Biodiversity Database Data Entry Manual
Organization:
revised 3/18/97 lhc
The purpose of this Manual is to help students entering data into the Biodiversity Database by describing the database structure and providing examples of data entries.
The Biodiversity Database is an interactive data repository designed to be a comprehensive listing of observations of biological organisms on the Eastern Shore of Virginia. It was created by Dr. Bruce Hayden, Dr. John Porter, and students in 1996 and further developed in 1997. It is a dynamic repository; new information is continually added and old information edited. It resides on a network operated by the Virginia Coast Reserve Long Term Ecological Reserve (VCRLTER) and housed in the Department of Environmental Sciences, Clark Hall, University of Virginia. It is programmed in the Structured Query Language (SQL) and has a Web interface for data entry and retrieval. No quality assurance or control measures have yet been integrated into the database.
The Biodiversity Database consists of three linked sub-databases (Figure 1): the Observation database, the Taxa database, and the Location database. The Observation database is designed to contain reported sightings of an organism and information regarding the name of the organism, the individual responsible for the sighting, the location and habitat in which the organism was found, its abundance therein, and the date it was sighted. Pictures associated with the sighting can also be included. The Taxa database was designed to include both basic as well as detailed information on each observed species. The Location database, likewise, was established to hold basic and detailed information on sites where observations have been made. Figure 1 displays these three databases and the specific information included in each.
In the event of difficulty finding material on your taxonomic group, make an appointment with Mr. Hayden for assistance.
The database is designed to capture detailed textual descriptions of species and locations. For example, you might do some research on a particular species (say the Atlantic silverside, an extremely common fish of the Eastern Shore). Based on your research, you put together a two-paragraph description of this species' life history and ecology. Approach these text entries the same rigorous way you would approach writing a paper - follow formal rules of citing references. If you used three books as the basis of your description, include all those complete references after the end of your paragraphs. See the examples in sections C.2. and C.3. of this Manual.
Graphical images must also be explicitly and thoroughly cited. You must include a caption with each image. This caption should include a complete formal reference to the source of the image. See the last section of this manual for more on how to include images in the Database.
There are two ways of typing in information into the Biodiversity database. One option is to type information into an Excel spreadsheet designed for this purpose ("BIODIN1"), available from the course instructors or downloadable from the Web. This method is suitable for entry of a list of observations, but is not suitable for entering descriptive, natural history-type or detailed location description-type information. Pages 12-13 of this manual provide an example of a completed BIODIN1 spreadsheet, ready for uploading to the main Biodiversity database.
The other option is to type information directly into the Biodiversity database. Direct entry is most suitable for inputting any detailed textual information on species or locations that you have developed from library and other materials. The process of direct entry is described in section D of this manual. Database operations during direct entry tend to move slowly and also require a terminal or computer that has Web access, so spreadsheet entry will be more convenient unless it is necessary to input detailed textual information into the database.
In general, the data entry objective is to enter observations of a particular organism on the Eastern Shore into the Database. Most of the observations will be taken from the scientific literature pertaining to research on the Eastern Shore. Let's take an example. A scientific journal article reported high abundances of the Atlantic silverside (Menidia menidia), a common fish in Eastern Shore waters, at three study locations: Wachapreague Channel and Inlet between Cedar and Parramore Islands; Sand Shoal Channel and Inlet between Cobb and Wreck Islands; and Fishermans Island.
How are these observations entered into the Database? How much additional information is desirable? Well, in order to enter an observation into the database, the species in question must already be registered in the database - within the TAXA listing of species. Second, the location in question must also be entered into the database within the LOCATION listing of geographical references. The species and location may have already been entered into the database - which you can easily check, by scrolling down the TAXA and LOCATION scrollbars on the data entry page - however, if they are not already entered, then you must enter them. This process is described in the following sections.
