Amazon Basin Biodiversity Information Facility (ABBIF)
Feasibility Study Report
Index
Executive Summary
Introduction
Methodology
Architecture, standards, and protocols
1
3
4
Elements of the Network .................................................................................................................. 5
Data Providers
5
Portal
7
Tools
8
Data archive
8
Standards ......................................................................................................................................... 8
Brazil
9
Bolivia
9
Colombia
9
Ecuador
9
French Guyana
10
Peru
10
Venezuela
10
Communication Infrastructure......................................................................................................... 10
ABBIF and Amazonian countries
13
Analysis based on the ABBIF survey .............................................................................................. 13
Peru
13
Venezuela
14
Bolivia
16
Colombia
16
Ecuador
16
Brazil
17
Strategy for data digitization ........................................................................................................... 19
Strategy for capacity building.......................................................................................................... 20
ABBIF and Non Amazonian countries
21
Evaluation ...................................................................................................................................... 21
Argentina
21
1
Museo Argentino de Ciencias Naturales Bernardino Rivadavia (MACN), Herbario Nacional de
Plantas Celulares
21
Museo de La Plata, División Zoología Invertebrados - MLP
21
Austria
22
Belgium
22
Bulgaria
23
Denmark
23
Estonia
24
France
24
Germany
25
Latvia
26
Netherlands
27
Poland
27
Portugal
27
Spain
28
Sweden
28
Switzerland
30
UK
31
USA
32
Analysis and Recommendations .................................................................................................... 35
Digitization and Collaborative Research Programs ......................................................................... 36
Natural History Museum Vienna, Dept. of Botany (W)
37
National Botanic Garden of Belgium, Dept. Spermatophyta-Pteridophyta and Dept. BryophytaThallophyta, Herbarium BR
37
Museúm National d'Histoire Naturelle, Herbier Unité taxonomie et Collection - Dept Systematique
et Evolution
37
Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, herbarium
Berolinense
37
Botanische Staatssammlung München, Dept. Vascular Plants
37
Royal Botanic Gardens, Kew, Herbarium
38
Harvard University, Museum of Comparative Zoology (MCZ)
38
New York Botanical Garden
38
Seed Money Program..................................................................................................................... 38
Thematic Information Systems ....................................................................................................... 38
Proposed Overall Budget (in US$ 1,000)
39
Final Comments
39
2
Executive Summary
The Centro de Referência em Informação Ambiental (CRIA) together with the Global Biodiversity
Information Facility (GBIF) conducted a study to determine the feasibility, need and convenience of
establishing an Amazon Basin Biodiversity Information Facility (ABBIF). As biodiversity data is a
critical resource for scientific and conservation purposes including better decision-making, ABBIF aims
at making available -freely and openly- non sensitive Amazonian biodiversity data via the internet.
The ABBIF feasibility study aimed at identifying the size, location, and availability of Amazonian data,
the existence of infrastructure, staff and the availability of resources. It also appraised the interest and
willingness of participation and sharing biodiversity data of different data providers within and outside
the region. In addition, this study also wanted to assess if an initiative like ABBIF was considered
important and/or needed and beneficial for the Amazon region and its institutions.
Based on an inclusive and participatory process that included: an on-line survey, 600 questionnaires
sent, direct interviews, a regional workshop with Amazonian scientists and consultation with
representatives from northern-based large Natural History institutions, the following results and reports
have been produced:
1) Proposal for digitization of biological collections: http://www.cria.org.br/abbif/docs/digit.doc
2) Report on data sharing and repatriation of biodiversity information: Setting-up a collaboration
program with collections from non-Amazonian Countries:
http://www.cria.org.br/abbif/docs/repatriation.doc
3) Proposal on architecture: http://www.cria.org.br/abbif/docs/Architecture.doc
This study concluded that there is a strong support and endorsement from the scientific community
from the Amazon region to promote and establish an initiative like ABBIF
(http://www.cria.org.br/eventos/abbif/ and share biodiversity data. Furthermore, scientists working in
northern-institutions that hold vast quantities of specimens collected in the Amazon expressed also
their keen interest in collaborating with ABBIF and in promoting activities of data sharing with countries
of origin.
Technology, standards, and protocols for distributed systems are readily available and ABBIF can be
structured following a decentralized and distributed architecture having GBIF as an articulator and
integrator. Siamazonia in Peru and Humboldt Institute in Colombia, both GBIF nodes, and CRIA in
Brazil are prepared to contribute with a distributed architecture. Most northern-based large Natural
History institutions are also serving data to GBIF. It is therefore expected that with appropriate funding,
data systems can be organized and made available very quickly, showing at an early phase the value
and importance of ABBIF.
ABBIF is envisaged as building upon existing expertise and national initiatives and projects. A three
year project is being proposed to the Betty and Gordon Moore Foundation to: (1) fully establish and
make ABBIF operational (2) help catalyze initiatives and (3) establish the basis of a regional and
decentralized network. Yearly evaluations based on clear indicators shall be carried out to help
institutions responsible for maintaining the information systems in Amazonian countries to analyze
their progress and to help promote the exchange of experiences and know-how.
For further information please contact:
Vanderlei Canhos
(vcanhos@cria.org.br)
Dora Canhos
(dora@cria.org.br)
Beatriz Torres
(btorres@gbif.org)
1
Introduction
Biodiversity information is critical to a wide range of scientific, conservational, educational and
governmental uses, and is essential for decision making. Most of the biodiversity information on the
Amazon Basin is neither readily available nor accessible. Access to taxonomic information (scientific
names and synonymic lists) and specimen data (primary data, including geospatial information) is
fundamental to build robust ecological niche models and environmental change scenarios. An initiative
to integrate worldwide distributed species and specimen information on the fauna, flora and microbiota of the Amazon Basin is urgently needed. An action plan must be carried out to digitize and
integrate all relevant information on the region in a structured manner, with the adoption of standards
and protocols that allow transparent data integration and systems interoperability.
Recent developments in the field of biodiversity informatics can directly benefit environmental
education programs, resource management, conservation efforts and biomedical and agricultural
research in the region. However, in order to benefit from the recent developments in information and
communication technologies a shared digital data infrastructure is a fundamental requirement.
Species and specimen data (scientific names and synonyms; localities and collection dates) and
associated environmental information (climatic, geological and geographical data) are the fundamental
building blocks for the comparative spatial analysis, synthesis and visualization of biodiversity
information.
ABBIF’s primary goal is to support the development of a shared data infrastructure associated to a
modeling framework, with a broad and inclusive participation of local stakeholders. This facility will be
developed adopting GBIF recommended standards and protocols and modern approaches of data
capture and management, increasing the value, visibility and usage of available data worldwide
through dynamic networking. The scheme of the proposed infrastructure integrating data, webservices, tools and products is shown in figure 1
DATA
Web Services
Specimen & Species Data
• Herbaria & Museums
• Checklists
Environmental Data
• Name Server
• Locality Server
• Map Server
Tools
• Data Quality
• Modeling
• Climate, soil, etc.
Maps
Standards & Protocols:
• interoperability
• integration
Products:
• Integrated Checklists
• Virtual Collections
• Species Distribution Maps
Figure 1. Biodiversity information infrastructure components
2
Methodology
In order to involve the greatest number of partners possible, the following activities were carried out:
(1) Internet survey. The first step was to carry out an internet-based survey to identify potential
data providers and custodians. Special attention was given to on-line species and specimen
data, with focus on biological collections and species and specimen data custodians. This
information is evidently biased as it is restricted to data and information that is available on-line.
But, as the objective is to develop an internet based information facility in order to quickly prove
its utility and usefulness, it is important that existing initiatives be integrated while non Internet
data providers organize and digitize their data.
(2) Questionnaire. A questionnaire was prepared in consultation with GBIF. Its objective was to
analyze a number of aspects in data providers and custodians such as:

Taxonomic group: plants, animals, microorganisms

Type of data: checklists, specimen data, observation data

Digitization: status, software used

Standards used: data models and protocols

Existing infra-structure: hardware, software, humanware

Internet access

Data and information access policy

Willingness to participate in the project
(3) Survey. The questionnaire was sent out to potential data providers and custodians known to
GBIF and CRIA and to those identified in the Internet survey. A web site1 was developed with
information about the project, inviting all interested players to answer the questionnaire that was
made available on-line. Over 600 emails were sent to 254 institutions from 15 countries. More
then 200 answers were received from 22 countries.
(4) Personal meetings, phone conferences and hired consultant. Personal meetings were held
at the American Museum of Natural History and at the New York Botanical Garden. Phone
conferences were carried out with specialists from the Instituto de Investigación de Recursos
Biológicos Alexander von Humboldt, Colombia, and the Instituto de Investigaciones de la
Amazonía Peruana – IIAP, Peru. A consultant was hired to contact interested parties in
Venezuela.
(5) Studies. Specific studies were carried out on architectures, standards, and protocols used in
different information systems.
(6) Analysis. The questionnaires were received and analyzed and together with the IT studies
were the basis for the production of the following reports:

Proposal for digitization of biological collections2
1
ABBIF website – http://www.cria.org.br/abbif
2
Report: Proposal for digitization of biological collections - http://www.cria.org.br/abbif/docs/digit.doc
3

Proposed Architecture3

Data Sharing and Repatriation of Biodiversity Information: Setting-up a Collaboration
Program with Collections from Non Amazonian Countries4
(7) Dissemination of reports. All reports were made available on the Internet for comments and
suggestions.
(8) Technical meetings. A workshop and a briefing meeting were organized to present and
discuss the reports and the results of the survey

A workshop was held with data providers and custodians of the Amazon region5 in
Campinas in March, 2006. 18 participants from Bolivia, Colombia, Ecuador, Venezuela,
Brazil, and Peru discussed with CRIA and GBIF first whether an information facility for the
Amazon Basin is needed and second, if it is necessary and important, would those
present be willing to collaborate. The answer was unanimous as to the necessity of
structuring an information facility for the region and in the participants’ willingness to
collaborate. A summary of the survey was presented and the architecture was discussed.
Contributions expressed during the workshop and after (sent by email) were included in
the feasibility study.

