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Last Saved: 2016-02-10
Welcome to SESTO - a Nordic Gene Bank documentation system ................................... 2
Introduction ......................................................................................................................... 2
SESTO menus ................................................................................................................. 2
Entry levels with seed store data ................................................................................. 2
Into the material: ................................................................................................................. 3
GENUS ........................................................................................................................... 3
TAXON........................................................................................................................... 3
CULTIVAR .................................................................................................................... 3
ACCESSION .................................................................................................................. 4
COLLECTIONS / DATASET ........................................................................................ 4
LIST Views ..................................................................................................................... 4
DETAIL views ................................................................................................................ 5
Cases in SESTO .................................................................................................................. 6
Search PGR information ................................................................................................. 6
Quick search................................................................................................................ 6
Quick search – google type ......................................................................................... 6
Quick search – Accession number .............................................................................. 7
Log in cases in seed store material ..................................................................................... 7
Edit and add data ............................................................................................................. 7
Add a taxon ..................................................................................................................... 7
Add cultivar .................................................................................................................... 9
Add an accession............................................................................................................. 9
Add a batch ................................................................................................................... 10
Add a batch to storage................................................................................................... 11
Add germination test ..................................................................................................... 12
Calculate seed amount .................................................................................................. 13
Material that is vegetatively Propagated ........................................................................... 13
Define storage cases and types ..................................................................................... 14
Add Collecting site ........................................................................................................... 15
References ......................................................................................................................... 16
Projects .......................................................................................................................... 16
Trait (C&E) Evaluation................................................................................................. 16
Picture ........................................................................................................................... 17
Library........................................................................................................................... 17
Transactions .................................................................................................................. 17
(Regeneration)............................................................................................................... 18
Contacts......................................................................................................................... 19
Correspondence............................................................................................................. 19
Utilities.............................................................................................................................. 19
Report Tool ................................................................................................................... 19
Label printer .................................................................................................................. 19
Admin ........................................................................................................................... 19
Welcome to SESTO - a Nordic Gene Bank
documentation system
SESTO is a gene bank data management tool, developed by the Nordic Gene Bank
(NGB), (since 2008 NordGen, Nordic Genetic Resource Center) with the purpose to
document the genetic variation in Nordic material from plant species used in agriculture
and horticulture. The stored material as well as the information about stored and
conserved material should be accessible to researchers, breeders and to the general
public.
This manual will describe the structure and briefly go through the most important
features of the documentation system. Access to the protected features require password
which is limited to staff at the genebank. See chapter “Log in cases”.
This manual is mainly written for Nordic circumstances. However, SESTO has been
implemented in other gene banks worldwide and adapted and adjusted to suit each gene
banks specific needs. Some of the descriptions in this manual may not be applicable to all
gene banks that run SESTO. Colours and design may also differ to this manual.
Introduction
The SESTO documentation system contains plant genetic information and related
information. SESTO is organized to list the material, to get an overview and with the
possibility to present the material in detailed levels.
SESTO menus
With SESTO follows other features, with a short explanation and introduction, such as:
 A Characterization and Evaluation module (not yet final developed)
 References: a picture archive, project archive, possibilities to search in the
library database
 Utilities: a Report tool for compiling datasets etc.
 User manual: guidelines and tutorials
 Links: to other SESTO scope, useful links and related topics
Entry levels with seed store data


Genus: A list with genus names belonging to a family preserved at the gene bank.
Genus is the taxonomic rank above the systematic nomenclatures of species
Taxon: A list with species preserved at the Nordic Gene Bank
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Cultivar: A list with cultivars, e.g traditional cultivars or landraces
Accession: This is the list with the actual seed samples conserved by the
genebank
Dataset: A list with thematic sub collections with germplasm conserved by the
genebank.
A quick search
Into the material:
One central idea of SESTO is to browse the information instead of using the classical
search filter that sometimes results in “no hits”. Select [genus], [taxon] [cultivar] [accession]
[dataset] in the menu above to start. Here follows an explanation and a description where
in the SESTO structure it can be found.
GENUS
Genus (plural genera) is a rank in a taxonomic classification between family and species.
