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Re: Comments on NAS-NRC Status of Pollinators study

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  • Michael Wilson
    Just trying to understand, To determine change in the health of oligolectic species, wouldn t one need to follow plant communities that often move dynamically
    Message 1 of 28 , Aug 15, 2008
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      Just trying to understand,
      To determine change in the health of oligolectic species, wouldn't
      one need to follow plant communities that often move
      dynamically across the landscape? How would this
      be done with static locations?
      Thanks,
      Michael Wilson


      --- In beemonitoring@yahoogroups.com, "Thompson, Chris"
      <chris.thompson@...> wrote:
      >
      > John Asher's comments on NAS-NRC are totally out-of-line and
      represent a personal resentment that he was not selected for the panel.
      >
      >
      >
      > Two museum-based taxonomists were included. So, to imply that a
      dipterist and a lepidopterist some how resulted in the "deemphasizes
      museum-based expeditions ..." is simply not true.
      >
      >
      >
      > We pushed for and got recommendation to support basic taxonomic
      research on pollinators. What came out of Congress in the new Farm
      Bill is not exactly what we recommended but that is another issue.
      >
      >
      >
      > However, for good defensible scientific monitoring, to document
      CHANGE, etc., you must have "monitoring of fixed study sites with
      sampling regimes chosen primarily to obtain "statistically verifiable
      measures." And that does include and require basic taxonomy.
      >
      >
      >
      > Yes, John is right about there being much to be discovered and the
      traditional museum taxonomists and their collecting techniques are
      ALSO needed. Things are changing, for example, the Smithsonian has
      finally re-filled its Curator of Bees, in the Hymenoptera Unit, with
      Dr. Seán G. Brady, who starts on August 18th.
      >
      >
      >
      > So, slowly ...
      >
      >
      >
      > F. Christian Thompson
      >
      > Systematic Entomology Lab., ARS, USDA
      >
      > c/o Smithsonian Institution MRC-0169
      >
      > PO Box 37012
      >
      > Washington, D. C. 20013-7012
      >
      > (202) 382-1800 voice
      >
      > (202) 786-9422 fax
      >
      > www.diptera.org Diptera Website
      >
      > ________________________________
      >
      > From: beemonitoring@yahoogroups.com
      [mailto:beemonitoring@yahoogroups.com] On Behalf Of John S. Ascher
      > Sent: Friday, August 15, 2008 12:27 PM
      > To: beemonitoring@yahoogroups.com
      > Subject: RE: [beemonitoring] Proposal to Hold a Meeting on The
      Development of a North American Bee Inventory and Monitoring Network
      >
      >
      >
      >
      >
      > Like Terry, I am concerned that the initial "global and continental
      > foundation" for the proposed project does not cite ongoing, successful
      > efforts by the global bee taxonomic community. These include compilation
      > of relevant taxonomic data, including distributional records, and
      > databasing and mapping of bee specimen records.
      >
      > I'm all in favor of this proposed effort, but if it is to transcend the
      > limitations of previous efforts such as the ALARM project
      (highlighted in
      > the NAS-NRC status report as a premiere example of pollinator
      monitoring)
      > then it is imperative that the essential role of taxonomists and their
      > institutions be made clear from the outset. For example, the
      expertise of
      > taxonomists must be fully incorporated when designing sampling
      protocols.
      >
      > The 15-member NAS-NRC Committee on the Status of Pollinators in North
      > America did not include a single bee taxonomist, and perhaps as a result
      > their recommended monitoring program emphasizes ecologically-oriented
      > monitoring at fixed sites and deemphasizes museum-based expeditions and
      > other sampling protocols that more efficiently yield certain essential
      > discoveries. Results best obtained from a systematic/taxonomic,
      > museum-based approach rather than from an
      > ecological/experimental/statistical approach include discovery of new
      > species and and life stages, of biogeographically significant new
      > distributional records, and of host-parasite and bee-plant
      relationships.
      >
      > We are still in a discovery phase in terms of bee species distributions
      > and basic natural history, including floral associations, so we must
      find
      > a way to efficiently obtain fill gaps in these data. While the
      ecological
      > approach emphasizes unbiased samples, necessarily consisting for the
      most
      > part of common and widespread species, much essential information can
      > better be obtained by biasing samples in favor of specimens and
      > observations of systematic/taxonomic interest. To do so we must make
      full
      > use of existing taxonomic expertise, e.g. knowledge of areas of
      endemism,
      > and support maintenance and enhancement of this. We simply cannot
      > efficiently fill gaps in knowledge of our bee fauna solely through
      > monitoring of fixed study sites with sampling regimes chosen
      primarily to
      > obtain "statistically verifiable measures."
      >
    • Sam Droege
      OK, I can see Matt s original message if I look on the listserv s web site...it was somehow corrupted by my email browser originally... For future reference
      Message 2 of 28 , Aug 15, 2008
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        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 3 of 28 , Aug 15, 2008
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          Oligolectic species would be in one of the groups more likely to be
          missed...depending on the survey technique.