A meeting was held in Curitiba, Brazil, during COP 8 with 30 participants, mostly from non
Amazonian countries. Here again the survey and architecture were presented and
partnerships were discussed. The idea is to try and make digitization of Amazonian data a
priority for collections held in Europe and North America. Here again, great interest was
shown and worldwide collaboration seems to be feasible if the necessary resources are in
place.
(9) Feasibility study. Based on the surveys, the studies, and the contributions received at the
workshop and technical meeting and through email, a feasibility study report was prepared and
is being submitted to the Gordon and Betty Moore Foundation.
Architecture, standards, and protocols
When designing and implementing the network, it is important to consider the fact that ABBIF should:

promote free and open access to taxonomic information and non-sensitive specimen data;

enable that each data provider or custodian be fully responsible for his/her own data;

enable frequent updating managed by each data provider;

enable data validation;

assure that full attribution to data and information sources are given;
3
Report on the Architecture: http://www.cria.org.br/abbif/docs/Architecture.doc
4
http://www.cria.org.br/abbif/docs/repatriation.doc
5
Workshop: Amazon Basin Information Facility, March 16-17, 2006 (http://www.cria.org.br/eventos/abbif/)
4

aim at strengthening local biological collections and data custodians;

be integrated to existing information systems at local, national, and regional levels; and,

be integrate to GBIF.
The proposed architecture for ABBIF is based on the study of existing systems that are disseminating
species and specimen data through the Internet and on the answers received to the questionnaire by
biological collections and data custodians as to what standards and protocols are being used.
The report on the architecture3 included the following elements:

Centralized, distributed and combined or mixed systems: main characteristics, advantages and
disadvantages.

Standards and protocols: what is available, what is being used or has been adopted by
networks of direct interest to ABBIF and what is the situation of local data providers and
custodians concerning infrastructure and expertise.