From a Web Browser, type in the URL "http://www.vcrlter.virginia.edu/"
Click on Biodiversity Project
Click on Prototype Diversity Database - Add Data
When prompted, input the username "biod" and password "mycritters"
When prompted, input your e-mail address (e.g., lhc4c@virginia.edu)
2. Entering a species description
To enter a species in the database, you need some basic information about that species. In particular, you should find out its taxonomic order, family, genus, species, the authority under which the name was assigned, and its common name. Even if you do not have all of this information, at a minimum you should have the genus, species, and common name. This is enough information on the species to go ahead and add a new taxa to the database. So, for example, in our example of menidia observations from the Norcross and Hata paper, I gathered several essential bits of information: the species menidia's genus name is also Menidia; the author notes that all species mentioned in the paper were named after Robins (this would be the authority); and menidia's common name is Atlantic silverside. The paper lacks information on menidia's taxonomic order and family, but I can easily find these from library books on fish taxonomy. With this information, I would select the Add New Species button on the data entry screen, enter MNDMND for the species identification, and fill in the rest of the data fields with the appropriate information.
A further piece of information that this database is designed to receive at this point is a (digital) picture of the organism. This procedure is described in section E of this Manual. Images can come from paper documents, from photo or slide archives, and also are something that you can search the Web for. Perhaps the best way to go about this is to take a couple of hours at some other time and browse the Web, looking generally for organisms in the taxonomic order that your group is covering. Record any URLs for images of organisms that you find, and enter the URLs for the correct species either when you are adding TAXA to the database or are editing them.
At this point, you have entered all the necessary basic species data, and you can submit the TAXA entry. The TAXA database is designed, however, to receive a great deal of descriptive (textual) information on species - descriptions of its physical characteristics, its natural history, its typical habitat, biological/reproductive/life cycle characteristics, and even its economic uses and human interactions. Inputting such descriptive information for a particular species is done by EDITing a TAXA entry - so, for example, I could research the natural history of menidia on the Web and in the library. Supplied with information about menidia's natural history, I could then add it to the existing record for menidia. I would highlight MNDMND on the TAXA scroll bar, and then select Edit Selected Species. A screen with buttons leading to places to type in descriptive textual information (species physical description, species natural history, typical habitat of species, species biological characteristics, and economic uses and human interactions for species) will appear, allowing me to flesh out the MNDMND entry. The following paragraph is an example of an entry under the typical habitat heading of the TAXA database:
The adults are associated with sandy rather than vegetated bottoms near beaches, tidal creeks, and river mouths. They are uncommon along rocky shorelines or over continental shelf. Exact details of salinity tolerance and preference are not available, but a significant portion (21%) of catch in Delaware tidal creeks was from freshwater. The temperature range in which the adults have been collected is 1.0 to 36.0 C; median tolerance limits range from 1-2 C to 32-34 C. Adults have been captured as deep as 49 m in beam trawl hauls. The adult follows the tidal ebb and flow in large schools and often enters flooded beach grass at high tide; limited information suggests that seasonal patterns in movement exist as well, but are not yet well characterized. The habitat of juveniles does not differ from adults except that smaller individuals occur in greater abundance over naturally vegetated bottoms rather than sand filled bottoms. The salinity and temperature ranges for the juveniles are approximately 1-14 ppt (mode = 7 ppt) and 3-31 C (concentrated at 18-25 C), respectively.
Excerpted from Martin, F.D., and G.E. Drewry, 1978. Development of Fishes of the Mid-Atlantic Bight. Volume VI. U.S. Department of the Interior, Fish and Wildlife Service. FWS/OBS-78/12. January, 1978, pp. 106-108.
To enter a LOCATION into the LOCATION database, you should have a few bits of information. First, you should develop a 10-character-or-less location ID - for example, the abbreviation, ESHORE was used to describe the Eastern Shore location, which encompasses the entire study area. For Wachapreague, one of the study sites in Norcross and Hata (1990), I used WACHPRG. Next, you should determine the latitude-longitude coordinates of an imaginary bounding box that would enclose the study site. A good way to do this for our Eastern Shore sites is to consult the Virginia Geographic Names Information Service (Virginia GNIS), to which there is a link from the VCRLTER homepage. You only need to input pairs of coordinates for only two corners of the imaginary bounding box - by convention, we are inputting only the upper left (UL) corner of the bounding box and the lower right (LR) corner. You can enter geographic coordinates by either degree decimal notation or degree-minute-second notation. The Virginia GNIS system uses the degree-minute-second notation. Figure 2 displays the approximate geographic location of the Eastern Shore. Alternatively, you can look at a road map or state or regional atlas for the location of your site, then use this information to get coordinates either from the GNIS system or from the ArcView system in the Department of Environmental Sciences computer room.
