CESP2021-007 “Extending knowledge on biodiversity data quality and publication in the Spanish-speaking
community”

How to use the Latin America and the Caribbean
Regional IPT
Table of Contents
How to use the Latin America and the Caribbean Regional IPT
1. The GBIF Integrated Publishing Toolkit (IPT)1.1. General description
1.2. Registered Users: Managers and Administrators
1.3. Quick walkthrough1.3.1. Home page
1.3.2. Creating and managing resources
1.3.3. Administration
2. The Latin America and the Caribbean IPT (IPT-LAC)
2.1. What is the IPT-LAC
2.2. Using the IPT-LAC: credentials and agreements
2.3. Who can use the IPT-LAC
2.4. Moving data from IPT-LAC to another IPT
2.5. Administrators in the IPT-LAC
2.5.1. Tips for Administrators in the IPT-LAC

1. The GBIF Integrated Publishing Toolkit (IPT)1.1. General description
The GBIF Integrated Publishing Toolkit (IPT) is a free, open source web application thatfacilitates the publication and sharing of biodiversity-related information, such as primary taxon
occurrence data, taxon checklists, sampling event data, and general metadata about data
sources.
This guide is a general overview of the IPT and its usage (see Section Quick
walkthrough). For details about specific IPT functions and management, please see the GBIFIPT User Manual.
1.1.1. Basics
To understand the function of the IPT correctly, it is important to understand thefollowing terms:● Instance: An IPT instance refers to a specific installation of the IPT software on a server.
For example, the IPT-LAC, is an IPT instance.
● Resource: An IPT resource is a specific dataset or checklist that has been prepared or
published on an IPT instance.
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●

●
●
●

Metadata: Within an IPT instance, metadata describes the data contained within any
occurrence set, sampling event, or checklist that has been prepared or published on an
IPT instance. It may also include data that describes the publishing organization andindividuals or groups associated with the collection of or maintenance of the data within
an IPT resource.
Public: A public resource is one that is accessible by the general public.
Private: A private resource is accessible to individuals who have been given thoseaccess rights.
Publisher: The organization, institution, or group to which a data resource belongs. For
example, Biodiversidata, Herbario ACOR, and the Institute of Marine Affairs are
publishing organizations, or publishers.

The IPT can be accessed in two primary ways: as a registered user and as a member ofthe general public. Any individual with the URL to an IPT instance (e.g.,https://cloud.gbif.org/lac/) can view the IPTs public home page (See 1.3.1. Home page below)
and can access all of the resources that have been made public. Registered users will haveaccess to the public home page, as well as any private resources to which they have been
granted access rights. Some registered users may have the ability to manage the function of
the IPT.
1.2. Registered Users: Managers and Administrators
The IPT permits a few types of registered users, including Managers with and without
registration rights, and Administrators. A Manager is an individual who has the ability to view,
edit and delete a specific resource. An individual can become a manager for a specific resource
if they are the creator of the resource or if they have been assigned to that resource by anothermanager or administrator.
To be assigned as a manager to a resource, the individual must first be added to the listof users for that IPT instance by an administrator. Once on the list, any manager oradministrator with access to a resource can select an individual from the drop down menu in
the Resource Managers section on the resource’s Overview page. Once selected, clicking the
Add button will add that individual as a manager. Conversely, an individual can be removed froma resource by clicking the Delete button next to their name in the same section.

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Each resource can have multiple Managers. If a given Manager has registration rights,
that person may also register the resource and update it in the GBIF registry through the IPT.
For details, see the Resource Managers section in the IPT Manual.
An Administrator is a “super manager” who can manage all of the resources (public andprivate) on a given IPT installation, modify the IPT settings (including setting data Cores andExtensions), and configure user and organization accounts and registration. The role of the
Administrators is to enable and facilitate the work of the Managers across the community andto maintain the IPT installation.
1.3. Quick walkthrough1.3.1. Home page
Every IPT installation has the same basic structure, starting with the view of a Home
page, showing all public resources hosted in the given IPT. This page can be accessed byregistered and non-registered users, but not all menus will be available to public users.

1.3.2. Creating and managing resources
When a registered user logs in, a new menu item, Manage Resources, appears as amenu option at the top of the window. The Manage Resources page displays all resources towhich a user has management rights and where new resources can be created. When an
Administrator logs in, an additional menu item for Administration is enabled.

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Creating a new resource involves five basic steps:
1.
2.
3.
4.
5.

providing the source data,
mapping the data to the Darwin Core standard,
providing the metadata,
publishing, andregistration (although this step happens only the first time a resource ispublished).

Once created, the resource overview page will display sections in which the above steps
can be updated as well as options for Auto-publishing, Visibility, Networks, and Resource
Managers.
Details on how to create and modify data resources are described in the section Manage
Resources Menu of the IPT User Manual, and will not be reproduced here.

