ANNUAL REPORT
ANNUAL REPORT
ANNUAL REPORT
ANNUAL REPORT
Leading Institute: Universidade Federal de Pernambuco Associated Institutions
Instituto de Botânica do São Paulo (IBt)
Instituto Nacional de Pesquisas da Amazônia (INPA) Jardim Botânico do Rio of Janeiro (JBRJ)
Museu Nacional (MN/UFRJ)
Universidade Estadual de Feira de Santana (UEFS) Universidade Federal de Paraíba (UFPB)
Centro of Referência em Informação Ambiental (CRIA) Rede Nacional de Ensino e Pesquisa (RNP)
IPA TEPB ASE UFG EAN UEL CEPEC HST BHCB EAC SPF UFRN MOSS IMA PEUFR UB HFSL RNP UFPE MNRJ JBRJ IBt UFPB INPA UEFS CRIA Colaboradores nacionais
NYBG MOBOT MNF CoL Colaboradores internacionais
International collaborators
TABLE OF CONTENTS
1.Introduction 1
2.Participants 2
3.Research Program in Taxonomy 5
4.Training 7
Best practices 7
New taxonomists 7
5.Virtual Herbarium 9
Baseline 9
Work carried out 11
Change of protocol (from DiGIR to Tapir) 11
Inclusion of new collections to the speciesLink network 15
Website 16
New outputs of the information system 17
Data repatriation 18
Defining a strategy for data repatriation 21
Maintenance 22
6.Bibliographic Production 22
7.Progress Indicators 22
8.Final Considerations 26
1. INTRODUCTION
The Virtual Herbarium of Flora and Fungi of Brazil is part of CNPq’s National Institutes of Science and Technology (INCT) Program. The Herbarium’s mission is to provide a free and open data infrastructure for the scientific community, for policy and decision makers, and for society in general. It intends to achieve these goals by integrating data from Brazilian herbaria and by repatriating data about plants collected in Brazil and deposited in herbaria outside the country.
To fulfill its mission the Virtual Herbarium aims to:
• Expand the knowledge base about the diversity of flora and macroscopic fungi in Brazil; • Improve the quality of the holdings in Brazilian herbaria;
• Encourage the formulation of public policies aimed at ensuring the sustainability of herbaria, the training of taxonomists, and the provision of support for biodiversity studies; • Make species occurrence data a fundamental instrument for decision making and for the
formulation of public policies concerning biodiversity;
• Encourage as a standard conduct, free and open data and information sharing in a comprehensive, useful and usable format; and,
• Offer data and information to make environmental sustainability just as important as social and economic development in the formulation and assessment of public policies. The Virtual Herbarium’s activities are focused on research, training, and knowledge transfer to society.
As to research, the Virtual Herbarium is involved in the study of the diversity and taxonomy of plants and macroscopic fungi and with the use of species-occurrence data in the formulation of public policies.
In the case of training, the Virtual Herbarium offers courses in taxonomy, curation of collections, and biodiversity informatics, aiming at providing researchers and technicians with better qualifications leading to an improvement in the quality of the Virtual Herbarium’s holdings. It also supports the training of Masters and PhD students taking graduate courses in botany.
Concerning the transfer of knowledge to society, the Virtual Herbarium is developing an open access, online data system about Brazilian plants and fungi. The integration and public availability of these data will support the analysis of specialists from different sectors, leading to a quicker advancement of knowledge.
2. PARTICIPANTS
Team Leader: Leonor Costa Maia
Assistant Team Leader: Maria Regina de V. Barbosa Steering Committee:
Leonor Costa Maia (UFPE)
Maria Regina de V. Barbosa (UFPB) Ariane Luna Peixoto (JBRJ)
Mariângela Menezes (MN-UFRJ) João Renato Stehmann (UFMG) Ana Odete Santos Vieira (UEL) Coordinators of specific areas:
José Rubens Pirani – USP (taxonomy of phanerogams) Kátia Cavalcanti Pôrto – UFPE (taxonomy of criptogams) Ariane Luna Peixoto – JBRJ (training)
Ana Odete Santos Vieira – UEL (articulation) Maria Regina Barbosa – UFPB (products)
Dora Ann Lange Canhos – CRIA (online information systems and products) Leading Institute: Universidade Federal de Pernambuco
Associate Institutions
Museu Nacional (MN/UFRJ) Instituto de Botânica (IBt)
Instituto Nacional de Pesquisas da Amazônia (INPA) Jardim Botânico do Rio de Janeiro (JBRJ)
Universidade Federal da Paraíba (UFPB)
Universidade Estadual de Feira de Santana (UEFS) Centro de Referência em Informação Ambiental (CRIA) Rede Nacional de Ensino e Pesquisa (RNP)
Associate Herbaria and Collaborators/Curators
Herbário da Embrapa Semiárido (HTSA)– Lúcia Helena Kiill
Herbário da Faculdade São Lucas, Roraima (HFSL) – Ana Cristina Ramos de Souza Herbário da Fundação do Meio Amb., Ciência e Tecnol. de Roraima (MIRR) – Andréia S. Flores
Herbário da Universidade de São Paulo (SPF) – Renato de Mello-Silva
Herbário da Universidade Estadual de Londrina (UEL) – Ana Odete Santos Vieira
Herbário da Universidade Estadual de Feira de Santana (HUEFS) – Luciano P. de Queiroz Herbário da Universidade Federal da Paraíba (EAN) – Leonardo Pessoa Félix
Herbário da Universidade Federal da Paraíba (JPB) – Maria Regina de V. Barbosa Herbário da Universidade Federal de Minas Gerais (BHCB) – Alexandre Salino
Herbário da Universidade Federal de Pernambuco (UFP) – Marlene C. de Alencar Barbosa Herbário da Universidade Federal de Pernambuco (URM) – Leonor Costa Maia
Herbário da Universidade Federal de Goiás (UFG) – José Angelo Rizzo Herbário da Universidade Federal de Brasília (UB) – Carolyn Proença
Herbário da Universidade Federal do Ceará (EAC) – Maria Iracema B. Loiola Herbário da Universidade Federal do Piauí (TEPB) - Roseli Farias M. de Barros. Herbário da Universidade Federal do Rio Grande do Norte (UFRN) – Jomar G. Jardim Herbário da Universidade Federal do Vale do São Francisco (HVASF) - José A. Siqueira Filho
Herbário da Universidade Federal Rural do Semiárido (MOSS) - Leandro de O. F. de Sousa
Herbário da Universidade Federal Rural de Pernambuco (HST) – Ângela M. de M. Freitas Herbário da Universidade Federal Rural de Pernambuco (PEUFR)– M.Elisabeth B. Pedrosa
Herbário do Centro de Pesquisas da Lavoura Cacaueira (CEPEC) – André Márcio Amorim Herbário do Instituto Agronômico de Pernambuco (IPA) - Rita de Cássia Araújo Pereira Herbário do Instituto de Meio Ambiente de Alagoas (IMA) – Rosângela P. de Lyra Lemos Herbário do Instituto de Botânica de São Paulo (SP) – Maria Candida Henrique Mamede Herbário do Instituto Nacional de Pesquisas da Amazônia (INPA) – Carlos H. Franciscon Herbário do Jardim Botânico do Rio de Janeiro (RB) – Rafaela C. Forzza
Herbário do Museu Nacional (R) – Luci de Senna Valle Researchers
Name Institution, State CNPq Fellow
Adriana de Mello Gugliotta IBt, SP -
Alexandre Salino UFMG, MG PQ 2
Amélia Iaeca Kanagawa UFPB, PB -
Ana Cristina Ramos de Souza FSL, RO -
Ana Luiza Du Bocage Neta IPA, PE -
Ana Maria Benko Iseppon UFPE, PE PQ 1D
Ana Odete Santos Vieira UEL, PR -
Andreia Silva Flores MIRR, RO -
Ana Paula Prata UFS, SE -
Andre Marcio Araujo Amorim UESC, BA PQ 2
Andréa Ferreira da Costa UFRJ, RJ -
Ângela Maria de Miranda Freitas UFRPE, PE -
Ariane Luna Peixoto JBRJ, RJ PQ 1B
Ariadna Valentina de F. e Lopes UFPE, PE PQ 2
Carolyn Elinore Barnes Proença UnB, DF -
Cássio Van Den Berg UEFS, BA PQ 1D
Célia Leite Sant’Anna IBt, SP -
Célio Ubirajara Magalhães Filho INPA, AM PQ 2
