could place on data of
            their own
            > specimens. This "lock" would allow the data to show up in certain
            contexts
            > (e.g. state species list queries), but not in full detail until any
            relevant
            > publications were completed.
            > (3) Data accuracy - a database such as this would require much
            effort from
            > competent individuals to ensure the accuracty of determinations,
            etc.
            > Including det. codes and dates in the database would be a minimal
            step to
            > help ensure the validity of records.
            > (4) Accessibility. Difficult decisions would need to be made about
            use of
            > the contributed data. I am in the open data-sharing camp, but many
            are not,
            > and I understand the reasons for that. If full funding could be
            found to
            > support the efforts of staff and taxonomists, it would compel open
            access to
            > the compiled data.
            >
            > I feel that this is the direction that we should be going in this
            > information age. We should all strive to overcome our own self-
            interests
            > and work toward a true collaborative effort!
            >
            > Sam, I apologize if I have hijacked your original intention, but it
            seems to
            > me that standardized methodologies are closely intertwined with
            this idea.
            >
            >
            > My two cents
            > Matt Sarver
            >
          • Sam Droege
            Oligolectic species would be in one of the groups more likely to be missed...depending on the survey technique. Males and females may sometimes nectar off
            Message 5 of 28 , Aug 15, 2008
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              Oligolectic species would be in one of the groups more likely to be
              missed...depending on the survey technique.

              Males and females may sometimes nectar off their host which would
              increase their probabilities of capture. Pantrap, malaise and other
              general traps often pick up oligolectic species, but there are many
              instances where they seem to be poor vehicles for capturing this group.

              This may be an instance where you would have to develop host-based
              special surveys, decide that general collecting would be sufficient, or
              decide that some groups simply will not be "monitored."

              I think that will be another topic area when surveys are being
              developed...that is, which species will be adequately covered, and
              which will not.

              sam

              --- In beemonitoring@yahoogroups.com, "Michael Wilson" <mwilso14@...>
              wrote:
              >
              > Just trying to understand,
              > To determine change in the health of oligolectic species, wouldn't
              > one need to follow plant communities that often move
              > dynamically across the landscape? How would this
              > be done with static locations?
              > Thanks,
              > Michael Wilson
              >
            • John S. Ascher
              This sounds good Sam. I have a few minor additions as follows: 1. Standardized vs. Opportunistic samples or surveys I m not sure that these can be broken
              Message 6 of 28 , Aug 15, 2008
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                This sounds good Sam. I have a few minor additions as follows:

                " 1. Standardized vs. Opportunistic samples or surveys"

                I'm not sure that these can be broken down so simply. My sense is that a
                wide array of sampling techniques are appropriate depending on the
                questions of interest and the circumstances. Much "Opportunistic" or
                taxonomically-focused sampling can be standardized to some degree, but
                using methods appropriate to descriptive and historical science (e.g.,
                historical biogeography) and therefore quite different from those applied
                to experimental studies such as those designed by statistically savvy bee
                ecologists.

                "3. Everyone does their own thing and keeps data in whatever
                database/spreadsheet they like and periodically contributes a text file
                with column headers to a central repository. Each database is owned by the
                contributor and is maintained (and included or excluded) by that group.
                Another body provides a service for extraction or
                display of these datasets...Discoverlife is a good example of this."

                A useful model, already implemented at Discoverlife, is for small
                contributors and those lacking computer resources to periodically send
                static data (e.g., from a spreadsheet) whereas larger and/or more
                computer savvy contributors can set up dynamic, continuously updating
                links (e.g. to a relational database) between their servers and the
                community resource.

                Many groups have already been developing useful standards for sharing
                pollinator data and we can usefully consult these and suggest that people
                adopt them. If people nonetheless persist in doing their own thing for
                whatever reason much of their data may still be rendered useful to all if
                a clever computer scientist can extract these.

                It is extremely important to note that there are already multiple linked
                central repositories in place. All data sent to one central repository can
                and should be shared dynamically with other collaborating repositories.
                Local repositories can enhance centralized (global) data by providing
                additional more particular services (e.g., customizable dynamic local maps
                and potentially analyses based on these) and by sending corrections
                discovered locally back to the general repositories.

                As a specific example, note that bee specimen records sent to GBIF can
                also be sent to other centralized data sources. This map of Bombus
                includes 135,000+ GBIF records and many others, all error-checked by the
                Global Mapper:

                http://www.discoverlife.org/mp/20m?kind=Bombus

                This example shows how the community can and should take advantage of
                multiple central repositories, as these have different strengths and can
                usefully link to each other to collectively display and error-check data.

                When planning this or any other project we should try to take full
                advantage of existing tools. Of these, web-based collaborative tools are
                already very powerful and are being improved every day.

                Images in particular can have a very wide array of uses once copyright
                issues can be addressed.

                In summary I suggest that we as a community assemble globally relevant
                data, which can of course easily be repackaged for local use, and
                establish dynamic links among central repositories (plural) and between
                these and local repositories.

                John

                P.S. On the subject of sampling oligolectic bees, these are not
                efficiently sampled using single-site/ecological protocols designed to
                obtain an unbiased cross-section of the community from an unbiased sample
                of floral resources. However these can be found very effectively using
                taxonomically-oriented methods, such as targeted collecting at sites were
                the particular taxa of interest have been recorded historically or at
                biogeographically similar sites. In this case sampling bias in favor of
                the oligolectic species of interest is a very good thing.