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The button to complete Step 5, Registration, appears beside the Publish button only
after the first public publication event for a resource. It will remain visible until the resource has
been registered.
To manage existing resources, a manager or administrator can click on the Manage
Resources tab to review the list of resources to which that user has access. When a resource
is selected, the resource overview page is displayed and the user can then select, edit, or update
the necessary data, metadata, or settings.
Remember that for any change to be indexed by GBIF and reflected in the GBIF portal,
the resource must be republished by clicking the Publish button, as shown in Step 4 above(every “Save” button in the IPT only saves changes within the IPT application). Resources canalso be deleted from the resource’s main page using the “Delete” button at the top of theresource’s overview page. Resources can be deleted from the IPT installation only or from boththe IPT and GBIF.org.
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1.3.3. Administration
The Administration tab is visible only to users with administrative rights. These rights
permit users to modify the IPT settings and to configure or add user and organization accounts.
For details about each option, see the Section Administration Menu in the IPT User Manual.

2. The Latin America and the Caribbean IPT (IPT-LAC)
2.1. What is the IPT-LAC
The Latin America and the Caribbean IPT (hereafter IPT-LAC) is an IPT installation
hosted by the GBIF Secretariat. The IPT-LAC was launched in 2021 to support data sharing andhost data resources generated by publishers in the LAC region for whom no other IPT
installation is available. See 2.3. “Who can use the IPT-LAC” to learn which users can use thisresource.
The IPT-LAC is maintained by the GBIF Secretariat with the support of a small group ofadministrators from the LAC community (see 2.5. “Administrators in the IPT-LAC”).
The IPT-LAC works just as any other IPT installation with the same basic functions,requirements and restrictions necessary to publish data resources (see general sections above
about IPT). The application is shared by members from across the LAC community, so
individual users or organizations cannot customize the installation’s appearance (e.g., change
skins).

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2.2. Using the IPT-LAC: credentials and agreements
Every organization that wishes to use the IPT-LAC, or any other IPT installation, mustregister as a Publisher with GBIF. To become a registered GBIF publisher, each organizationmust complete a simple form (https://www.gbif.org/become-a-publisher) and submit it to theappropriate GBIF Participant Node for endorsement. Endorsement is normally granted by the
GBIF Node established in the same country of the organization applying to become a publisher.
When a national node (or a regional node) is not available, then another suitable node may be
assigned by GBIF’s Nodes Steering Group.
Please contact the GBIF Regional Representative for Latin America and the Caribbean
with questions about Node selection and endorsement.
When publishing through the IPT-LAC, all organizations will agree to abide by the Datapublisher agreement, and GBIF’s Terms of Use, which state that all data accessible via the GBIF
network are openly and universally available to all users within the framework of the Data users
agreement, under one of three possible Creative Commons licenses or waivers: CC0, CC-BY, or
CC-BY-NC.

2.3. Who can use the IPT-LAC
The IPT-LAC may be used to publish data resources by any organization in the LAC
region. If a more appropriate IPT instance exists, such as a national node IPT (e.g., Argentina or
SiB Colombia) the organizations may be requested by GBIF or a participant node to use a
specific IPT. Publishing organizations should explore national and regional options before
resorting to IPT-LAC. Please refer to the decision tree below to determine if and where an
appropriate IPT is available.

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2.3.1. Selecting an IPT and Node for Endorsement
Steps for collections/organizations:
1. Check to see if the organization is already registered with GBIF via the GBIF
Registry. If the organization is not registered, continue to Step 2. If theorganization is registered, skip to Step 4.
2. To register the organization, first identify if a national or regional node exists
where the organization is located.
a. If a national or regional node exists, contact the Node Manager forassistance with the registration process. Please review the Voting
Participants, Associate Country Participants and Other Associate
Participants to find a Node in the GBIF Directory.
b. If a national or regional node does not exist, contact the GBIF Regional
Representative for LAC for assistance.
3. Once it has been determined if a Node exists, complete the registration form tobecome a data publisher with GBIF. Please note that the appropriate node may
be selected automatically after the form section for organizational details has
been completed.
a. If no node exists or an alternative node was recommended by the GBIF
Regional Representative or Nodes Steering Group, select thehttps://www.gbif.org/project/CESP2021-007/extending-knowledge-on-biodiversity-data-quality-and-publication-inthe-spanish-speaking-community