Architectures: how data custodians and information systems of direct interest to ABBIF are
being structured
Elements of the Network
The aim is the establishment of a shared data infrastructure open to all interested, where the data
provider has complete control over his/her data.
Data Providers
It is important to determine target data providers for ABBIF’s initial phase. Focus should be given to
specimen and specie data, and the organization of data providers must be country driven, meaning
that the articulation and involvement of different providers will be carried out nationally.
Biological collections, due to the nature of their activities, are information centers. They must have
sufficient infrastructure and expertise to set up their own information system for internal purposes.
Those that also have the necessary infrastructure and expertise to hold an internet information system
available 24 hrs a day can serve their data directly to the network. Those that don’t have or don’t want
to maintain dynamic links should have a mechanism to submit, alter, and delete their data at a
regional server (or cache node).
Figure 2 shows a diagram of the network.
5
ABBIF Portal
Regional Servers
Collections with
dynamic links
Collections mirroring their data in
regional servers
Figure 2. Component data provider: biological collections
Collections with dynamic links and regional servers must adopt compatible standards and protocols
and must be held in institutions capable of maintaining the system and serving data through fast
Internet connections.
Observation data and taxonomic descriptions represent two other groups of data providers,
individuals or research groups. This is the case where facilities must be offered by data custodians
where researchers may deposit their data for full and open access on the internet. This is not a task
for amateurs. There must be a specialized staff that has as its main activity the development and
maintenance of information systems that guarantee the preservation and dissemination of data.
Based on the concept of open and free access to non-sensitive data, this element of the network will
be called digital data commons space6. The network may have more then one server that will
guarantee the necessary infrastructure for preservation, maintenance, recuperation, and
dissemination of the data. Internet connectivity must be stable and fast (figure 3).
6
see National Science Board. Long-Lived Digital Data Collections: Enabling Research and Education in the 21st
Century. NSB-05-40. September, 2005. http://www.nsf.gov/pubs/2005/nsb0540/
6
portal
Internet 2
Data commons space
Observation data
“data commons”
Taxonomic data
“data commons”
Other data
Figure 3. Architecture element: digital data commons space
This element could involve stakeholders from the conservation community with important observation
data that are normally disseminated through books and reports.
Portal
GBIF today has a data index that serves data to the system. A subset of over 96 million records, with
name and locality data is harvested from 174 data providers and maintained at a centralized
database. This makes the basic search system much quicker and solves problems such as slow or
unstable connectivity. After carrying out the basic search the user obtains a list of providers with the
number of records found. Users can then display the list of records corresponding to each provider.
Users can also download the selected records and may choose to do so directly from the data
providers or from the GBIF index (faster), and may also select the format of the downloaded file. There
is also a map illustration of the distribution of the requested records that can be produced dynamically.
CRIA developed a fully distributed system. When a query is processed it is sent out to the providers
that search the databases and dynamically send the results. At the moment, the speciesLink Network
has 6 regional servers (mirroring data from 38 collections) 2 collections with dynamic links, one
centralized database with observation data (at CRIA), and one centralized information system of
microbial collections (with 9 collections). This architecture is interesting for advanced users that can
search any field and retrieve the full data set as a file. Speed and the “fragility” of the network is a
disadvantage. If a server for any reason is off-line, that “branch” of the network will be unavailable.
Maps are also produced dynamically.
CRIA developed an indexing service of a subset of the data which is used for data cleaning. At the
moment CRIA is planning to provide a service to users of searching its index for the data subset to
provide faster results and a more stable system. But the distributed search system will continue to be
offered as it is very powerful and important to advanced users.
7
Tools
Another important activity is the development of tools for data providers and users. These tools should
be preferably developed as web services to be able to be used more freely at all levels (local, country,
and regional).
Data archive
An important element to be addressed in the network design is long term data archiving. This may
also be a task for country data custodians or their partners. It is important that the scientific council
discusses this issue to determine priorities as to what data should be added to a permanent archive
and identify an institution or a pool of institutions responsible for this activity.
Figure 4 below presents a diagram of the system.
Web services
•Maps
•Modeling
•Data cleaning
•automatic
georeferencing
•Other services
portal
regional server
biological collections
data commons
space
data commons
space
observation data
taxonomic data
long term data archive
Figure 4. Diagram of the system
Standards
In order to build a distributed or combined system, basic standards must be used. Of immediate
interest to ABBIF are: DarwinCore; ABCD – Access to Biological Collection Data; DiGIR; BioCASe;
and TAPIR. The report on the proposed architecture offers a brief description of each one. Basically,
the data model and communication protocol DarwinCore/DiGIR has been adopted by information
systems in the Americas and ABCD/BioCASE has been adopted by Europe. Tapir is being developed
to meet the needs of both DiGIR and BioCASE protocols.
8
Information systems of Amazonian countries were analyzed to see whether an interoperable system
could be developed.
Brazil
Brazil has two very important projects underway that are of direct interest to ABBIF: the speciesLink
network7 and PPBio – MCT8, the biodiversity research program of the Ministry of Science and
Technology. The speciesLink network involves 40 collections, one centralized information system of
observation data from São Paulo State (SinBiota9) and one centralized network with 9 microbial
collections (SICol10). The network adopted DarwinCore and DiGIR as data model and protocol. PPBio
of the Ministry of Science and Technology is adopting the speciesLink architecture as a model. Data
from the network could be immediately linked to ABBIF.
Bolivia
Bolivia does not have an on-line information facility in place but the Noel Kempff Mercado is willing to
participate in this effort. Due to slow connectivity, at a first stage perhaps the best solution would be
for Bolivian collections to deposit their non-sensitive data in a regional server with good connectivity.
Capacity should be built in order to address the problems associated with connectivity and biodiversity
informatics.
Colombia
Colombia has a GBIF node established at the Alexander von Humboldt Biological Research Institute,
responsible for the Biodiversity Information System SIB (Sistema de Información sobre
Biodiversidad11). The interface for distributed searches is not available yet.
SIB’s communication protocol was being developed concurrently with DiGIR and is now aiming at
compatibility. The “Standard for exchanging biodiversity information to the organisms’ level Estándar
para intercambiar información sobre biodiversidad al nivel de organismos was built based on the
mandatory elements indicated in Darwin Core V2, and in some data elements proposed in the
Estándar para la documentación de registros biológicos developed by SIB. It seems clear now that in
order to share data with other initiatives it is important to use a common protocol and GBIF
recommended that SIB should use TAPIR that should be ready for testing in the near future.
Meanwhile, in order to integrate SIB in the network it may be necessary to implement some translation
routines from one standard to another, which is not a big problem.
Ecuador
Ecuador does not have an information system, responsible for integrating data from biological
collections, but the herbarium of the Pontificia Universidad Católica del Ecuador (QCA) is in the
process of digitizing its data and is willing to share non-sensitive data through the Internet. This is the
7
http://splink.cria.org.br/
8
http://ppbio.inpa.gov.br/
9
http://sinbiota.cria.org.br/atlas/
10
http://sicol.cria.org.br/cv/
11
http://www.siac.net.co/Home.php
9
case where a regional server could be installed to start the process of sharing biological collection
data in Ecuador. The herbarium would either have to adopt data model standards such as DarwinCore
or some translation routines would have to implemented.
French Guyana
Although French Guiana is an overseas department of France and, consequently, is politically a part
of Europe, it is located in South America, within the Amazon region, and for this reason was included
in the analysis of Amazonian countries. The “Herbier de Guyane (CAY)”, a Center of the Institute de
Recherche pour le Developpment (IRD) in Cayenne adopted the data model RIHA (Réseau
Informatique des Herbiers Africains) that is compatible to ABCD. Biocase is used as a communication
protocol and CAY already serves data through GBIF.
Peru
Peru has developed Siamazonia12, the information system for biological and environmental diversity of
the Peruvian Amazon (Sistema de Información de la Diversidad Biológica y Ambiental de la Amazonía
Peruana). Siamazonia was created in 2001 through the BIODAMAZ project (Proyecto Diversidad
Biológica de la Amazonía Peruana), an agreement between Peru and Finland, and was developed by
the Instituto de Investigaciones de la Amazonía Peruana (IIAP). IIAP is a GBIF node and therefore is a
natural partner of the ABBIF network. Its structure is based on nodes, similar to GBIF. Siamazonia is
already serving data to GBIF using DarwinCore/DiGIR.
Venezuela
Venezuela does not have an information system in place but is beginning to develop an integrated
information system on Collections of Vertebrates (Sistema Integrado de Información de Colecciones
de Vertebrados de Venezuela). There are 3 institutions participating in this initiative: Museo de
Historia Natural La Salle (MHNLS), Museo de Biología de la Universidad Central de Venezuela
(MBUCV), and Museo Estación Biológica Rancho Grande (EBRG). Although the intention is to set up
a web interface for on-line access, the idea is to control access, having different levels of accessibility
according to the user. This restriction, if maintained, will mean that the system will not be
interoperable.
Communication Infrastructure
Another important element to be considered in the design is the existing or potential communication
infrastructure or connectivity. An analysis of research and education networks in Latin America was
carried out to see whether there are any serious constraints that may hinder the full participation of a
node in the network.
Bolivia, Brazil, Colombia, Ecuador, Peru, and Venezuela are all members of RedClara, an association
of Latin American networks that aims at connecting academic networks to stimulate cooperation and
promote scientific and technological development in the region and with European scientific
communities.
5 Amazonian countries are already operating with installed capacity between 10 and 155Mbps. There
is a direct link to Europe of 622 Mbps and to the United States (figure 5).
12
www.siamazonia.org.pe/
10
Figure 5. RedClara: Connections established and planned (April, 2006)
Bolivia is the only Amazonian country where the connections have not been established. Unfortunately
the Guyanas are not members of the network. Table 1 shows the status of connectivity of Amazonian
countries.
11
Table 1. Network Status of Amazonian countries
Capacity
Internal
External
Number
institutions
connected
Country
Network
Status
Brazil
RNP/Ipê
operating 8M - 10G
155M (EU)
1G (USA)
400
Colombia
Renata
planned
10M
43
Peru
RAAP
operating 2M - 10M
45M
7
Ecuador
Cedia
operating 4M - 45M
16M
21
45M
78
34M
34M
Venezuela REACCIUN2 operating 155M
of
-
It is important to stress the fact that even if the country has an operating network this does not
guarantee that the institutions that are important to ABBIF have a good and reliable connectivity.
The conclusion of this study is that all information systems developed by Amazonian countries that
were analyzed are compatible with GBIF, meaning that the development of an Amazon Basin
Biodiversity Information Facility is technically feasible. Some systems are centralized other distributed,
so the architecture must be a combined system (Figure 6).
users
queries
virtual
catalog
HTTP / XML
DiGIR
Portal
HTTP / XML
DiGIR
Provider
DiGIR
Provider
DiGIR
Provider
DiGIR
Provider
Regional
Server
SOAP
Collections (data providers)
Figure 6. Diagram of a combined system
ABBIF should be built upon existing expertise and national initiatives. A three year project is being
proposed to help catalyze initiatives and to establish the basis of the network. Yearly evaluations
based on clear indicators shall be carried out to help institutions responsible for maintaining the
information systems in Amazonian countries to analyze their progress and to help promote the
exchange of experiences and ideas. Three institutions are ready to receive investments and support to
12
carry out this initiative in their countries: Siamazonia, Humboldt, and CRIA. Venezuela is in the
process of structuring a system for vertebrates. In other countries where there isn’t an institution with
capacity and expertise to hold an information system, it is recommended that the collections link
directly to the closest node or, in the case of low or unstable connectivity, to a regional server that will
be established for this purpose.
We recommend a yearly budget of US$ 2 million for the system.
ABBIF and Amazonian countries
This section will focus on the size of the holding, the degree of digitization and the needs of the
collections. The results of the ABBIF survey, sponsored by the Gordon and Betty Moore Foundation,
which aimed at identifying the location and size of the relevant collections within and outside the
region, highlights the size of the universe that needs digitizing, as well as the location and size of
these collections.
The strategy is not only to involve biological collections and offer resources to digitize data, but to
promote a greater integration between the collections and local GBIF nodes or information networks.
Most collections that haven’t digitized their data or are very behind in the process, besides hardware,
software, and humanware, require training in collection management, databases and on internet
connectivity. It is very important to promote local expertise, and GBIF nodes and other local initiatives
have a role to play and should be involved in the process.
Analysis based on the ABBIF survey
All questionnaires from collections from the Amazonian countries were analyzed. Only collections
willing to participate in ABBIF and share their data, even if with some restrictions, were considered.
Institutions that don’t have species or specimen data were not included in this analysis.
Peru
The Instituto de Investigaciones de la Amazonía Peruana is responsible for Siamazonia
(www.siamazonia.org.pe/) and is a GBIF node. They are natural partners to the ABBIF network.
Siamazonia is developing a system to integrate biodiversity data including that of biological
collections. They have 60,000 records on-line 50% of which are georeferenced.
The ABBIF questionnaire was sent to 5 institutions and 15 individuals in Peru and 7 answers were
received. The numbers of questionnaires sent obviously does not include possible downloads from the
internet. The answers from 6 institutions were sent by Siamazonia which already shows the important
role Siamazonia has in the region.
Numbers are as follows:
Collection
Plants Animals total records
Digitized (no. & % Georeferenced (no. &
of total)
% of digitized)
Herbário
MOL-FCF
1
11.428
6.857
130.000
32.500
Herbário
Amazonense 1
22.750
Hérbário
Regional de
Ucayali
1
13
Collection
Plants Animals total records
Digitized (no. & % Georeferenced (no. &
of total)
% of digitized)
Herbário
Herrerensi
1
6.000
3.300
2.640
UNMSM (11
collections)
1
10
1.500.000
200.000
Personal
collection of
leafbeetles
and
their
hostplants
1
1
100.000
5.000
5.000
Total
11
1.747.428
247.657 (14%)
30.390 (12%)
6
Only considering records from the Amazon region one has the following:
total
records
amazon
Collection
PERU
Siamazonia
–
Herbário MOL-FCF
60.000
Digitized
Georeferenced
(no. and % (no. and % of on-line
of total)
digitized)
60.000
30.000
5.000
www.darwintreediversity.org.pe
Herbário
Amazonense
www.siamazonia.org.pe
Hérbário Regional
de Ucayali
Herbário
Herrerensi
UNMSM
collections)
www.siamazonia.org.pe
No
answers
5.000
3.200
400.000
40.000
0 - 2500
(11
Personal collection
of leafbeetles and
their hostplants
5.000
Total (Siamazonia
wasn’t included in
the total)
415.000
100.000
(24%)
www.siamazonia.org.pe
no
30.000 (30%)
Where there was no information the table or cell is blank.
One can see that all collections require resources for digitization of data. This group is also concerned
with digitizing images and making it available on-line. A digitization grant involving Siamazonia could
be very effective.
Venezuela
Questionnaires were sent to 21 institutions and 28 individuals. As there is no local organization
working on an information system to integrate biodiversity data, a local consultant was hired to visit the
collections. 9 answers with information from 4 herbaria and 6 zoological collections were received.
14
Animals
total
records
Digitized (no.
Georeferenced (no.
and % of
and % of digitized)
total)
EBRG
1
61.529
61.529
6.153
MIZA
1
2.500.000
5.289
5.289
Collection
Plants
PORT
1
100.000
7.500
GUYN
1
18.625
18.625
13.037
53.000
53.000
40.000
350.000
113.000
35.000
1
5.399
5.399
5.399
MBUCV
1
14.898
14.898
10.000
ULABG
1
200
0
0
6
3.103.651
279.240 (9%)
114.878 (41%)
Museu
de
BioCentro
Zoologia,
1
VEN
1
MHNLS
1
Total
4
Only considering records from the Amazon region one has the following:
Collection
Digitized
Georeferenced
total
records
(no. and % (no. and % of on-line
amazon
of total)
digitized)
EBRG
7.404
MIZA
500.000
7.404
768
740
no
768
www.mizafpolar.info.ve
PORT
no
GUYN
no
Museu
de
BioCentro
VEN
Zoologia,
10.000
10.000
27.200
27.200
no
no
MHNLS
no
MBUCV
1.628
1.628
1.628
no
ULABG
200
0
0
no
Total
546.432
47.000 (9%)
3.136 (7%)
Venezuela shows a need of resources to digitize data and to develop a system to make biodiversity
data available on the Internet. They are beginning to develop a project that aims at developing an
integrated information system for vertebrate collections.
15
Bolivia
The questionnaire was sent to 14 institutions and 13 individuals. Answers were received from one
herbarium and two zoological collections.
Collection
Plants
USZ
1
Animals
total
records
68.500
MNK-Zoologia
1
92.970
MNKEntomologia
1
500.000
2
661.470
Total
Digitized Georeferenced
1
0
0
There was no information on the percentage of digitized or georeferenced data as they were not able
to organize a meeting with all curators to obtain this information. No site on the Internet that makes
data available was indicated. An interesting aspect mentioned is the necessity of collaboration with
other institutions for identification (entomology). This may be another interesting activity to be funded
by Moore: visits from experts to collections to help identify specimens.
Colombia
Based on the web survey on possible data providers that was carried out in the beginning of the
project, 124 questionnaires were sent out to Colombian institutions and 133 to individuals. At first, only
9 answers were received, but the Alexander von Humboldt Biological Research Institute,
(www.humboldt.org.co/sib), carried out a very good survey on 93 institutions involving 29 herbaria, 60
zoological and 9 microbial collections. These institutions together hold a total of 4.071.632 records,
more then 50% digitized and about 10% of the digitized records georeferenced. Approximately 2% of
the records are from the Amazon region, but this is undoubtedly an important initiative to be
sponsored. As in the case of Peru with Siamazonia, a digitization project should involve the Humboldt
Institute.
Ecuador
The questionnaire was sent to 16 institutions and 23 individuals, based on the Internet survey. Six
answers were received, including 2 collections that have interest in participating in ABBIF.
Collection Plants Animals Checklists total
records
Digitized
Georeferenced (no. total
(no. and and % of digitized)
records
% of total)
amazon
CHEP
1
8,700
5,000
1,500
QCA
1
250,000
30,000
10,000
11,500
10,220
7,200
270,200
45,220
(17%)
7,200 (16%)
QCAZ
Total
1
2
1
0
11,500
(4%)
These collections would require training and support to help digitize and make data available on the
internet.
16
Brazil
Brazil has two important projects underway that are of direct interest to ABBIF: the speciesLink
network (http://splink.cria.org.br/) and PPBio – MCT, the biodiversity research program of the Ministry
of Science and Technology.
The speciesLink network involves 40 collections (table 2), including some very specialized collections
with important holding from the Amazon Basin such as:

the fish collection of the São Paulo State University Museum (MZUSP) that have 36% (26.348)
of their digitized records (72.705) from the Amazon region, 11% (2.891) of which are
georeferenced; and,

