Network Accessible Taxanomic Resources

Peter Rauch anamaria at GARNET.BERKELEY.EDU
Fri Mar 12 18:04:38 CST 1993

This problem description should be of interest to lots of others. Peter
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>From key at Fri Mar 12 17:01:15 1993
>Date: Fri, 12 Mar 93 16:44:52 -0800
>From: Gerry Key <key at>
>To: Jim Beach <beach at>,
>        Peter Rauch <anamaria at>,
>        Julian Humphries <jmh at>, Stan Blum <mnhod025 at sivm.bitnet
>Subject: Network Accessible Taxonomic Resources
>Cc: Jeff Grovhoug <grovhoug at>, Evan Evans III <evans at>,
>        Gerry Key <key at>

>I am seeking information about the availability of taxonomic information
>from network accessible sources.  I got your name from Peter Wilson at the
>Missouri Botanical Gardens and from poking around in the biosystematics
>and biodiversity gopher servers.

>We are in the process of designing a database to support an ecological
>risk assessment project getting underway in San Diego Bay.  The database
>will be used as a repository for a variety of biological, chemical,
>physical and geological data collected by our project and by other
>concurrent projects, and data extracted from reports prepared from past
>surveys conducted in the Bay.  It is our desire that the database become a
>long-term repository of data so researchers can gain sufficient spatial
>and temporal perspectives to begin addressing system-level processes in
>the Bay.

>Having done this before (but some time ago), I know we have neither the
>time nor the resources to maintain complete taxonomic information for all
>the organisms that may be referenced in the database.  The most I can hope
>for is to have correct field identifications of the organisms being
>sampled.  I know we'll have to turn to outside sources for current
>information on synonymies, higher-order taxonomy, authorities, etc. for
>these critters.

>Which brings me back to the purpose of this message.  Ten years ago or so
>I was involved in a project called the Natural Resources Data Base (NRDB),
>in which we incorporated a taxonomic coding system developed by the Hawaii
>Coastal Zone Data Bank (HCZDB) at the University of Hawaii.  That
>taxonomic coding system was eventually folded into similar systems that
>had been developed by EPS as part of their BIO-STORET system and by the
>National Oceanographic Data Center (NODC) as part of their oceanographic
>database.  That project also lead to a number of contacts with the Flora
>North America project, the Association of Systematic Collections, etc. who
>were also dabbling in computerized taxonomies back then.  Knowing how much
>work it was to create and maintain those coding systems then, I thought I
>would first nose around to see who was doing what in these fields today.
>I found Peter Wilson through a mutual friend, Ron Foreman at UBC, and
>Peter pointed me down a path the lead to you.

>Let me outline what I would like to be able to do, and you can tell me
>whether efforts in the systematics community are at, or headed in, the
>direction I am trying to go.  In general, I would like to be able to
>record the taxa in the database as reported by the field scientists.  In
>most cases the identification will be a bi- or tri-nomial name, perhaps
>with the accompanying authority.  Obviously, because this is a study of
>San Diego Bay, we will be recording predominantly marine taxa in the
>database.  Because the project will be studying the fate and effect of
>materials released in the Bay, there is no apriori reason to assume the
>measurements will be predominated by avian, fish, molluscan, algal, or
>bacterial taxa.

>For many applications, being able to retrieve data for an organism by
>searching on its scientific name will suffice. However, I can envision at
>least three scenarios where we will required broader taxonomic
>information.  First, some researchers will know taxa by their common name,
>and thus we will need a common-to-scientific name cross-reference.
>Second, some users will want to retrieve data by aggregating taxa into
>higher-order groupings - for example, searching by family and picking up
>all genera and species that belong to that family.  And third, taxonomic
>names will change and we'll need to be able to find organisms by both
>their current name and their synonymies.

>The poking around I have done so far indicates that some museums,
>systematics organizations, etc. have begun to put their collections
>on-line and make them accessible via the Internet and other pathways.  Can
>you give me any indication of what the status of this work is and whether
>any of these servers are addressing marine taxa for the Western U.S.?
>Second, are any of these servers organized such that I could feed them a
>list of taxa from the database and they could send back the Kingdom,
>Order, Class, ..., Authority, and Common Name(s) of those taxa?  And
>finally, blue sky-of-all-blue skies, has there been any discussion of
>designing these systems to be true database servers that could become part
>of the logical database design of remote client applications?  In other
>words, design a client application like ours environmental database to
>recognize that a query like Family = requires it to connect to a remote
>taxonomic server, retrieve a list of the taxa that belong to that family,
>and then incorporate those taxa into query specification.

>As long as we're dreamin', of course the client/server relationship should
>be reversible.  A systematist should be able to query his client taxonomic
>application and have it go out on the network to query environmental
>databases such as ours for distribution and abundance data for the
>requested taxa.

>Finally, I should add that we have the same requirement for chemical,
>geological, and other taxonomies.  Have you seen evidence that the
>chemical, geological, or other scientific societies are endeavoring to put
>their taxonomies on-line like the biosystematics community is?

>Simple request, huh?  But, who knows?  I've been amazed at how much
>information from worldwide sources is already available on-line through
>Gopher, WAIS, Archie, and related systems.  I'd be surprised if there
>weren't a goodly number of researchers out there speculating about how the
>client/server model can be extended to allow seamless queries against
>interdisciplinary databases from far flung client applications.

>Oh, I lied.  One more item.  I noticed that some of the systematics
>collections are offering a service in which the user sends a formatted
>Email message with his request and gets back via Email the requested
>information for that taxon or locality.  This is interesting development
>because Email-enabled applications are just about to burst on the scene in
>a big way.  I think database interfaces will be one of the growth areas
>for these products.   With standards like X.400 and X.500 I should be able
>to compose a query in English on my PC using cc:Mail, send it out across a
>Novell LAN to the Internet and then to the target server, and get the
>table, report, graph, etc. back by the reverse pathway.

>--Gerry Key
>Computer Sciences Corporation
>4045 Hancock Street
>San Diego, CA  92110-5164
>Internet:      key at (NeXTMail OK)
>FAX:           619.225.2583
>Voice:         619.225.2504

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