In the nomenclature used worldwide, the name of an organism is composed of two parts:
its genus name (always capitalized) and a species modifier. An example is Allium
porrum, the name for the leek species which belongs to the genus Allium.
Click the Genus button and all genera are listed in descending alphabetic order and report
which family every genus belongs to. It is also marked how many taxons this genus has.
The letter bar allows you to browse amongst genus names in alphabetical order. To take a
closer look into the material, click the [select] text or the Genus name. This will show
you information on the specific genus. From here you can go further and find information
about Genus details, all taxons that belong to the genus, accessions, collecting sites and
images (if any).
TAXON
A taxon (plural taxa), or taxonomic unit, is a grouping of species recognized as distinct
by a taxonomist. It will usually be assigned a name and rank and can be placed at a
particular level in a hierarchy.
Click the Taxon button. The features are similar to the Genus hierarchy. The scientific
names appear in alphabetic order with the crop name, which working group it belongs to
and how many cultivars and accessions it has. To se more details click the [select] option
or the specific name of the taxon.
CULTIVAR
A cultivar is a cultivated variety. For this, it must be distinct from other cultivars and it
must be possible to propagate it reliably, in the manner prescribed for that particular
cultivar. (The word cultivar is a portmanteau coined from "cultivated" and "variety" but
is not interchangeable with the botanical rank of variety, nor with the legal term "plant
variety".) Cultivars are identified by uniquely distinguishing names. In botanical
nomenclature, variety is a rank below that of species: As such, it gets a ternary name (a
name in three parts).
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When clicking the Cultivar button, all cultivars appear in an alphabetic list, with cultivar
type, breeder country, year of release, which taxon it belongs to and how many
accessions the gene bank stores. The [select] option gives more detailed information.
CulTyp stands for cultivation code and correspond to “SAMPSTAT” (biological status of
accession in EURISCO’s Multi Crop Passport Descriptors, MCPD). The different types
of cultivars are as follows:



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
CV – Advanced cultivar
L – Traditional Cultivar, Landrace
LP – Primitive local material
B – Breeding, research material, genetic stock
P – Pending, unknown cultivar type
W – Wild population, weedy
The list can be sorted in different ways by clicking the preferred selection.
ACCESSION
An accession is a distinct sample (can e.g. be seed material from a variety, breeding line,
landrace or seed material collected from a specific wild population) in the collections of
the gene bank. The sample is given a separate and unique number when it is accessioned
into the collections. The accessions are listed with accession number, which are a unique
catalogue number assigned to the seed (or clone) sample, accession name and country of
origin and taxon.
The accession button lists all accessions. When clicking an accession in the list,
information on taxon level (if relevant also the cultivar level) and accession level is
presented. Beneath the accession level there are submenus with more information about
Accession details, Stored material, Collecting site, Evaluation, Transaction, Regeneration
and Images.
COLLECTIONS / DATASET
The germplasm is divided into thematic sub collections and special collections. The
special collections are of high value and of international interest from researchers and
breeders worldwide.
LIST Views
When listing the material there is some features that are in common for each level no
matter if it’s listing genus, taxons, cultivars or accessions.
In a 'list' view you will find a letter bar above the listed entries. The letter bar
provide a 'quick jump' to filter the listed entries by the selected letter. Clicking
'Z' will result in a list of the values beginning with 'Z'. You may click again to
limit the listed entry to the corresponding first two letters and so on...
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The field names in a list are clickable. Clicking a field name will sort the list by
this column. Clicking the same field name again will order the list in reversed
order (Z-A). A small arrow indicates the field name the list is sorted by. The
arrow will point down for an ordinary sort and up for a reversed sort. You will
also notice that the 'quick jump' letterbar reflecting the selected column.
The list will only show 25 entries at a time. You may 'walk' in these
entries by using the 'Next 25' and 'Previous 25' at the bottom of the list.
You may wish to see the full list without the limitation of
25 items at a time. This is done by clicking the number
indicating the total hits.
DETAIL views
The SESTO documentation system is presenting its seed store data in divided levels,
according to which level you have selected. When, for example an accession is chosen,
the different levels are presented. Beneath is an example of Allium porrum with its
information on taxon, cultivar and accession levels. (To see all the detailed information,
you have to be logged in.)