Dora Ann Lange Canhos CRIA, SP -
Francisca Araújo UFC, CE -
Gladstone Alves da Silva UFPE, PE -
Isabel Cristina Sobreira Machado UFPE, PE PQ 1B
Name Institution, State CNPq Fellow
Jefferson Prado IBt, SP PQ 1B
João Renato Stehmann UFMG, MG PQ 1D
José Alves de Siqueira Filho UNIVASF, PE -
José Laurindo C. dos Santos INPA, AM -
José Luis Bezerra CEPLAC, BA PQ 1D
José Rubens Pirani USP, SP PQ 1A
Kátia Cavalcanti Porto UFPE, PE PQ 1D
Laíse de Holanda C. Andrade UFPE, PE PQ 1A
Leandro de O.F. de Souza UFERSA, RN -
Leonardo Pessoa Félix UFPB, PB
Leonor Costa Maia UFPE, PE PQ 1B
Lígia Queiroz Matias UFC, CE -
Luci de Senna-Valle MN-UFRJ -
Lucia Garcez Lohmann USP, SP -
Luciano Paganucci de Queiroz UEFS, BA PQ 1D
Luis Fernando P. Gusmão UEFS, BA -
Marcela Eugênia da S. Cáceres UFS, SE PQ 2
Marcelo Tabarelli UFPE, PE PQ 1A
Marcos Sobral UFSJ, MG -
Marcus Alberto Nadruz Coelho JBRJ, RJ -
Marccus Vinícius Alves UFPE, PE -
Maria Auxiliadora Cavalcanti UFPE, PE PQ 2
Maria Alice Neves UFPB, PB -
Maria Candida Henrique Mamede IBt, SP PQ 2
Maria das Graças M. de Souza UnB, DF -
Maria de Fátima Figueiredo Melo INPA, AM -
Maria Elizabeth B. Pedrosa UFRPE, PE -
Maria Iracema Bezerra Loiola UFC, CE -
Maria Regina de V. Barbosa UFPB, PB PQ 2
Mariângela Menezes UFRJ, RJ PQ 2
Marlene de Alencar Barbosa UFPE, PE -
Marli Pires Morim JBRJ, RJ -
Rafaela Campostrini Forzza JBRJ, RJ PQ 2
Regina Célia de Oliveira UnB, DF -
Rita Baltazar de Lima UFPB, PB -
Rita de Cássia Araújo Pereira IPA, PE -
Rosângela P. de Lyra Lemos IMA, AL -
Roseli Farias M. de Barros UFPI, PI -
Ruy José Válka Alves JBRJ, RJ PQ 2
Sérgio Romaniuc-Neto USP, SP
Tatiana Gibertoni UFPE, PE PQ 2
3. RESEARCH PROGRAM IN TAXONOMY
The Virtual Herbarium’s research program has the following aims: increase the number of networked herbaria by 100%; improve the quality of taxonomic identification; increase the level of digitization of all holdings to 80%; define strategies to guarantee taxonomic research of less studied groups; and increase the levels of interaction between different research groups.
In 2009 efforts were made to promote a greater level of involvement within participating herbaria. As a result three new herbaria were incorporated into the program (two from Pernambuco – HVASF and HTSA – and one from Espírito Santo – VIES) and the number of records that were digitized and made available online increased significantly (see Table 6).
Two activities that have been very important for the future of the Virtual Herbarium are: (a) the definition of taxonomic groups whose identification represents a bottleneck for the advancement of knowledge due to the large number of species or to the complexity of the relationships between taxa; and (b) the development of tools that enable the evaluation of the size of the problem and the determination of priority actions to be implemented.
A survey of plant herbaria data available on the speciesLink network was carried out to identify the number of records lacking identification at the genus and species level (Table 1). A specialists’ visiting program to selected herbaria was planned based on these data. The number of unidentified or partially identified fungi data records is still being evaluated.
Table 1. Families and corresponding number of records without data for genus and/or species (source speciesLink, May 2009)
Families Number of records Families Number of records
Fabaceae 33.000 Eriocaulaceae 5.100 Euphorbiaceae 16.041 Bignoniaceae 5.044 Rubiaceae 13.324 Cyperaceae 4.824 Asteraceae 11.752 Lauraceae 4.563 Malpighiaceae 10.336 Orchidaceae 4.143 Myrtaceae 10.276 Solanaceae 4.123 Melastomataceae 10.228 Clusiaceae 4.061 Apocynaceae 6.529 Piperaceae 4.023 Malvaceae 5.976 Acanthaceae 3.718 Poaceae 5.785 Sapindaceae 3.159
In 2009 specialist teams made visits to ten selected herbaria in order to help reduce the number of unidentified records (Table 2). 16,639 samples were examined.
Table 2. Visits of specialist to selected herbaria to revise or identify specimens in 2009 Specialist / Institution
of origin Visited Herbaruim / Institution / State / Períod of Visit Families revised/ Number of exsiccates examined
Haroldo Cavalcante de Lima and collaborators; Jardim Botânico do Rio de Janeiro, RJ
BHCB, Universidade Federal de Minas Gerais, MG; OUPR, Universidade Federal de Ouro Preto, MG; April, 2009
Leguminosae from the Atlantic Rain Forest, BHCB (3.500); OUPR (3.000); Total: 6.500 Haroldo Cavalcante de
Lima and collaborators Jardim Botânico do Rio de Janeiro, RJ
MBM, Museu Botânico Municipal de Curitiba, PR
UPCB, Universidade Federal do Paraná HBR, Herbário Barbosa Rodrigues, SC ICN, Universidade Federal do Rio Grande do Sul, RS
PACA, Instituto Anchietano de Pesquisas/ Unisinos, RS
May, 2009
Leguminosae from the Atlantic Rain Forest MBM (3.000); UPCB (300); HBR (600); ICN (1.100); PACA (400) Total: 5.400
Ariane Luna Peixoto Jardim Botânico do Rio de Janeiro, RJ
HUEFS, Universidade Estadual de Feira de Santana, BA
CEPEC, Centro de Pesquisas da Lavoura do Cacau, BA July, 2009 Monimiaceae and Siparunaceae: CEPEC (50+30), HUEFS (35+28). Total: 143 Tatiana Baptista Gibertoni Universidade Federal de Pernambuco, PE and Leif Ryvarden Universidade de Oslo, Noruega
INPA, Instituto de Pesquisas da Amazônia, AM
September – October, 2009
Fungos poliporóides: Ganoder-mataceae (391); Meruliaceae (96); Hymenochaetataceae (463); Polyporaceae (2.095); Fomitopsidaceae (142); Gloeophyllaceae (72); Penio-phoraceae (6); Schizophylla-ceae (7); SchizoporaSchizophylla-ceae (20); Stereaceae (5) Total: 3.297 Jadergudson Pereira Universidade Estadual de Santa Cruz, BA
INPA, Instituto de Pesquisas da Amazônia, AM September, 2009 Xylariaceae (161) Marccus V. Alves Universidade Federal de Pernambuco, PE
INPA, Instituto de Pesquisas da Amazônia, AM September, 2009 Cyperaceae (350); Juncaceae (17) and Rapateaceae (15). Total: 382 Marcos E. G. Sobral Universidade Federal de Ouro Preto, MG
VIES, Universidade Federal do Espírito Santo, ES
October, 2009
Myrtaceae and others (65)
Jorge Fontella Pereira Museu Nacional – UFRJ, RJ
IMA, Instituto de Meio Ambiente, AL UFP, Universidade Federal de Pernambuco November, 2009
Apocynaceae Asclepiadoideae IMA (43), UFP (50). Total: 93 Olga Yano
Instituto de Botânica SP
HUCS-Universidade de Caxias do Sul, RS PACA- Instituto Anchietano de Pesquisas/ Unisinos, RS,
ICN-Universidade Federal do Rio Grande do Sul, RS,
HAS- Fundação Zoobotânica do Rio Grande do Sul, RS.
November, 2009
Musgos: HUCS (60); PACA (157); ICN (120). Total: 337
José Iranildo M. de Melo
Universidade Estadual da Paraíba, PB
HVASF,Universidade Federal do Vale do São Francisco
HTSA, Embrapa Semiárido November, 2009
Boraginaceae
HVASF (198), HTSA (63). Total: 261
4. TRAINING
B
EST PRACTICESThe Virtual Herbarium initiated a training program aimed at curators and technicians working in the herbaria of associated institutions. In July 2009 a short course was offered in database management in the Northeast and another course about herbaria management is planned for May/June 2010 in the Southeastern region of the country. The content of each course focuses on the most common problems presented by the institutions and tries to disseminate the most modern and appropriate techniques for the different taxonomic groups of interest. The courses also train technicians to help in collecting, drying, and documenting plants and fungi.