Figure 2. Approximate lat-long position of Eastern Shore.
Another piece of information you may include in the LOCATION description at this point is a description of the habitat at this location. Finally, you can also include the URL (if you can find one) of an image of this site.
Like the TAXA database, however, the LOCATION database is designed to receive more detailed descriptive information about a location. Specifically, you may enter a detailed text description of the site. For example, for the three study sites at the center of the Norcross and Hata (1990) paper, the following site description can be developed:
Site is located in channels directly behind the barrier islands, and adjacent to the marsh complex. A variety of depths, habitats, and substrates are found. Sand substrate is found at inlets, creek mouths, and along river margins. Mud substrate predominates in the creeks of the saltmarshes. The site is part of a contiguous system of shallow bays, extensive saltmarshes, and barrier islands which constitute the seaside of the eastern shore of Virginia. These bays and saltmarshes are transected by main channels approximately 400-1000m wide near inlets and 40-250 m wide at the upstream end. Channel depths range from 3-20 m at Mean High Water (Norcross and Hata, 1990).
B.L. Norcross and D. Hata, 1990. Seasonal composition of finfishes in the lagoonal waters behind Virginia Barrier Islands. Virginia J. Science 41(4a): 441-461.
Please note that when I enter a description such as the one above, I include complete references to any sources I used in putting the description together. Again, approach these textual entries the same rigorous way you would approach writing a paper - follow formal rules of citing references.
In addition, the authors describe the basis for their site selection - information that the LOCATION database is also designed to capture.
The Norcross and Hata (1990) study objective was to describe the utilization of the waters behind the barrier islands of Virginia by finfish. It has been speculated that the seaside bays of the eastern shore are primary nursery grounds for juvenile flatfish but this has never been documented with direct observation. While preliminary sampling at many eastern shore sites was conducted prior to this study by the same author, three sites - Wachapreague, Sand Shoal, and Fishermans Island - were selected for this study based on presence of juvenile finfish, accessibility, and diversity of habitat.
B.L. Norcross and D. Hata, 1990. Seasonal composition of finfishes in the lagoonal waters behind Virginia Barrier Islands. Virginia J. Science 41(4a): 441-461.
Again, note the complete citation to the Norcross and Hata (1990) paper from whence the location description was taken. Like the TAXA database, you must go back and EDIT an existing LOCATION record in order to input this detailed descriptive information. Also, if you have the capability of simultaneously having a Web browser and a word processing window open simultaneously, it may be more efficient for you to input all your textual data beforehand with your word processor, then just cut and paste entries from your word processed file into the correct fields of the database. Try it and see if it turns out to be a time- and effort-saver for you.
Now you are finally ready to enter the species observation. The major pieces of information you will need to enter the observation are: the species code name (MNDMND for this example), a full citation for the study (see Footnote on page 1 for the complete citation), the location ID (WACHPRG for this example), the kind of habitat in which the species was observed (for this example, "lagoonal waters behind Virginia barrier islands" will do), and the name of the primary observer (the first author of the paper, B.L. Norcross, will usually suffice). Once you have entered this data, you have completed the observation entry.
The spreadsheet is available from the Web at the Biodiversity project address. In addition, each of the course instructors can provide you with a copy of the spreadsheet (please bring a disk). The spreadsheet is available as an Excel 7.0 file, but can also be made available in different spreadsheet formats.
See pages 12-13 of this manual for an example of a completed spreadsheet. The spreadsheet does not have to be entirely completed in order to be uploaded to the main Biodiversity database. If you have questions about whether your spreadsheet is sufficiently complete, ask one of the course instructors. When you are ready to submit a spreadsheet (you may submit multiple spreadsheets, instead of one spreadsheet with all your data) please give it to the class T.A. on a disk that has your name, e-mail address, and the name of the spreadsheet file.
