Hello, everyone today. I’ll be introducing you to specify seven and showcasing
some of our features and functionalities navigation menu
items and our data entry forms.
specify as a database platform for collections research data
It manages species and specimen information for computerizing biological
Tracking transactions linking images and attachments
to specimen records and Publishing record data to data
Our software is open source and available on GitHub.
It supports data from specimens determination slash
identifications locality and geography data
taxonomic and stratigraphic classifications
field notebooks DNA sequences literary references
and other information sources
It manages the information associated with accession records documents conservation
treatments repository agreements loans exchanges
and other interactions.
Specify has been an active development for decades exciting the standard for
Museum database management software.
Is used by hundreds of Institutions around the world spanning the
large number of disciplines and collections.
Specify uses Maria DB is the database management software underlying
all of the relationships Within.
All installations of specify have the
same database tables relationships and Fields. However, the
schema can be configured for your individual needs.
the schema configuration tool includes the fields labels visibility
all records within specify exist as records within a database table.
Such as the collection object record that then contains many
relationships to other records and other tables.
There are relationship fields in the collection object table that connect the
specimen record to the accession records. The terminations collecting event
data specimen preparations attachments and
It is important to study the specified data model when preparing data
for import or before entering data into a new database.
You can see now. We’re on the home screen.
At the top you see a list of items. This is the navigation
At the top left, you will find the specify logo.
This will return you to the homepage at any time from anywhere
The first item in the navigation menu is data entry.
When selected you will choose a table when specify that
you would like to create a record in.
Data forms are used for entering editing and viewing
Because specify uses related fields to link information.
Most data can be entered using the collection object form. However,
it may be useful to enter background information such as
agents and collecting events before entering collection object records.
Each discipline has a default set of forms for viewing entering and
editing data appearing in this data entry list.
Specify shows the most frequently used forms for each discipline in the dialogue. However,
this can be customized.
Next we have trees.
In this collection, we have three trees available. The geography tree
storage tree and the taxon tree specify visually
presents some data types in hierarchical tree displays. This includes
the taxon geography storage chronostratigraphy and
These data types are also included in the form system. But the
tree displays offer a more convenient single screen view of the
data and some data tasks are more intuitive when performed and
tree displays compared to forms.
The taxon geography chronostratigraphy and lithostratigraphy trees
and tables our scope of the discipline level meaning that
all collections within a discipline share the same tree.
Storage tree is scoped at the institution level. But as
with the other trees only collection objects with the current collection will
be shown when querying the associated collection objects from
the context menu.
Next up we have interactions.
Interactions and specify allow users to create and manage documentation
associated with the movement of specimens or data into or
outside of the collection.
This includes information about loans gifts borrowed items
permits shipments accessions disposals deaccessions
and information requests.
For example The Collection manager May respond to the request for a
loan of a specimens for research by creating a loan record in specify.
The record would include the list of specimen being loaned along with
other required loan information. The loan number date of
loan due date agents Etc.
When the loan is returned the manager would then update the
loan record to note the date of return in which
specimens were returned.
Next we have one of the most important specified features queries.
What are the benefits of entering data into a structured database is the ability
to retrieve the data efficiently and consistently?
The query Builder offers a flexible interface for
defining and running searches.
Queries are precise request for information retrieval that
can restrict the return records based on the contents of any specified
The results from queries can then be used to export data
to CSV create record sets Google Earth KML
files and browse in a form viewing mode.
The query dialog displays a list of existing queries within the
database as well as the date. They were created and the date
they were last modified.
Can be sorted by name date created or the date
You can click new to create a new query.
You will see a list of tables and specify that can be queried.
We have a video introducing and explaining the query building functionality of
specify available in the community form.
Let’s just open one up to show you.
You’ll see that they’re very complex relationships here. You can query and pull
data from that specific field.
Next we have record sets record sets are collections of
Records, but then the database from any table.
In this instance, we have collection object records contained in a record
set that can be navigated using these buds up
here. You can type in the specific number within this
grouping of items that you’d like to navigate to and you
can add and remove records from this grouping.
Next we’ve got the reports menu item.
The reports menu contains the reports and labels for the current collection.
A label a report is a document that specify creates containing the desired
information from a table in the database.
Labels are commonly attached to a jar the container or
the specimen itself.
They often contain details about the determination whether or not it is
the type specimen the catalog number field number coordinates and
other important details.
Reports are used for invoices loans exchanges and more and contain
any information from any related table to the record as
Reports and labels can be made to display field values from any table.
Now I’m going to run an example to show you I’m talking about.
You can see the specify was able to quickly create these labels
on the Fly.