N
EW TAXONOMISTSThrough its associated institutions the Virtual Herbarium is participating in six graduate programs where new taxonomists are being trained. It is the aim of this Project to promote a greater integration between these programs by organizing advanced courses on the taxonomy of specific groups, disseminating new techniques, and establishing partnerships with collaborating foreign institutions.
One of the strategies is to bring foreign visiting specialists to run specific courses within these programs, as well as to contribute to broader courses covering all interests. The courses offered in 2009 are listed in Table 3. These include courses offered as part of the graduate programs at INPA and UFPE, as well as a training course for new taxonomists at undergraduate level offered in Maceió, Alagoas, where there are no graduate courses in Botany.
Table 3. Disciplines offered in Graduate Programs, short courses carried out in scientific events, and courses offered in partner institutions in 2009.
Title of the course/place/date Professors/Institution workload/Number of students/Origin of students
Introduction to the use of tools for the computerization of herbaria;
Universidade Federal de Pernambuco; Recife, june 2009
Itamar Barbosa de Lima
(Universidade Federal da Paraíba) 40 hours; 18 students; UFPE, IPA, UFRPE, UNICAP, UFAL UFPB, UFRN
Computerization of botanical collections using Brahms and the speciesLink network; 60º Congresso Nacional de Botânica ; Feira de Santana, July, 2009
Alexandre Marino (CRIA) e; Gracialda Ferreira (Universidade Federal Rural do Amazonas)
16 hours; 13 students; CEPEC, HUEFS, UMAC, UNEB, UFBA, FUEL, HUEM, HSTA, IPA, R, UFRN
New Approach on Taxonomy of arbuscular mycorrhizal fungi (Glomeromycota); PPG Biologia de Fungos, UFPE; Recife, August 2009
Fritz Oehl (Agroscope Reckenholz-Tänikon Research Station ART, Suíça) and Bruno Goto
(Universidade Federal do Rio Grande do Norte)
30 hours;14 students; UFPE, FUNESO
Techniques for Identification of Tropical Polipore; PPG-Botânica, INPA; Manaus, September 2009
Dra. Tatiana B. Gibertoni (Universidade Federal de Pernambuco) and Leif Ryvarden (University of Oslo)
30 hours; 15 students: INPA, MG
Title of the course/place/date Professors/Institution workload/Number of students/Origin of students
Training in species identification of the families Cyperaceae, Juncaceae, and Rapateaceae; INPA; Manaus,
September 2009
Dr. Marcus Alves (Universidade
Federal de Pernambuco); 15 hours; 3 students; UNESP, MG, INPA
Botanical Nomenclature; PPG Biologia Vegetal, UFPE; Recife, November 2009
Dr. Jorge Fontella Pereira (Museu Nacional do Rio de Janeiro and do Herbário Bradeanum) and Dr. Maria Regina de Vasconcellos Barbosa (Universidade Federal da Paraíba)
60 hours; 25 students: UFPE UFRPE, UNIVASF, UNB, UNESP, IMA
Botanical Nomenclature; Instituto do Meio Ambiente de Alagoas; Maceió, November 2009
Dr. Jorge Fontella Pereira (Museu Nacional do Rio de Janeiro e do Herbário Bradeanum)
40 hours, 10 students; UFAL, CESMEC Taxonomy of Plants from the
Caatinga; Universidade Federal do Vale de São Francisco; Petrolina, November 2009
Dr. José Iranildo Miranda de Melo (Universidade Estadual da Paraíba)
12 hours; 34 students: UNIVASF, EMBRAPA Semiárido
The following graduate programs are linked to the leading and associated institutions:
• Graduate course on Fungal Biology – UFPE (Concept 5 at CAPES) – unique in the country as it is exclusively about the study of fungi. It has been in existence for over 25 years and is recognized for its emphasis on training of taxonomists. Nine teachers from the program participate in the project.
• Graduate program in Plant Biology – UFPE (Concept 5). This program is also consolidated and is recognized for the large scope of its research. Six teachers of the program participate in the project.
• Graduate program in Plant Biodiversity and the Environment – IBt-SP (Concept 4). The objective of the program is to train professionals to interpret situations of environmental impact by assessment of their impact on the vegetation. Three teachers of the program participate in the project.
• Graduate program in Botany and Plant Biodiversity – JBRJ (Concept 3). This program follows JBRJ’s strategy to become a center of excellence in the dissemination of botanical and environmental studies. Three teachers of the program participate in the project.
• Graduate program in Botany – UEFS (Concept 5). The main objective of this program is to train new taxonomists to work in Brazil’s semi-arid region. Two teachers of the program participate in the project.
• Graduate program in Biological Sciences (Botany) – Museu Nacional (Concept 4). This course began in 1972 (masters) and in 1998 a PhD course was initiated. It is one of the
oldest graduate courses in botany of the country. Four teachers of the program participate in the project.
5. VIRTUAL HERBARIUM
B
ASELINEThe information system of the Virtual Herbarium uses the speciesLink1 network as its
platform. In order to be able to follow the project’s progress concerning free and open availability of data through the Internet, a baseline was established as the project’s starting point (Table 4). Table 4. Status of collaborating and associate collections (January, 2009)
Institution Project
Commitment Herbarium estimated holding online data
Universidade Federal de Pernambuco Coordinator URM 78,852 12,014
UFP - Herbário 51,020 14,463
UFP- Carpoteca 390 390
Universidade Federal de Sergipe Collaborator ASE 13,000 10,333
Universidade Federal do Ceará Collaborator EAC 42,000 21,149
Universidade Federal da Paraíba Collaborator EAN 13,000 4,574
Universidade Federal Rural de
Pernambuco Collaborator HST PEUFR 15,500 349 12,909 349
Instituto do Meio Ambiente do Estado
de Alagoas Collaborator MAC 32,000 18,584
Instituto de Botânica Associate SP 350,000 35,699
SP-Algas 30,000 26,240
Instituto Nacional de Pesquisas da
Amazônia Associate INPA - Herbário INPA - Fungos 220,000 8,840 210,683 8,840 Empresa Pernambucana de Pesquisa
Agropecuária Collaborator IPA 81,000 26,654
Jardim Botânico do Rio de Janeiro
(JBRJ) Associate RB RBdna 450,000 2,583 336,065 2,583
RBw 8,200 7,600
Universidade Federal Rural do
Semi-Árido Collaborator MOSS 9,782 7,500
Universidade de São Paulo Collaborator SPF 133,500 21,270
SPF – Algas 22,828 22,132
Universidade Federal do Piauí Collaborator TEPB 23,130 8,257
Universidade Estadual de Londrina Collaborator FUEL 44,000 42,058
Universidade Federal do Rio Grande
do Norte Collaborator UFRN UFRN - Fungos 8,200 500 7,249 0
Universidade Federal da Paraíba (UFPB)
Associate JPB 40,000 35,865
Departamento de Botânica da UFMG Collaborator BHCB 125,000
1
Institution Project Commitment Herbarium estimated holding online data
Centro de Pesquisas do Cacau Collaborator CEPEC 114,000 Faculdade São Lucas, Porto Velho Collaborator HFSL 4,241
Museu Nacional (MN/UFRJ) Associate R 375,000
Universidade de Brasília Collaborator UB 200,000
Universidade Federal de Goiás Collaborator UFG 120,000 Universidade Estadual de Feira de
Santana (UEFS) Associate HUEFS 100,000
Total Collaborators and Associated Institutions
23 32 2,716,915 893,460
Names in green indicate the collaborating and associate institutions that were not sharing data through the speciesLink network when the project began. Participating herbaria in January 2009 contributed a total of 2.7 million exsiccates of which 893.460 data records were online. This baseline includes only collaborating and associate institutions of the project, but the speciesLink network has data from other herbaria, both in Brazil and abroad that are repatriating their Brazilian records (Table 5).