                > OK, I can see Matt's original message if I look on the listserv's web
                site...it was somehow corrupted by my email browser originally...
                >
                > For future reference all these messages are archived at:
                >
                > http://tech.groups.yahoo.com/group/beemonitoring/
                >
                > I believe that anyone can see these.
                >
                > So, this will be another important set of topics at any meeting.
                >
                > 1. Standardized vs. Opportunistic samples or surveys
                >
                > 2. Databasing and datasharing.
                >
                > In regards to topic one...Both general approaches are very useful, in
                their places and there is no reason not to develope systems for both.
                >
                > A survey or set of surveys can be established (likely at several
                geographic scales) that is systematic, standardized, and repeatable that
                will provide the most statistically rigorous means of looking at change
                and another complementary system can be established that
                > compiles unstandarized studies, data collections, museum information,
                general collecting etc.
                >
                > In regards to topic number 2. Sharing data and databasing are often big
                bottlenecks in collaborative projects. I have seen a number of ways for
                the NOT to work in the past, but only 3 that seem to work well.
                >
                > 1. One agency or group pays for, collects, analyzes, databases ALL the
                data (relatively unrealistic in this case). North American
                > Waterfowl Surveys or the Breeding Bird Survey are good examples of these.
                >
                > 2. One group maintains a data entry web site in which everyone
                > shares and produces reports and dataset of equal value to the
                > stakeholders. The North American Amphibian Monitoring program and
                FrogwatchUSA are good examples.
                >
                > 3. Everyone does their own thing and keeps data in whatever
                > database/spreadsheet they like and periodically contributes a text file
                with column headers to a central repository. Each database is owned by
                the contributor and is maintained (and included or excluded) by that
                group. Another body provides a service for extraction or display of
                these datasets...Discoverlife is a good example of this.
                >
                > sam
                >
                >
                >
                >
                >
                >
                > --- In beemonitoring@yahoogroups.com, "Matthew Sarver" <mjsarver@...>
                wrote:
                >> All -
                >> Clearly, we each have different opinions on this topic, biased by
                > our own
                >> interests and specializations. Such is the challenge of
                > collaborative work
                >> in the age of academic globalization! The common ground, as I read
                > it, is
                >> threefold:
                >> (1) A desire for some level of standardization in methods of
                > inventorying
                >> bees for the specific purpose of monitoring long-term population and
                distributional trends (Sam's original point, and the goal of his
                > work, if I
                >> understand it correctly)
                >> (2) A way to incorporate and make available the massive amount of
                non-standardized data already available in museums, and that will
                > continue
                >> to be generated by taxonomists and ecological field workers. This
                > data, as
                >> John points out, is of tremendous importance in natural history,
                > taxonomy,
                >> and biogeography, and can add to the standardized data in (1), and
                > may
                >> supersede it in many cases of rare or infrequently collected
                > species.
                >> (3) Following from the first two points, and as has been alluded to
                > by John
                >> and others, the need for a collaborative and
                > accessible "clearinghouse" for
                >> the resultant data from both standardized and non-standardized
                > origins.
                >> As a bit of an outsider (I often find myself walking a tightrope
                > between
                >> academia, government, non-profits, etc) perhaps I can offer a start. It
                seems to me that the standardization of protocols is only useful
                > if that
                >> data ends up in a common database for analysis and sharing. If we
                > are to
                >> build a common database for bee records, it would be foolish not to
                > include
                >> all of the records from non-standardized methodology, including
                > museum
                >> specimens, expert-identified photographs, etc.
                >> While the georeferenced specimen mapping tools in the Discover Life
                > guides
                >> are a good start, I would argue that an expanded version of that
                > database,
                >> with a much fuller feature set and search functions, and including
                > more
                >> fields, would be highly desirable. This North American Bee
                > Database (or
                >> whatever it might be called) could become the standard location for
                > storage
                >> of all bee specimen and photo records for the continent, and could
                > be made
                >> accessible on the web.
                >> Issues of standardization could be dealt with by populating, for
                > each import
                >> of records, a selection of fields indicating the type of record, the
                collection methods used, etc. This would hopefully not be as hard
                > as it
                >> might seem. Most bee specimens could be assigned to one of the
                > following
                >> collection methods: malaise, net/hand, bowl, vane trap, photograph
                > only, or
                >> unknown method (for museum specimens). Another field could ask for
                > the
                >> specific protocol used. Still more linked fields would hold floral
                association, habitat data, etc
                >> In this way, all relevant data could be compiled in a centralized
                > clearing
                >> house. Researchers interested in monitoring trends could simply
                > filter the
                >> database and view only specimens from standardized methods, while
                > those
                >> interested in floral associations or distributions could make use
                > of the
                >> complete data set.
                >> Several challenges come to mind here:
                >> (1) Funding / Personnel - such a project would require full time
                > attention
                >> from at least a few people building and managing the database, in
                > addition
                >> to much time from taxonomists (who, as John points out, are already
                overextended).
                >> (2) Academic intellectual property - Regrettably, this is a major
                > issue when
                >> dealing with such an endeavor, but that is the nature of our field,
                > and
                >> everyone should get due credit for their contributions. Perhaps
                > this could
                >> be overcome by a lock that contributors could place on data of
                > their own
                >> specimens. This "lock" would allow the data to show up in certain
                > contexts
                >> (e.g. state species list queries), but not in full detail until any
                > relevant
                >> publications were completed.
                >> (3) Data accuracy - a database such as this would require much
                > effort from
                >> competent individuals to ensure the accuracty of determinations,
                > etc.
                >> Including det. codes and dates in the database would be a minimal
                > step to
                >> help ensure the validity of records.
                >> (4) Accessibility. Difficult decisions would need to be made about
                > use of
                >> the contributed data. I am in the open data-sharing camp, but many
                > are not,
                >> and I understand the reasons for that. If full funding could be
                > found to
                >> support the efforts of staff and taxonomists, it would compel open
                > access to
                >> the compiled data.
                >> I feel that this is the direction that we should be going in this
                information age. We should all strive to overcome our own self-
                > interests
                >> and work toward a true collaborative effort!
                >> Sam, I apologize if I have hijacked your original intention, but it
                > seems to
                >> me that standardized methodologies are closely intertwined with
                > this idea.
                >> My two cents
                >> Matt Sarver
                >
                >
                >


