Loading ...
Sorry, an error occurred while loading the content.

Standardized Sampling Methodologies and a Common Database

Expand Messages
  • Matthew Sarver
    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
    Message 1 of 28 , Aug 15, 2008
    • 0 Attachment
      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
      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 2 of 28 , Aug 15, 2008
      • 0 Attachment
        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 3 of 28 , Aug 15, 2008
        • 0 Attachment
          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

           

          The information contained in this message is intended only for the recipient, and may otherwise be privileged and confidential. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, please be aware that any dissemination or copying of this communication is strictly prohibited. If you have received this communication in error, please immediately notify us by replying to the message and deleting it from your computer. This footnote also confirms that this email has been scanned for all viruses by the Hampton University Center for Information Technology Enterprise Systems service.



        • 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 4 of 28 , Aug 15, 2008
          • 0 Attachment
            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 5 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 6 of 28 , Aug 15, 2008
              • 0 Attachment
                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 7 of 28 , Aug 15, 2008
                • 0 Attachment
                  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 8 of 28 , Aug 15, 2008
                  • 0 Attachment
                    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 9 of 28 , Aug 15, 2008
                    • 0 Attachment
                      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 10 of 28 , Aug 15, 2008
                      • 0 Attachment
                        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 11 of 28 , Aug 15, 2008
                        • 0 Attachment
                          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 12 of 28 , Aug 15, 2008
                          • 0 Attachment
                            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 13 of 28 , Aug 15, 2008
                            • 0 Attachment
                              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 14 of 28 , Aug 16, 2008
                              • 0 Attachment
                                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 15 of 28 , Aug 16, 2008
                                • 0 Attachment
                                  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 16 of 28 , Aug 16, 2008
                                  • 0 Attachment
                                    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 17 of 28 , Aug 16, 2008
                                    • 0 Attachment
                                      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>
                                      >
                                    Your message has been successfully submitted and would be delivered to recipients shortly.