Table 5. Herbaria that are making their data available through the speciesLink network and will be invited to become part of the Virtual Herbarium
Institution Estimated holding Online records
BOTU 24,000 1,399 CPMA 2,150 2,072 ESA 120,000 94,179 HISA 10,235 1,287 HRCB 40,000 6,541 HSJRP 28,000 12,600 HSJRP Algae 691 691 HSJRP Bryophyta 4,866 4,866 HSJRP Pteridophyta 28,000 7,557 HUEM 14,343 372 HUMC 7,000 4,672 HUPG 15,000 2,386 IAC 50,000 43,116 INCAPER 998 99 MBM 320,000 238,153 MBML Herbario 33,143 33,143 SPSF 37,903 36,045 UEC 148,083 55,523 VIES 15,000 10,113
Total Not Associated 899,412 554,814
Repatriated data
MOBOT BR 157,087 157,087
NYBG BR 225,061 225,061
Total Repatriation 382,148 382,148
Adding all data from Brazilian herbaria, the Virtual Herbarium’s baseline holdings sum to 3,616,327 records, of which 1,448,274 are online. As the estimated number of exsiccates deposited in Brazilian herbaria is 6 million, the Virtual Herbaria begins with about 60% of the total holdings directly or indirectly associated with the project. Furthermore, about 497 thousand records are geo-referenced, representing 34% of the online data.
Concerning data repatriation, the Project begins with the Botanical Gardens of New York and Missouri which are repatriating 382,148 records, 135,628 (35%) of which are geo-referenced.
This is the project’s base line and will in future serve as a parameter to evaluate the project’s progress.
W
ORK CARRIED OUTChange of protocol (from DiGIR to Tapir)
In 2001/2002 CRIA’s team, with the support of Fapesp, participated actively in an international initiative led by the Universities of Kansas and California at Berkeley to develop a data model and communication protocol to integrate data systems for biological collections. The data model adopted was DarwinCore2 and involves 48 data fields for all taxonomic groups. The
communication protocol based on a Client-Server architecture is called DiGIR3 (Distributed Generic Information Retrieval).
Figure 1 shows the basic architecture adopted by most collections from the Americas. The portal is a software package responsible for receiving queries from the search interface, redirecting them to providers, receiving the answers and returning them to the search interface. The portal can send a request to several providers, communicating through the protocol and can also determine which provider should be consulted based on existing metadata.
The provider is a software package responsible for serving data and metadata to the portal from multiple data sources in a structured way. The provider is implemented as a web application that answers questions from the portal. The provider receives an XML document, validates the document, generates the search, and prepares the answer in the required format, also as an XML document. The communication protocol between the Portal and the Provider is DiGIR.
2
See http://splink.cria.org.br/digir/darwin2.xsd
3
website Presentation Layer DiGIR Portal (Java) Data ProviderPHP Collection Management System SQL Biological Collection Lib DiGir
Fast and stable connectivity
Figure 1. Basic architecture for a DiGIR network
Three elements are required in order to serve data through a distributed network: fast and stable connectivity; an online data server accessible 24 hours a day; and qualified personnel that can guarantee a permanent service. Most Brazilian collections do not have even one of these. The speciesLink network has introduced a new element to the architecture, a cache node, responsible for mirroring data from the collections and in serving the data to the network (Figure 2).
Data PostgreSQL Provider PHP Mirror SOAP server SQL
Data spLinkerJava
Collection Management System SQL Collections (A, B, C, D) Data Repository SOAP Portal DiGIR Cache node Translator
Fast and stable connectivity
Slow or unstable connectivity
B A
C D
Figure 2. Architecture of the speciesLink network
European collections have developed a data model and data transfer protocol that are different from DarwinCore and DiGIR. Their data model is called ABCD (Access to Biological
Collection Data) and includes more than 500 data fields. The protocol used to serve data is called BioCase.
The two systems are incompatible and GBIF (Global Biodiversity Information Facility)4 must run a system using both protocols in order to integrate data from all its members. A new protocol TAPIR (TDWG Access Protocol for Information Retrieval)5 has been developed to deal with both data models so that eventually only one global protocol, common to all networks of biological collections, will be needed. DiGIR networks are migrating to the new protocol and as time passes all programs written for DiGIR will become obsolete. That is why changing the protocol is considered a priority and was carried out at the beginning of the project, before increasing the number of herbaria on the network.
Both protocols DiGIR and TAPIR are based on a client-server architecture. A TAPIR provider was installed in all cache nodes of the speciesLink network and a new TAPIR portal was developed by CRIA. This work also required the development of a new search engine (indexer) to collect, parse, and store data to facilitate fast information retrieval and to enable the production of indicators and the use of other applications such as data cleaning through a centralized database (Figure 4).
The migration to TAPIR began with the servers in São Paulo State due to their proximity to CRIA and because they were the first servers of the network and were already requiring updates. The actual physical distribution of the servers was also optimized. The distribution of cache nodes and the location of the collections can be seen at Figure 3. Besides three servers in the state of São Paulo, the network has cache nodes in Manaus, Vitória, Rio de Janeiro and Curitiba. All collections (in green) send their public data to one of these cache nodes which then serves the network.
4
Find out more about GBIF at http://data.gbif.org
5
Figure 3. Geographic distribution of the cache nodes (in blue) and of the collections (in green) of the
speciesLink network
The work carried out in each cache node included:
• Installation and update of all software of all providers. Subversion 1.4.x; PHP 5.x and Perl modules
• Compatibility of the PostgreSQL database with TapirLink
• “Debug” and changes in the TapirLink code that was presenting errors in some servers. Once all necessary software had been installed, the next step was to install the Tapir provider in accordance to the following steps:
• Download of the TapirLink6 software
• Configuration of the connection module with PostgreSQL of the PHP • Configuration of the Apache web server
6
• Configuration of the user and password in order to have access to the administration page of the provider
After installation on the provider had been completed the resources that were on the DiGIR provider were transferred to Tapir. The new indexer/harvester was installed and became responsible for updating the centralized database. A web service was also made available in order for the openModeller7 framework to have access to the data (Figure 4).
DiGIR Portal
Cache node Cache node
Indicators Network Manager
Query interface
Data cleaning
Web Site webservicemapcria
Data analysis Maps PostGIS Central Repository Data Harvester Collections with a TAPIR provider Collections with spLinker TAPIR SOAP TAPIR Tapir provider webservice
Figure 4. Diagram with the complete architecture of the speciesLink network
Inclusion of new collections to the speciesLink network
The following procedure was carried out in order to integrate new collections to the network: • A standard mandatory questionnaire8 was sent to each collection.
• The questionnaire was analyzed as to the data structure, software used, number of digitized records, and total holdings.
• The cache node was prepared to receive data from the collection.
• The collection was visited by technicians or a remote access to the computer was made in order to install the software spLinker, developed by CRIA, responsible for mapping
7
Formore information about OpenModeller access http://openmodeller.sourceforge.net
8
data fields following the DarwinCore standard and in sending the data to the selected cache node.
• If necessary, filters to mark sensitive data were created.
• Data was transferred to cache nodes and possible transmission errors were identified. This part of the work had to have one technician at the collection (or logged on to the computer of the collection) and one at CRIA monitoring the transmission.
• When the technician was physically at the collection, local staff was trained in the use of
spLinker and other tools9 available at the speciesLink network were demonstrated.
Special attention was given to the data cleaning and collection profile reports produced by the system based on online records.
In 2009 the speciesLink network integrated 29 new collections, six of which were herbaria, one being from abroad.
• FURB, Herbário Dr. Roberto Miguel Klein • HTSA, Herbário do Trópico Semi-Árido • HVSF, Herbário Vale do São Francisco
• UFACPZ, Herbário da Universidade Federal do Acre
• HUEFS, Herbário da Universidade Estadual de Feira de Santana
• NMNH-Botany_BR, Smithsonian Department de Botany - Brazilian records
Besides the inclusion of these new collections, 68% of herbaria that are part of the speciesLink network updated their data in 2009. The network is serving approximately 2.27 million records, of which 930,000 are geo-referenced (December 10, 2009).
Website
The development of the website INCT Herbário Virtual da Flora e dos Fungos began in 2009 and can be accessed at http://inct.florabrasil.net. It is a dynamic system with regular updates.
A Linux Server was prepared to receive the site (Debian GNU/Linux “Lenny”). The database MySQL was installed on an Apache web server, together with programming language PHP, and Ws-ftp file transfer protocol. Wordpress was also installed. A number of adjustments were made such as the configuration of the database, configuration of users and names. All software was installed with the latest versions and all were free. Those responsible for implementing the site have full access to Wordpress and ftp.
9
New outputs of the information system
Although this activity was scheduled to begin during the project’s second year, due to the fact that the project began with a very large amount of data, the first product was developed to offer data to help determine the specialists’ visiting program by identifying herbarium material at partner institutions that required identification.
For all records classified as "Plantae", those that had an entry in the field "family" but no entry in the field "genus" were selected. The exercise was designed to verify if this information indicated gaps (local, regional, national) in taxonomic knowledge. A list of a total of 68,051 records from 558 families which matched these criteria were sent to the Steering Committee..
