About Collection Presenter and NRM Ichthyology Collection database
Collection Presenter Version 0.7beta17a
This implementation of Collection Presenter enables searches in the NRM Ichthyology Database. Primarily one searches for objects (one or more specimens with the same catalog number), but one may also search directly for images of specimens or localities, or for expedition information. Images and maps are provided with all kinds of data. Since images and maps may be large (50kb or more) they are normally downloaded only when requested.
Collection Presenter was designed and coded by Sven O Kullander using PHP. The backend is a MySQL database based on the Darwin Core 2, v.1 concepts. The design and standard permits rapid customization to suit other databases and taxonomic groups. The source code is available under the GNU General Public Licence 3.
Collection Presenter can be configured to display the user interface in any language. English, Swedish and Spanish are available by default. You can help translating Collection Presenter to other languages. Contact the author of Collection Presenter to learn how.
Search collection
The "Search Collection" search form provides the following query options
- Category:
- Family — a valid scientific family name
- Genus — a valid scientific generic name
- Species — a valid scientific species name, e.g., Gadus morhua
- Species epithet — a valid scientific species epithet (the second word in a species name)
- Svenskt artnamn — a national common name
- Continent/Ocean — the name of a continent or ocean, e.g., Europe or Pacific Ocean
- Country — a valid country name in English, generally the short ISO name. If you suspect that the database is not using the country name you expect it to, try searching a random country, and from the results page locate the desired country name in the dropdown list
- Province/State — a state or province name, you may try with or without a qualifier
- River drainage — a valid name of a major river, e.g., Amazon River
- Locality — a description of the collecting site, best use with precision "contains" and just one word in the locality description
- Field No — a valid field number/collecting site number as used at NRM
- Collector — a valid collector name. Collector names may be single, in the format Lastname, Initials (Kullander, SO), or binomial (Kullander, SO & Larson, AB), or abbreviated using the ending et al. (Kullander, SO et al.)
- Catalog Number — a valid NRM catalog number (between 1 and 55000)
Expedition — a valid expedition name. It may be more convenient to search the Expedition database - Date — a valid collecting date in the form d MMM yyyy (e.g., 1 May 1922)
- Precision options:
- equal to, begins with, ends with, contains
- Data field:
- blank field for entering the text to search for. Letters A-Z, å,ä,ö, Å,Ä,Ö, and figures 0-9, and a few other characters are allowed
- Ordering options:
- Default — ascending by Family, Genus, Species epithet, Catalog number, Country, Locality
- Catalog Number — ascending
- Species — ascending
- Country — ascending
- Restriction options:
- All — outputs all records, including types
- Images only — outputs only records with associated images
- Types only — outputs only records for types
- Check options:
- Simple — if you check this box the results page does not show a dropdown list of selectable terms in the database. If left unckecked, the results page will feature a helpful dropdown box from which you can select among available values in the database, rather than guessing at what it might contain
- Maps — if you check this box and the search result yields georeferenced objects, the results page will feature a small map with the localities plotted. This option only works with precision set to "equal to"
- Output record number options:
- Select 10, 50, 100, 250, 500, or 1000 records to be output
- Output format options:
- Full catalog record — formatted, detailed excerpt from the database, with image availability
Tabular listing — catalog number, species name, field number, type status and image availability presented in a table
Sorting is possible by clicking up and down arrows in table headers
The "Full text" search field is independent from the above. Follow the intructions below the search field. Using full text search you may perform highly advanced queries, but you also need to be careful with operators and keywords. Keywords must be at least 3 characters long. The only option is whether output should be in table or catalog record format.
- Example (1) to find all Swedish roach
- type: +Sweden + "Rutilus rutilus".
- Example (2) to find all non-Swedish roach
- type: -Sweden + "Rutilus rutilus"
The "Quick Browse" option gives you a possibility to browse through species, genera, families and countries for which objects are available in the collection. This is particularly useful if you frequently get a negative response from normal searches.
For most parameters, the results page also offers a quick pick selection form displaying all available values of same parameter.
Tabular query results can be downloaded as spreadsheet in MS-Excel format, comma-separated-value text file (CSV), xml output, or as a table in a portable document format (PDF) file. Spreadsheet, CSV, xml and PDF outputs contain displayed information but also geographical coordinates (longitude/latitude in decimal degrees)
Images
Images are typically 1000 pixels wide, shown reduced by on the fly conversion, with a resolution of 96dpi or more. Clicking the review button under a thumbnail image opens an image manipulation page displaying the image at full size and with options for enhancing it. Images show either specimens in the collection or collecting sites. The uploaded images represent only a subset of the available image bank. Images not directly relevant to specimens or field activities are not available online. If several images show the same specimen or same view of a field site, only one is selected for online display.
