Users of BioLink -- feedback?
Paul J. Morris
mole at MORRIS.NET
Tue Jan 16 09:51:27 CST 2001
>"Also, I have yet to discover if customized fields are available to the
>user. Biota has a limited number of fields that could be customized, but
>not enough to accomplish adding the extra info I wanted to include. For
>example, ... the conservation status of each taxon based on various local,
>state, and federal resource agencies, conservation groups, etc. Depending
>upon the taxon, it may have one to many conservation statuses depending upon
>who tracks it."
Custom fields in Biolink are available in two forms: keywords and
traits. Both allow the user to add an unlimited list of new fields.
Keywords work as a flexible controlled vocabulary. You can specify keyword
categories (e.g. conservation status) and a controlled vocabulary for each
category (phrases such as endangered species, threatened, etc...).
Biolink includes a phrase manager to allow privileged users to create and
edit this controlled vocabulary, unfortunately it does not work properly in
the current release version 1.0. Picklists for the controlled vocabulary
are generated from a select distinct query on the values currently in use
in the database rather than from the phrases entered in the phrase manager.
The work around for this is to create a 'work around' record in the
database and add all of the desired keywords to it.
Traits are very flexible fields - they can be set up to enter
essentially any data that a user wants. They can be used to import data
that does not exactly map onto biolink's field structures. Traits are a
very flexible and powerful aspect of biolink, especially if you use biolink
with the full version of MS SQL Server 7. With biolink and SQL Server, it
is possible to import data that does not exactly map onto biolink fields
into traits, and then manipulate it within sql server to fit biolink's
Each taxon or specimen or publication record can be associated with as
many keywords or traits as desired. Multiple publications can be
associated with at taxon. Keywords, however, cannot be associated with a
publication, except by storing the name of the source in a text 'qualifier'
field for the keyword. It is possible to set biolink up to track the
conservation status of a taxon according to different authorities, but it
will not be easy to run a search using the authorities (further detail
At ANSP we have been using Biolink since its initial release last
summer to support a grant to capture all of the names of indopacific
molluscs, and are beginning to try using it for managing collections
information. We have had reasonable success with multiple users in
Australia and the US connecting to a biolink database at ANSP and entering
data. This has not been entirely without problems, and our biggest
difficulty with biolink has been getting user support.
Paul J. Morris, Biodiversity Information Manager
The Academy of Natural Sciences
1900 Benjamin Franklin Parkway, Philadelphia, PA 19103, USA
215-299-1161 mole at morris.net AA3SD PGP public key available.
How biolink handles references and keywords in a bit more detail:
Each taxon has zero to many references.
Each reference comes from one and only one publication
A reference includes Reference type, page, and Qualifier (uncontrolled
(thus a reference can be identified as a source for conservation status
Each taxon has zero to many keywords
A keyword includes Keyword Type, Keyword Value, and Qualifier (uncontrolled
Thus it is possible to record two sources for conservation status
information about a taxon, but it is not possible to directly link these
sources with the status (without an extensive work around: one could create
a long list of reference types that includes each value for conservation
status and use the reference type as a work around for a vouchered keyword,
or one can duplicate the source information in the qualifier field for the
keyword, but it will not be possible to control what gets typed into that
field, and errors may creep in).
Conversely, for associated taxa it is possible to link to a source for the
information about the association
Each taxon has zero to many associations with other taxa.
Each association has zero to one reference.
More information about the Taxacom