                --
                John S. Ascher, Ph.D.
                Bee Database Project Manager
                Division of Invertebrate Zoology
                American Museum of Natural History
                Central Park West @ 79th St.
                New York, NY 10024-5192
                work phone: 212-496-3447
                mobile phone: 917-407-0378
              • Gretchen LeBuhn
                All- While I was at ESA, I spoke with Matt Jones, the bionformatics guru at NCEAS about how to archive bee data sets that used a common protocol. NCEAS has
                Message 7 of 28 , Aug 15, 2008
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                  All-

                  While I was at ESA, I spoke with Matt Jones, the bionformatics guru at  NCEAS about how to archive bee data sets that used a common protocol.  NCEAS has been working toward becoming a clearinghouse for exactly these types of data and has particular expertise in the issues of sharing scientific data tat Matthew has outlined below.  They archive all of the LTER and NRS datasets among many others. 

                  Gretchen

                  On Fri, Aug 15, 2008 at 11:36 AM, Matthew Sarver <mjsarver@...> wrote:

                  All - 
                   
                  Clearly, we each have different opinions on this topic, biased by our own interests and specializations.  Such is the challenge of collaborative work in the age of academic globalization!  The common ground, as I read it, is threefold:
                   
                  (1) A desire for some level of standardization in methods of inventorying bees for the specific purpose of monitoring long-term population and distributional trends (Sam's original point, and the goal of his work, if I understand it correctly)
                   
                  (2) A way to incorporate and make available the massive amount of non-standardized data already available in museums, and that will continue to be generated by taxonomists and ecological field workers.  This data, as John points out, is of tremendous importance in natural history, taxonomy, and biogeography, and can add to the standardized data in (1), and may supersede it in many cases of rare or infrequently collected species.
                   
                  (3) Following from the first two points, and as has been alluded to by John and others, the need for a collaborative and accessible "clearinghouse" for the resultant data from both standardized and non-standardized origins
                   
                  As a bit of an outsider (I often find myself walking a tightrope between academia, government, non-profits, etc) perhaps I can offer a start.
                   
                  It seems to me that the standardization of protocols is only useful if that data ends up in a common database for analysis and sharing.  If we are to build a common database for bee records, it would be foolish not to include all of the records from non-standardized methodology, including museum specimens, expert-identified photographs, etc. 
                   
                  While the georeferenced specimen mapping tools in the Discover Life guides are a good start, I would argue that an expanded version of that database, with a much fuller feature set and search functions, and including more fields, would be highly desirable.  This North American Bee Database (or whatever it might be called) could become the standard location for storage of all bee specimen and photo records for the continent, and could be made accessible on the web.
                   
                  Issues of standardization could be dealt with by populating, for each import of records, a selection of fields indicating the type of record, the collection methods used, etc.  This would hopefully not be as hard as it might seem.  Most bee specimens could be assigned to one of the following collection methods: malaise, net/hand, bowl, vane trap, photograph only, or unknown method (for museum specimens).  Another field could ask for the specific protocol used.  Still more linked fields would hold floral association, habitat data, etc
                   
                  In this way, all relevant data could be compiled in a centralized clearing house.  Researchers interested in monitoring trends could simply filter the database and view only specimens from standardized methods, while those interested in floral associations or distributions could make use of the complete data set.
                   
                  Several challenges come to mind here:
                   
                  (1) Funding / Personnel - such a project would require full time attention from at least a few people building and managing the database, in addition to much time from taxonomists (who, as John points out, are already overextended).
                  (2) Academic intellectual property - Regrettably, this is a major issue when dealing with such an endeavor, but that is the nature of our field, and everyone should get due credit for their contributions.  Perhaps this could be overcome by a lock that contributors could place on data of their own specimens.  This "lock" would allow the data to show up in certain contexts (e.g. state species list queries), but not in full detail until any relevant publications were completed.
                  (3) Data accuracy - a database such as this would require much effort from competent individuals to ensure the accuracty of determinations, etc.  Including det. codes and dates in the database would be a minimal step to help ensure the validity of records.
                  (4) Accessibility.  Difficult decisions would need to be made about use of the contributed data.  I am in the open data-sharing camp, but many are not, and I understand the reasons for that.  If full funding could be found to support the efforts of staff and taxonomists, it would compel open access to the compiled data. 
                   
                  I feel that this is the direction that we should be going in this information age.  We should all strive to overcome our own self-interests and work toward a true collaborative effort! 
                   
                  Sam, I apologize if I have hijacked your original intention, but it seems to me that standardized methodologies are closely intertwined with this idea.
                   
                   
                  My two cents
                  Matt Sarver 



                  --
                  Gretchen LeBuhn
                • Matthew Sarver
                  John - It is extremely important to note that there are already multiple linked central repositories in place. Thanks for pointing this out. I am obviously
                  Message 8 of 28 , Aug 15, 2008
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                    John -
                     
                    "It is extremely important to note that there are already multiple linked
                    central repositories in place."
                     