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

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

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

          sam

          --- In beemonitoring@yahoogroups.com, "Michael Wilson" <mwilso14@...>
          wrote:
          >
          > Just trying to understand,
          > To determine change in the health of oligolectic species, wouldn't
          > one need to follow plant communities that often move
          > dynamically across the landscape? How would this
          > be done with static locations?
          > Thanks,
          > Michael Wilson
          >
        • John S. Ascher
          This sounds good Sam. I have a few minor additions as follows: 1. Standardized vs. Opportunistic samples or surveys I m not sure that these can be broken
          Message 4 of 28 , Aug 15, 2008
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            This sounds good Sam. I have a few minor additions as follows:

            " 1. Standardized vs. Opportunistic samples or surveys"

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

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

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

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

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

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

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

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

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

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

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

            John

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





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


            --
            John S. Ascher, Ph.D.
            Bee Database Project Manager
            Division of Invertebrate Zoology
            American Museum of Natural History
            Central Park West @ 79th St.
            New York, NY 10024-5192
            work phone: 212-496-3447
            mobile phone: 917-407-0378
          • Gretchen LeBuhn
            All- While I was at ESA, I spoke with Matt Jones, the bionformatics guru at NCEAS about how to archive bee data sets that used a common protocol. NCEAS has
            Message 5 of 28 , Aug 15, 2008
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              All-

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

              Gretchen

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

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



              --
              Gretchen LeBuhn
            • Matthew Sarver
              John - It is extremely important to note that there are already multiple linked central repositories in place. Thanks for pointing this out. I am obviously
              Message 6 of 28 , Aug 15, 2008
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                John -
                 
                "It is extremely important to note that there are already multiple linked
                central repositories in place."
                 
                Thanks for pointing this out.  I am obviously not as well-versed in bioinformatics databases as I could be.  I did not mean to suggest reinventing the wheel on this, but wasn't sure how many of these existing databases are flexible enough in their data input to allow us to work with the specific fields that the bee community would find useful / neccessary.  Generating a map for a species is one thing, but a fully searchable database that allows one to find flower records, flight periods, etc for a certain part of the world or a certain species is another.  Right now, the Discover Life specimen view includes a number of very useful data fields, but there are certainly many more that might be of interest, particularly in terms of habitat and floral associations.  As far as I know, there is no easy way to search the fields in that database, other than by viewing a specimen record from the mapper.  Likewise, GBIF is primarily biogeographical data.  I was thinking about the creation of a database web portal with a design and front end that would be specifically geared toward pollinator records, and the associated ecological data that might not fit the mold of available broader repositories.
                 
                Such a customized portal could also be expanded to include an EBird or Bugguide-like citizen science component, where photos could be posted by amateurs.  I agree that bugguide already serves that purpose admirably, but its structure does not encourage the entry of scientifically useful data along with submitted records in the way that a custom-tailored user interface like Ebird does.  The already useful information generated by bugguide could be made even more useful by asking users for more information about their sighting.
                 
                "Local repositories can enhance centralized (global) data by providing
                additional more particular services (e.g., customizable dynamic local maps
                and potentially analyses based on these) "
                 
                I guess this is more along the lines of what I am thinking.  But "local" in the sense of specificty of purpose or usage, rather than geography.  Thoughts?
                 
                Matt
                 
                 
              • Dan Kjar
                As a database person I have to just say I am surprised savvy and relational database ended up in the same sentence... ;) Remember that old saying you can
                Message 7 of 28 , Aug 15, 2008
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                  As a database person I have to just say I am surprised 'savvy' and
                  'relational database' ended up in the same sentence...

                  ;)


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

                  Dan
                • Dan Kjar
                  Discoverlife s fields are whatever the submitter wants them to be. The only thing required is a taxonomic name and hopefully a location in whatever format you
                  Message 8 of 28 , Aug 15, 2008
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                    Discoverlife's fields are whatever the submitter wants them to be.
                    The only thing required is a taxonomic name and hopefully a location
                    in whatever format you like.

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

                      Thanks for another thoughtful response.

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

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

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

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

                      http://libraryportals.com/PCDL

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

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

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

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

                      You are correct. The search function needs improvement.