Taxon level
With summary
data
Cultivar
level
Accession level
Shows storage data for this specific
accession
Accession subunits listed
(Here: Stored
material)
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This is an example of browsing and drilling down to some specific and detailed
information about the material. See also Search PGR information below.
Cases in SESTO
The Sesto documentation system has a wide variety of search options and data structures
to be examined. Here follows a description list or different scenarios or SESTO cases.
Search PGR information
You can browse through the material if you are familiar with the nomenclature (I.e. If
you know the Genus, Taxon, Cultivar you can choose your way to which level you want
to examine.) If you for instance, are interested in all the Allium taxons, click on Genus
level, and you will have a list with the Scientific names, which Crop name and to which
Working Group it belongs to. You can, if you have this option, choose in which language
it will be listed in and you can also se how many cultivars there are within the taxon and
how many accessions. If you are especially interested in Allium porrum, click it and you
will have information on taxon level and all the accessions listed. You can select and list
the cultivars of Allium porrum and select which cultivar you are interested in. Select for
instance CONORA, and you will se the accessions of this stored cultivar. (At this
moment two)
Quick search
The very simple search function in the menu to the top right of the page
is only providing a 'quick jump' into the information.
Clicking the search 'button' will result in a pop-up search window. In the first pulldown
menu (to the left) you select a property (database field). The middle pulldown menu
specifies the search operator. Selecting equals mean your search pattern must exactly
match the value in the database. E.g. when searching an accession name CAMILLA
using the operator equals will only hit accessions with this name. If you try to search for
accession name contains MILLA, will result in hits for both CAMILLA and
ILGERMILLA II. The operators less than and more than can be used for text fields as
well as numbers.
Quick search – google type
With the simple search form in the first sesto page you can either do a numeric search for
accessions, or cultivars or searching for names in taxon, cultivar and accession levels.
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The result will be presented in the same site with a link from the search
hits that list the material.
Quick search – Accession number
When the material is in list view and if you know the accession number
you can search for it and directly retrieve information about the certain
accession. The search box is to be found at the bottom of the listed
material.
Log in cases in seed store material
The SESTO information system has a variety of features that are valuable to use if you
want to take advantage of the entire documentation system. Your administrator will then
provide you with a log in password. You log in by clicking the [Login staff version] link
at the bottom at every SESTO –site. If you are logged in and have the right permissions
you have the authorization to add and edit much of the seed store material
Edit and add data
When seed store data is listed, and presented in the different hierarchic taxonomic levels
you will encounter [edit] –links where you can edit the material. This is also the case
when you add data.
Add a taxon
To add a new taxon into the genebank, use the drop down menu by clicking add:[mandate
taxon]. You will find this link under ‘Taxons’ or under a chosen Genus. The
documentation of taxons (often species) is divided into two entities; backbone and
mandate taxons. Backbone taxon is containing a list of taxons from which the mandate
taxon is containing the specific taxon for your gene bank. When editing the backbone
taxon you change the attributes for the taxon and when you edit the mandate taxon you
change the characteristics for the species in your gene bank.
If the taxon is not yet among the ‘mandate taxons’,
you have to add the taxon by filling in information
about the taxon in the pop up window by clicking the
link add:[backbone taxon]. NB! When adding a new
taxon, be careful and use strictly approved and
accepted sources for nomenclature and names. (E.g.
http://www.itis.gov/, http://www.ars-grin.gov/cgi-
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bin/npgs/html/taxgenform.pl, http://mansfeld.ipkgatersleben.de/pls/htmldb_pgrc/f?p=185 )
See first if the taxon you want to add is in the taxonlist in the taxon library (backbone),
by clicking the drop down list. To add the new taxon, click submit.
This pop up window is used to edit
and add data about the taxon that are
gene bank specific. Here you can
document to which working group
the taxon belongs to and the
thousand grain weight (which will be
used in other calculations) and the
minimum germination percent it can
reach before you have to propagate
new seeds.
This is where you add and edit the
superior data about the taxon.
Under Taxon name, write the whole
name with Genus, species and if
applicable, subspecies.
Use the drop down list to document
Family name and Genus name. If they
don’t appear in the list, ask your
database administrator to add them in
the database.
