BioMa - BIODIVERSITY DATA MANAGER  

Is BioMa for you? PDF Print E-mail

Is BioMa for you?


BioMa in five minutes

Think of BioMa as your field notebook: typically, you collect a specimen and take several notes about it. Main notes are sample number, where it was collected from, and the date. Later, in the lab, you name this specimen according to international codes of Taxonomical Nomeclature.

The specimen can be an insect, a plant, a part of a plant, etc, etc. The place can be --for instance-- a quadrat belonging to a transect, within a site, at a given municipality. And the date can be simply day-month-year (or some reverse combination of these, depending on your national standards). The name given to the specimen can be a morphospecies code or even a valid species name.

In BioMa you start by entering the specimen then assign it to a locality, a date collected, and a collector. You may make things a bit more complicated, by creating sublocalities within that locality, or creating a range of dates, or a group of collectors. BioMa keeps track of everything, based on who collected what, where and when. This means that you may have different collectors working together, or collect everything yourself, in different places, or different dates. BioMa makes it easy to recover all information.

Access privileges

BioMa retains a complete hierarchy of access privileges, in a manner similar to Unix/Linux systems.

Each BioMa System installed has three kinds of users: a single Administrator, who has all privileges; Project Leaders, who act as Administrators inside their own project; and Users, who change data they've collected for a given project, as long as they are listed as members of that project. Two users from the same project do not change each other's data.

A single user can be, simultaneously, Project Leader in a project and User in another project.

Projects

A feature that distiguishes BioMa from similar software, is its ability to set groups of data to different sub-projects, all belonging to the same project. This is rather useful when you lead a laboratory that run several experiments simultaneously, by different people. You need to keep track of all specimens of all experiments independently, and also, you may need to combine all data in a single metada analysis.

BioMa's Project facility makes it easy. Simply create a project and assign the respective specimens to that project. In creating the project you will be given oportunity to describe its respective Material & Methods, for future reference.

Creating new fields

Although we have tried to cover most of the basic necessities of biodiversity data's gathering, we know that you will need specific field notes to be taken. To make those notes easy to recover, we've designed BioMa's data bank flexible enough to accept new fields to be inserted.

Suppose, for instance, you need to take note of the trees height at each sublocality we have collected specimens from. Simply go to the sublocality input screen and click the "Auxiliary field" buton. You'll be then asked which are the new fields to be inserted and the unit of measurement used. In the example above, your new field will be "tree height" and the measurement unit can be "meters". This last definition (unit of measurement) is mandatory. You will also be given the oportunity to attach a note to this field explanning how it was collected in the field, so that you can use it in future, say, for the Material & Methods section of an article on this data.


BioMa for Ecologists

Ecologists often need to take note of y and x variables. It is common that y-vars are something related to the specimens collected (number of individuals, number of species, etc..) and x-vars are the "ecological determinants" of the pattern under study. For instance, you may want to record the number of species (y-var) in a given site along with the total area in hectares (x-var) of that site, in order to be able to produce a nice "species-area" graphs aftewards.

So far, so good: each specimen you collect is named and recorded into BioMa as belonging to a given locality. In our example above, the site is recorded in BioMa as a locality, along with its characteristics, such as total area in hectares. Then, you ask BioMa to produce the list of species that have been collected in each of the sites, which is the basis for your calculus of species-area.

Environmental heterogeneity studies

The problem
Imagine that you, as an Ecologist, want to test whether or not resource heterogeneity determines species richness of an insect group, say termites.wink

Logs and twigs on the site's floor are the "resources". Your hypothesis is that the number of species of termites inhabiting a locality is related to how variable (=how heterogeneous) is the spatial distribution of resources within that locality.

In this example, in order to calculate resource heterogeneity of a given site you need to produce a sequence of numbers that reveal how resources are distribuited within that site and apply a given variability statistics upon such sequence. You also need to record the total number of species at each site, so that you may later to check wheter site heterogeneity (x-var) affects site species richness (y-var).