Coleção Camargo (RPSP) a bee collection with 68.598 digitized records on-line, 60% of which
are from the Amazon region, but only 3% of these are georeferenced.
Table 2. Number of records available through the speciesLink network
Collections
no. of records
Digitized
% of total Georeferenced % of digitized
Plants (herbaria, algae, wood) 1.431.750
486.987
34,0
191.945
39,4
Zoological collections
2.228.666
377.952
17,0
193.053
51,1
Microbial Collections
8.724
8.724
100,0
0
0,0
Observation Data
88.717
88.717
100,0
88.717
100,0
Total records
3.757.857
962.380
25,6
473.715
49,2
There is a clear need for resources for digitization, especially for large collections that have historical
data and that normally require some interpretation and validation, besides the use of data cleaning
and georeferencing tools.
PPBio in its first phase is concentrating on the Amazon and the semi-arid regions. Partner institutions
include INPA – Instituto Nacional de Pesquisas da Amazônia; MPEG – Museu Paraense Emílio
Goeldi; and INSA-CF – Instituto Nacional do Semi-Árido Celso Furtado. These institutions will have
support from the Brazilian government to digitize and make their data available on-line.
The tables that follow present a summary of the status of the institutions that answered the
questionnaire.
Collection
Plants Animals Micro. total
records
Digitized (no.
and % of total)
Georeferenced (no.
and % of digitized)
DZSJRP - pices
1
7.500
7.500
4.684
UNIR - Fish
1
23.229
23.229
23.229
UNIR - Mammals
(CRM)
1
MEFEIS
1
10.200
1.000
2.751
2.751
191.992
0
5.914
4.666
24.536
17.000
UFRR
1
UFAM Coleção
Zoológica
MIRR
INPA - Peixes
1
1
1
0
17
Collection
Plants Animals Micro. total
records
INPA - CMIM
1
Digitized (no.
and % of total)
7.459
7.459
Georeferenced (no.
and % of digitized)
0
INPA - Mammals
1
4.819
4.819
INPA - invert.
1
303.015
1.022
INPA - Amphi
1
13.500
13.500
6.750
215.000
200.000
86.000
631
631
400
INPA - Herbaria
1
INPA - Aves
1
JBRJ
1
410.000
40.000
SPF - USP
1
145.000
15.000
Herbário MG
1
174.000
165.000
9.298
2.295
593
40.000
5.000
0
Instituto Butantan
- IBSP
1
HRCB
1
7.000
MPEG - Invert
1
2.000.000
20.000
MPEG - Fish
1
11.000
8.500
MPEG - Herp.
1
60.000
58.000
2.000
19.500
7.600
0
1.000
IPT - BCTw
(xiloteca)
1
MPEG - Masto
1
34.000
16.000
MPEG - Coleção
Ornitológica
1
74.965
71.200
10.392
3.100
3.798.701
695.272 (18%)
INPA - xiloteca
1
Total
9
16
1
131.656 (19%)
Records from the Amazon Basin:
Collection
Plants
Animals
Micro.
total
records
amazon
Digitized
Georef.
on-line
(no. and (no. and
% of total) %
of
digitized)
DZSJRP - pices
1
390
309
343
splink.cria.org.br
UNIR - Fish
1
23.229
23.229
23.229
no
UNIR
Mammals
(CRM)
-
MEFEIS
UFRR
UFAM Coleção
Zoológica
1
no
(100%
digitized - Word)
1
splink.cria.org.br
1
1
2.751
2.751
191.992
0
no
0
no
18
Collection
Plants
MIRR
1
INPA - Peixes
Animals
total
records
amazon
Digitized
Georef.
on-line
(no. and (no. and
% of total) %
of
digitized)
Nno
1
INPA - CMIM
INPA
Mammals
Micro.
no
1
-
1
INPA - invert.
1
INPA - Amphi
1
INPA - Herbaria
no
4.819
4.819
no
no
13.500
13.500
6.750
1
INPA - Aves
no
no
1
631
631
400
JBRJ
1
splink.cria.org.br
SPF - USP
1
splink.cria.org.br
Herbário MG
1
no
Instituto
Butantan - IBSP
HRCB
1
splink.cria.org.br
1
splink.cria.org.br
MPEG - Invert
1
no
MPEG - Fish
1
8.000
8.000
MPEG - Herp.
1
59.000
58.000
no
2.000
IPT - BCTw 1
(xiloteca)
MPEG - Masto
MPEG
Coleção
Ornitológica
-
INPA - xiloteca
1
Total
9
no
splink.cria.org.br
1
32.000
16.000
no
1
63.720
60.500
no
8.300
16
1
408.332
no
187.739
(46%)
32.722
(17%)
Strategy for data digitization
To be more effective, a digitization effort of the region should be based on establishing partnerships
with local institutions (giving preference to existing GBIF nodes or partners) that will be responsible for
offering support to local biological collections. Where a local partner specialized in information
systems does not exist an institution that can give this support locally should be identified. There are
clearly three institutions that can play this role in their countries:

The Instituto de Investigaciones de la Amazonía Peruana (IIAP) in Peru, contact person:
Victor Miyakawa (vmiyakawa@iiap.org.pe)
19

The Alexander von Humboldt Biological Research Institute in Colombia, contact person:
Ximena Franco Villegas (xfranco@humboldt.org.co); and,

The Reference Center for Environmental Information (CRIA) in Brazil, contact person:
Vanderlei Perez Canhos (vcanhos@cria.org.br).
It is recommended that the Gordon and Betty Moore Foundation should reserve US$ 200,000 for
digitization projects a year during a three year period in each of these countries (total of US$ 600,000
per year). Each institution together with GBIF should present a proposal or a set of proposals, clearly
stating which collections were selected for digitization and why, what are their holdings and what is the
digitization strategy. A clear statement on open and free access to non sensitive data must also be
made. When an institution capable of integrating partners and structuring an on-line data system is
structured in Venezuela, the same procedure is recommended, that is, involve this institution in the
selection of holdings and the formulation of a digitization strategy and proposal. In order to involve all
other countries that may have greater difficulties with on-line communication and may have interest
and people willing to become involved, it is also recommended that an extra budget of US$ 200,000
be made available for GBIF per year to send out a call for proposals to try and identify these possible
partners.
It is important that all proposals include:

a digitization plan;

a clear policy for data sharing, with free and open access to non-sensitive data on the Internet;
and,

a definition or strategy as to how data will be made available on the Internet.
GBIF must provide the means to share data for those institutions that do not have local data providers.
This is the “digitization” component of the strategy that is being formulated for ABBIF. The budget
recommended up to USD 1 million per year for a period of 3 years, after which the effectiveness of this
activity will be evaluated together with the necessity of new investments in data digitization. This
activity may have a great impact on local scientific development, on international partnerships and on
open and free access to scientific data important for research, conservation and policy making.
Strategy for capacity building
An important component is capacity building in the region. The questionnaire and workshops identified
four basic areas for training:

collection management: ABBIF should concentrate on information management)