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Add cultivar
In the cultivar level you have these options: edit [cultivar] (the main table), [advanced
cultivar] (or type of cultivar), [synonyms] (if the cultivar is known under other names or
has synonyms), and [mandate] (in which country the cultivar is a mandate). There are
also other examples of editing and add complementary data to the documented material.
(E g [other designations], add [image], add [reference], add [breeder] etc).
Add an accession
To add an accession into the documentation system you have to be at the taxon ( or
cultivar) level. First select the taxon of the accession, then click the add: [accession] to
the right of the T a x o n –line. This brings up a form:
Name of person who
identified the taxon
Which mandate the
accession has, for
example ACC if
accepted
For example “winter”
Fill in all data about the accession you have and click the submit button. Some of the
fields are mandatory and you will be asked to fill them in if you try to submit the form.
The different conservation responsibilities for accession mandate are:
 ACC – accepted for long term storage
 TEM – temporary, accepted for short term storage
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
PEN – pending, new and unverified material
REJ – rejected material
LST – the accession is lost or not viable
The new accession will display under the taxon it belongs to:
To change or add more information about the accession click [edit]
The procedure of adding an accession to a cultivar is the same.
Add a batch
When an accession is defined, you can enter data about the seed sample you have of the
accession. This is done by creating a “batch”. Batches are different seed samples of the
same accession. Click the add: [batch] link to the right in the accession level.
The batch number is suggested automatically. You usually don’t need to change it. (Do
not set it to zero). Batches are separated by different harvest years, pollen sources or by
selective influences. This means that seeds harvested from the same mother plants, but in
different years, will not belong to the same batch. Generation is the chronological order
with parents, offspring and siblings arranged in a linear fashion.
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The pedigree number tells which batch has been used for regeneration. The purpose is to
show whether the same batch has been used for more than one regeneration. Pedigree
number 2 is regenerated from number batch 2.
The figure below is an example of how the designations should be used:
AccNum.1 (1992)
generation 1
AccNum.2 (1992)
generation 2
pedigree 1
AccNum.4 (1996)
generation 3
pedigree 2
AccNum.3 (1994)
generation 2
pedigree 1
Figure: an imagined example of a regeneration story. It exemplifies the meaning of batch
number, pedigree, and generation number. Year of harvest is within parentheses.
AccNum is the same for all cases
Donor institutes and Donor persons have to be registered in the “contacts” section and
given the role as donor. Submit the form when you have filled in all data you have.
The batch will appear under the submenu Stored material:
Add a batch to storage
What you have done so far is only to define a batch – to register a seed sample. Now you
need to register where the seed sample is stored (in what collection), the amount of seeds
and how they are distributed in bags. Start by selecting in which collection (active, base
or safety) the batch will be stored, by clicking the relevant link. In this example we add
the batch to the active collection. Click
Add: [add batch to activ]
A new popup windows appears. Here we
have selected batch number 2 and a storage
date. The number of distribution bags is 4,
each of them containing 100 seeds. There
are 2 bulk bags, each of them with a mass of
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500g. All bags are put in freezer with number 1. Inside the freezer the bags are put in
paperbox nr 2.
The batch will now appear in the storage where you assigned it:
Add germination test
The seed material is regularly tested for viability. (That is, germination is only an
indicator of viability. Viability is “power to sprout” not only ability to germinate.) To add
data about germination test, click the Add: [add grm test] link. Enter all data from the test
result and submit data.
The test result will then appear in the seedstore display.
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Calculate seed amount
To get the seed amount calculated, you need to perform a weight measurement of the
accession and enter the result.
When you have submitted your data, you’ll see that the thousand grain weight is added.
Also notice that the seedstore status now is updated and the number of seeds is
calculated. The calculated number of seeds depends on germination and tgw (thousand
grain weight) registered.
Material that is vegetatively Propagated
SESTO is from the beginning a seed storage documentation system, but a need has over
time evolved to safeguard and document vegetatively propagated material, clonal
material. The circumstances and settings of seed and clonal material differ. To separate
the different storage settings you have to ‘tag’ the accession if it is vegetatively
propagated. When you edit the accession you have a box to tick if the accession has
individuals of clones (instead of seeds).
