Quick start Manual for SEAD
Overview
The SEAD data entry application is a module based data entry system for environmental
archaeology data. The system is comprised of three major parts; the Site explorer where the
site-sample hierarchy is visible; the metadata component where editing of metadata is possible;
and, finally, the data entry sections. These sections open up as separate components within the
entry system. The SEAD data entry application will be henceforth be referred to by SEAD.
The SEAD data model is based on a three tier exchange system. Firstly, a public database exists
that is readily available through the SEAD data portal online. Secondly, a private database
interacts with the SEAD data entry application and is kept in sync with the public version for
newly accepted data. Thirdly, an upload data holder exists where newly contributed data is
vetted for inconsistencies, errors and data formatting policies exists to reduce the number of
problematic data points in the public database.
The metadata is centred on a three level hierarchy with a site being to top level. Each site can
have any number of sample groups but must have a minimum of one, and finally a sample group
can have as many samples as needed, with a minimum of one. Each of these levels have their
own metadata entry form which will be presented below.
Since the system is based off of a local database and uploading is optional it is encouraged to
click around the interface and explore and create sites, samples and data values as needed.
However, the system have a difficult time to handle erroneous uploads that have passed clearing
house and become part of the public database. Once data have been pushed out to other clients
they have become part of the collective and are very hard to remove. Therefore, care should be
put towards thinking about what to upload. Parts of the SEAD interface will encourage “greedy”
thinking from the SEAD project perspective and will try to upload as much data as possible,
although still voluntarily. Consider the option to delete erroneous values before uploading.
New Site
A site in SEAD refers to a single location excavated or sampled for the purpose of building
environmental pre- and historical data records. A site is sampled and each sample belongs to a
sample group.
Begin to enter information in SEAD by creating a new site.
Figure 1 Start screen of the SEAD data entry application. The left side shows the Site Explorer
component and to the right the Meta data editor for site metadata is visible.
-
Right click on the mouse and choose “New site”
-
Enter the name of the site, ex. “Medåker Raä 176”
The site name is now shown in “Site Explorer” window. To your right you now see a window
called “MetaDataEditor Window”. A site must have a least one location (specifically a country)
associated with it. This is shown in the interface by a reddish border around the box of locations.
In order to be able to save the site this error must be resolved. Add or create a location by
pressing Edit Locations
-
Enter location name in the top box, start with a country, e. g. Sweden. Choose a location
type from the drop down list, in this case “country”, unless it is already selected.
-
Press Add
When entering text in the name field a list will pop up with locations that already exist starting
with the same text. Select one of these if the location fits the site. Generally, when lists pop up
upon text entry always use the predefined value listed, if it fits the context.
Now do the same for the rest of the site information, ex county, parish etc. Try to be as detailed
as possible. If you are insecure which location type to choose, hold the mouse over the type of
interest and more information about it will appear. (A recurrent option throughout the entry
system).
After removing the reddish border on the location box continue with the other fields for
metadata about the site. If you want to be able to upload your data, enter a Site description, a
brief yet detailed introduction to the site.
Add coordinates about the site. Select the entry method from the drop down and enter values.
The fields support paste functionality.
If you have references to add use the Edit References button and either search for an existing
reference or create a new one (See the section for editing bibliography entries).
Do not forget to save once in a while. The snowflake by the name in the Site explorer indicates
that something needs to be saved. Press ctrl+S or use File>Save. If there are errors found for an
item listed in the Site explorer a red exclamation sign is drawn over the icon of the erroneous
item. Select the item and correct the error, otherwise the save cannot be performed.
New sample group
A sample group is a group of samples associated by site and the context (i.e. why the samples
are gathered) and finally, by the sampling method. The philosophy of sample groups and how
samples are grouped are detailed in the full SEAD manual (LINK).
In order to add sample groups right click on the site item in the Site explorer and choose New
Sample Group. Enter a group name (be descriptive, yet succinct) and click OK. A group should
now be displayed beneath the site item in the Site Explorer. If that is not the case, click on the
Figure 2 Meta data entry view for sample group.
‘+’ sign to the left of the site name in the Site explorer. This will expand the sample groups for
that site.
Click on the sample group item in the Site explorer will open the metadata entry form for sample
groups. Select Sampling context and Sampling method to fix the errors displayed (The
sampling methods are explained briefly by hovering the mouse over each selectable item in the
drop down list for the method box).
Here you can also add references the same way as on site level, mainly if there are different
references between sample groups that need to be separated. As a general rule, try to keep the
reference associated with as high a level as possible in the site – sample hierarchy. More
information regarding the sample group can be added through Lithology, Dimensions, Images,
Descriptions and Positions.
Press ctrl + S to make the snowflake go away.
Create new samples
There is a range of different ways to add samples depending on how they are named. Right
click on the sample group item in the Site explorer and choose Create samples.
1. MAL samples follow the pattern AA_BBBB:CCCC. As and Bs denotes a serial number
and the Cs denotes a formatted running number with a fixed width of 4. MAL numbers
are used at the Environmental Archaeology laboratory in Umeå.