taxonomy: ABBIF should concentrate on taxonomic information processing

database management, tools, and information systems

use of biodiversity data
It is recommended that ABBIF holds yearly workshops and or training courses on these themes, so a
yearly budget of US$ 200,000 for this purpose is proposed. An extra US$ 100,000 is proposed for
technical meetings.
20
ABBIF and Non Amazonian countries
In 2003 a survey was carried out to study the theme “Data-sharing with Countries of Origin” (Contract
no. GBIFS/OCB/2003/04)13. This study showed that collections were already working on digitizing their
data and were willing to share this if properly acknowledged. A very strong tendency to openly share
data was observed. This new survey carried out with the support of the Gordon and Betty Moore
Foundation focuses on Amazonian collections outside of the Amazon region. The 33 responses
received from institutions around the globe, highlight their interest in digitizing and making data
available, as well as the need to establish partnerships with experts in taxonomy/systematics that can
assist in the identification of materials.
Evaluation
The evaluation process was carried out based on the questionnaires answered by each institution
and, when possible, further information was sought analyzing each web site. The existence or not of a
GBIF node in the country was also considered as, in principal, if a node is in place, the technology to
openly share data is available. The objective was to evaluate whether there was interest and whether
it would be feasible to set up a collaboration program with collections from non Amazonian countries
aiming at data and expertise sharing.
Argentina
Argentina joined GBIF in 2002 as an Associate participant. Seven (7) institutions serve data through
GBIF (approximately 135,000 records). Two of these institutions answered the questionnaire.
Argentina is establishing a national network of biological collections (Red Nacional de Colecciones
Biológicas Argentina – RNCB14) as a GBIF node, using the protocol DiGIR.
Museo Argentino de Ciencias Naturales Bernardino Rivadavia (MACN), Herbario
Nacional de Plantas Celulares
Holdings: 100 specimens of Algae, all georeferenced and 70 digitized (Excel), 32 of which are
from the Amazon region.
Infrastructure: Inadequate hardware and software with adequate staff. Internet access through
modem.
Comments: The museum serves data to GBIF (a total of 40,292 records), so all data of interest
to ABBIF could be serviced through the GBIF node in Argentina.
Website: www.macn.secyt.gov.ar/colnac/herbario.htm
Museo de La Plata, División Zoología Invertebrados - MLP
Holdings: non-arthropod invertebrates, Arachnida and Myriapoda. 230 digitized records of
Molluscs, Platyhelmintha, Myriapoda
Infrastructure: Sufficient hardware and software, insufficient staff for data entry.
13
http://www.gbif.org/prog/ocb/sdco
14
http://www.gbifargentina.org.ar/
21
Contact: Cristián Ituarte (cituarte@fcnym.unlp.edu.ar)
Comments: This collection also serves data through GBIF (a total of 19,419 records), and as
the case of MACN, all data of interest to ABBIF could be serviced through the GBIF node in
Argentina.
Website: www.fcnym.unlp.edu.ar/museo/
Austria
Austria is an Associate Participant, having joined GBIF in September 2001, and has established its
national focal point of GBIF15. Ten institutions serve over 2 million records through the GBIF’s portal.
Natural History Museum Vienna, Dept. of Botany (W)
Holdings: The museum holds many historical collections including probably several thousand
types. There are approximately 5.5 million records, with only 5,000 digitized. There are several
ten thousand records from the Amazon region with several thousand types, but nothing has
been digitized.
Infrastructure: The museum requires additional scanning and PC facilities and has inadequate
staff (only 2 curators)
Contacts: Ernst Vitek (ernst.vitek@nhm-wien.ac.at) & Anton Igersheim
Comments: This herbarium is part of the Virtual Herbaria Austria. 4 herbaria have added data to
the system which has approximately 45,000 records on-line. This initiative is being partially
funded through GBIF's DIGIT program. It would be interesting to establish a digitization program
of Amazonian specimens. The Museum is a GBIF data provider and serves almost 8 thousand
records through the network.
Website: herbarium.botanik.univie.ac.at/database/search.php
Belgium
Belgium is a voting participant, having joined GBIF in February 2001. The Belgian Biodiversity
Platform16 is the Belgian node of GBIF and is serving over 160,000 records.
National Botanic Garden of Belgium, Dept. Spermatophyta-Pteridophyta and Dept. BryophytaThallophyta, Herbarium BR
Holdings: The herbarium holds 3 million specimens, of all plant groups including fungi. There is
important historical material such as the collections of Funck and Schlim (Venezuela), Claussen
(Brazil) and Herbarium Martii (~60,000, 24,000 from Brazil, 11,000 from Central & South
America). Of the 3 million specimens, 40,000 are nomenclatural types; 200,000 are databased,
20,000 imaged, and 100,000 georeferenced. There are 200,000 records from the Amazon
region, 2,000 of which are digitized, but none are georeferenced. Fungi are 100% digitized and
plants only 1%. The software used are BGBASE, Progress (fungi), and Microsoft Access.
15
http://www.biodiv.at/gbif/
16
http://www.biodiversity.be/
22
Infrastructure: The herbarium requires more server storage capacity and additional staff. They
especially require expertise with knowledge of the Neotropics.
Contact: Piet Stoffelen (stoffelen@br.fgov.be)
Comments: The institution is open to collaboration. It would be important to establish
collaborative programs with Amazonian countries to database data from the Amazon (~200,000
specimens). The herbarium serves the Martius collection data through the Belgium GBIF node.
Websites:
fungi:ww.br.fgov.be/RESEARCH/COLLECTIONS/HERBARIUMS/FUNGI/SURVEY/index.html
vascular plants: projects.bebif.be/enbi/martius
Bulgaria
Bulgaria is an associate participant of GBIF since August, 2001 and holds a GBIF node, BULBIONET
(BULgarian BIOdiversity NETwork). They are not yet providing data through the GBIF portal.
National Museum of Natural History, BAS (NMNHS), Fossil and Recent Birds Dept. (FRBD NMNHS)
Holdings: The museum was established in 1889 and holds specimens collected 140 years ago.
Over 250 specimens of 60 species are referred to as extinct, endangered or vulnerable. The
collection has 31,029 specimens. Nothing has been digitized. 400-500 records are from the
Amazon region.
Informed infrastructure: The museum requires one computer and 1 person for data entry.
Contact: Zlatozar Boev (boev@nmnh.bas.bg)
Comments: GBIF could look into this collection and analyze its holdings. As the resources
requested are very small, it might be interesting to help the collection in digitizing its data.
Website: www.nmnh.bas.bg/
Denmark
Denmark is a voting participant since January 2001, and has structured the Danish Biodiversity
Information Facility (DanBIF)17 as a National Node of GBIF. DanBIF serves over 250,000 records
through the GBIF portal.
Copenhagen University, Institute of Biology, Dept. Microbiology
Holdings: The department holds fungal specimens from Ecuador. There are more then 10,000
digitized records using FileMaker.
Comments: The responses to the questionnaire were incomplete, with no indication as to
protocols and standards used. The on-line system is very interesting, with a lot of images and an
identification key, but does not include information about any counterpart in Ecuador. This group
should be contacted to evaluate how this data could be served through GBIF and ABBIF.
Contact: Thomas Læssøe (thomasL@bi.ku.dk)
17
http://www.dk.gbif.net/
23
Website: www.mycokey.com/Ecuador.html
University of Aarhus, Herbarium (AAU)
Holdings: The herbarium holds 750,000 specimens worldwide including those from Ecuador,
Peru, Bolivia and Colombia. 118,000 records are digitized and georeferenced. 60,000 records
are from the Amazon region, of which 41,200 are digitized and georeferenced (41,000). 100% of
the records from Ecuador are databased and available through GBIF. Standard and protocol
used are DarwinCore, and DiGIR)
Contact: Finn Borchsenius (finn.borchsenius@biology.au.dk)
Comments: The herbarium received an award (GBIF DIGIT 2004) to digitize data and to set up
Danish herbaria as data providers to GBIF. This herbarium today serves almost 12,000 records
and the Danish Biodiversity Information Facility over 250,000 through GBIF. We recommend that
ABBIF should filter the data directly through GBIF. A search for "Ecuador" carried out in
January/2006 retrieved 96,640 records.
Website: herb42.bio.au.dk:591/AAUbase/
Estonia
Estonia is a voting participant, and although it hasn’t an established node, the Institute of Zoology and
Botany of the Estonian Agricultural University is serving 439 records through GBIF’s portal.
Estonian Agricultural University, Institute of Agriculture and Environment
Holdings: The institute holds Geometridae of the world including from French Guyana,
Venezuela, and Ecuador. There are 8,000 records from the Neotropical region, 200 of which are
digitized (Excel), and none are georeferenced. There is no information on-line.
Infrastructure: The institution has sufficient hardware, software, and staff.
Contact: Jaan Viidalepp (jaan@zbi.ee)
Comments: The institution states that it is willing to participate in ABBIF but doesn't indicate any
specific needs and can't be automatically linked to the network. Perhaps this would be the case
for GBIF node in Estonia to offer a data commons space for deposit of data.
France
France is a voting participant but also hasn’t set up a GBIF node. Three (3) institutions are serving
over 600,000 records to GBIF’s portal.
Laboratoire Dynamique de la Biodiversité, Université Paul Sabatier, Naturhistorisches Museum
Wien
Holdings: The collection is still housed in Toulouse University with the exception of types. They
hold Ephemeroptera from French Guyana. There are 1000 digitized records (Excel) not on-line
Informed infrastructure: The questionnaire indicates that the institution has sufficient
hardware, software, and staff.
Contact: A.Thomas (alain3d@cict.fr) & Y. Dominique (y.dominique@epoc.u-bordeaux1.fr
Comments: The institution indicates that it is willing to participate in ABBIF but doesn't indicate
any specific needs and can't be automatically linked to the network. Perhaps this would be the
case for GBIF or ABBIF to offer a data commons space for deposit of data.
24
Museúm National d'Histoire Naturelle, Herbier Unité taxonomie et Collection - Dept
Systematique et Evolution
Holdings: Relevant to the Amazon region, the herbaria holds collections of Humboldt-Bonpland,
A. de St. Hilaire, Alexandre R. Ferreira, A. Glaziou, Gaudichaud, Poeppig, among others. The
collection includes phanerogams, cryptogams, fungi, and lichens. There are 10 million records of
which 500,000 are types. 520,000 records have been digitized and 81,000 georeferenced. There
are 500,000 records from the Amazon Region, of which only 18,000 are digitized.
Infrastructure: The collection has insufficient hardware and staff for digitization and for making
information available via the Internet.
Contact: Odile Poncy (Curator American Plants)
Comments: This is a very important collection with only 3.6% of its holdings digitized. The
online information system seems to have all the necessary elements for data sharing through
interoperable systems. The Museum is a GBIF data provider and serves almost 600,000 records
to the network. It would be very important for both GBIF and ABBIF to have a digitization project
with this herbarium.
Website: www.mnhn.fr/base/sonnerat.html
Germany
Germany is a voting participant and has structured GBIF – Deutschland18, as its node. Germany
serves over 5 million records to the GBIF portal.
Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin, herbarium
Berolinense
Holdings: The herbarium holds 3.5 million specimens, 296,000 of which are digitized and 145,
000 georeferenced. The total amount of records from the Amazon region is unknown to the
herbarium. There are 5,600 digitized records from Brazil 1,700 of which are georeferenced,
including 1,950 high resolution images.
Informed infrastructure: The herbarium requires personnel for digitization, georeferencing,
quality control; and for curatorial and technical tasks.
Contact: Walter Berendsohn (w.berendsohn@bgbm.org)
Comments: Several datasets are offered through GBIF (over 150,000 records) and BioCASE.
Standard and protocol used are ABCD and BioCASe. This herbarium should receive support for
the digitization of its holding. ABBIF should filter data through GBIF.
Website: www.bgbm.org/BioDivInf/databases.htm
Botanische Staatssammlung München, Dept. Vascular Plants
Holdings: This is a state herbarium with 2.5 million specimens from all plant and fungal groups
and areas. It includes approximately 7,000 species and 25,000 specimens from the Martius
expedition, and the herbarium of P. von Luetzelburg (1910-1938) with the Amazonian Colombian
border expeditions of General Rondon, and Amazonian collections by Prance, Krukoff, and
18
http://www.gbif.de/
25
Kubitzki. 1.5 million records are of vascular plants, but only 6,000 are digitized and
georeferenced. Approximately 25,000 records are from the Amazon region, but only 200 have
been digitized and georeferenced. There are 330,000 records of fungi, 25,000 digitized and
georeferenced. Very few of these records are from the Amazon region. There are 150,000