Requests for using an image should be adressed to Sven O Kullander for further processing. Images copyright NRM or NRM staff are free to use for academic, non-commercial purposes, but you must check with us first. Images showing persons may under no circumstances be displayed in other contexts, commercial or non-commercial. Commercial use of our images is subject to charges. You may not use our images on websites or in publications without express permission. You may not maintain a permanent link from our image gallery to web pages under your control. Citation of images should be avoided as they may be removed, modified, replaced, or otherwise made inaccessible at a particular web address.
Maps
Application native maps are generated on the fly, based on georeferenced records, i.e., there may be additional records corresponding to the search in the database, but these records do not have associated coordinate data. The symbols are 7X7 pixels, and symbols may overlap or completely cover each other. Clicking a symbol opens a page showing the details of the objects displayed by the visible symbol only; and holding the pointer over a symbol displays the Field Number and decimal degree coordinates for that symbol only.
Native maps are optimized for screen display. Printing maps rarely yields satisfactory results, and results vary with browser, printer settings, and user settings. Usually the symbols are displaced relative to the map on printed output including print previews.
You can print records for up to four species using the "Plot Distribution" option, which is independent from the database search. If you just need a map quickly, use this option instead of maps generated from searches.
Localities may also be plotted using the c-squares mapper, developed by Tony Rees, CSIRO. C-squares mapping is currently only available from the menu, not from within database searches. C-squares based on latitude/longitude data are submitted to an external c-squares mapper, by default the NRM FishBase server.
Another mapping option is available from within search output: Under the small map provided with query output from collection database searches, is a link to "Google Earth". Clicking the link creates a kml file which can be saved to disk for later use, or opened with Google™ Earth. Google Earth is available in a free version. It must be installed separately on your computer and runs as a local application. In Google Earth, localities are displayed on a representation of the Earth. If Google Earth is not available on your computer, you will be given an option to view the output file in Google Maps instead, using a service from Google.
Yet another mapping option is available from within search output: Under the small map provided with query output from collection database searches, is a link to "Google Maps". Clicking the link opens a Google Maps window with the localities plotted. In Google Maps, localities are displayed on a 2D map. Clicking a marker produces an information call-out showing the catalog number, species name, locality, date, collector, field number, and the coordinates for the particular record. Clicking anywhere on the map produces the coordinate for that point displayed below the lower left portion of the map. Attempting to plot a large number of records may result in long waiting time, or produce an "unresponsive script" warning in Mozilla Firefox. This is a known problem with Google Maps which will be resolved eventually.
RSS
The 25 most recently added object records and images as well as references are available through RSS feed from each page. The RSS file is accessible in its native xml format or, more conveniently, with a newsfeed application. A link to the object RSS file is also provided on the main page and here: 
Disclaimer
The entire database is available online except objects temporarily excluded because they may be under study or the information may suffer abuse from malicious data miners.
No information in the database should be used without first checking with the staff of the NRMIchthyology Collection. Any information is potentially incorrect, such as identification, classification, locality and collecting event information, spellings of personal and place names. Photographs may have been manipulated or miscoded, and the colors may vary from one computer system to another. National borders on maps are not necessarily correct; locality symbols plotted on maps may be incorrectly placed because of mistakes in georeferencing or because the browser does not display the symbols correctly.
Technical aspects
This online database represents an extraction from the NRM Ichthyology Database exported to MySQL 5. All original code is written in PHP 5 using HTML-Kit and tested against Opera and Mozilla Firefox browsers. Graphs are produced dynamically using the JpGraph library. Native maps were produced in MapInfo 7 or ArcGIS 8.3 and further processed with PaintShop Pro 8.
Image manipulation uses MagickWand for PHP, installed as a PHP extension to ImageMagick. Graphs are produced with JPGraph, incorporated as source code. Rounded corners employ Nifty Corners, a free java script with cascading style sheet, copyright © HTML.it and Alessandro Fulciniti. PDF output was created using the FPDF class and the MySQL Report code by Philip Clarke.
Collection Presenter was first released under the name The Web Artedian, so named because it was developed using output from the collection management system, The Artedian.
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