                    Thanks for pointing this out.  I am obviously not as well-versed in bioinformatics databases as I could be.  I did not mean to suggest reinventing the wheel on this, but wasn't sure how many of these existing databases are flexible enough in their data input to allow us to work with the specific fields that the bee community would find useful / neccessary.  Generating a map for a species is one thing, but a fully searchable database that allows one to find flower records, flight periods, etc for a certain part of the world or a certain species is another.  Right now, the Discover Life specimen view includes a number of very useful data fields, but there are certainly many more that might be of interest, particularly in terms of habitat and floral associations.  As far as I know, there is no easy way to search the fields in that database, other than by viewing a specimen record from the mapper.  Likewise, GBIF is primarily biogeographical data.  I was thinking about the creation of a database web portal with a design and front end that would be specifically geared toward pollinator records, and the associated ecological data that might not fit the mold of available broader repositories.
                     
                    Such a customized portal could also be expanded to include an EBird or Bugguide-like citizen science component, where photos could be posted by amateurs.  I agree that bugguide already serves that purpose admirably, but its structure does not encourage the entry of scientifically useful data along with submitted records in the way that a custom-tailored user interface like Ebird does.  The already useful information generated by bugguide could be made even more useful by asking users for more information about their sighting.
                     
                    "Local repositories can enhance centralized (global) data by providing
                    additional more particular services (e.g., customizable dynamic local maps
                    and potentially analyses based on these) "
                     
                    I guess this is more along the lines of what I am thinking.  But "local" in the sense of specificty of purpose or usage, rather than geography.  Thoughts?
                     
                    Matt
                     
                     
                  • Dan Kjar
                    As a database person I have to just say I am surprised savvy and relational database ended up in the same sentence... ;) Remember that old saying you can
                    Message 9 of 28 , Aug 15, 2008
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                      As a database person I have to just say I am surprised 'savvy' and
                      'relational database' ended up in the same sentence...

                      ;)


                      Remember that old saying "you can choose two of the following:
                      quality, quantity, and currency. You cannot have all three."

                      Dan
                    • Dan Kjar
                      Discoverlife s fields are whatever the submitter wants them to be. The only thing required is a taxonomic name and hopefully a location in whatever format you
                      Message 10 of 28 , Aug 15, 2008
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                        Discoverlife's fields are whatever the submitter wants them to be.
                        The only thing required is a taxonomic name and hopefully a location
                        in whatever format you like.

                        --- In beemonitoring@yahoogroups.com, "Matthew Sarver" <mjsarver@...>
                        wrote:
                        >
                        > John -
                        >
                        > "It is extremely important to note that there are already multiple
                        linked
                        > central repositories in place."
                        >
                        > Thanks for pointing this out. I am obviously not as well-versed in
                        > bioinformatics databases as I could be. I did not mean to suggest
                        > reinventing the wheel on this, but wasn't sure how many of these
                        existing
                        > databases are flexible enough in their data input to allow us to
                        work with
                        > the specific fields that the bee community would find useful /
                        neccessary.
                        > Generating a map for a species is one thing, but a fully searchable
                        database
                        > that allows one to find flower records, flight periods, etc for a
                        certain
                        > part of the world or a certain species is another. Right now, the
                        Discover
                        > Life specimen view includes a number of very useful data fields, but
                        there
                        > are certainly many more that might be of interest, particularly in
                        terms of
                        > habitat and floral associations. As far as I know, there is no easy
                        way to
                        > search the fields in that database, other than by viewing a specimen
                        record
                        > from the mapper. Likewise, GBIF is primarily biogeographical data.
                        I was
                        > thinking about the creation of a database web portal with a design
                        and front
                        > end that would be specifically geared toward pollinator records, and the
                        > associated ecological data that might not fit the mold of available
                        broader
                        > repositories.
                        >
                        > Such a customized portal could also be expanded to include an EBird or
                        > Bugguide-like citizen science component, where photos could be posted by
                        > amateurs. I agree that bugguide already serves that purpose
                        admirably, but
                        > its structure does not encourage the entry of scientifically useful data
                        > along with submitted records in the way that a custom-tailored user
                        > interface like Ebird does. The already useful information generated by
                        > bugguide could be made even more useful by asking users for more
                        information
                        > about their sighting.
                        >
                        > "Local repositories can enhance centralized (global) data by providing
                        > additional more particular services (e.g., customizable dynamic
                        local maps
                        > and potentially analyses based on these) "
                        >
                        > I guess this is more along the lines of what I am thinking. But
                        "local" in
                        > the sense of specificty of purpose or usage, rather than geography.
                        > Thoughts?
                        >
                        > Matt
                        >
                      • John S. Ascher
                        Matt - Thanks for another thoughtful response. I did not mean to suggest ... existing ... with ... neccessary. As Dan already noted Discoverlife can
                        Message 11 of 28 , Aug 15, 2008
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                          Matt -

                          Thanks for another thoughtful response.

                          I did not mean to suggest
                          > reinventing the wheel on this, but wasn't sure how many of these
                          existing
                          > databases are flexible enough in their data input to allow us to work
                          with
                          > the specific fields that the bee community would find useful /
                          neccessary.

                          As Dan already noted Discoverlife can accommodate virtually any field as
                          long as data are linked directly to a species name. Only fields with data
                          appear when you pull up specimen records; blank fields are not displayed.

                          > Generating a map for a species is one thing, but a fully searchable
                          database
                          > that allows one to find flower records, flight periods, etc for a
                          certain
                          > part of the world or a certain species is another.

                          There are web portals being designed specifically to fulfill precisely
                          these needs, e.g.:

                          http://libraryportals.com/PCDL

                          Stuart Roberts in the UK is developing an excellent database optimized to
                          record these data.

                          Right now, the
                          > Discover
                          > Life specimen view includes a number of very useful data fields, but
                          there
                          > are certainly many more that might be of interest, particularly in terms of
                          > habitat and floral associations.