A second spread sheet was prepared by selecting records classified as “Plantae” with both fields “family” and “genus” not blank and the field “species” blank or sp (and its variations such as spp. sp., etc.). In this case, data was presented for each herbarium. This second spreadsheet contained about 200 thousand records. By knowing which were the unidentified records and where they were located it was possible to develop a strategy to improve data quality and to program training courses.
At the time New York also had some records with incomplete identification, and we believe this could lead to an opportunity of collaboration and training.
These reports were generated through direct access to the database and will now serve as an example for the development of an advanced search interface that will be launched in 2010. Through this new interface it is expected that all interested may carry out this type of analysis independently.
Another important application developed in 2009 involved the automatic geo-referencing of records with data of the municipality where the sample was collected. All collections that have records of samples from Brazil that are not geo-coded but have municipality data, have a spreadsheet available produced by an automatic geo-referencing application with the values for latitude, longitude, datum, and maximum error. For users that are searching the database, the system presents new columns with this data, making it clear that this is not original data, but data produced by an application.
In December 2009 there were 2.27 million records, of which 842 thousand were geo-referenced at the origin and an additional 800 thousand which had been geo-geo-referenced automatically, using the geo-referencing tool. This way, for those questions that require a precision at the municipality level, these new data are good and these users are now able to count with about double the amount of data they had before.
Data repatriation
At the beginning of the project, Brazilian data from the botanical gardens of New York and Missouri had already been integrated to the speciesLink network.
Visits were made to the National Museum of Natural History in Paris, France, Kew Gardens in the UK and to the Smithsonian Institution in the USA with the aim of understanding the type of data system in each institution and to study whether a repatriation program could be initiated. All three institutions have two features in common: they are serving data to GBIF; and they have received support from the Mellon Foundation to produce high resolution images of their type specimens from Latin America.
Another important initiative was the project being developed through a cooperation between the Paris Museum, the Botanical Institute of São Paulo, and CRIA, with the support of Fapesp (São Paulo Research Foundation) to develop a prototype of the Virtual Herbarium of A. de Saint-Hilaire10. All samples collected by Saint-Hilaire are being scanned and the images are being sent
to CRIA for online dissemination.
The diagram of the strategy adopted for the prototype is presented on Figure 5.
Sonnerat DB França SH@CRIA DB Brasil Transcrições DIGiR
Servidor de imagens eRez
Figure 5. Diagram of the data repatriation system for the holdings of Saint-Hilaire at the Paris Museum
10
An important concept when defining a data integration strategy is that only one database should be used as reference. Each update must be done at this reference database and data repatriation or transfer must be carried out from this same database.
In the case of Paris, any transcription or data entry must be fed into the Sonnerat database in Paris. For this project an application was developed to transfer data from Sonnerat to a database at CRIA through the DiGIR protocol to serve as the informational base of the system in Brazil. The system checks every hour whether there is an update in Paris. Special software tools were developed to make high resolution images available through the Internet and a prototype was launched with excellent results.
A visit was also made to the Royal Botanic Gardens, Kew in order to know more about its digitization process and quality control of the images that are part of the Mellon Foundation project. The first step is to attribute a bar code to each species of each sample. This barcode is entered into the information system and the exsiccate is cleaned so that dust does not affect the quality of the scanning.
Figure 6. First step: cleaning, barcoding, and digitizing metadata
Figure 7. Scanning
In the case of samples with volume, a high resolution camera is used at Kew (Figura 8).
Figure 8. Digital camera used in the case of material with more volume
The images then go through a thorough quality control check and if not approved the process is carried out again.
Defining a strategy for data repatriation
Many herbaria that have type specimens from Latin America are receiving grants to digitize their material and therefore are acquiring expertise and equipment in this area. It is important for the Virtual Herbarium to develop an image server to receive these high resolution images and associated metadata in order to make all this material publicly accessible and integrated with the other data. This can then be linked to a cyber identification service with specialists from Brazil and abroad aiming at improving the identification of material collected in Brazil.
Since different institutions have adopted different information systems and different procedures for treating and computerizing their holdings, it is important to qualify these different situations in order to define specific strategic actions that are compatible with long term programs.
The following situations can be found and require different strategies: • Holdings are digitized and data is available online
• Samples are identified but are not digitized • Samples are not identified nor digitized; and, • Holdings with all examples above.
In order to repatriate data that is already available online it is necessary to evaluate the compatibility of the data fields with DarwinCore and to study mechanisms of data export and indexing. If the collection already serves data to GBIF, repatriating this data and making it available through the speciesLink network technically speaking is practically immediate and will most probably be carried out by harvesting an existing DiGIR provider.
Many collections abroad do not have teams to process data associated to samples collected in Brazil. If this is the case, possible strategies to be agreed upon with each herbarium are:
• Digitization services are hired in Brazil or abroad (funding from the Brazilian government and/or partners)
• Brazilian specialists and technicians are sent to work on the digitization of data and identification of the material at the partner organization.
A third possibility is to take low resolution pictures of each sample and send them to Brazil so that the label data can be digitized. All data that is digitized must be sent and imported into the local system at the partner institution. Data repatriation will be carried out accessing the local system.
In some international herbaria the characterization and taxonomy of the samples must be revised. In places where specialists for specific groups do not exist or are insufficient it is important to establish a research program where Brazilian specialists and graduate students may be involved with work on taxonomic revisions, cataloging and identification of material with local or remote
supervision. Again, we suggest that all data digitization be carried out in the system used by the partner institution in order to guarantee continuity of the dynamic repatriation process of data from all samples collected in Brazil.
Maintenance
Routine maintenance includes hardware maintenance, software updating, backup, problem solving, and a help desk to support curators and other people responsible for the data of the herbaria and a help desk to attend user needs.
6. BIBLIOGRAPHIC PRODUCTION
The bibliographic production of the Virtual Herbarium team members is presented in Annex and demonstrates advances in taxonomic studies, revisions, new references, and plant and fungi species descriptions from different regions of Brazil.
7. PROGRESS INDICATORS
The first criterion used to evaluate the project’s progress is the increase in the quantity of data freely and openly available through the network. Table 6 presents the evolution of online data availability for the herbaria that are part of the project together with other herbaria from Brazil and abroad that are disseminating their data through the speciesLink network.
Table 6. Growth of the number of data available online (December, 2009)
Online Records 2008 2009 Growth
Total records available online
INCT 893,460 1,144,194 28.0%
Brasil not INCT 554,814 671,141 5.9%
Repatriation 382,148 456,817 14.5%
Online georeferenced records
INCT 442,599 559,446 26.4%
Brasil not INCT 80,661 128,626 59.5%
Repatriation 151,966 154,485 1.7%
Herbaria involved with the INCT Project increased their contribution to the amount of data available online by 28%, whereas herbaria that are not participating grew only 5.9%. Data repatriated from foreign herbaria increased by 14.5%. The increase in the amount of geo-referenced data, which increases data value, was another important feature. Those herbaria that have been involved with the speciesLink network for a longer time contributed only about 6% of new data, but the number of geo-referenced records in their holdings grew in the order of about 60% during 2009.
Another interesting parameter is th this project and are sharing their data
represented such as Minas Gerais and Rio Grande do Sul object of an action plan in the near
Figure 9. Number of herbaria participating of the INCT Project The next indicators include a
be able to analyze the indicators based on data that are openly available and accessible to all.
Figure 10. Number of records per geographic region of Brazil Amazonas; 2
Paraíba; 2 Piauí; 1
Ceará; 1 Sergipe; 1 Santa Catarina; 1
Another interesting parameter is the number of herbaria in each state that are participati this project and are sharing their data (Figure 9). One can see that important states are not
Minas Gerais and Rio Grande do Sul, just to mention two. object of an action plan in the near future.
Number of herbaria participating of the INCT Project sharing their data online (December, 2009)
The next indicators include all herbaria data, e.g. INCT project added to all others, in order be able to analyze the indicators based on data that are openly available and accessible to all.
Number of records per geographic region of Brazil (Source: species Pernambuco; 5 São Paulo; 5 Rio de Janeiro; 4 Rio Grande do Norte; 3 Amazonas; 2 Santa Catarina; 1 Paraná; 1 Alagoas; 1
e number of herbaria in each state that are participating in mportant states are not , just to mention two. These should be
sharing their data online per Brazilian State ll herbaria data, e.g. INCT project added to all others, in order to be able to analyze the indicators based on data that are openly available and accessible to all.
speciesLink 10/12, 2009)
The southeast is the best represented region with 0.79 records per km2, followed by the
South Northeast, Center-West and the North which is the third largest region in terms of the number of records contributed but last in terms of records per km2 (0.09) . This region includes
important centers such as Embrapa and Museu Paraense Emílio Goeldi that must be integrated to the network.