The storage of clonal material will be visible below the Accession-level under menu
‘Clonal material’.
The term ‘batch’ is not applicable for clonal material. The term used is now ‘individual’
of an accession. This term is used in many other databases all over the world. The
individual is the actual tree or plant of the accession.
To edit and add a individual you have to be logged in. To add a new individual click on
the link add:[individual to clonal archive].
The system is keeping track of the sequence of the individuals. An accession plus the
individual will always be unique and thus identify each plant.
An individual can also be ‘a group of’ if several individuals grow together, e.g. onions or
strawberry.
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Every clonal archive can have different
‘Cases’ to define several possibilities of
storage situations. Example of Cases
could be; Field, Greenhouse, In vitro,
Cold room, Hop collection, Fruit and
berry etc…
Each case can have one or more ‘Types’
to be as detailed as you need. A Type is a
more detailed level of information
belonging to a Case. A Type could consist
of a textbox or a predefined selectbox
with values.
If an individual is being moved, you will
be asked to document a reason why the
plant is transferred. The old locality and
the reason are saved in the database for
further information and for traceability of
the places the plant has been growing.
Define storage cases and types
The definitions of Cases and Types are documented once. See link in menu Admin (you
must be a member in group pg_admin)
Define storage data (Cases) for a certain institute.
Name them, order them and document a
description. You can decide as many cases as
applicable. At least one Case must be documented
to be able to choose a institute or a clonal archive in
the edit-individual window.
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Every Case must have at least one Type. Types
could be text boxes or you could administrate a
list of predefined values in a selectbox.
When adding a Type or editing a Type to a
Case, select the Case and then click edit: type
[nr].
Name the label (the name that will show in the
website), a description and in which order it will
appear. Type of info is either a textbox (t) or a
drop down list (s).
The name and the value in a select list should
preferably be the same.
Add Collecting site
The link Collecting site is one of the menus of the accession sub menus. By clicking it the
site will expand and you have links to [edit collecting data] and [edit collecting site data].
When adding information about the coordinates where the accession was collected, it will
show up as a red mark in the map application. (Notice in which format Latitude and
Longitude will be written in [edit collecting data]).
If the accession has
been collected in the
wild, you have to enter
collection data. Select
the Collecting site
sublevel, and click the
add collecting data link.
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Enter all data about the collection event
and the material and submit the form.
Click the edit collecting site data link to
enter geographical data about the site.
References
The menu References contains different features, depending if you are logged in or not.
The common public user is able to access the menus: Projects, Evaluation, Pictures and
Library.
Projects
This is the activity database with a list of all projects from working groups, the National
Programs and other activities. Click the Project Name to read a more exhaustive
description about it.
Trait (C&E) Evaluation
A new module for characteristics and evaluation is under development and described
essentially on the site.
A list of evaluation projects and a list of methods (descriptors) are presented. This site
also describes a Dynamic Evaluation Data Analyzer which presents Statistical
characteristics, Distribution Graphs etc.
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Picture
In the picture archive you have the opportunity to both search and add images (if you
have the images rights). Click the [add image] and
follow the guidelines. If you are logged in you also
have the possibility to edit the description or image
relation by clicking these links. To make the
picture searchable, please add some Keywords.
You have also the possibility to link a picture to an
entity when editing the material, for instance to a
certain species or to an accession by clicking the
link [Edit] the image relations.
Keywords
and
Copyrights
Library
The Gene Bank has a small library and this form gives you the opportunity to search for a
certain book, a certain article or topic, etc. There is a variety of search options.
Transactions
Under Reference choose Transactions. Transaction contains information about who sent
out seeds, what was sent out, why it was sent out, when and to whom.
When adding a new transaction, sent out or received, it is
automatically given a unique transaction number. With
this transaction number (TraNum) you can search for a
certain transaction and get information, for instance how
many accessions were sent to which person. All
transactions are linked to the person who carried out the
transaction.
Mark if the transaction is sending or
receiving seeds
Click the workgroup (and/or other boxes)
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Every seed transaction contains one or more samples and each sample contains one
accession. After creating a new transaction, search this, click Add samples and fill in
information about which accession number, batch number, weight and distribution bags
the transaction consists of. Every seed sample will get a unique sample number and you
can search after this number to see what has happened with a particular sample or
accession.