                          These can already be mapped. These and other fields you can dream up can
                          certainly be displayed. Sam even has a field where he notes brand of
                          soap!

                          As far as I know, there is no easy way
                          > to
                          > search the fields in that database, other than by viewing a specimen record
                          > from the mapper.

                          You are correct. The search function needs improvement.

                          Likewise, GBIF is primarily biogeographical data. I was
                          > thinking about the creation of a database web portal with a design and
                          front
                          > end that would be specifically geared toward pollinator records, and the
                          associated ecological data that might not fit the mold of available
                          broader
                          > repositories.

                          As noted above this may already exist:

                          http://libraryportals.com/PCDL

                          > Such a customized portal could also be expanded to include an EBird or
                          Bugguide-like citizen science component, where photos could be posted by
                          amateurs. I agree that bugguide already serves that purpose admirably,
                          but
                          > its structure does not encourage the entry of scientifically useful data
                          along with submitted records in the way that a custom-tailored user
                          interface like Ebird does. The already useful information generated by
                          bugguide could be made even more useful by asking users for more
                          information
                          > about their sighting.

                          I would advocate an all of the above solution, i.e. improving Bugguide
                          itself, improving relevant tools at other sites such as Discoverlife, and
                          establishing useful links between sites with complementary emphases.

                          > "Local repositories can enhance centralized (global) data by providing
                          additional more particular services (e.g., customizable dynamic local
                          maps
                          > and potentially analyses based on these) "
                          >
                          > I guess this is more along the lines of what I am thinking. But "local" in
                          > the sense of specificty of purpose or usage, rather than geography.
                          Thoughts?

                          I meant both.

                          In terms of geography, one example of a local site would be a global or
                          regional ID guide customized for a specific site by filtering out
                          extralimital taxa.

                          For example, here is the eastern Bee Genera guide customized for the
                          Fingerlakes region of NY:

                          http://www.discoverlife.org/mp/20q?guide=Bee_genera&cl=US/NY/Fingerlakes

                          In terms of specificity of purpose, a local site could highlight and
                          extend a subset of data, e.g., pollinator-plant interactions, derived by
                          querying one or more central repositories.

                          John


                          > Matt
                          >
                          >
                          >


                          --
                          John S. Ascher, Ph.D.
                          Bee Database Project Manager
                          Division of Invertebrate Zoology
                          American Museum of Natural History
                          Central Park West @ 79th St.
                          New York, NY 10024-5192
                          work phone: 212-496-3447
                          mobile phone: 917-407-0378
                        • Matthew Sarver
                          Great! I didn t know discoverlife was set up that way until Dan pointed it out. A query interface for this database now seems like an obvious starting point.
                          Message 12 of 28 , Aug 15, 2008
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                            Great!  I didn't know discoverlife was set up that way until Dan pointed it out.  A query interface for this database now seems like an obvious starting point.  As for PCDL - I thought they were only tackling literature, at least for now.  Do they have plans to incorporate specimen data as well?  I've certainly used it for plant/pollinator interactions a number of times already. 
                             
                            The "citizen science" thing for insects has great potential - as long as those who can ID the pics can keep up!  An integration of bugguide and discover life would be really cool!
                             
                            Matt


                            From: beemonitoring@yahoogroups.com [mailto:beemonitoring@yahoogroups.com] On Behalf Of John S. Ascher
                            Sent: Saturday, August 16, 2008 1:16 AM
                            To: beemonitoring@yahoogroups.com
                            Subject: Re: [beemonitoring] Re: Standardized Sampling Methodologies and a Common Database


                            Matt -

                            Thanks for another thoughtful response.

                            I did not mean to suggest

                            > reinventing the wheel on this, but wasn't sure how many
                            of these
                            existing
                            > databases are flexible enough in their data input
                            to allow us to work
                            with
                            > the specific fields that the bee community
                            would find useful /
                            neccessary.

                            As Dan already noted Discoverlife can accommodate virtually any field as
                            long as data are linked directly to a species name. Only fields with data
                            appear when you pull up specimen records; blank fields are not displayed.

                            > Generating a map for a species is
                            one thing, but a fully searchable
                            database
                            > that allows one to find
                            flower records, flight periods, etc for a
                            certain
                            > part of the world
                            or a certain species is another.

                            There are web portals being designed specifically to fulfill precisely
                            these needs, e.g.:

                            http://libraryporta ls.com/PCDL

                            Stuart Roberts in the UK is developing an excellent database optimized to
                            record these data.

                            Right now, the
                            > Discover
                            > Life specimen view
                            includes a number of very useful data fields, but
                            there
                            > are certainly
                            many more that might be of interest, particularly in terms of
                            > habitat
                            and floral associations.

                            These can already be mapped. These and other fields you can dream up can
                            certainly be displayed. Sam even has a field where he notes brand of
                            soap!

                            As far as I know, there is no easy way
                            > to
                            > search the fields in that database, other than by viewing
                            a specimen record
                            > from the mapper.

                            You are correct. The search function needs improvement.

                            Likewise, GBIF is primarily biogeographical data. I was
                            > thinking about the creation of a database web portal with a
                            design and
                            front
                            > end that would be specifically geared toward
                            pollinator records, and the
                            associated ecological data that might not fit the mold of available
                            broader
                            > repositories.

                            As noted above this may already exist:

                            http://libraryporta ls.com/PCDL

                            >
                            Such a customized portal could also be expanded to include an EBird or
                            Bugguide-like citizen science component, where photos could be posted by
                            amateurs. I agree that bugguide already serves that purpose admirably,
                            but
                            > its structure does not encourage the entry of
                            scientifically useful data
                            along with submitted records in the way that a custom-tailored user
                            interface like Ebird does. The already useful information generated by
                            bugguide could be made even more useful by asking users for more
                            information
                            > about their sighting.