records of algae, 25,000 of which are digitized and georeferenced, but none are from the
Amazon region. As to lichens, there are 250,000 records, 3,200 digitized and georeferenced and
perhaps 2,000 records are from the Amazon region but maybe only 50 are digitized and
georeferenced. As to Bryophytes, there are 300,000 records but nothing has been digitized or
georeferenced and there aren’t any records from the Amazon region.
Infrastructure: This department considers itself understaffed at all levels, stating that there are
no tenured IT staff.
Contact: Hans-Joachim Esses (esser@bsm.mwn.de - Vascular Plants);
Dagmar Triebel (triebel@bsm.mwn.de - GBIF-D Mycolocy Node Manager)
Comments: Museum is a GBIF dataprovider, serving over 30 thousand records to the network,
and adopted ABCD and BioCASE as standards. Amazon basin biodiversity data is a priority and
is stated as a research focus of Munich's scientific staff. They hold important vascular plants'
collection from the Amazon (quantity, historical significance, types) and have expertise in
Amazonian Euphorbiaceae, Melastomataceae, and Siparunaceae. Besides recommending data
integration with ABBIF possibly through GBIF, it would be interesting to study future
collaboration with specialists from Amazonian countries associated with a digitization project of
Amazonian vascular plants.
Website: www.botanischestaatssammlung.de/projects/coll_online.html
Museum für Naturkunde Berlin, Zoology/Ornithology
Holdings: This is a large ornithological collection of the 19th century of the Amazon region
(collectors: Sello, von Hoffmannsegg, Olfers). There are 200,000 records, 20,000 of which are
digitized, but not georeferenced. 5,000 records are from the Amazon region, 500 are digitized in
a SQL database. There is no information on-line
Infrastructure: The museum requires personnel for technical work in the collection
Contact: S. Frahnert (sylke.frahnert@museum.hu-berlin.de)
Comments: The museum is a GBIF data provider and serves approximately 3,000 records. It
might be interesting to include this institution in a digitizing program.
Latvia
Latvia is not a GBIF member.
The Entomological Society of Latvia
Holdings: Coleoptera (Anthicidae) worldwide. There are 50,000 records, all digitized (Excel)
and georefenced, 500 of which are from the Amazon region. There is no information on-line
Infrastructure: The society indicates that it has sufficient hardware, software, and staff.
Contact: Dmitry Telnov (telnov@parks.lv)
Comments: It is willing to participate. As all records are digitized but not on-line, perhaps this
would be the case for GBIF to offer a data commons space for deposit of data
Website: www.lubi.edu.lv/les/kafernieki.htm
26
Netherlands
The Netherlands are voting members and joined GBIF in February, 2001. They have structured the
Netherlands Biodiversity Information Facility - nlbif19 which serves over 2 million records to GBIF’s
portal.
Centraalbureau voor Schimmelcultures (CBS)
Holdings: This collection holds 46,000 filamentous fungi and yeasts, and 15,000 specimens
from the herbarium. Its status in June, 2005 was all fungi and yeasts and 12,000 herbarium
specimens digitized. No material is georeferenced. Expectations were that the holdings would be
fully digitized by the end of 2005. 5,000 fungi and yeast cultures and 500 digitized specimens
are from South America.
Infrastructure: The institute indicates that it has sufficient hardware, software, and staff, but not
enough time for new projects.
Contact: Gerrit Stegehuis (stegehuis@cbs.knaw.nl)
Comments: CBS uses DarwinCore & CABRI as data models and DiGIR protocol and are willing
to participate. They are a GBIF data provider and serve more than 35,000 records to the
network. ABBIF could filter data through GBIF.
Website: www.cbs.knaw.nl
Poland
Poland is an associate participant and joined GBIF in March, 2001. They have established a GBIF
node20 and nine (9) institutions are serving approximately 80,000 records to the GBIF portal.
Polish Academy of Sciences - Institute of Systematics and Evolutions of Animals, Dept. of
Invertebrate Zoology (IZ)
Holdings: The collection has Lepidoptera from Brazil, French Guyana, Peru. There are 12,000
specimens that have not been databased and most have not been identified. Part of the
Microlepidoptera (Tortricidae) are identified and could be databased.
Informed infrastructure: Hardware and software are considered insufficient, but the staff (2
technicians) is considered adequate.
Contact: Lukasz Przybylowicz (lukasz@isez.pan.krakow.pl)
Comments: They offer facilities for visitors to database Tortricidae and Arctiidae.
Website: www.isez.pan.krakow.pl
Portugal
Portugal is a voting member and joined GBIF in 2001. It does not have a node and is not serving data
to the GBIF portal.
19
http://www.nlbif.nl/
20
http://www.ksib.edu.pl/
27
Jardim Botânico - Museu Nacional de História Natural, Universidade de Lisboa, Herbário de
Alexandre Rodrigues Ferreira
Holdings: This herbarium holds the collection of Alexandre Rodrigues Ferreira when he traveled
to Brazil between 1783 and 1793. This collection has 1187 angiosperms, 69 pteridophytes, and
4 algae, but nothing has been digitized or georeferenced.
Infrastructure: Insufficient hardware, software, and staff. Specimens require revision and
identification.
Contact: Ana Isabel D. Correia (aicorreia@fc.ul.pt)
Comments: This may be another case of promoting collaboration with Brazilian specialists and
offering a data commons space for data deposit.
Website: www.www.jb.ul.pt/
Spain
Spain is a voting member and joined GBIF in February, 2001. The Spanish GBIF Node21 is in place
and serves over 600,000 records to the portal.
Museu Darder d'História Natural de Banyoles
Holdings: The museum was founded in 1916 and has a small collection with fish (2), reptiles
(5), birds (<100), mammals (<18), and insects (168) all digitized and 124 are georeferenced.
There are 250 specimens from the Amazon. The database is not on-line.
Informed infrastructure: insufficient staff
Contact: Georgina Gratacós i Teixidor (mdhn@ajbanyoles.org)
Comments: If these holdings are of interest to GBIF or ABBIF perhaps the easiest/fastest
solution would be to offer a data commons space at the GBIF node in Spain, where the data can
be deposited.
Website: www.banyolescultura.net/mdhncat.htm
Sweden
Sweden joined GBIF in February, 2001, is a voting participant and holds a GBIF node22.
The Swedish Museum of Natural History
The Swedish Museum of Natural History is serving over 6 million records through GBIF’s portal. As
standards they are using DarwinCore and DiGIR. Amazonian data can therefore be served to ABBIF
through GBIF.
Ichthyology Collection, Department of Vertebrate Zoology (NRM)
Holdings: The fish collection holds 50,000 records, 41,000 of which are digitized and 6,000
georeferenced. Amazonian collections come mostly from Peru and some from Venezuela,
21
http://www.gbif.es/
22
http://www.gbif.se/
28
Brazil, Colombia, and Bolivia. There are 5,000 digitized records from the Amazon region, 3,000
of which are georeferenced.
Informed Infrastructure: Sufficient hardware and software and adequate staff.
Contact: Sven O. Kullander (sven.kullander@nrm.se)
Comments: The collection uses the Artedian (MS-Access) and is interoperable with Fishbase
and GBIF, using DarwinCore and DiGIR. As to access to data, it restricts the access to its work
in progress and is willing to collaborate with ABBIF.
Website: http://www.nrm.se/ve/pisces/
Department of Invertebrate Zoology
Holdings: The collection holds about 560,000 records, 14% of which are digitized (78
thousand). There are only 296 records from Amazon countries (not necessarily of the Amazon
region).
Infrastructure: Sufficient hardware and software and adequate staff
Contact: Elizabeth Watson (elizabeth.watson@nrm.se)
Comments: The collection is using FileMaker Pro and DarwinCore and DiGIR as standards.
Digitized data is available on-line through GBIF. As is the case of the Fish collection, access is
only restricted in the case of work in progress.
Website: http://www2.nrm.se/ev/welcome.html.en
Bryophytes
Holdings: The collection has 706,000 records of which 100,000 are digitized. There are 3,236
digitized records from Amazon countries, and they hold about 400,000 specimens from South
and Central America and from the Caribbean. There are about 25,000 type specimens and a
separate Ecuador herbarium with about 35,000 specimens.
Informed Infrastructure: sufficient hardware and software and adequate staff.
Contact: Elizabeth Watson (elizabeth.watson@nrm.se)
Comments: This collection has significant material for South and Central America and from the
Caribbean. They don’t indicate what standards are being used, but they serve their data to
GBIF, so there shouldn’t be any problems with interoperability. As is the case with the other
collections of Swedish Museum of Natural History, access is only restricted in the case of work
in progress.
Website: http://www2.nrm.se/kbo/welcome.html.en
Lichens
Holdings: There are 295,000 records of which 100,000 are digitized. There are 2,652 digitized
records from Amazon countries.
Infrastructure: Sufficient hardware and software and adequate staff
Contact: Elizabeth Watson (elizabeth.watson@nrm.se)
Comments: All digitized records are served through GBIF’s portal.
Website: http://www2.nrm.se/kbo/saml/lavkoll.html.en
29
Botanical Museum, University of Lund
Holdings: The Botanical Museum (LD) holds 2.5 million specimens, mostly vascular plants but
also lichens, mosses, fungi and algae. 175,000 records are digitized, of which only 362 records
are from Amazon countries (not necessarily from the Amazon region). Access to data is
protected in the case of work in progress.
Infrastructure: Sufficient hardware and software and adequate staff.
Contact: Elizabeth Watson (elizabeth.watson@nrm.se)
Comments: Although there are only very few digitized records from Amazon countries, there
are a number of types, with digitized images. This may be important data to be integrated to
ABBIF.
Website: http://www.biomus.lu.se
Gothenburg Herbarium (GB)
Holdings: This herbarium has focused on exploring the Neotropical flora, mainly the flora of
Ecuador. They hold 1.6 million records, of which only approximately 100,000 are digitized. This
data is not available on-line.
Infrastructure: no information was offered.
Contact: Elizabeth Watson (elizabeth.watson@nrm.se)
Comments: The contact person is Elizabeth Watson from the Swedish Museum of Natural
History. The best strategy for access of this important data is most probably through the GBIF
portal.
Website: http://www.systbot.gu.se/
Switzerland
Switzerland is an associate participant and joined GBIF in February 2001. It established GBIF
Switzerland23 and the country serves approximately 50,000 records to the portal.
Muséum d'histoire naturelle (MHNG), Dept. herpetology and ichthyology
Holdings: The department holds specimens of freshwater fish, amphibians, and reptiles and
their parasites. Nothing has been digitized. They have a checklist of pseudoscorpians of South
America. The questionnaire does not indicate the size of the holdings.
Infrastructure: They require one student to digitize Amazonian fauna
Contact: Volker Mahnert (volker.mahnert@mhn.ville-ge.ch)
Comments: There is an interest in cooperating as a data provider. The answers and the web
site seem to indicate that a lot of resources would be necessary to make this possible as nothing
has been digitized. As there is no indication as to the size of the holdings, it is difficult to
evaluate.
Website: www.ville-ge.ch/musinfo/mhng/
23
http://www2.unine.ch/gbif
30
Natural History Museum Bern, NMBE
Invertebrate Dept.
Holdings: The collection holds 1.7 million insect and 1.2 mollusk specimens. The actual state of
inventoried specimens include: 250.000 insects and spiders, 150.000 mollusks. The museum
holds the collection assembled by Emílio Augusto Goeldi and collaborators in Brazil (18941910). They hold 9,500 insects, mainly Coleoptera, Lepidoptera, and Hymenoptera - among
them 90 Ducke type specimens. All records are digitized, not georeferenced and are available in
Excel on request.
Vertebrate Dept.
Holdings: They hold the collection assembled by Emílio Augusto Goeldi and collaborators in
Brazil (1894-1910). There are 3,600 vertebrates, mainly birds & mammals. All records are
digitized but not georeferenced. Excel lists are available on request.
Infrastructure: They do not have specialists in neotropical fauna.
Contact: Marcel Güntert (marcel.guentert@nmbe.unibe.ch)
Comments: This would be an interesting museum for GBIF to contact as a data provider. They
hold their data in an oracle database. No information is offered as to standards or protocols. If
they do not wish to disseminate their data themselves, maybe Amazonian data could be stored
in a data commons service held by ABBIF.
Website: www.nmbe.ch
UK
The United Kingdom is a voting participant, having joined GBIF in August, 2001. They have
established a National Biodiversity Network24 as the GBIF node and are serving over 11.6 million
records to the GBIF portal.
Royal Botanic Gardens, Kew, Herbarium
Holdings: Kew holds 7 million specimens (plant & mycological diversity), 350,000 of which are
types. They have significant collections from Guyana (formerly British Guyana), but only a small
portion of the Amazon specimens have been digitized - specimens collected by Richard Spruce
from 1849 to 1864 in Peru (2902 records) and Ecuador (4081 records). They don't have an idea