You can configure your database to automatically create labels upon the
creation of a new specimen record in the data set.
Next is the workbench.
Our tool that allows importing datasets in a specify.
It can import data from a range of file types link images to existing
records create View and edit data in
a grid View.
Visualize Gia referenced objects in geolocate convert coordinates
to different formats and Export and
re-import data sets while maintaining the same mapping.
This tool can handle Imports of large sets of data during digitization
of a collection after collecting in the field or when
moving to specify from another database system.
We have videos demonstrating how to use the workbench available
in our community form for our members.
You can see here how a data set looks once it’s
been uploaded to the database.
You can roll it back.
See the number of new records created during each upload.
Each column in the data set can be assigned to a specific field within
Finally, we have the attachments page.
This allows you to view all of the attachments in your database in a
grid view that can be sorted by any field or filtered by the table. The attachment
was uploaded to
On the far right of the navigation menu, you will see a grouping of
First we have the username the current user displayed as a
This button brings you to the user tools menu.
The left column contains the sections for the user account which includes
changing the password logging out.
It also includes customization options like the user preferences, which
we’ll have an upcoming video on the schema configuration tool.
We also have the administrative tools the ability to generate a
master key repair the trees see your
app resources and view resources security and
configuration options, which we have a webinar covering.
The right column includes Darwin core exporting options links
to our documentation.
And resources for developers including the API and database schema.
We have documentation covering all the functions and Links of this menu on the community form
To the right of the user account button is the
collection pick list. This pick list allows you to choose
the current collection.
When new collection is selected in that list the page will
refresh bring you to the other collection in that database.
And now we’re in the fish collection.
notifications exist beneath the user button
These are created anytime there is data being exported from something like
a query or an app resource.
Now you can see the simple search to the right of the notifications. These
are searches that are configured to search data fields that
are indexed by default and specified databases.
The purpose of simple searches to eliminate the need to create a structured field
by field query for relatively simple and commonly executed searches.
Simple search to be configured to show results from index fields and other tables or related
searches. For example a search for
an agent name can display the name and the agent table as well as all
determinations owned by that agent in the determination table.
We’ll be learning about collection objects the data associated with them and
understanding the basics of the collection object form.
Let’s start at the beginning with what a collection object is.
we talk about a collection object as either a specimen or a lot
depending on which kind of collection you have.
In most collections a collection object is a single specimen.
For example a single mammal bird or insect would
be considered a collection object.
Some such as fish collections capture multiple fish
in a single collection object that they call a lot.
Collection objects are most often identified by a unique catalog number.
These are assigned each individual collection object.
So now we’re going to go into what is a collection object and
what data is associated with it, and I’m going to try to make it so you
can understand and open a collection object form and
see the data.
So let’s look at the structure of a collection object.
Due to the relational structure of a database a collection object is made
up of a collection of fields that connect each record to another
table containing related information.
The information that can displays on the form is often being pulled from
other tables in the database that have a relationship with the collection object record.
And its simplest form it is made up by a determination our species
name that is associated with your collection object from a taxonomic Authority
that you have entered into your collection.
The database is a taxon tree that contains all taxonomic records
within the database.
Determinations table can reference attacks on record and Associate
Which would then be present and related to The Collection object record itself?
A determination means that somebody has looked at a specimen and
said it is this particular species so you can record that person’s
name and the date that that particular determination was made.
There’s a one too many relationship from collection object to
determinations. So you can keep a determination history for the specimen in
your collection. If someone determines the specimen is one tax
on but later the record is redetermined. This data will be preserved.
The current determination will appear on the form and in
the history will be sorted in order from the most recent determined date to the oldest.
preparations describe the physical status of a specimen and its storage
specify provides an extensive array of utilities for curatorial management
of species preparations
and Fishes you often have wet specimens dry skeletal
specimens cleared and stained specimens and all of
those specimens are associated with a single lot or a single collection object
and that would maintain the same catalog number.
There can be as many preparations entered as necessary for that
Next there is the collective event table relationship.
Collected event is a place and time that a collection is made as well
as the collectors involved.
This has relationship field that extends to the locality table which
includes the name of the location where species was collected
This data often includes the latitude and longitude coordinates elevation data
uncertainty and measuring units.
Some taxonomic disciplines are collectors may use locality name instead
of a field number to associate a collecting event with a specimen.
From the locality table. There is a relationship to the geography
tree. This includes all geography ranks desired
typically including country state county or Province
Township or other regions of desired.
To reiterate the geography data is connected
to the collection object through two relationships first through
collecting event and then locality.
