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Malacolog Version 4.1.1

A Database of Western Atlantic Marine Mollusca

The Academy of Natural Sciences, Philadelphia

About Malacolog:

Malacolog is a database for research on the systematics, biogeography and diversity of mollusks. Malacolog attempts to document all names that have ever been applied to marine mollusks in the Western Atlantic from Greenland to Antarctica. Gastropod species have the most complete coverage, bivalves, polyplacophorans, aplacophorans, monoplacophorans and scaphopods are a work in progress, and cephalopods include only a small subset of names. The database was originaly described in Rosenberg (1993).

Search Malacolog

Search tips:

The following wildcards are available ? [match any one character], * [match zero or more characters]. Wildcards can be placed before, within or after a string. The wildcards _ [match any one character] and % [match zero or more characters] are also recognized and are shown in sql queries listed with results. Wildcards will work in most fields, but not in fields for years.

Each search displays the sql query that was run against the database. As data relevant to your criteria may exist in more than one field, this query may be quite complex. Some searches will provide a link allowing you to edit the where clause of your query. Some of the relevant field structures are shown below. Searches have been designed to hide most of the complexity of the database from you, and should produce reasonable results most of the time. Results may well contain records you did not expect due to automatic insertion of wild cards for some fields in some searches.

If you are not sure where to start searching, you can browse molluscan families and geographic regions.

Geographic regions searches will return those taxa having records in the particular geographic region selected, not those having only records in that region's children or parents.

Author Search Search for names in current use by authors of names. This search returns all current names where the author searched on occurs in the synonymy. Author names may include apostrophies or diacritic marks, and the search engine will only find exact matches against those characters. If you are not finding an author you expect to find, try inserting diacritics or wild cards into that author's name. Cut and paste diacritic marks from this list ‰ · Â È Ë Ì Ò Û ˆ ¸ ˙ if you cannot generate them from your keyboard. Alternately, use ? in place of character with diacritic mark. For example: d?orbigny finds d'Orbigny, and m?ller finds Müller and Möller. The following are all valid author searches: *Adams* A. Adams* A. Adams auct. non A. Adams Adams & Reeve


Enter only one search term in each field. To find all species listed in both Patella and Helcion run two searches, one on Patella, the other on Helcion.

Citing Malacolog

If you use data from Malacolog in a scientific paper, please use this citation: Rosenberg, G. 2009. Malacolog 4.1.1: A Database of Western Atlantic Marine Mollusca. [WWW database (version 4.1.1)] URL It is not necessary to cite the date on which Malacolog was queried, as a new version number is assigned each time the data are updated.

Malacolog was first described in: Rosenberg, G. 1993. A database approach to studies of molluscan taxonomy, biogeography and diversity, with examples from Western Atlantic marine gastropods. American Malacological Bulletin 10:257-266.

To cite the search interface or information model, please use this citation: Morris, P.J. and G. Rosenberg, 2005. Search interface and documentation for Malacolog, an online database of Western Atlantic marine Mollusks. [WWW database (version 4.1.1)] URL

Data structures:

tables in Malacolog: Current name, WASP, Biblography, etc...

Tables in Malacolog 3 and 4 web database.

Tables and fields in Malacolog 3 and 4 Web Database

Details for several of these tables are listed below, see also the more complete information model for Malacolog 4. The web database tables contain several departures from normal forms. Some of these are legacy fields from the early development of the database as a flat file in paradox 3. Others are redundant fields used to reduce joins between tables or text concatenation, and to improve the performance of queries on the web.

Table wasp

Field Name Type
ext_waspid int(11) [Primary key]
currentnameid int(11) [Foreign key to link to current name table]
currentfullname varchar(255) [Redundant, name found from currentnameid link]
originalcombination varchar(60) [The literal string that the original author used in creating this name]
originalgenus varchar(18) [Genus in which associated name was originaly described]
associatedname varchar(23) [Trivial epithet that this record is based upon. Taken together, the original genus and associatedname form the original combination sensu ICZN. The literal text of the original combitnation used by the describing author is held in the originalcombination field.]
author varchar(36) [Author of this name]
attributedto varchar(50) [Author to whom this name has been attributed to]
year int(11) [year of publication of name]
abc char(1) [e.g. Smith 1932a]
parentheses char(1) [Should Author, year be placed in parenthesies]
status_1 varchar(50) [Fields indicating status of name]
statussort char(1) [Redundant, legacy from codes in Paradox]
status_sort varchar(50)
status_2 varchar(50)
systematicnumber int(11) [Used to sort original data in phylogenetic order]
family varchar(18) [Current family placement of name]
waspid int(11) [Original primary key from paradox tables]
pagination varchar(30) [Pages of original description]
illustration varchar(101) [Illustrations of original description]
refid int(11) [Foreign key to bibliography table, reference in which name was created]
north double [Furthest point North from which species has been reported]
south double
west double
east double
shallow double [Shallowest reported depth]
deep double
liveshallow double [Shallowest reported depth of live taken specimen]
livedeep double
size double [Largest reported size]
nameid int(11) [Not used on web] referencez text [Legacy field: List of references providing information about this name along with codes indicating kind of information in each reference]
comments text
typelocality varchar(180)
combininggenera text [Legacy Redundant list of genera with which the name in the available name field has been combined. Now parsed out as additional records in this table
shellmeans varchar(50) [Not used on web]

Table currentname

Field Name Type
intcommonnameid int(11) [Primary key]
currentfullname char(255)
genus char(18)
subgenus char(18)
species char(18)
subspecies char(18)
author char(36)
year int(11)
parenthesies char(1)
currentnameid int(11)
Wasp paradox tables converted to mysql database through vb scripts in a MS Access db, mysql database web served with php.

Network architecture for Malacolog 3 and 4.

The master tables for malacolog are paradox files on a file server. These data are imported into a MS Access database, and massaged with visual basic scripts to bring the data to a more normal form, to search for inconsistencies, and to prepare them for the web. The Access db is used to upload a clean set of the data to a mySQL database via an odbc connection. The data are then provided to the world using php embedded in html.

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