SysTax - a Database System for Systematics and Taxonomy

Documentation
Web Search

Collection data (+ "portal")

Data ready for search

The new collection query uses a full text index, which is being created with ORACLE interMedia text ™.

The following data from SysTax are indexed:

• name and acronym of collection, subcollection
• project (e.g. GBIF or EDIS, sub-projects GloMyris or DORSA)
• determination: taxon, all higher taxa, vernacular names, type status
• collector, collection number
• Referenced place including complete geographical hierarchy,  description of location, description of locality, all "free text fields" (original text of label, original quotations, without "private" or "internal" remarks of an institute)
• geographical coordinates
• sex, developmental stage, reproduction type, material type
• illustrations: title, description, copyright, picture type, view, used filter
• sound: title, description, copyright, songtype

When standard lists are uses for assigned values, all language variants stored in SysTax are indexed, so that e.g. for "type" and "type" can be searched. Likewise each "holotypus" is found when searching "type". A multi-language query is also possible for all geographical data (Asien - Asia, Brasilien - Brazil). For each taxon the complete systematic hierarchy is indexed, so that also these higher taxa at any level can be searched (example: the search pattern "Annonaceae Gottsberger Brazil" gives all objects, that had been collected by  Gottsberger in Brazil and that has a determination of Annonaceae or any taxon below this family)

The collection search is available in a simple and an expert mode. The search result can be displayed in a short and in a detailed list. For the simple mode  the short list is preset, for the expert mode  the detailed list.

The search can also be carried out in such a way that the query fields are omitted in the result lists. By doing so, for example, type lists or lists of collection items of a certain taxon can be dynamically created for a certain institute.

At the end of the result the links are shown to get the collections displayed in the map created by the web-service of GBIF-Canada and of Google local™.

Technique of indexing

For each collection item an appropriate word list (see illustration) from the data listed above is created. This word list is stored in a separate table in a field of the type "CLOB" (character large object). ORACLE InterMedia Text™ then provides the actual full text index from these lists. At present the index is calculated once a week which takes about up to 4-5 hours.

The marking of the data in the word list in so called "sections" allows for a direct search for certain data in the expert mode (e.g. taxon, collector, ...).

You can  incorporate the collection search presented here in your own web site - just like the SysTax "taxon browser" and the "quick-search".

Search sample

Abbreviation (wildcard) is a "%" or "*".

The following search patterns can be used :

• Peter Miller: Peter AND Miller
• "Peter Miller": character string "Peter Miller"
• Peter -Miller: Peter AND NOT Miller
• -"Peter Miller ": all data sets WITHOUT the character string "Peter Miller"

Parameter and their use

Query field for simple search:

• query = { search pattern }; simple query field for combined search
  The following data are excluded from the search:
  Institution name: because these data contain geographical names
  acronym: because it might be identical with a Town; e.g. the Ulm Herbarium has the Acronym „ULM“
  determinator: in order to enable a search for collector names
  project: because it might contain geographical names
  copyright: same reason
• wrapper= { ID }; ID of the wrapper to be queried
  -1 = Systax
  0 = all (default)
  1 = IPK Gatersleben - Genebank accessions
  2 = Zoologisches Forschungsinstitut und Museum Alexander Koenig
  3 = Senckenberg - Wrapper 1
  4 = Senckenberg - Wrapper 2
  5 = Museum für Naturkunde, Humboldt-Universität zu Berlin
  6 = HBGSpermatophyta
  7 = HBGBryophyta
  8 = HGB Impetus
  9 = Bryophyte herbarium, Göttingen
  10 = Type herbarium, Göttingen
  11 = Forster herbarium, Göttingen
  12 = BGBM - Bridel Herbar
  13 = BGBM - HerbarImages
  14 = BGBM - Fruit and seed collection database
  15 = Staatliches Museum für Naturkunde Stuttgart, Herbarium
  16 = BGBM-Algaterra Types
  17 = Alfred-Wegener Institute for Polar and Marine Research, Herbarium
  18 = BGBM-BoGART

Search field for the expert mode:

• tquery = { taxon }
• cquery = { collector }
• locquery = { location_habitat }
• longfrom = { coordinates_longitude_from }; coordinates in degrees and decimals; direction W and S as negative values; example: "- 10,323456".
• longto = { coordinates_longitude_to }
• latfrom = { coordinates_latitude_from }
• latto = { coordinates_latitude_to }
• labquery = { original_label_text }
• iquery = { institute_name_acronym }
• acro = { zfmk | ulm | k | smns | ... }; acronym of an institute

Further options for both query modes (defaults underlined):

• proj = { edis | glomyris | dorsa, ... }; project or sub-project
• data = { all | herb | coll | bg }; all data or restricted to herbaria, zoological collections or botanic gardens
• type = { no | yes }; type material only 
• img = { no | yes }; collection items with illustrations only
• snd = { no | yes }; collection items with with sound files only

Options for formatting the result lists (default underlined):

• lang = { e | d }; language
• expert = { no | yes }; expert mode or not; "no" ignores all parameters of the expert mode 
• dsearch = { yes | no }; display search fields or not
• pr = { systax | gbif_e1 | gbif_e2 | gbif_v1 | edis | ... }; code for the selection of a style sheet
• displ = { s | l }; display result in short or long list. 
• sort = { tax | inst }; sort result by taxon or by name of institute 

SysTax collection search on your own web-site

You can incorporate the collection search into your web site as follows (shown for the GBIF Vertebrata web site) :

• set a link to the collection query like:  http://www.biologie.uni-ulm.de/cgi-bin/portal/portal.pl?pr=gbif-v1&lang=e
• Place two marks (html comments) in your web page, for example
  <! - - start: SysTax -->
  <! - - end: SysTax -->
  SysTax will place the query result between theses two marks. 
• Send us the URL of the desired web page, the exact text of the marks and the project code  as well as the desired formatting of the text and background colors for the css file.

Installation of a simple suchfeldes into arbitrary web pages

The following HTML code gives you a simple query field in your web page.  The result is displayed in simple form without query fields (dsearch="no") in English language.

It will look like this:

Link to lists using the parameters

You can display a various lists of collection items by suppressing the display of the search fields using the parameters listed above.

Here as an example the list of  "all types of birds from the ZFMK in short display mode and in English language":

http://www.biologie.uni ulm.de/cgi bin/portal/portal.pl?tquery=aves&acro=zfmk&typus=yes&sort=tax&displ=s&lang=e&expert=yes&dsearch=no