2. Dendrochronological samples are numbered in series starting from a specific value. This
method can be used for any samples that use a single numerical value as its name.
3. If you have a large amount of samples with different names in no specific order it is
possible to copy the samples from its source (e.g. an excel sheet) and paste the sample
names into the sample group item either by right clicking on the sample group item and
choose Paste or by pressing ctrl+V.
Edit sample information
By selecting a sample in the Site explorer window the metadata associated with the sample can
be edited. It is also possible to select more than one sample and edit all of the selected ones,
setting the metadata points to the same value. By right-clicking on the sample group item and
choosing the Select all children option all samples within the sample group is selected
automatically.
Figure 3 Data entry for plants and pollen data type. Species metadata is to the left, actual abundance data
is to the right.
Edit the sample metadata (only sample type is mandatory) and save the samples. The samples
for your site is now ready for data entry. Note that sample coordinates has the status of data and
is entered elsewhere.
Some metadata cannot be entered when multiple samples are selected. These will be greyed out
when such selections occur.
Please read the SEAD manual for instructions on how to use the different metadata values. For
instance, dimensions refer to many different types of dimensions for a sample, such as size and
volume.
Add samples to data entry
Data entry is divided into different groups based on type of data. The major groups are species
data, soil chemistry / physical properties, positions (coordinates), dendrochronologica data, and
ceramics data. All groups may not be available in SEAD depending on the installed plugins.
Select the samples that you are going to add data to. Right click and choose Add sample(s) to
entry. Select the appropriate data type and open the data entry sheet by clicking on the menu
option matching your needs. For new data use the “new” version of the menu item. These will
create a new dataset for the specified data type. When returning to a dataset use the other version
of the menu item and a list of editable dataset will be opened for you to select from. This list is
based on the selected samples to avoid unnecessary listings. See also information about datasets
in the SEAD manual (LINK).
For all data entry components, if the text in the bane if the component you are working is bold,
it means the data for that component is not saved.
Position data
Choose a coordinate system from the drop down list and press Add coordinate system. Add
coordinate data for each sample, or copy and paste the coordinate data. For each coordinate
value two different values exists; measurement value (X/North (meas.)) and accuracy value
(X/North (accu.)). Accuracy is not mandatory as some coordinate systems have the accuracy
built into the measurement value. A basic plot displays the coordinates visually for your
convenience.
Plants and pollen
Species data are grouped based on the actual data (abundance value) and metadata for the
specimen. The metadata part contains four different data types: the species of the specimen, the
abundance element of the specimen, the identification level, and modifications.
To add species start entering text into the species column. Species are entered by specifying
genus and species separated by space. The system will start searching for genera starting with
the added text and search results will be more refined the more text is entered. Partial searches
are possible by entering the first couple of characters of the genus name, add a space and enter
the first couple of characters of the species name. Select the species from the list occurring
during searching.
If the species requested cannot be found, use the Species Editor button from the toolbar in the
data entry component. With the Species Editor synonyms can be entered too (see below).
If you have a list of plant names in column separated data source, you can copy paste it into the
Species column. The paste function disregards column boundary on the copied data so species
names can exists in separate columns in the source data. For each species not found SEAD will
prompt for user action, such as creating a new species. For synonyms, create a new species and
attach it to the target species using the Species Editor. Note that if all species are found with a
literal search (i.e. exact match and no uncertainties) the dialog prompting for intervention will
not be displayed and the list will be pasted directly into the data entry sheet. Further editing is
still possible however.
Species Editor
Use the Species Editor, accessible from both the data entry component toolbar and from the
menu Tools, to edit and create species. The species are organized from order level down to
species. Sub-species are represented as pseudo-taxa species with the sub-species name
following the species name. Click around the existing taxa to see how it looks.
From order to genera only the name is editable. For species several items can be edited,
including, but not limited to, authority, associations and ecological information. Try to be as
detailed as possible when adding new species. To add a new species right click on the item in
the taxa tree to the left and use the option New. Then, select the empty, newly created item and
edit the species in the panel to the right. Use Save changes to save the newly created species,
or close the dialog with OK.
Synonyms
Synonyms are handled in a special way in SEAD. A synonyms is considered a species
association, from the synonym to the synonymed taxon. To add a synonym, create the synonym
species at the correct place in the taxa tree and click the Edit speciesAssociation button. Follow
the instructions in the opened dialog. Note that species with different authorities (yet same
species) are considered synonyms and the SEAD root list is considered target for such
associations (i.e. synonymed).
Plant metadata
Along with the specimen species the plant (or insect) part can be specified using the abundance
element column, the types of modifications the specimen have been subjected to, and at what
identification level the specimen is named at.
Abundance element allows you to select which part of the plant, or insect, remains that has
been identified ex, needle, cone scale or straw.
Figure 4 Example view of the Species Editor.
Identification level can be added if some of the samples have an uncertainty, cf. or you just
want to be clear how detailed the identification is.
Modifications are used to specify external affects to the species remain. These include
carbonisation and fragmentation.
For both Identification level and Modifications the whole list of species can be set to the same
types by clicking on the header of the column and selecting the appropriate choices. This will
set the values for each species in the list to the same value.