Say I did a search on the Web and found some Web pages that had high-quality images of Menidia menidia. I'd like to include these in our Biodiversity Database under the Menidia menidia taxa entry. How do I to this? I simply have to make a note of the Web address, or URL, at which the fish picture can be found, as well as information about the institution or individual responsible for the Web site which can be used to write a "caption" for the figure. The URL should be entered into the TAXA database by editing the MNDMND entry and clicking on the button for adding a URL. Please also provide the caption information for the URL at this point as well.
Is this legal? We may add hypertext links (which is what we do when we add a URL to the Biodiversity database that points to another Web site) to the database.
As it stands now, there appears to be a doctrine of implied public access on the Web. The Web was created on the basis of being able to attach hypertext links to any other location on the Web. Consequently, by putting yourself on the Web, you have given implied permission to others to link to your Web page, and everyone else on the Web is deemed to have given you implied permission to link to their Web pages (taken from The Copyright Website, maintained by Benedict O'Mahoney, http://www.benedict.com/index.html; resource listed on UVA Digital Image Center home page (http://www.lib.virginia.edu/dic/info/webinfo.html).
Although Web etiquette suggests that we notify the other Web sites to which we point with our URLs, current technology makes this unnecessary since a Web manager can easily find out who is linking/pointing to their site.
Continuing with the Menidia menidia example, say I found high-quality, detailed drawings of this species in a book I checked out from the Alderman or SEL (for example, the drawing attached to the last page of this Manual). I had consulted a professor who specializes in fish physiology regarding sources of drawings of fish of the Eastern Shore, and he pointed me to a 6-volume series available in our library: Development of Fishes of the Mid-Atlantic Bight: An Atlas of Egg, Larval, and Juvenile Stages. This document was compiled by the U.S. Department of the Interior, Fish and Wildlife Service - so, as a federally-produced document, the content is considered public domain and no permissions need to be requested for scanning the image and including it in the Biodiversity database.
I'd like to add this image to the Biodiversity Database - but how do I go about doing this? First, you need to make a best-possible xerox of the picture you want to scan in. The image to be scanned needs to be on a single sheet of paper (it may not be a book, report, journal article, or other document that may not be placed flat on a scanner). You also need to bring a formatted 3.5" diskette with you when you use a scanner, since you must save your scanned image to a file to give to the course instructors for uploading to the Biodiversity database.
Second, you need to locate a scanner. Scanners are available in the Bryan Computer Lab in room 235 of Bryan Hall; in the E-tech center in Alderman Library (4-3230); and in the Science and Engineering Library. The following example was developed using the PC scanning station in Bryan Hall. See the ITC help pages on scanning (address is all one line: http://www.itc.virginia.edu/cgi-contrib/gopherit.cgi/minerva.acc.virginia.edu*70*itc
/acc.docm/doc.tibm/tib171.gwis) for more detail.
Follow the ITC instructions for using the "Image Assistant" software on the PC scanning station in Bryan Hall, I scanned in the image on the last page of this manual and saved it as a CompuServe GIF file onto my diskette in drive A. The file on this disk can then be given to the course T.A. to be uploaded onto the main Biodiversity Database. For each image file, please develop a "caption" which includes a complete formal reference to the source of the image. For example, the caption used for the Menidia menidia image is as follows:
Kendall, W.C., 1902; found in Martin, F.D., and Drewry, G.E., 1978. Development of Fishes of the Mid-Atlantic Bight. Volume VI. U.S. Fish and Wildlife Service. FWS/OBS-78/12. P. 106.
When the image has been uploaded by the course T.A., a new URL and accompanying caption will appear in the TAXA database for the species. To view the image and caption, edit the specie's TAXA entry and click on on the new URL. The image you scanned in should appear.
Please be aware that for all copyrighted material (e.g., any material such as figures, drawings, tables in a copyrighted book) you must get permission to use the material. In general, unless a document is a government document, assume that it is copyrighted and be prepared to write to the copyright holder for permission to use the material. Some tips: the publishing company, Dover, generally does not copyright their publications and is a rich source of biological images. Also, copyrights expire 50 years after date of issuance. Therefore, if you find a publication which is over 50 years old, you may assume that the material is public domain and you do not need to request permission to duplicate it.