If the transaction is sent out for regeneration, tick the box Regen, and fill in data about
project code, institute number, contact person, gene bank handling person and date when
the seeds were sent out. Search the transaction and click the link Add traNum to
regeneration. For every sample that goes to regeneration, click the link Add regeneration
data and fill in the information.
(Regeneration)
(There are three collections: the active, the base and the safety duplicate collection. The
purpose of the base and safety collections is conservation, while the primary purpose of
the active collection is utilization of the germplasm. The documentation system has to
keep track of regenerated material as well as be able to search for detailed information
about a certain project. The reason to regenerate seeds or other germ plasm could be that
the amount of seed is low or that the germination percent is sinking to an unacceptable
level. All material that is ACCEPTED and PENDING should be maintained by
regeneration.
A regeneration project can regenerate seeds from one or many accessions. The
regeneration projects are registered as ‘PRF + country code’ and ‘locality number’. D
stands for Denmark, F Finland, I Iceland, L Lithuania and Latvia, N Norway and S for
Sweden. A list with different projects can be found under menu References, Projects.
When first entering the regeneration site, you will be presented a search form. You have a
variety of options to search. Some examples: the accession number, the project code or
the country of origin. Click the Go -button. Results from this search are presented below
the web form, and the different values that are presented are clickable and linked to more
information.
When adding a new regeneration project, add information about locality (project code
and number), number of seeds and viability, price, currency, source of financing, sowing
year and year for expected return. Useful information can also be: reason for
regeneration, number of plants to be grown, field or glasshouse culture, bulk or single
plant harvest as well as method for isolation. If a regeneration fails (maybe all plants of
an accession die and no seed can be harvested), document this in the database by clicking
the tick box for Failed. If the partner, after all, will not regenerate one or more accession,
the record should be updated and the sample should be removed. Edit this record by
finding the transaction, the valid sample and, the regeneration recNum and click the link
Edit record.
The link [update received samples] is used to accept each individual accession )
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Contacts
Under menu References, Contacts, you can search or add information about persons as
well as about institutions. All persons in contacts are committed to an institute, a task, a
working group, or a seed request etc. To add a person click on link [add person] and fill
in the personal information. If you don’t now the institute of this person, write 0. If the
person is a breeder fill in the tick box ‘Breeder’ and this persons name will show up when
you document information about germplasm that is breeding material. (See pop up
window ‘Edit breeder data for accession’ when clicking the link edit [breeder] on the
accession level). Information if the user is a collector and/or donor will also be used in
other modules, for instance when you edit collecting information and donor information
for an accession.
You have plenty of search options. You can search for all breeders by clicking the box
Breeder and then the Search button. You can also search on names and countries, and you
have the option to search for Persons or Institutes. From here, you also have access to
print address labels (currently only for NordGen settings)
Correspondence
This is to document and hold track of NGB’s correspondence. All correspondence is
linked to a person in Contact.
Utilities
The features under menu Utilities consist of entities that are valuable and useful for gene
bank staff. To have access to some submenus, you have to have the right permissions.
The Report Tool are accessible to everyone that visits SESTO.
Report Tool
This is a report tool for plant genetic resource (PGR) data that allows you to choose what
combination of data you want to search for. The procedure is in three steps and the result
will be presented in a table and a link to MS excel spreadsheet report.
To have additional options to display person names and some seedstore administrate data,
please log in.
Label printer
By using the label printer in the library you can compose your own labels. Under menu
Utilities, choose Label Printer in menu below or further down on website.
If you are in the position to manage the seedstore, click on the [label] –link under sub
menu Stored material for an accession, and you are able to print seed bag labels to
SESTO Seedstore
Admin
Useful only for administrators. The administration web sites contain information about
technical matters and administrative tasks. Here you can find information about the
database model and database nodes hosted from the NGB etc. According to your rights
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you have access to different tasks. (For instance if you have the admin rights you are able
to administrate a password for new SESTO-users)
Supplementary information:
An exhaustive manual about regenerating seeds can be red in the manual “Seed
regeneration at the Nordic Gene Bank”
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