Figure 11. Number of records per Brazilian State (Source: speciesLink December 10, 2009)
All states are represented even when there are no collections from that state sharing their data through the network. This fact shows the importance of data sharing where each state benefits from local samples and associated data deposited in collections located in other states.
The indicator of the types (Figure 12) demonstrates the use of a data field for observations and demonstrates the necessity to train people working with data input on the use of standards. One can see that this field was filled out with terms such as “possible” or “probable”, when this should be expressed in an observation field.
Figure 12. Graphic with the number of types available on line (Source: speciesLink 10/12, 2009)
The “family” indicator (Figure 13) presents the 20 families most collected, based only on online data. Throughout the Project more detailed reports should be produced to evaluate taxonomic and geographic information gaps.
To evaluate the cost to digitize data of the herbaria that are already making their data online there is another indicator called “databasing” (Figure 14).
Figure 14. Percentage of off-line data from participating herbaria
Some studies indicate a cost of R$ 2.00 per exsiccate just considering man power costs. So for this cost we have an estimate of R$ 3.6 million to fully computerize these holdings.
8. FINAL CONSIDERATIONS
The work is being carried out satisfactorily, as scheduled and keeping track of the established goals. In terms of public availability of data, the network is growing at about 28% a year. The inclusion of new herbaria should maintain this level of growth for some time, but when the larger herbaria are integrated into the network, it is expected that this level of growth will diminish as it will then depend mostly on digitizing new data and not on the integration of new holdings of digitized data.
Activities concerning integrating new collections into the network and training will continue as will the maintenance and continuous development of existing systems and routine services.
Besides increasing the amount of data available, improving data quality is also an important objective. The INCT specialist network has examined over 16.6 thousand samples, identifying and validating material observed. This activity will continue. Also concerning data quality and adding value to data, the tool to automatically georeference data has been very successful. Other
applications will be evaluated and developed throughout the project aiming at increasing data usage.
Training activities related to short courses, graduate disciplines, workshops and visiting specialists will continue to try to reach an ever increasing number of people (students, technicians, researchers) and regions of the country, disseminating and increasing taxonomic knowledge on the diversity of plants and fungi of the country.
9. ANNEX. BIBLIOGRAPHIC PRODUCTION
Journal papersAbrahao, M. C.; Gugliotta, A.M.; Gomes, E. Poliporóides (Basidiomycota) em fragmentos de mata no perímetro urbano de São José do Rio Preto, São Paulo, Brasil. Revista Brasileira de Botânica, v. 32, p. 427-440, 2009.
Almeida, V.R.; Costa, A.F.; Mantovani, A.; Esteves, V.G.L.; Arruda, R.C.O.; Forzza, R.C. Morphological phylogenetics of Quesnelia (Bromeliaceae, Bromelioideae). Systematic Botany, v. 34, p. 660-672, 2009.
Alvarenga, L.D.P.; Pôrto, K.C.; Silva, M.P.P. Relations bBetween Regional Local Habitat Loss and Metapopulation Properties of Epiphyllous Bryophytes in the Brazilian Atlantic Forest. Biotropica, v. 41, p. 682-691, 2009.
Alves, R.J.V.; Kolbek, J. Summit vascular flora of Serra de São José, Minas Gerais, Brazil. Check List (UNESP), v. 5, p. 35-73, 2009.
Alves, Ruy J.V.; Kolbek, J. Can campo rupestre vegetation be floristically delimited based on vascular plant genera?. Plant Ecology, p. 1-13, 2009.
Alves-Araujo, A.; Alves, M. Amaryllidaceae s.s. e Alliaceae s.s. ocorrentes no Nordeste do Brasil. Rodriguesia, v. 60, p. 311-331, 2009.
Alves, M.; Araújo, A.C.; Prata, A. P.; Vitta, F. ; Hefler, S. ; Trevisan, R. ; Gil, A. ; Martins, S.; Thomas, W. W. Diversity of Cyperaceae in Brazil. Rodriguesia, v. 60, p. 771-782, 2009.
Baltazar, J.M.; Gibertoni, T.B. A checklist of the aphyllophoroid fungi (Basidiomycota) recorded from the Brazilian Atlantic Forest. Mycotaxon, v. 109, p. 439-442, 2009.
Barbosa, F.R.; Maia, L.C.; Gusmão, L.P. Fungos conidiais associados ao folhedo de Clusia
melchiorii Gleason e C. nemorosa G. Mey. (Clusiaceae) em fragmento de. Acta Botanica
Brasilica, v. 23, p. 79-84, 2009.
Barbosa, F.R.; Maia, L.C.; Gusmão, L.P. Novos registros de Hyphomycetes decompositores para o estado da Bahia, Brasil. Acta Botanica Brasilica, v. 23, p. 323-329, 2009.
Barros, I.C.L.; Xavier, S.R.Silva. Pteridófitas do estado de Pernambuco: Gleicheniaceae. Bradea, v. 14, p. 11-20, 2009.
Bastos, C.J.P.; Yano, O. O gênero Lejeunea Libert (Lejeuneaceae) no Estado da Bahia, Brasil. Hoehnea, v. 36, p. 303-320, 2009.
Berg, C.C.; Pirani, J.R. Flora de Grão-Mogol, Minas Gerais: Urticaceae s.l. Boletim de Botânica, v. 27, p. 107-108, 2009.
Bordin, J. ; Yano, O. Novas ocorrências de Musgos (Bryophyta) para o Estado do Rio Grande do Sul, Brasil. Revista Brasileira de Botânica, v. 32, p. 455-477, 2009.
Bordin, J. ; Yano, O. Novas ocorrências de antóceros e hepáticas para o Estado do Rio Grande do Sul, Brasil. Revista Brasileira de Botânica, v. 32, p. 189-211, 2009.
Bordin, J. ; Yano, O. Briófitas do Centro Urbano de Caxias do Sul, Rio Grande do Sul, Brasil. Hoehnea, v. 36, p. 7-71, 2009.
Campacci, T.V.S.; Gugliotta, A.M. A review of Amauroderma in Brazil, with the new record of A.
oblongisporum in the neotropics. Mycotaxon, v. 110, p. 423-436, 2009.
Carrijo, T.T.; Freitas, M.F.; Peixoto, A.L. The identity and typification of Stylogyne laxiflora (Myrsinaceae). Nordic Journal of Botany, v. 27, p. 454-455, 2009.
Carvalho-Sobrinho, J.G.; Santos, F.A.R.; Queiroz, L.P. Morfologia dos tricomas das pétalas de espécies de Pseudobombax Dugand (Malvaceae, Bombacoideae) e seu significado taxonômico. Acta Botanica Brasílica, v. 23, p. 929-934, 2009.
Cervi, A.C.; Bona, C.; Moço. M.C.C.; Linsingen, L.V. Macrófitas aquáticas do Município de General Carneiro, Paraná, Brasil. Biota Neotropica, v. 9, p. 1-8, 2009.
Chiron, G.R.; Oliveira, R.P.; Santos, T.M.; Bellvert, F.; Bertrand, C.; Van Den Berg, C. Evolution of
Baptistonia (Orchidaceae, Oncidiinae): phylogeny and floral oil evolution. Plant Systematics and
Evolution, v. 281, p. 35-49, 2009.
Christo, A.G.; Guedes-Bruni, R.R.; Silva, A.G.; Peixoto, A.L. Structure of the shrub-arboreal component of an Atlantic Forest fragment on a hillock in the central lowland of Rio de Janeiro, Brazil. Interciencia, v. 34, p. 232-239, 2009.
Coelho, M.A.N.; Mayo, S.J. ; Waechter, J.L. Revisão taxonômica das espécies de Anthurium (Araceae) seção Urospadix subseção flavescentiviridia. Rodriguesia, v. 60, p. 799-864, 2009. Conceição, A.S.; Queiroz, L.P.; Lewis, G.P.; Andrade, M.J.G.; Schnadelbach, A.S.; Van Den Berg,
C. Phylogeny of Chamaecrista Moench (Leguminosae-Caesalpinioideae) based on nuclear and chloroplast DNA regions. Taxon, v. 58, p. 1168-1180, 2009.
Corrêa, I.P.; Pirani, J.R. Flora de Grão-Mogol, Minas Gerais: Umbelliferae (Apiaceae). Boletim de Botânica, v. 27, p. 103-106, 2009.
