Webinar: Introduction to Specify 7

Transcript (Autogenerated)

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

and formatting

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

within specify.

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

collection data.

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

lithostratigraphy tables.

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

data field.

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

last edited.

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

as well.

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.

and specify

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

the taxoname.

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

collection object.

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

or observed.

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

field needs.

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

of 96290.

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

locality table.

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

the database.

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

object citations

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

the guid

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 support@specifysoftware.org.

Specify 7 Introduction & Demo Database

User Tools Menu


All Specify 7 Topics

Data Entry in Data Forms

Specify 7 Wiki on GitHub