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recommended node from the drop down list in the Endorsing nodesection.
b. Complete the remainder of the form and click “Register Organization”.
c. After submission, an email should be sent to the email address provided
in the form notifying the organization that the application was received
and to provide additional instructions and information about theendorsement process. If no communication has been received within 5business days, please contact the GBIF Regional Representative formore assistance.
4. When the endorsement has been approved, or if the organization is alreadyregistered, the organization can move forward with publication to theappropriate IPT instance. If the IPT-LAC is the IPT to be used, please contact the
GBIF Regional Representative for LAC for access and instruction.
Steps for researchers:
Individuals who wish to publish resources through an IPT must be affiliated with anorganization. Currently, GBIF does not publish data resources from unaffiliatedindividuals.
1. If the individual is affiliated with an organization, then the steps for collections
and organizations described above should be followed.
a. If the affiliated organization has been registered, then the researcher canbegin with Step 4 above.
b. If the affiliated organization has not been registered, the researcher
should begin with Step 1 above.
2. It is recommended that researchers contact the Point of Contact (PoC) for
organizations that have been registered with GBIF so that any inquiries sent to
the PoC can be forwarded accordingly.
3. Every publishing organization participating in GBIF has at least one individual
who serves as the primary Point of Contact (PoC) or Administrative Point ofContact. Researchers who plan to publish one or more data resources under theumbrella of an existing publishing organization should notify the PoC, so that
any inquiries received by that individual about the researcher’s publishedresources can be forwarded as needed.
Steps for private sector organizations:
Private sector organizations and collections are encouraged to participate in the GBIF
data-sharing community. Those organizations seeking to publish data should proceedwith the same steps as described for collections and organizations above.
Additional guidance for the private sector is available and recommended.
Please contact the GBIF Regional Representative for Latin America and the Caribbean
with questions about Node selection and endorsement.

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2.4. Moving data from IPT-LAC to another IPT
For some organizations, using IPT-LAC to share data may be a temporary solution, e.g.,while waiting for a national node or IPT to be implemented. Data resources can be migrated
from one IPT instance to another. Using the IPT-LAC does not imply any commitment from theuser or organization to maintain any resources through this IPT for any specific length of time.
If a more appropriate IPT becomes available at a future date, resources can be moved from
IPT-LAC to that IPT. Conversely, if an existing IPT is removed or ceases to be maintained,
resources can be moved from that IPT to the IPT-LAC.
The process to move a resource is simple, but careful attention should be paid to thedetails. When possible an administrator for each IPT involved (in some cases the proper
administrator may be the Node Manager, for IPT LAC any administrator can be notified) should
be notified and engaged in the process to avoid any unnecessary duplication or confusion. The
general steps are as follows:
1. A copy of the data resource, specifically the Darwin Core Archive (DwC-A),
should be downloaded from the IPT from which the resources will be removed,
henceforth referred to as the “old” IPT. This can be done from the Published
Versions section in the Overview Page for the resource using the DwC-A
download button.

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2. Next, the Node Manager or other IPT administrator for the new IPT will need to
add the publishing organization to the new IPT.
a. This is done by clicking the Organizations section under the
Administration menu tab.
b. This process will require the organization’s password, or IPT key, which
was issued when the organization was endorsed as a publisher. If thepassword has been lost, it can be retrieved through the GBIF Registry or
by contacting the GBIF Helpdesk.

3. A new resource will need to be created on the new IPT under the Manage
Resources tab. Instead of giving this resource a new short name, the option to“Import from an archived resource” should be selected and the DwC-A file thatwas downloaded from the old IPT should be selected. When the new resource
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is created it will upload the entire DwC-A, including data files, mappings, and theentire version history of the resource into the new IPT. Any core types andextensions used on the old IPT for this resource must be installed and active on
the IPT for this import to be successful.

4. Once the resource is up on the new IPT, it should be inspected to confirm that
all of the data files, mappings and metadata have been imported correctly. In
particular, the Alternative Identifiers should be updated as needed in the
Additional Metadata section of the resource metadata.

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5. After everything has been uploaded and confirmed, the new resource needs tobe published. The resource on the old IPT should be deleted or made private sothat it is no longer accessible by GBIF or the public.

6. Finally, the GBIF Helpdesk should be notified that these changes have takenplace. They will confirm the process or notify the node managers or publisher if
any additional steps need to be taken.
It is recommended that after a transition from one IPT to another, the resource manager should
check the GBIF Registry to confirm that everything has been updated.

2.5. Administrators in the IPT-LAC
As mentioned in the general description of the IPT, an Administrator is a “supermanager” whose role is to enable and facilitate the work of the Managers across thecommunity, and to maintain the IPT installation. Anyone who wishes to help the LAC
community may propose her/himself as an Administrator of the IPT-LAC. Preferably an
Administrator will have a solid understanding of the data mobilization process, including data
capture, data management (including data quality and improvement), and data publication. A
strong familiarity with data sharing standards, such as the Darwin Core Standard, and GBIF’s
data mobilization documentation is important so that the Administrator can assist publishers
as well as manage the function of the IPT. Members of the GBIF Data Products and Informatics
teams are available to provide support as needed. Finally, a good Administrator will be able torespond to user requests and troubleshoot basic problems with the IPT in a reasonable
timeframe. To join the IPT-LAC as an Administrator, please contact the GBIF Regional
Representative for LAC.