For instance:

Amount of twigs+logs in quadrats within a site
Site
Quadrats
Site 1
Site 2
Q1 0
5
Q2
12
6
Q3
0
5
Q4
4
4
number of species
10
4



How to solve it in BioMa

In BioMa, you record each specimen assigning it to a given locality (=site), as usual. The trick here is to create sublocalities (= quadrats) which do not hold any specimen, but keep the information about the respective amount of resources present within them. Later, you ask BioMa to produce the final table as above.

BioMa for Taxonomists

The problem
As a Taxonomist, you may want to keep track of where a given specimen was collected, when, by whom, how, and where is it located in your Museum. You may also want to know which are the papers you've published using that specimen (say, a description of a species new to science).

How to solve it in BioMa
Simply enter the specimen in BioMa, assigning it to a locality, a collector, and a date, and link that specimen to its respective bibliographic reference.

Museum curacy

If you are the curator of a Museum which holds several different taxonomical sections, each section run by a different researcher, just assign each section to a BioMa project and give to the respective researcher the necessary privileges to change his (her) own specimens.

When the researcher comes to a decisive identification of the specimen, he (she) propose to the curator to include this specimen in the main collection. Upon your (the curator) approval, the specimen is assigned to the Museum.

Please note that each researcher is allowed to change everything within his (her) own project, but has no privileges to change specimens which are assigned to the main collection.

Species catalogue

Taxonomists often compiled catalogues of species, including determination history of the taxa, geographical distribution, and even drawings/pictures of specimens of a given species.

BioMa allows all this, even if you do not have specimens for all species to be present in the catalogue. Simply record "fake" specimens, including all info you will need in the catalogue, and instruct BioMa to produce the list of species as the final catalogue. To create "fake" specimens, simply create a new project and insert specimens in it, without transfering those specimens to you main collection.  These specimens are, actually, information on a given species, collected from the literature rather than from the field.

Alternatively, if you do not want to mix the catalogue with your actual collection, install a new instance of BioMa in you computer, and run it independently.

NOTE: since BioMa is web-oriented, you can even publish an online catalogue.

Geographical distribution of species

The problem
A typical demand of Taxonomy and Sistematics is to produce distribution maps for a taxonomical entity, say, a Genus. To do so, you need the recordings of the geographic reference for each locality the genus was recorded from.

How to solve it in BioMa

Simply enter the specimens as usual. Even when you do not know the geographic coordinates for the locality, BioMa will use the closest reference to the site, subjected --of course-- to the level of detail you have supplied when entering locality. If you inform the name of the municipality (anywhere in the globe), BioMa will find its coordinates automatically for you.

Of couse, you'll be given to oportunity to record the geographic reference yourself.

NOTE: You may even enter "fake" specimens (i.e., specimens that are not physically present at your Museum) as long as you inform BioMa so. Simply create a new project, enter the data as if the specimens actually exist, and inform BioMa that no specimen from that project will be inserted in your main Museum.

The Problem
Biogeographers normally face another very typical trouble with data managing software: it is not possible to record that a species have been searched --but not found-- in a given locality. That is, most software will reject to record a 'non-existent specimen', because this produces null records in the database.

How to solve it in BioMa
In BioMa, you simply record a locality, but do not assign any specimen do it. This wil keep the information that such a locality actualy exists in your research protocol, but no specimen has been found in it.

BioMa for theses' supervisors

Theses' supervisors may often need to keep track of all data generated by all thesis under his (her) supervision, as long as being able to analyse data from a single thesis.

This is easily achieved by BioMa, by assigning the data from each thesis to a distinct project. Upon thesis completion, the student may retain some of the specimens for his (her) own collection and let some specimens to be included in the Supervisor's main collection. This is done by transfering specimens from the thesis' project to the main collection in BioMa. The point here is that all data is kept in BioMa, even for the specimens which have not been included in the main collection (that is, specimens which have been retained by the student and, therefore, do not exist physically in the lab. This is useful for future reference, say, statistical analysis of a pertinent publication.
Last Updated ( Friday, 04 May 2007 )
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