Costa, A.F.; Takata, R.M. Flora de Grão-Mogol, Minas Gerais: Ulmaceae. Boletim de Botânica, v. 27, p. 101-102, 2009.
Costa, N.M.S.; Van Den Berg, C. A new species of Stylosanthes Sw. (Leguminosae-Papilionoideae) from Paraná, Brazil. Neodiversity, v. 4, p. 9-13, 2009.
Costa, A. F.; Rodrigues, P.J.P.; Wanderley, M.G.L. Morphometric analysis and taxonomic revision of Vriesea paraibica complex Wawra (Bromeliaceae). Botanical Journal of the Linnean Society, v. 259, p. 161-181, 2009.
Drechsler-Santos, E.R.; Gibertoni, T.B.; Góes-Neto, A.; Cavalcanti, M.A.Q. A re-evalutation of the lignocellulolytic Agaricomycetes from the Brazilian semi-arid region. Mycotaxon, v. 108, p. 241-244, 2009.
Ferreira, F.M.; Costa, A.F.; Forzza, R.C. Aristidoideae, Chloridoideae, Danthonioideae e Pooideae (Poaceae) no Parque Estadual do Ibitipoca, Minas Gerais, Brasil. Boletim de Botânica, v. 27, p. 189-202, 2009.
Ferreira, F.M.; Costa, A.F.; Forzza, R.C. Bambusoideae (Poaceae) no Parque Estadual do Ibitipoca, Minas Gerais, Brasil. Boletim de Botânica, v. 27, p. 203-218, 2009.
Fiaschi, P.; Pirani, J.R. Review of plant biogeographic studies in Brazil. Journal of Systematics and Evolution, v. 47, p. 477-496, 2009.
Filgueiras, T.S.; Prado, J. Proposal to maintain the terminations of plant names cited in a validating Latin description or diagnosis in a new protologue. Taxon, v. 58, p. 663-664, 2009.
Garcia, R.J.F.; Longhi-Wagner, H.M.; Pirani, J.R.; Meirelles, S.T. A contribution to the phytogeography of Brazilian campos: an analysis based on Poaceae. Revista Brasileira de Botânica, v. 32, p. 703-713, 2009.
Giulietti, A. M. ; Andrade, M. J. G. De ; Parra, L. R. ; Van Den Berg, C. ; Harley, R. M. . (1902) Proposal to conserve the name Syngonanthus against Philodice (Eriocaulaceae). Taxon, v. 58, p. 1008-1009, 2009.
Gomes-Silva, A.C.; Ryvarden, L.; Gibertoni, T.B. New and interesting species of Hymenochaetaceae from the Brazilian Amazonia. Mycological Progress, v. 8, p. 273-279, 2009. Goto, B.T.; Costa, C.M.C.; Maia, L.C. Glomus halonatum Rose & Trappe (Glomeromycota) in South America: comments on the morphological characteristics of the species. Acta Botanica Brasílica , v. 23, p. 1167-1170, 2009.
Grokoviski, L.; Cervi, A.C.; Tardivo, R.C. O Gênero Piptocarpha R. Br. (Asteraceae: Vernonieae) no Estado do Paraná, Brasil. Acta Botanica Brasilica, v. 23, p. 486-498, 2009.
Iganci, J.R.V.; Morim, M.P.; Abarema (Leguminosae, Mimosideae) no Estado do Rio de Janeiro. Rodriguesia, v. 60, p. 581-594, 2009.
Iganci, J.R.V.; Morim, M.P. Three new species of Abarema (Leguminosae Mimosoideae) from south-eastern Brazil. Kew Bulletin, v. 64, p. 271-277, 2009.
Linsingen, L.V.; Cervi, A.C.; Guimarães, O. A. Sinopse Taxonômica da Família Combretaceae R. Brown na Região Sul do Brasil. Acta Botanica Brasílica , v. 23, p. 738-750, 2009.
Linsingern, L.V.; Cervi, A.C. Acrocomia aculeata (Jacq.) Lodd ex Mart., nova ocorrência para a flora do Estado do Paraná. Acta Biologica Paranaense, v. 38, p. 187-192, 2009.
Lopes, R.F.M.; França, G.S.; Silva, F.R.G; Sposito, T.C.; Stehmann, J.R. Estrutura do componente arbóreo de Floresta Estacional Semidecidual Montana Secundária no Alto Rio Doce, Minas Gerais, Brasil. Rodriguesia, v. 60, p. 1037-1053, 2009.
Lopes, R.C., Pirani, J.R. 2010. Agavaceae. In: Lista de Espécies da Flora do Brasil. Jardim Botânico do Rio de Janeiro. (http://floradobrasil.jbrj.gov.br/2010/FB000037).
Mantovani, A.; Pereira, T.E.; Coelho, M.A.N. Leaf midrib outline as a diagnostic character for taxonomy in Anthurium section Urospadix subsection Flavescentiviridia (Araceae). Hoehnea, v. 36, p. 269-277, 2009.
Marquínez, X.; Lohmann, L.G.; Salatino, M.L.F.; Salatino, A.; González, F. Generic relationships and dating of lineages in Winteraceae based on nuclear (ITS) and plastid (rpS16 and psbA-trnH) sequence data. Molecular Phylogenetics and Evolution, v. 53, p. 435-449, 2009.
Martins, E.G.A.; Pirani, J.R. Flora da Serra do Cipó, Minas Gerais: Cannabaceae. Boletim de Botânica, v. 27, p. 247-251, 2009.
Medeiros, D.; de Senna Valle, L.; Alves, R.J.V. ; Alves, R.J.V. Two new species of Croton L. (Euphorbiaceae) from campos rupestres of Minas Gerais State, Brazil. The Journal of the Torrey Botanical Society, v. 136, p. 186-191, 2009.
Melo, J.I.M.; Alves, M.V.; Semir, J. Padrões de distribuição geográfica das espécies de Euploca e
Heliotropium (Heliotropiaceae) no Brasil. Rodriguesia, v. 60, p. 1025-1036, 2009.
Moran, R.C.; Prado, J.; Labiak, P. H. Megalastrum (Dryopteridaceae) in the West Indies. Brittonia, v. 61, p. 273-292, 2009.
Moran, R.C.; Prado, J.; Labiak, P.H. Megalastrum (Dryopteridaceae) in Brazil, Paraguay, and Uruguay. American Fern Journal, v. 99, p. 1-44, 2009.
Mota, R.C.; Barros, F.; Stehmann, J.R. Two New Species of Orchidaceae from Brazil:
Bulbophyllum carassense and Lepanthopsis vellozicola. Novon, v. 19, p. 380-387, 2009.
Olmstead, R.G.; Zjhra, M.L.; Lohmann, L.G.; Grose, S.O.; Eckert, A.J. A molecular phylogeny and classification of Bignoniaceae. American Journal of Botany, v. 96, p. 1731-1743, 2009.
Pereira, J.; Bezerra, J.L.; Maia, L.C. Revision of taxa of the URM Herbarium 2. Hypoxylon species described by A.C. Batista. Mycotaxon, v. 104, p. 405-408, 2009.
Pereira, M.S.; Barbosa, M.R.V. Uma nova espécie de Coussarea Aubl. (Rubiaceae) para a Mata Atlântica no Estado da Bahia, Brasil. Acta Botanica Brasílica v. 23, p. 549-551, 2009.
Prado, J.; Moran, R.C. Checklist of the ferns and lycophytes of Acre State, Brazil. Fern Gazette, v. 18, p. 230-263, 2009.
Romaniuc-Neto, S.; Gaglioti, A.L.; Guido, B.M.O. Urticaceae Juss. do Parque Estadual das Fontes do Ipiranga, São Paulo, SP, Brasil. Hoehnea, v. 36, p. 193-205, 2009.
Santiago, A.L.C.M.A.; Cavalcanti, M.A.Q.; Trufem, S.F.B. The first record of Dimargaris bacillispora (Dimargaritales) in South America. Mycotaxon, v. 108, p. 201-204, 2009.
Silva, A.C.G.; Gibertoni, T. B. Checklist of the aphyllophoraceous fungi (Agaricomycetes) of the Brazilian Amazonia. Mycotaxon, v. 108, p. 319-322, 2009.
Silva, A.C.G.; Gibertoni, T.B. Revisão do herbário URM. Novas ocorrências de Aphyllophorales (Basidiomycetes) para a Amazônia brasileira. Revista Brasileira de Botânica, v. 32, p. 587-596, 2009.