                            I would advocate an all of the above solution, i.e. improving Bugguide
                            itself, improving relevant tools at other sites such as Discoverlife, and
                            establishing useful links between sites with complementary emphases.

                            > "Local repositories can enhance centralized (global) data
                            by providing
                            additional more particular services (e.g., customizable dynamic local
                            maps
                            > and potentially analyses based on these) "
                            >
                            >
                            I guess this is more along the lines of what I am thinking. But "local" in
                            > the sense of specificty of purpose or usage, rather than
                            geography.
                            Thoughts?

                            I meant both.

                            In terms of geography, one example of a local site would be a global or
                            regional ID guide customized for a specific site by filtering out
                            extralimital taxa.

                            For example, here is the eastern Bee Genera guide customized for the
                            Fingerlakes region of NY:

                            http://www.discover life.org/ mp/20q?guide= Bee_genera& cl=US/NY/ Fingerlakes

                            In terms of specificity of purpose, a local site could highlight and
                            extend a subset of data, e.g., pollinator-plant interactions, derived by
                            querying one or more central repositories.

                            John

                            >
                            Matt
                            >
                            >
                            >

                            --
                            John S. Ascher, Ph.D.
                            Bee Database Project Manager
                            Division of Invertebrate Zoology
                            American Museum of Natural History
                            Central Park West @ 79th St.
                            New York, NY 10024-5192
                            work phone: 212-496-3447
                            mobile phone: 917-407-0378

                          • Sam Droege
                            I wasn t aware of some of those new, more flexible database features, it will be good to have representation at the meeting from that group. While one could
                            Message 13 of 28 , Aug 16, 2008
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                              I wasn't aware of some of those new, more flexible database features,
                              it will be good to have representation at the meeting from that
                              group. While one could argue that you could develop those features
                              later, I think that more and more that database functions will help
                              guide the development of what gets monitored. Its also clear that
                              internet functions can be built directly into monitoring schemes
                              rather than having paper surveys that get entered later.

                              The possibilities of expanding Bugguide.net are intriguing. It seems
                              particularly good at detetecting the spread of introduced
                              species...and the digital libraries that are produced are going to
                              become invaluable.

                              sam


                              --- In beemonitoring@yahoogroups.com, "Matthew Sarver" <mjsarver@...>
                              wrote:
                              >
                              > Great! I didn't know discoverlife was set up that way until Dan
                              pointed it
                              > out. A query interface for this database now seems like an obvious
                              starting
                              > point. As for PCDL - I thought they were only tackling literature,
                              at least
                              > for now. Do they have plans to incorporate specimen data as well?
                              I've
                              > certainly used it for plant/pollinator interactions a number of
                              times
                              > already.
                              >
                              > The "citizen science" thing for insects has great potential - as
                              long as
                              > those who can ID the pics can keep up! An integration of bugguide
                              and
                              > discover life would be really cool!
                              >
                              > Matt
                              >
                              > _____
                              >
                              > From: beemonitoring@yahoogroups.com
                              [mailto:beemonitoring@yahoogroups.com]
                              > On Behalf Of John S. Ascher
                              > Sent: Saturday, August 16, 2008 1:16 AM
                              > To: beemonitoring@yahoogroups.com
                              > Subject: Re: [beemonitoring] Re: Standardized Sampling
                              Methodologies and a
                              > Common Database
                              >
                              >
                              >
                              >
                              > Matt -
                              >
                              > Thanks for another thoughtful response.
                              >
                              > I did not mean to suggest
                              > > reinventing the wheel on this, but wasn't sure how many of these
                              > existing
                              > > databases are flexible enough in their data input to allow us to
                              work
                              > with
                              > > the specific fields that the bee community would find useful /
                              > neccessary.
                              >
                              > As Dan already noted Discoverlife can accommodate virtually any
                              field as
                              > long as data are linked directly to a species name. Only fields
                              with data
                              > appear when you pull up specimen records; blank fields are not
                              displayed.
                              >
                              > > Generating a map for a species is one thing, but a fully
                              searchable
                              > database
                              > > that allows one to find flower records, flight periods, etc for a
                              > certain
                              > > part of the world or a certain species is another.
                              >
                              > There are web portals being designed specifically to fulfill
                              precisely
                              > these needs, e.g.:
                              >
                              > http://libraryporta <http://libraryportals.com/PCDL> ls.com/PCDL
                              >
                              > Stuart Roberts in the UK is developing an excellent database
                              optimized to
                              > record these data.
                              >
                              > Right now, the
                              > > Discover
                              > > Life specimen view includes a number of very useful data fields,
                              but
                              > there
                              > > are certainly many more that might be of interest, particularly
                              in terms
                              > of
                              > > habitat and floral associations.
                              >
                              > These can already be mapped. These and other fields you can dream
                              up can
                              > certainly be displayed. Sam even has a field where he notes brand of
                              > soap!
                              >
                              > As far as I know, there is no easy way
                              > > to
                              > > search the fields in that database, other than by viewing a
                              specimen
                              > record
                              > > from the mapper.
                              >
                              > You are correct. The search function needs improvement.
                              >
                              > Likewise, GBIF is primarily biogeographical data. I was
                              > > thinking about the creation of a database web portal with a
                              design and
                              > front
                              > > end that would be specifically geared toward pollinator records,
                              and the
                              > associated ecological data that might not fit the mold of available
                              > broader
                              > > repositories.
                              >
                              > As noted above this may already exist:
                              >
                              > http://libraryporta <http://libraryportals.com/PCDL> ls.com/PCDL
                              >
                              > > Such a customized portal could also be expanded to include an
                              EBird or
                              > Bugguide-like citizen science component, where photos could be
                              posted by
                              > amateurs. I agree that bugguide already serves that purpose
                              admirably,
                              > but
                              > > its structure does not encourage the entry of scientifically
                              useful data
                              > along with submitted records in the way that a custom-tailored user
                              > interface like Ebird does. The already useful information generated
                              by
                              > bugguide could be made even more useful by asking users for more
                              > information
                              > > about their sighting.
                              >
                              > I would advocate an all of the above solution, i.e. improving
                              Bugguide
                              > itself, improving relevant tools at other sites such as
                              Discoverlife, and
                              > establishing useful links between sites with complementary emphases.
                              >
                              > > "Local repositories can enhance centralized (global) data by
                              providing
                              > additional more particular services (e.g., customizable dynamic
                              local
                              > maps
                              > > and potentially analyses based on these) "
                              > >
                              > > I guess this is more along the lines of what I am thinking.
                              But "local" in
                              > > the sense of specificty of purpose or usage, rather than
                              geography.
                              > Thoughts?
                              >
                              > I meant both.
                              >
                              > In terms of geography, one example of a local site would be a
                              global or
                              > regional ID guide customized for a specific site by filtering out
                              > extralimital taxa.
                              >
                              > For example, here is the eastern Bee Genera guide customized for the
                              > Fingerlakes region of NY:
                              >
                              > http://www.discover
                              > <http://www.discoverlife.org/mp/20q?
                              guide=Bee_genera&cl=US/NY/Fingerlakes>
                              > life.org/mp/20q?guide=Bee_genera&cl=US/NY/Fingerlakes
                              >
                              > In terms of specificity of purpose, a local site could highlight and
                              > extend a subset of data, e.g., pollinator-plant interactions,
                              derived by
                              > querying one or more central repositories.
                              >
                              > John
                              >
                              > > Matt
                              > >
                              > >
                              > >
                              >
                              > --
                              > John S. Ascher, Ph.D.
                              > Bee Database Project Manager
                              > Division of Invertebrate Zoology
                              > American Museum of Natural History
                              > Central Park West @ 79th St.
                              > New York, NY 10024-5192
                              > work phone: 212-496-3447
                              > mobile phone: 917-407-0378
                              >
                            • Dan Kjar
                              Here is a quick break down of relational vs flat databases. Relational databases link tables to tables and those links allow you to do some very powerful
                              Message 14 of 28 , Aug 16, 2008
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                                Here is a quick break down of relational vs flat databases.