The relational database structure is advantageous so that you can reuse the
same locality for future collecting event records. And so
that multiple events can share the same locality.
Next we have the collection object catalogger which access
relationship to the agent table which contains the information about
the people groups and organizations in the database.
Some other roles for an agent besides catalog are include collector determiner
prepare donor issuer of
permits and so on and so forth.
Having agent data be entered only once eliminates unnecessary
duplication and allows agent data modification to be
reflected everywhere all at once.
Finally for this example. We have the collection object
Which may include any additional attributes for the specimen or
This table often contains additional texts number and relationship fields
that can be customized to fit your collection of desired specifications and
This commonly includes life stage sex weight length
Once we view a collection object record and specify you will see
that the record is an amalgamation of the specimen record itself and these
Now as an example, we have a collection object here that has a catalog number
A collecting event that occurred on the 15th of April in 2005.
Locality that Kansas South Wind Nature Preserve and
the geography which is Lawrence, Kansas United States. This is
a series of relationships that go from The Collection object table
to the collecting event table the locality table and
finally geography table.
Denormalized data is going to be just like your typical spreadsheet where every
single item and each field is unique from each other.
So you have 96290 the specimens collection
object number go into the collecting event on
the 23rd of September 2004. The locality is
the Fitch Natural History reservation.
You can see that the specimen with the number nine six five nine
zero has the same locality.
However, these two records are independent from each other. So any changes
would not be reflected on the other.
With normalized data data is going to be shared through relationships.
So in this instance
both the specimen number 96290 and 96590
have separate collecting events, but those collecting events are referencing
the same locality.
We can see the specimens with a number 96475 and 96476
both the referencing the
same collecting event and the Kansas Southwind Nature
Preserve as their locality.
Specimen nine six four seven eight has the
collecting event of the 19th of April 2005 and its
referencing the Kansas Southwind Nature Preserve.
If any changes are made to the details in the
locality table of the kansas-southwind Nature Preserve.
Both the collecting event on the 15th of April 2005 and the 19th of
April 2005 will receive those updates
because they are pointing to the same record in the
You can configure your database to have shared collecting events such as
these where multiple specimen with different catalog numbers
can point to the same collecting event record.
Or you can configure them to be embedded so that
every collecting event is specific to that specimen record.
So even if they have similar characteristics, they are pointing
to a locality. That’s the same but the
collecting events are independent.
You can see here the scoping and visibility of each table.
So you can see that at the institution level. The storage tree is
shared between everyone agents or shared at each division the
locality geography lithostrat and chronostrat are
share at the discipline level at the collection level prep
type and pick lists or shared and that collection object
level determinations and preparations.
This will give the best indication of how data is shared in
You can see the data that shared at the institution level which is all of
those tables at the division level the discipline level
collection and Institution.
Now that we’re viewing the collection object form we can see which Fields we’ve
made visible from this table.
We have the catalog number.
the previous and Exchange number
the catalog date and year
And then many linkages to other tables within the database.
You can see that there can be many determinations added by clicking
on the plus or minus to the right of the subview heading.
You can even see the relationship to the tax entry by clicking the
pencil to the right of the taxon field here
with the query combo box functions.
And you can see the details about that taxon node
in the taxon tree.
Relationships can be viewed as a subview.
Like the determinations is being displayed as here or as
a query combo box.
Such as the succession one here.
where this allows you to search
from the list of
items within that table. So if I want to attach the
accession number 5048 to this
form, I can quickly search it using this query combo
box and click on the pencil to view more about that specific
if I want to associate a new determination
With a node that I know exists within our tax
I can use the query combo box to find that record
and make an association.
using the relationship from The Collection object form
to the determinations table to the tax on table.
You can see that the sub views like the subview for Preparation can be
displayed as a grid.
or in a form View
By default the preparations is shown as a grid here
where you see that you can add records to it where
you can fill in information and collapse it and then view
the sub View and all of its records as a grid.
The appearance and behavior of these forms can be customized entirely based
on your collections preferences and applied to the entire institution a
group of users or a single one based
on your requirements.
Other table relationships are presented as buttons.
such as the collection object attachments
DNA sequence samples and collection
some Fields act as links to external websites opining the
value of the field to the end of an external URL.
The bottom of this form displays even the agent who last modified
the date edited
and it even contains a regular text field added in
the form definition.
Now that you’ve seen a basic example of the collection object record. There are
many more tables within specify with more Fields relationships capabilities
and features that I have not yet introduced.
You can follow along on this video series as we continue into the many
other functions within specify.
Please let us know if you have any questions members can
send any support inquiries to email@example.com.