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

                      As noted above this may already exist:

                      http://libraryportals.com/PCDL

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

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

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

                      I meant both.

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

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

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

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

                      John


                      > Matt
                      >
                      >
                      >


                      --
                      John S. Ascher, Ph.D.
                      Bee Database Project Manager
                      Division of Invertebrate Zoology
                      American Museum of Natural History
                      Central Park West @ 79th St.
                      New York, NY 10024-5192
                      work phone: 212-496-3447
                      mobile phone: 917-407-0378
                    • Matthew Sarver
                      Great! I didn t know discoverlife was set up that way until Dan pointed it out. A query interface for this database now seems like an obvious starting point.
                      Message 10 of 28 , Aug 15, 2008
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                        Great!  I didn't know discoverlife was set up that way until Dan pointed it out.  A query interface for this database now seems like an obvious starting point.  As for PCDL - I thought they were only tackling literature, at least for now.  Do they have plans to incorporate specimen data as well?  I've certainly used it for plant/pollinator interactions a number of times already. 
                         
                        The "citizen science" thing for insects has great potential - as long as those who can ID the pics can keep up!  An integration of bugguide and discover life would be really cool!
                         
                        Matt


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


                        Matt -

                        Thanks for another thoughtful response.

                        I did not mean to suggest

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

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

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

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

                        http://libraryporta ls.com/PCDL

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

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

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

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

                        You are correct. The search function needs improvement.

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

                        As noted above this may already exist:

                        http://libraryporta ls.com/PCDL

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

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

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

                        I meant both.

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

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

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

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

                        John

                        >
                        Matt
                        >
                        >
                        >

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

                      • Sam Droege
                        I wasn t aware of some of those new, more flexible database features, it will be good to have representation at the meeting from that group. While one could
                        Message 11 of 28 , Aug 16, 2008
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                          I wasn't aware of some of those new, more flexible database features,
                          it will be good to have representation at the meeting from that
                          group. While one could argue that you could develop those features
                          later, I think that more and more that database functions will help
                          guide the development of what gets monitored. Its also clear that
                          internet functions can be built directly into monitoring schemes
                          rather than having paper surveys that get entered later.