Abundance values
The abundance data is entered into the right part of the species data entry component. Copypaste is possible across both rows and columns. Make sure that the samples are in the same
order on both the source data and the data entry component. The abundance data type is set in
the dataset dialog accessible form the data entry component toolbar (see below).
Save your species data by clicking File>Save or use ctrl+S. This will pop up a dataset editor if
your data currently have no associated dataset (See dataset editing below).
Soil chemistry
Data for soil chemistry and physical properties for samples are added using the Soil Chemistry
option after selecting the samples from the Site explorer. These data are organised in columns
with samples being the rows.
Select your methods of choice in the curtain cell above the sample names, e.g. Phosphate
degrees, Magnetic Susceptibility and Loss on ignition. If there are any methods that have a
special preparation, e.g. “Heating 550” for MS, select one, or more, columns by clicking on
them and click the Set preparation method button that is activated. Select the preparation
methods used for these columns and close the dialog. All columns with an associated
preparation have now a dark shade column header. Hover the mouse of this header to see a list
of preparation methods for the column.
Copy-paste functionality for each method column work. However, only one method at a time
is pastable.
When everything is done, save. An edit dataset dialog will appear if no dataset have been
created for the data (See dataset editing below).
Figure 5 Dataset editor with name and data type missing
Datasets
In order to save a set of data it must be bound by a dataset object. These are created by clicking
on the Edit Dataset button in each data edit component. It will also appear if no dataset have
been set and the save functionality is invoked. A dataset groups data based on the method of
analysis and the associated samples.
The dataset require a name and a method. The method may be optional if it is set through other
means. SEAD will keep track of this. Give the dataset a useful name and add appropriate
metadata to it. These include data type and, at least one contact, such as data enterer. A dataset
reference can be given if the data are only referenced in one bibliographical item which is not
coupled with any of the samples, except through analysis. For instance, re-evaluating data or
re-doing analyses should be referenced from the dataset. Otherwise attach the reference to the
sample group or site.
It is also possible to add a project to the dataset. A project is a loosely defined set that group
data together from a top down perspective. A project also denotes the type of data and
investigation the data is stemming from. To add a project to a dataset enter the name in the
project entry box. If no match is found a new project is created and the Edit project dialog is
opened.
A dataset can exist in two states. First it is added to the local database by a data entry, this is
the unfinished state. During this state new data and new samples can be attached to the dataset.
When the dataset is considered complete (i.e. no new data or samples should be added) it can
be marked as finished by deselecting the Unfinished dataset option in the edit dataset dialog.
This is a sign that tells the SEAD that the dataset is presumably ready to upload. If a dataset has
been marked finished, yet new data should be added, or some samples have been reanalysed a
new dataset must be created with a link to the finished, re-analysed, dataset. SEAD will create
these tasks for you when added or updating information about a finished dataset. SEAD will
also mark all uploaded datasets as finished when that task is undertaken.
Methods
Central to the SEAD analysis are methods. These define how data is analysed and how it should
be interpreted. SEAD include many methods for different purposes, notable species analysis
and significant soil chemistry /physical property methods, as well as methods use for sample
preparation.
A method is highly specific and new methods should be created if the one used does not fit the
existing ones. Use the menu option Edit methods found under the Tools menu to create a new
method. When describing the method be as specific as possible. The method should be
reproducible by others by just using the method description. Also consider that some methods
have sub-methods that can be created as preparation methods. For example, flotation can be a
preparatory method, since that is used on samples regardless of the following analysis method,
yet carry meaningful information about the results of the analysis method.
Two different methods can, theoretically, have the same name. That is unencouraged however,
and it will be difficult to both separate the two methods within SEAD and to create a new, rather
than edit the existing method.
Note that accepted methods, methods that have passed through the clearing house process
cannot be edited.
Figure 6 Edit methods dialog. All items have been blocked for edit since this is an
accepted method.
Upload data
After completing the data entry for your project you can opt to disseminate the data to the public
SEAD. This is done by uploading the data to a clearing house where professional, domain
knowledgeable, clearing house officers will review the data and communicate any mistakes or
divergences from policy back to the uploading data provider. After acceptance through the
clearing house the datasets will be available to the general public through the SEAD public
database.
By uploading you are part of building the foundation for stronger models and broader research
through the use of SEAD.
SEAD maintenance
The data entry application require some maintenance from time to time. These will generally
be in the form of updates rolled out through the automatic update system. This will be indicated
to the user through a small icon in the lower right hand corner of the application. By clicking
this icon and accepting an update the program will download and install the necessary updates
and, generally, restart. Note that you should save before clicking through the update.
In the event of malfunction (bugs), a page for reporting such anomalies exist. Errors will be
stored in a file called messages.log located in the user space of the application. The user
space
exist
in,
on
windows
$user/AppData/roaming/
.seadapplication/dev/var/log where $user is the user home directory. Attach this
file
to
any
bug
reports
created
on
the
error
reporting
page
(http://snares.idesam.umu.se/sead/bugzilla)