Silva, M.P.P.; Pôrto, K.C. Effect of fragmentation on the community structure of epixylic bryophytes in Atlantic Forest remnants in the Northeast of Brazil. Biodiversity and Conservation, v. 18, p. 317-337, 2009.
Simon, M. F.; Grether, R.; Queiroz, L.P.; Skema, C.; Pennington, R.T.; Hughes, C. E. Recent assembly of the Cerrado, a neotropical plant diversity hotspot, by in situ evolution of adaptations to fire. Proceedings of the National Academy of Sciences of the United States of America, v. 106, p. 20359-20364, 2009.
Singer, R.B.; Azevedo, C.O.; Van Den Berg, C.; Aguiar, D. Prescottia ostenii Pabst (Orchidaceae): a new record for Brazil, with a complete morphological description. Kew Bulletin, v. 64, p. 543-547, 2009.
Sobral, M.; Stehmann, J.R. An analysis of new angiosperm species discoveries in Brazil (1990 - 2006). Taxon, v. 58, p. 227-232, 2009.
Souza Muñoz, M.E.; Giovanni, R.; Siqueira, M.F.; Sutton, T.; Brewer, P.; Pereira, R.S.; Canhos, D. A.L.; Canhos, V.P. OpenModeller: a generic approach to species potential distribution modelling. Geoinformatica, p. 1-20, 2009.
Teles, A.M.; Nakajima, J.N.; Stehmann, J.R. Senecio albus, a new species of Senecio sect.
Adamantina (Senecioneae Asteraceae) with an emendment to the section. Kew Bulletin, v. 64,
p. 161-165, 2009.
Thomas, W.W.; Araújo, A.C.; Alves, M. A preliminary molecular phylogeny of the Rhynchosporeae (Cyperaceae). The Botanical Review, v. 75, p. 22-29, 2009.
Valente, E.B.; Pôrto, K.C.; Boas-Bastos, S.V.; Bastos, C.J.P. Musgos (Bryophyta) de um fragmento de Mata Atlântica na Serra da Jibóia, município de Santa Teresinha, BA, Brasil. Acta Botanica Brasilica, v. 23, p. 369-375, 2009.
Van Den Berg, C.; Higgins, W.E.; Dressler, R.L.; Whitten, W.M.; Soto-Arenas, M.A.; Chase, M.W. A phylogenetic study of Laeliinae (Orchidaceae) based on combined nuclear and plastid DNA sequences. Annals of Botany, v. 104, p. 417-430, 2009.
Vianna Filho, M.D.M.; Carrijo, T.T.; Romaniuc-Neto, S. Sorocea carautana (Moraceae): A new species from Southeastern Brazil. Novon, v. 19, p. 549-551, 2009.
Wartchow, F.; Tulloss, R.E.; Cavalcanti, M.A. Amanita lippiae - a new species from semi-arid caatinga region of Brazil. Mycologia, v. 101, p. 864-870, 2009.
Yano, O.; Peralta, D.F. Flora de Grão Mogol, Minas Gerais: Briófitas (Bryophyta e Marchantiophyta). Boletim de Botânica, v. 27, p. 1-26, 2009.
Yano, O.; Bordin, J.; Peralta, D.F. Briófitas dos Estados do Ceará, Maranhão, Paraíba, Piauí e Rio Grande do Norte (Brasil). Hoehnea (São Paulo), v. 36, p. 387-415, 2009.
Zuquim, G.; Prado, J.; Costa, F.R.C. An Annotated Checklist of Ferns and Lycophytes from the Biological Reserve of Uatumã, an Area with Patches of Rich-soils in Central Amazonia. Fern Gazette, v. 18, p. 286-306, 2009.
Zuquim, G.; Costa, F.R.C.; Prado, J.; Braga-Neto, R. Distribution of pteridophyte communities along environmental gradients in Central Amazonia, Brazil. Biodiversity and Conservation, v. 18, p. 151-166, 2009.
Books
Alves, M.; Lucena, M.F.; Maciel, J.R.; Martins, S. Flora de Mirandiba. 1. ed. Recife: Associação Plantas do Nordeste, 2009. v. 1. 357 p.
Cervi, A. C.; Bernacci, L.C.; Nascimento, D.S. Passifloraceae. In: Stehmann, J.R.; Forza, R.C.; Salino, A., Sobral, M.; Costa, D.P.; Kamino, L.H.Y. (Org.). Plantas da Floresta Atlântica. Rio de Janeiro: Instituto de Pesquisa Jardim Botânico do Rio de Janeiro, 2009.
Giulietti, A.M.; Rapini, A.; Andrade, M.J. .; Queiroz, L.P.; Silva, J.M.C. (Orgs.) Plantas Raras do Brasil. Belo Horizonte: Conservação Internacional & Universidade Estadual de Feira de Santana, 2009. v. 1. 196 p.
Matos, E. ; Queiroz, L. P. Árvores para Cidades. 1ª ed. Salvador: Solislina, 2009. v. 1. 340 p. Mohr, L.V.; Castro, Alencar, J.W.; Alves, R.J.V. (Org.). Ilhas Oceânicas Brasileiras - da Pesquisa
ao Manejo, Vol. 2. Brasília: Ministério do Meio Ambiente, 2009. 300 p.
Queiroz, L.P. Leguminosas da Caatinga. 1ª ed., Feira de Santana: Universidade Estadual de Feira de Santana, 2009. v. 1. 443 p.
Stehmann, J.R.; Forzza, R.C.; Salino, A.; Sobral, M.; Costa, D. P.; Kamino, L. H. Y. (Org.). Plantas da Floresta Atlântica. Rio de Janeiro: Instituto de Pesquisa Jardim Botânico do Rio de Janeiro 2009. v. 1. 500 p.
Book chapters
Alves, M.; Alves-Araujo, A. Alliaceae. In: Giulietti, A. et al. (Org.). Plantas Raras do Brasil. Feira de Santana: CI, 2009, v. 1, p. 46-46.
Alves, M.; Alves-Araujo, A. Amaryllidaceae. In: Giulietti, A. et al. (Org.). Plantas Raras do Brasil. Feira de Santana: CI, 2009, v. 1, p. 51-51.
Alves, M.; Araújo, A.C.; Vitta, F. Cyperaceae - Plantas Raras Brasil. In: Giulietti, A. et al. (Org.). Plantas Raras do Brasil. Feira de Santana: CI, 2009, v. 1, p. 154-158.
Alves, M.; Araújo, A.C. Cyperaceae e Juncaceae. In: Stehmann, J.R.; Forzza, R.C.; Sobral, M., Salino, A. & Kamino, L.H.Y. (Org.). Plantas de Floresta Atlântica. Rio de Janeiro: Jardim Botânico do Rio de Janeiro, 2009, v. 1, p. 232-236.
Barbosa, M.R.V.; Lourenco, C.E.L.; Pessoa, M.C.R.; Melo, A.S. Rubiaceae. In: Lucena, M.F.; Maciel, J.R.; Martins, S. (Org.). Flora de Mirandiba. 1ª ed. Recife: Associação Plantas do Nordeste, 2009, p. 321-328.
Cabral, E.L.; Macias, L.; Di Maio, F.R. Germano Filho, P. Rubiaceae. In: Giulietti, A.M., Rapini, A., Andrade, M.J.G. Queiroz, L.P., & Silva, J.M.C. (Org.). Plantas raras do Brasil. 1 ed. Belo Horizonte: Conservação Internacional, 2009, p. 351-357.
Coelho, M.A.N.; Sakuragui, C.M.; Gonçalves, E.G.; Temponi, L.G. Valadares, R.T. Araceae. In: João Renato Stehmann; Rafaela Campostrini Forzza, Alexandre Salino, Marcos Sobral, Denise Pinheiro da Costa; Luciana Yoshino Kamino. (Org.). Plantas da Floresta Atlântica. Rio de Janeiro: Jardim Botânico do Rio de Janeiro, 2009, p. 141-145.
Coelho, M.A.N.; Sampaio, D. Elaeocarpaceae. In: João Renato Stehmann; Rafaela Campostrini Forzza, Alexandre Salino, Marcos Sobral, Denise Pinheiro da Costa; Luciana Yoshino Kamino. (Org.). Plantas da Floresta Atlântica. Rio de Janeiro: Jardim Botânico do Rio de Janeiro, 2009, p. 240-240.
Gonçalves, E.G.; Coelho, M.A.N. Araceae. In: José Ângelo Rizzo. (Org.). Flora dos Estados de Goiás e Tocantins. Goiânia: Universidade Federal de Goiás, 2009, v. 39, p. 1-109.