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

                          sam


                          --- In beemonitoring@yahoogroups.com, "Matthew Sarver" <mjsarver@...>
                          wrote:
                          >
                          > Great! I didn't know discoverlife was set up that way until Dan
                          pointed it
                          > out. A query interface for this database now seems like an obvious
                          starting
                          > point. As for PCDL - I thought they were only tackling literature,
                          at least
                          > for now. Do they have plans to incorporate specimen data as well?
                          I've
                          > certainly used it for plant/pollinator interactions a number of
                          times
                          > already.
                          >
                          > The "citizen science" thing for insects has great potential - as
                          long as
                          > those who can ID the pics can keep up! An integration of bugguide
                          and
                          > discover life would be really cool!
                          >
                          > Matt
                          >
                          > _____
                          >
                          > From: beemonitoring@yahoogroups.com
                          [mailto:beemonitoring@yahoogroups.com]
                          > On Behalf Of John S. Ascher
                          > Sent: Saturday, August 16, 2008 1:16 AM
                          > To: beemonitoring@yahoogroups.com
                          > Subject: Re: [beemonitoring] Re: Standardized Sampling
                          Methodologies and a
                          > Common Database
                          >
                          >
                          >
                          >
                          > Matt -
                          >
                          > Thanks for another thoughtful response.
                          >
                          > I did not mean to suggest
                          > > reinventing the wheel on this, but wasn't sure how many of these
                          > existing
                          > > databases are flexible enough in their data input to allow us to
                          work
                          > with
                          > > the specific fields that the bee community would find useful /
                          > neccessary.
                          >
                          > As Dan already noted Discoverlife can accommodate virtually any
                          field as
                          > long as data are linked directly to a species name. Only fields
                          with data
                          > appear when you pull up specimen records; blank fields are not
                          displayed.
                          >
                          > > Generating a map for a species is one thing, but a fully
                          searchable
                          > database
                          > > that allows one to find flower records, flight periods, etc for a
                          > certain
                          > > part of the world or a certain species is another.
                          >
                          > There are web portals being designed specifically to fulfill
                          precisely
                          > these needs, e.g.:
                          >
                          > http://libraryporta <http://libraryportals.com/PCDL> ls.com/PCDL
                          >
                          > Stuart Roberts in the UK is developing an excellent database
                          optimized to
                          > record these data.
                          >
                          > Right now, the
                          > > Discover
                          > > Life specimen view includes a number of very useful data fields,
                          but
                          > there
                          > > are certainly many more that might be of interest, particularly
                          in terms
                          > of
                          > > habitat and floral associations.
                          >
                          > These can already be mapped. These and other fields you can dream
                          up can
                          > certainly be displayed. Sam even has a field where he notes brand of
                          > soap!
                          >
                          > As far as I know, there is no easy way
                          > > to
                          > > search the fields in that database, other than by viewing a
                          specimen
                          > record
                          > > from the mapper.
                          >
                          > You are correct. The search function needs improvement.
                          >
                          > Likewise, GBIF is primarily biogeographical data. I was
                          > > thinking about the creation of a database web portal with a
                          design and
                          > front
                          > > end that would be specifically geared toward pollinator records,
                          and the
                          > associated ecological data that might not fit the mold of available
                          > broader
                          > > repositories.
                          >
                          > As noted above this may already exist:
                          >
                          > http://libraryporta <http://libraryportals.com/PCDL> ls.com/PCDL
                          >
                          > > Such a customized portal could also be expanded to include an
                          EBird or
                          > Bugguide-like citizen science component, where photos could be
                          posted by
                          > amateurs. I agree that bugguide already serves that purpose
                          admirably,
                          > but
                          > > its structure does not encourage the entry of scientifically
                          useful data
                          > along with submitted records in the way that a custom-tailored user
                          > interface like Ebird does. The already useful information generated
                          by
                          > bugguide could be made even more useful by asking users for more
                          > information
                          > > about their sighting.
                          >
                          > I would advocate an all of the above solution, i.e. improving
                          Bugguide
                          > itself, improving relevant tools at other sites such as
                          Discoverlife, and
                          > establishing useful links between sites with complementary emphases.
                          >
                          > > "Local repositories can enhance centralized (global) data by
                          providing
                          > additional more particular services (e.g., customizable dynamic
                          local
                          > maps
                          > > and potentially analyses based on these) "
                          > >
                          > > I guess this is more along the lines of what I am thinking.
                          But "local" in
                          > > the sense of specificty of purpose or usage, rather than
                          geography.
                          > Thoughts?
                          >
                          > I meant both.
                          >
                          > In terms of geography, one example of a local site would be a
                          global or
                          > regional ID guide customized for a specific site by filtering out
                          > extralimital taxa.
                          >
                          > For example, here is the eastern Bee Genera guide customized for the
                          > Fingerlakes region of NY:
                          >
                          > http://www.discover
                          > <http://www.discoverlife.org/mp/20q?
                          guide=Bee_genera&cl=US/NY/Fingerlakes>
                          > life.org/mp/20q?guide=Bee_genera&cl=US/NY/Fingerlakes
                          >
                          > In terms of specificity of purpose, a local site could highlight and
                          > extend a subset of data, e.g., pollinator-plant interactions,
                          derived by
                          > querying one or more central repositories.
                          >
                          > John
                          >
                          > > Matt
                          > >
                          > >
                          > >
                          >
                          > --
                          > John S. Ascher, Ph.D.
                          > Bee Database Project Manager
                          > Division of Invertebrate Zoology
                          > American Museum of Natural History
                          > Central Park West @ 79th St.
                          > New York, NY 10024-5192
                          > work phone: 212-496-3447
                          > mobile phone: 917-407-0378
                          >
                        • Dan Kjar
                          Here is a quick break down of relational vs flat databases. Relational databases link tables to tables and those links allow you to do some very powerful
                          Message 12 of 28 , Aug 16, 2008
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                            Here is a quick break down of relational vs flat databases.

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

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

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

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

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

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


                            Dan
                          • Matthew Sarver
                            Dan wrote: the way you make flat file databases scream is by indexing the information and holding the indexes in hash tables (at the file system/OS/Perl/C++)
                            Message 13 of 28 , Aug 16, 2008
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                              Dan wrote: "the way you make flat file databases scream
                              is by indexing the information and holding the indexes in hash tables
                              (at the file system/OS/Perl/ C++) level."

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

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

                            • Dan Kjar
                              There is no real limit on the hashes since they can be stored in various ways on filesystems. They can be loaded into memory and accessed very quickly. The
                              Message 14 of 28 , Aug 16, 2008
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                                There is no 'real' limit on the hashes since they can be stored in
                                various ways on filesystems. They can be loaded into memory and
                                accessed very quickly. The limit on this method is exactly what you
                                state... we need to know the searches a priori of the visit. If
                                someone suddenly wants to map all of the 5 legged male bees found in
                                southern utah we will have a problem.

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

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

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

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

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

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

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

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

                                Dan


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