                                Relational databases link tables to tables and those links allow you
                                to do some very powerful queries. However, as the tables grow the
                                queries slow and as the relationships become more complex the database
                                gets kludgy to deal with and nearly incomprehensible to people that
                                did not design it.

                                Flat file databases are always meaningful to humans and any human that
                                can read text. Flat files do not allow you to do some of the more
                                wizbang pull it out of your *** searches that relational databases
                                allow you. However, if you know what people are going to search
                                (genus/species/whatever), the way you make flat file databases scream
                                is by indexing the information and holding the indexes in hash tables
                                (at the file system/OS/Perl/C++) level. This is how pick can put
                                300,000 points on a map in just a few seconds. His database currently
                                has over 1.4 million records and when he gets all of th GBIF info it
                                will be over 15 million records (if I remember correctly). The
                                difficult part here is that you need to predetermine what queries the
                                user will be doing. The big search engines all work along the same lines.

                                I have mostly made relational databases, including my last one for the
                                Smithsonian. That database is limited to the exact number of type ant
                                specimens the museum holds. I made the decision that 1200 specimens
                                would not slow the searches to any appreciable level so I went with
                                the ease and power of a relational database. If it were going to
                                30,000 I would go with a flat file design.

                                If you would like to see the difference do a search on aphaenogaster
                                at this website
                                http://ripley.si.edu/ent/nmnhtypdb

                                and compare it to an author search on wheeler
                                at this website
                                http://ripley.si.edu/ent/nmnhtypedb/wlb/wlbsearch.cfm

                                The first is relational and allows me to easily assign multiple
                                taxonomies and specimens for a single type. The second is a flat
                                file. The first has 1400 or so entries in the typetable hooked to a
                                variety of other tables through relationships. The second has 10,000
                                records and is not hooked to other tables.


                                Dan
                              • Matthew Sarver
                                Dan wrote: the way you make flat file databases scream is by indexing the information and holding the indexes in hash tables (at the file system/OS/Perl/C++)
                                Message 15 of 28 , Aug 16, 2008
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                                  Dan wrote: "the way you make flat file databases scream
                                  is by indexing the information and holding the indexes in hash tables
                                  (at the file system/OS/Perl/ C++) level."

                                  John replied: "Clearly I need to learn more about this, at least enough to understand
                                  something about what the experts are doing."

                                   
                                  The whole topic is way over my head, but maybe this will help with some very basic info about different ways of indexing a database, including hash tables (I hope the info presented in this brief article is correct):
                                   
                                   
                                  So, Dan - what you're telling us is that a db of the size that could store all of the potentially-contributed bee specimen records from North America would HAVE to be a flat db (eg Discover Life), rather than relational, right?  So, the question is, is it possible to create some kind of front end web interface for a db like Discover Life that would allow queries on the basis of host plant, locality, collection method, month, etc.?  Or would the amount of indexing required to do this screw up data entry?  It doesn't seem very useful to store all this information with a specimen record, but effectively have no way to access it via a query.  Being able to sort by collection method and collection protocol would go a long way toward the goal of increasing standardization without sacrificing information.  
                                   