of the total number of specimens from the Amazon.
Infrastructure: Kew requires hardware and staff for new digitization and databasing projects. As
to standards, they have adopted HerbCore, and use Microsoft Access.
Contact: William Milliken (w.milliken@kew. org)
Comments: The institution is open to digitize Amazonian collections if funded through a project.
This would certainly be an important partnership for ABBIF. Kew serves over 85,000 records
through GBIF.
Website: internt.nhm.ac.uk/jdsml/research-curation/projects/spruce/index.dsml
24
http://www.nbn.org.uk/
31
School of Geography, University of Leeds, RAINFOR project (Amazon Forest Inventory
Network)
Holdings: This is not a collection but a collaborative scientific project assembling permanent
plot data. Its objective is to monitor the biomass and dynamics of Amazonian forests. According
to the questionnaire they have data on phanerogams, but it is not available on-line.
Infrastructure: They require investment in data basing and data management for the project
and at individual Amazonian institutions.
Contact: Tim Baker (t.r.baker@leeds.ac.uk)
Comments: This project apparently does not have a plan for disseminating data or a policy for
data sharing. There are links to project documents and publications but no access to data. At
this point, it would be difficult to interact with the project.
Website: www.geog.leeds.ac.uk/projects/rainfor/index.html
USA
The USA is a voting participant and jointed GBIF in January, 2001. They have structured a US GBIF
node25 at NBII (National Biological Information Infrastructure) and serve over 30 million records to the
GBIF portal.
ant.base
Holdings: 11,833 species; online digital library with more then 4,000 publications on ant
systematics. There are basically two sources of data: distribution and specimen description that
is extracted from legacy publications; and input of data matrices from field surveys - Ants in the
Neotropics. There are 80,000 pages of publications and they are using DarwinCore and DiGIR.
Infrastructure: The project requires one additional programmer; resources for OCR-ing existing
publications and data extraction.
Contact: Donat Agosti (agosti@amnh.org)
Comments: Antbase is being built and maintained at the American Museum of Natural History
(Donat Agosti) and the Ohio State University (Norman F. Johnson) (Also see additional
information below).
Website: antbase.org/
Ohio State University C.A. Triplehorn Insect Collection, Dept. Entomology
Holdings: Taxonomic name service for hymenoptera (180,000 names - collaborate with ITIS),
DiGIR interface for all specimen records. They hold 100,000 digitized records of hymenoptera,
95% of which are georeferenced. 26,648 records are from the Amazon of which 25,746
georeferenced.
Infrastructure: They require support for a programmer (PL/SQL, Perl) and personnel for data
entry.
Contact: Norman Johnson (johnson.2@osu.edu)
25
http://gbif.nbii.gov/
32
Comments: They are responsible for maintaining an ant name server and specimen data
(extraction project and leaf litter ant surveys). “Ants” are an interesting theme for ABBIF to
explore (see item “Themes”). Ohio State University Insect Collection is a GBIF data provider with
almost 115,000 records.
Website: iris.biosci.ohio-state.edu/hymenoptera/
Fairchild Tropical Botanic Garden, Herbarium
Holdings: The herbarium’s specialty is native plants of Florida and the West Indies. It has
recently expanded its scope to plants from all tropical regions. It holds 165,000 records, 52,000
of which are digitized, 3,454 georeferenced. There are between 2 and 3,000 specimens from
Amazon, 135 of which are digitized.
Contact: Lauren Raz (lraz@fairchildgarden.org)
Comments: Data is compatible as they have adopted Darwin core & DiGIR and they are willing
to share data. They already are a GBIF data provider with 93,000 records. Amazon data could
be filtered for ABBIF.
Website: www.virtualherbarium.org
Field Museum, Division of Mammals
Holdings: The mammals division holds 182,000 digitized records worldwide 170,000 of which
are georeferenced. 22 thousand digitized records are from the Amazon region, 21,000 of which
are georeferenced.
Contact: Bruce Patterson (bpatterson@fieldmuseum.org)
Comments: Field Museum serves almost one million records through GBIF, who could create
filters to serve data to ABBIF.
Website: fm1.fieldmuseum.org/collections/search.cgi?dest=mml
Harvard University, Museum of Comparative Zoology (MCZ)
Holdings: The MCZ holds 10 scientific collections with 21 million specimens, 12 million records,
900,000 of which are digitized and 200,000 georeferenced. 22 thousand are from the Amazon
region and only 8,000 are digitized and 6,200 are georeferenced. They hold important historical
material collected from the Amazon by Louis Agassiz and party on the Thayer Expedition (186566),
Infrastructure: personnel for data entry of catalogued data
Contact: Linda Ford (lford@oeb.harvard.edu)
Comments: MCZ serves almost 700,000 records through GBIF, so it would be interesting to
filter its data to ABBIF through GBIF. It would also be interesting to study a digitizing program of
the records from the Amazon region. Online collections available include fish, herpetology
(amphibians and reptiles), invertebrates, invertebrate paleontology, mammals, mollusks, and
birds.
Website: collections.oeb.harvard.edu/
IUCN/SSC-CI/CABS Biodiversity Assessment Unit
Holdings: Databases available: Global Amphibian Assessment and IUCN Red List. Incomplete
databases: fish, reptiles, and insects (25% digitized). The contact person informed that the
Global Mammal Assessment is also complete.
Contact: Simon Stuart (simon.stuart@iucn.org
33
Comments: IUCN is an important institution to liaise with. In our search for the Global Mammal
Assessment we only found explanatory texts. Apparently no online database is available. IUCN
is heading the Conservation Commons Initiative (www.conservationcommons.org) and aims at
making its data freely and openly available. It would be important for GBIF (and ABBIF) to study
means of making their systems interoperable.
Website: www.globalamphibians.org; www.iucnredlist.org
Missouri Botanical Garden (MO)
Herbarium
Holdings: MO holds 5.6 million specimens, 5.2 million vascular plants and 450,000 bryophytes,
of which 42% are digitized. Its Tropicos database system has 978,000 scientific names,
2,677,000 specimen records of which 1,299,000 are georeferenced. There are 887,000 digitized
records from the Amazon Region, 559,000 of which are georeferenced.
Contact: James Solomon (jim.solomon@mobot.org)
Comments: MO received grants (GBIF DIGIT 2004) for georeferencing and imaging over 200
thousand Mesoamerican Vascular Plant Specimens. They are a GBIF data provider and serve
almost 2 million records to the network. It would be important that this data be filtered for ABBIF.
Website: www.tropicos.org
CEEB - Ethno and Economic Botany
Holdings: CEEB is indexing collections of Ethno- and Economic Botany around the world and
aims at setting standards, databases, and to disseminate information on-line. Some data is
available on-line for only some collections and only through individual institutions.
Infrastructure: They state that they require support for the network.
Contact: Jan Salick, Curator of Ethnobotany (jan.salick@mobot.org
Comments: This is an interesting initiative to follow as the theme is of great interest for the
region. Serving data to the network may be achieved through the existing infrastructure in the
herbarium.
Website: www.ceeb.info
New York Botanical Garden, Herbarium
Holdings: The herbarium holds 6.5 million specimens of all plant groups and fungi. Of the
vascular plants, 925,000 are from South America, 550,000 from Brazil and 330,000 from
Amazonian Brazil. Approximately 800,000 records have been digitized and are available online.
Of these about 200,000 are georeferenced. Of the 330,000 records from the Amazon region,
82,500 are georeferenced. There is a large backlog of unidentified Neotropical plant specimens
because of the Flora Amazônica project the Garden led in the 1970s and 1980s (rough estimate:
is 8,000 specimens).
Infrastructure: They require students to identify specimens in the backlog. The number of
students possible depends on how much supervision/training they would need -as the
herbarium, at the moment, only has one staff member who oversees the entire visitor program.
Contact: Jacquelyn Kallunki (jkallunki@nybg.org) & Barbara M. Thiers (bthiers@nybg.org)
Comments: The digitized data can be immediately integrated through interoperable links as
NYBG already serves GBIF with over 200,000 records. A collaborative project for identifying and
digitizing backlog from the Amazon is recommended. According to information offered the
34
groups for which they don't have specialists, and for which there are likely to be specimens in
need of identification, are Aquifoliaceae (Ilex), Celastraceae (Maytenus), and Nyctaginaceae.
While they do have specialists for some genera of Poaceae, Cyperaceae, and legumes, there
are probably some specimens of these families in the backlog, such as Scleria in the
Cyperaceae and legumes from Acre collected since Rupert Barneby's death in 2000. If there are
graduate or post-graduate students with expertise in the Amazonian taxa of these groups, they
certainly could make a contribution by identifying them. There are also unidentified specimens
filed at the end of each family in the herbarium itself. The large families, such as Poaceae,
legumes, Cyperaceae, are bound to have many undetermined specimens that would be much
more useful when catalogued if they are accurately identified. Their virtual herbarium holds
important on-line specimen catalogues such as: Neotropical Flora and Mycota Catalog;
Neotropical Lecythidaceae Catalog; Ericaceae of Ecuador, Flora and Mycota of Acre, Brazil, and
Plant Diversity of Central French Guiana (among many others).
Website: sciweb.nybg.org/science2/VirtualHerbarium.asp
University of California, Berkeley, Museum of Vertebrate Zoology (MVZ), Mammal Collection
Holdings: The mammal collection of the museum holds 215,900 specimens of mammals, with
approximately 5,500 from the Amazon. All records are digitized and georeferenced, and are
accessible on-line through mvz.berkeley.edu and MaNIS (dlp.cs.berkeley.edu/manis/).
Contact: James Patton (Patton@berkeley.edu)
Comments: The Museum of Vertebrate Zoology is a GBIF data provider, serving about 650
thousand records.
Website: mvz.berkeley.edu
Analysis and Recommendations
There is a lot of digitized data that, once ABBIF is structured, would only require to be integrated into
the system. The table below shows the number of records and taxons collected in Amazon countries
available through GBIF (May, 2006).
Country
records
taxons
Bolivia
202,298
24,611
Brazil
228,426
40,044
Colombia
214,228
29,832
French Guiana
56,442
5,489
Guyana
61,018
7,366
350,179
32,102
Suriname
32,889
5,012
Venezuela
128,911
21,498
1,274,391
165,954
Peru
Total
These records are not all from the Amazon region, but the table gives an idea as to the possibility of
very quickly serving data to ABBIF and of the necessity of establishing partnerships to increase the
amount of data available.
Data from large scientific expeditions in the past are practically all held in museums and herbaria in
Europe. US collections also hold a large amount of specimens collected in South America (including
the Amazon region) which are fundamental for building the Amazonian Basin Biodiversity Information
35
Facility. Just to compare the magnitude of the data housed in collections outside of the Amazon
region, the total number of specimens in Brazil’s more than 100 active herbaria is estimated as being
5 million. Individual herbaria such as Kew, Harvard, Missouri, New York, and France, each
individually, hold more then that.
All collections that answered the questionnaire are willing to share data, and hold over 65 million
records, less than 4% of which are from the Amazon region. Even so, there are over 1 million digitized
records (more than 70% are georeferenced) which could relatively quickly be made available on-line.
In fact, most of this data is already available on-line and would require an integration mechanism. Of
the 16 countries that hold the collections that answered the questionnaire all, with the exception of
one, are either voting or associate participants of GBIF and fourteen provide data to GBIF’s portal.
The results presented also show a number of smaller collections wishing to make their data available
requiring hardware, software or just expertise. In these collections, the percentage of records from the
Amazon region is very small, and it may be difficult to justify a project based on the digitization of less
then 500 records. It would be important for GBIF to analyze their holdings to see whether seed money
through digitization grants could integrate these collections to the network. In some cases it would be
important if GBIF and its nodes studied the possibility of holding a data commons space where
providers could, through a password controlled interface, deposit, control, and make their data
available. A technical solution for this is already available in the form of the GBIF Data Repository Tool
(DRT). The DRT allows individual scientists to upload their datasets which are in document format,
such as a spreadsheet. From there they automatically become parsed, validated, and entered into a
database connected to an embedded DiGIR provider.
There are specific collections that could be quickly integrated such as:

Department of Microbiology, Institute of Biology, Copenhagen University – with 10,000 digitized
records of fungal specimens from Ecuador;

AAU Herbarium from the University of Aarhus, with a digitization process in place, already
providing data through GBIF, with 60,000 specimens from the Amazon (70% digitized and
georeferenced);

The collections from the Swedish Museum of Natural History that already serve more then 6
million records through GBIF;

Antbase and the Ohio State Insect Collection with the ant name server and specimen data;

Division of Mammals from the Field Museum with 22 thousand digitized records from the
Amazon region;

Missouri Botanical Garden (MO), with its Tropicos database system with over 978,000 scientific
names and approximately 900,000 digitized records from the Amazon Region; and

The Mammal Collection of the Museum of Vertebrate Zoology (MVZ) from the University of
California, Berkley with approximately 5,500 digitized and georeferenced records from the
Amazon, already accessible on-line.
Digitization and Collaborative Research Programs
In principle, all collections are important, and those with smaller holdings or with a small
representation of specimens from the Amazon region could be linked through GBIF nodes. It would be
important for GBIF to look carefully at the questionnaires and identify holdings that can be easily
linked and others that, although with a small representation of Amazonian species, may be important
for other regions. The ABBIF architecture document suggests using the GBIF UDDI registry to link
collections.
36
As resources are scarce important holdings for the Amazon region must be prioritized. Of those
collections that answered the questionnaire, it would be very important to develop a digitizing program
with the following institutions:
Natural History Museum Vienna, Dept. of Botany (W)
This is a herbarium with 5.5 million records with less then 0.1% digitized and with only 2 curators.
Against it is the fact that they have very little digitized data and lack of specialized personnel, so it is
probably correct to affirm that a digitization project in this case would demand a lot of resources. In its
favor is the fact that Austria has a GBIF node and they are developing the Virtual Herbaria Austria, so
the technology is in place and there already is a movement to digitize and openly disseminate data.
This may be a good opportunity to establish bilateral or multilateral research programs to help identify
and digitize material.
National Botanic Garden of Belgium, Dept. Spermatophyta-Pteridophyta and
Dept. Bryophyta-Thallophyta, Herbarium BR
The Herbarium BR has important historical collections and is open to collaboration. The herbarium
holds 200,000 records from the Amazon region with approximately 1% digitized. For ABBIF it would
important to set up a digitization project associate with bilateral or multilateral research programs as
specialist knowledge of the Neotropics is required.
Museúm National d'Histoire Naturelle, Herbier Unité taxonomie et Collection Dept Systematique et Evolution
This is a very important herbarium for South America with many historical collections. The herbarium
holds 10 million records with only 5.2% digitized. As to Amazon specimens the total is 500,000 26 with
less then 4% digitized. A very solid project for digitizing and georeferencing the holdings should be in
place. This project could involve, GBIF Secretariat, its node in France and multilateral agreements for
the exchange of experts to help identify and digitize material.
Botanic Garden and Botanical Museum Berlin-Dahlem, Freie Universität Berlin,
herbarium Berolinense
For ABBIF, this herbarium should be further studied to know whether its holdings are significant for the
Amazon region. In general, it would be interesting if GBIF could help set a digitization program with
them due to the fact that they hold 3.5 million specimens with less then 10% digitized. Data of
importance to ABBIF could then be filtered through GBIF.
Botanische Staatssammlung München, Dept. Vascular Plants
From ABBIF’s perspective, even though this herbarium only holds 25,000 records from the Amazon
region, it is relevant as they are the result of important expeditions. Less then 1% is digitized, but at
the same time the digitization process could perhaps be carried out in a very short period of time.
GBIF – Germany could maybe help the herbarium in this initiative. Multilateral and bilateral
agreements should be sought as the Amazon Basin is a research focus of its staff.
26
Note: 500,000 specimens would be the holding of the largest herbaria in Brazil
37
Royal Botanic Gardens, Kew, Herbarium
It would be very important to fund a digitization project with Kew. They hold 7 million specimens which
includes significant collections for the Guyana. A partnership could perhaps be established between
GBIF, the National Biodiversity Network, and Kew Gardens to digitize this data. Bilateral and
multilateral agreements could be established to send students and experts to Kew to help in the
identification and data validation process.
Harvard University, Museum of Comparative Zoology (MCZ)
This is a very large group of collections with 21 million specimens and 12 million records, with less
then 8% digitized. Of direct interest to ABBIF are the 22,000 records from the Amazon region, 36% of
which is digitized. Perhaps these records could be digitized through graduate student programs
involving bilateral or multilateral agreements.
New York Botanical Garden
NYBG has a very important collection, especially for Brazil. Their digitization process is in place, but
they have a backlog of unidentified Neotropical plant specimens. It would be important to establish
bilateral agreements (especially with Brazil) to send students and specialists to help identify this
backlog.
Seed Money Program
This is an important component, as a complementary activity to support the core ABBIF project. Seed
money calls for proposal will help in the in the identification of Amazonian holdings in large collections
and help smaller collections to organize their data. Preliminary candidates for this type of program
include:

Museum für Naturkunde Berlin, Zoology/Ornithology with 5,000 records from the Amazon
region collected during the 19th century;

Jardim Botânico, Museu Nacional de História Natural, Universidade de Lisboa, Herbário de
Alexandre Rodrigues Ferreira with Ferreira’s collection when he traveled to Brazil between
1783 and 1793; and

The Invertebrate and Vertebrate Departments of the Natural History Museum in Bern with the
collection assembled by Emílio Augusto Goeldi and collaborators in Brazil (1894-1910) to help
georeference the records that are all digitized.
A yearly grant of US$ 400,000 for this purpose is proposed and an exercise in identifying additional
key collections with material collected from the Amazon region should be carried out.
Thematic Information Systems
The survey did not directly addressed the issue of thematic information systems, however, as part of
this study we have found several examples that showcase the importance of adding content, specific
to a certain taxa or geographic region. One such example is the positive and important outcome of
Antbase (http://www.antbase.org/). Another interesting example, based on the number of botanical
institutions that responded to the questionnaire and are willing to share their data, would be a Virtual
Herbarium. This should be further discussed, once the basic infrastructure with species and specimen
data is in place or under development.
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Proposed Overall Budget (US$ 1,000)
Item
Information Systems
Digitization in Amazonian Country Collections
Capacity building
ABBIF seed money grant
Total
Year 1
2,000
1,000
300
400
3,700
Year 2
2,000
1,000
300
400
3,700
Year 3
2,000
1,000
300
400
3,700
Total
6,000
3,000
600
1,500
11,100
Final Comments
The ABBIF feasibility study has raised a huge interest from small to large collections from developed
to developing countries. The ABBIF project could be an excellent exercise to address cross-cutting
issues ranging from data capture (from high throughput to hand digitization) to the deployment of
emerging modeling tools. All this could be addressed as a large scale international project, promoting
technology transfer, capacity building and training. The core project could be carried out in
coordination with GBIF seed money projects. The challenge now is to develop a detailed project
proposal and secure the necessary funds to do the job, possibly from multiple funding sources. The
ABBIF feasibility study experience should be considered in the development of studies to define
priority topics/issues/areas to be addressed by GBIF campaigns.
The ABBIF survey focused on data custodians and species and specimen data providers. There are
gaps in this survey, as some large institutions did not reply, such as the Smithsonian Institution, the
Natural History Museum in London, and the American Museum of Natural History in New York. This
does not invalidate the work, but indicates that the development of partnerships with key players
should be an ongoing process. Another gap refers to conservation NGOs, as only one representative
answered the questionnaire.
This community is very important and should be involved and motivated to collaborate with ABBIF, not
only as data providers, but as data users as well. The Conservation Commons27 initiative should
support ABBIF’s development, as both initiatives basically follow the same principles concerning data
sharing.
An important issue to be dealt with is to explore existing mechanisms for bilateral and multilateral
collaboration, identifying opportunities for joint projects and programs with focus on taxonomy,
digitization and data sharing and repatriation of species and specimen data. This should be carried out
in association with an effort to link the digital observational/monitoring databases resultant from large
scale projects and programs in the in the Amazon Basin.
The task of identifying, describing, and classifying all live species of the planet is one of the great
challenges of the 21st century. The lack of knowledge of the Amazonian biota and its importance
makes the region fragile and more vulnerable to destruction and misuse. We believe that once
operational, ABBIF will help promote a collaborative environment to study, discover, and describe
27
http://www.conservationcommons.org
39
species diversity in the region, to analyze, synthesize, and share information and knowledge for the
sake of science and society.
40