2.5.1. Tips for Administrators in the IPT-LAC
In general, the IPT is a stable and intuitive tool for data publishing. There may be times
when things do not work as expected. The following are some recommendations foradministrators when the unknown presents itself.
●

If you don’t know, ask

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This simple rule will help administrators avoid unnecessary frustration. If something
unexpected has happened with the IPT or if an administrator simply doesn’t know how to dosomething, the best practice is to ask somebody who knows.
1. The first place to look for answers should be the GBIF IPT User Manual. Many
questions may be answered with this document.
2. Sometimes it is just easier, and more informative, to ask a real person and the
GBIF Helpdesk is run by well-informed real people who will help you to answer
any questions you send to them.
3. Asking other IPT administrators is also a great option. Not only is it a good
networking opportunity, but there is also an excellent chance that anotheradministrator or Node Manager has had to address the same issue at somepoint in time. If none of the other IPT LAC administrators know the answer, it ispossible that someone from SiB Colombia or Argentina or CONABIO Mexico or
VertNet or GBIF.es knows. Do not be afraid to reach out to those Node Managers
or members of the Nodes Steering Group with questions.
●

Something is not working

Sometimes when something doesn’t work as expected with the IPT it is because theinstance of the IPT in use is out of date. A check to see if the IPT is using the most current
version might explain why certain features, functions or outputs are not working as expected.
The GBIF Secretariat has the responsibility to maintain the IPT-LAC and keep it up todate, but if the latest release is more current than the production version in use, an IPT-LAC
Administrator or GBIF Regional Representative can request that the IPT instance be updated. If
an update is applied and the problem persists, ask someone who might provide help using thethree options above (If you don’t know, ask).
●

Keep the IPT Extensions and Cores up-to-date

Administrators have the ability to add, update and remove Core Types and Extensions
within the IPT. Sometimes the cores and extensions are updated, but these updates need to be
applied manually. To check to see if updates are available, Administrators can use theAdministration tab to navigate to the Core Types and Extensions section. This section contains
a list of all of the available cores and extensions.
Installation of a core or extension is simple. Find the core or extension to be installed on
the list and click the green “Install” button. The IPT will complete the installation automatically.
If an error is encountered, contact the GBIF Helpdesk. After installation, a red button to“Remove” the core or extension becomes available.
If an update is available for a core or extension, a new green button will be visible. To
update, simply click the “Update” button and the IPT will complete the process automatically. In
some cases, updating a core or extension may fix errors or unexpected issues within the IPT.
Checking for updates a few times throughout the year is recommended to keep the IPT
up-to-date.

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This graphic demonstrates options to manage extensions. Managing cores is exactly
the same.
●

Learn more

An excellent way to learn more about data publication and the IPT is to participate in a
training workshop when one is offered. GBIF maintains a collection of training and learning
resources that can be reviewed or completed at any time, such as the Biodiversity Data
Mobilization Course. Other opportunities for training and resources can be found on the GBIF
list of Events and in GBIF News releases.
In the LAC Region, the Biodiversity Information for Diversity (BID) Programme is a great
way to learn new skills and meet people from the region.
●

Adding new resource managers

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IPT-LAC administrators may be consulted by individuals or organizations in the region
about publishing data resources in the IPT-LAC. When this occurs, remember these tips:● Make sure the individual or organization wanting to join the IPT-LAC meets thecriteria described in section 2.3. A few reminders:○ If there is no national or regional IPT available in the region, then:.
■ Guide the individual or organization through the registration andpublication processes using IPT-LAC.
■ Seek help from others as needed (see above If you don’t know,ask)○ If there is a national or regional node in the country of the individual’s ororganization’s origin, but no IPT is available, then:■ Make sure the existing node is informed and engaged theconversation at all times.
■ Ideally, there should be a shared understanding between theexisting node and the organization about the use of the IPT-LAC.
If any conflicts arise, seek advice from the Nodes Steering Group.
■ If a more appropriate IPT becomes available (e.g., a new national
IPT) after publication on the IPT-LAC, and if the existing node andpublishing organization agree, help them to move resourcesfrom the IPT-LAC to the new IPT (see section 2.4. Moving datafrom IPT-LAC to another IPT).
● Encourage the individual or organization to read this manual, the IPT Manual,and provide support by answering inquiries, offering technical support andsharing other relevant information. If these tasks are not possible, please engage
another IPT-LAC administrator, region-based node manager, or the Nodes
Steering Group for help.

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