                                  I didn't realize how limited relational dbs were in terms of number of records - thanks for enlightening us on all of this!
                                   
                                  Apologies for ignorance about database design. :(
                                   
                                  Thanks
                                  Matt

                                • Dan Kjar
                                  There is no real limit on the hashes since they can be stored in various ways on filesystems. They can be loaded into memory and accessed very quickly. The
                                  Message 16 of 28 , Aug 16, 2008
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                                    There is no 'real' limit on the hashes since they can be stored in
                                    various ways on filesystems. They can be loaded into memory and
                                    accessed very quickly. The limit on this method is exactly what you
                                    state... we need to know the searches a priori of the visit. If
                                    someone suddenly wants to map all of the 5 legged male bees found in
                                    southern utah we will have a problem.

                                    Relational databases get around this by caching common searches and
                                    renewing the cache occasionally. Products like cold fusion have
                                    included this for years (yuck, but easy, that is what I wrote the
                                    Smithsonian site in. MYSQL for the database if you are interested. Now
                                    I only use perl and MYSQL. Pick uses berkeleyDB, luddite that he is).

                                    Let me run down a simple search using a relational database.
                                    You have three tables. One is a taxonomic data, another is specimen
                                    data, and another is locale data. You can have multiple specimens
                                    tied to single entries in the taxonomic data table and multiple
                                    specimens tied to the locale data (e.g. all the specimens of one
                                    species, and all of the specimens from one site). You would do this
                                    to avoid having the exact same taxonomic or locale data for all 150
                                    million specimens. The more crap in the table the longer it takes to
                                    search it.

                                    The problem is if you search on the fly and you have 300,000 records,
                                    a simple search for the bees of Wisconsin takes a very long time (but
                                    not nearly as long as searching a flat file without the hash table).
                                    If you have a hash table of locales all you need to do is search down
                                    the locales and then grab all of the records included.

                                    example hash table based on previously searched terms
                                    key value
                                    Minnesota 1,3,5,6,9,10,23,35
                                    Wisconsin 2,3,4,8,11,20,34

                                    It only takes a split second to reach into the flat database and grab
                                    everything in records 2,3, etc. It takes a little longer to reach in
                                    to a relational database and check each specimen record to see if it
                                    has a link to a locale table entry that includes Wisconsin (or vice
                                    versa, but you would still need to check the taxonomic table to make
                                    sure it is a bee or whatever you are interested in). Every time there
                                    is a comparison statement it takes much more time. Like I said though,
                                    this only really matters with very large datasets and people at places
                                    invested in relational datasets spend most of their time figuring out
                                    how to make things move more quickly.

                                    There are many other ways to get relational datasets moving fast but
                                    in the business world it is a bit easier for the consumer. If you log
                                    onto your bank account they can cache all information dealing with
                                    your accounts so you can have quick access to it after a short login
                                    wait. However, they know you are only going to look at your own stuff
                                    (hopefully). Since it takes this kind of magic to get relational
                                    databases to move I have decided that I might as well skip all that
                                    nonsense and move to the indexing right away and leave the data in a
                                    human readable format in case I kick off.

                                    The other nice thing about flat files is that anyone can write queries
                                    or index it however they see fit. As soon as you decide to put it
                                    into a relational setup (e.g. speciesname table, genusname table,
                                    specimen table, source table, locale table, alien invasive status
                                    table etc..) You are tied to that setup to create queries. Of course
                                    you could right a query that would flatten it (I did this with some
                                    Fish data from STRI and it WAS AWFUL), but that begs the question why
                                    not just leave the data in human readable form and cut it up for
                                    individual uses?

                                    Not that any of this needs to be worried about at this point....

                                    Dan


                                    --- In beemonitoring@yahoogroups.com, "Matthew Sarver" <mjsarver@...>
                                    wrote:
                                    >
                                    > Dan wrote: "the way you make flat file databases scream
                                    > is by indexing the information and holding the indexes in hash tables
                                    > (at the file system/OS/Perl/C++) level."
                                    >
                                    > John replied: "Clearly I need to learn more about this, at least
                                    enough to
                                    > understand
                                    > something about what the experts are doing."
                                    >
                                    >
                                    > The whole topic is way over my head, but maybe this will help with
                                    some very
                                    > basic info about different ways of indexing a database, including hash
                                    > tables (I hope the info presented in this brief article is correct):
                                    >
                                    > http://20bits.com/2008/05/13/interview-questions-database-indexes/
                                    >
                                    > So, Dan - what you're telling us is that a db of the size that could
                                    store
                                    > all of the potentially-contributed bee specimen records from North
                                    America
                                    > would HAVE to be a flat db (eg Discover Life), rather than relational,
                                    > right? So, the question is, is it possible to create some kind of
                                    front end
                                    > web interface for a db like Discover Life that would allow queries
                                    on the
                                    > basis of host plant, locality, collection method, month, etc.? Or
                                    would the
                                    > amount of indexing required to do this screw up data entry? It
                                    doesn't seem
                                    > very useful to store all this information with a specimen record, but
                                    > effectively have no way to access it via a query. Being able to sort by
                                    > collection method and collection protocol would go a long way toward the
                                    > goal of increasing standardization without sacrificing information.
                                    >
                                    > I didn't realize how limited relational dbs were in terms of number of
                                    > records - thanks for enlightening us on all of this!
                                    >
                                    > Apologies for ignorance about database design. :(
                                    >
                                    > Thanks
                                    > Matt
                                    >
                                    >
                                    <http://geo.yahoo.com/serv?s=97359714/grpId=17598545/grpspId=1705083125/msgI
                                    > d=406/stime=1218922240/nc1=3848642/nc2=4025291/nc3=5202316>
                                    >
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