Taxonomic Collection, Departamento de Ecologia e Biologia Evolutiva (DCBU) from UFSCar is on-line
The collection includes specimens of Hymenoptera parasitoids, Braconidae and Ichneumonidae especially from the Brazilian fauna, identified at subfamilies and genera levels. They are approximately 200,000 dry preserved specimens mounted on pins or blankets and in alcohol. There are also 1,500 samples in freezers awaiting sorting. Hosts of many species are included in the collection.
Joinvillea Herbarium (JOI) is on-line
The Joinvillea Herbarium, whose name was given in tribute to Joinville city and to the Joinvillea genus, was built in 2003 with the aim of documenting local and regional flora, as well as neighboring states. It is integrated with the Botanical Garden of UNIVILLE, and linked to the following courses: Biological Sciences, Pharmacy and Environmental Engineering. The collection is composed of more than 12.000 exsiccates in the database, mainly of Atlantic Rainforest plants, Restinga and Mangrove. The collection counts with Angiosperms (the largest group), Gimnosperms, Pteridophytes, Bryophytes and Lichens. Among the botanical families, the most frequent are: Asteraceae, Bromeliaceae, Fabaceae, Lauraceae, Melastomataceae, Myrtaceae, Orquidaceae e Rubiaceae.
Leopoldo Krieger Herbarium(CESJ) is on-line
The Herbarium Leopoldo Krieger (CESJ) was created in 1940 through the initiative of the priests Luiz Roth and Leopoldo Krieger. In 1983 the collection was incorporated by the Federal University of Juiz de Fora. The Herbarium CESJ holds collections of algae, fungi, bryophytes, pteridophytes, gymnosperms and angiosperms, besides a carpoteca (dried fruits) and xiloteca (woods), with over 56,000 records of plants, mainly from the Zona da Mata of Minas Gerais region.
CPAP Herbarium is on-line
CPAP Herbarium was founded in 1984 by the researchers Vali Pott and Arnildo Pott. It is part of the Brazilian Agricultural Research Corporation. It is a local herbarium, with vouchers collected in all subdivisions of Pantanal Wetland drainage basin. It is one of the most representative collections of this Biome, with about 25,000 specimens. CPAP also has specimens from Chaco, Cerrado (brazilian savanna), and Deciduous and Semideciduous forests of the non flooded part of the Pantanal Wetland.
Yersinia pestis Collection (Fiocruz-CYP) is on-line
The collection is composed of 917 Yersinia pestis strains isolated from human cases, rodents and fleas from plague epidemics or during plague surveillance activities in endemic periods in plague areas in northeastern Brazil since 1966. Besides its historical significance this collection is representative of biodiversity and a genetic patrimony and is used in research and services. The cultures are maintained in peptone agar stubs in refrigerator in the BSL3 laboratory at CPqAM, Fiocruz-PE.
speciesLink Balance 2012
The speciesLink network closes the year with a total of 5,725,729 records online, of which 2,119,954 are georeferenced by the data providers (37%) and 2,039,684 are georeferenced through a tool (36%). In one year the network grew 17%, an increase of about 836 thousand new records. The repatriation of data grew 21% and reflects the support of the program Reflora INCT Virtual Herbarium of Flora and Fungi. The new repatriated collection is Field Museum of Natural History and includes samples collected by naturalists of the 19th century.
The number of collections and subcollections grew from 235 in 2011 to 293 in 2012.
Another important component of the network are the images of herbarium specimens that began to be shared in 2011 through INCT Virtual Herbarium of Fungi and Flora thanks to funding from the project Reflora. We closed the year 2011 with 9 Brazilian herbaria and 2 abroad sharing more than 72 000 images. These numbers in December 2012 are: 17 Brazilian herbaria and 2 abroad sharing about 205 thousand images.
Regarding Brazil’s List of the Brazilian Flora, a system developed and maintained by CRIA since its development in 2009 under the coordination of JBRJ, we closed the year with a total of 49,223 accepted names and 50,603 synonymous in the administrative interface (closed by JBRJ in December 2012). The list open to public access closes the year with 43,448 validated and published names, with 5133 images associated to the vouchers.
The Moure Catalog of Bees was updated in June 2012, from 14.074 to 14.700 published names.
Regarding new developments: (i) new tools have been added to the data cleaning report and now indicate data incompleteness and a "buffer" of 1km was added when verifying geographic coordinates with the municipality polygon, (ii) the architecture of network was modified in order to improve the availability, reliability, performance and balance of the whole network, and (iii) a new search interface was developed with features such as maps, graphics, inventories, mechanisms to download data, and a tool that allows users to post their comments about a specific record and send it to the curator. With this we hope to enable users to participate in the process of correcting possible errors or identifying material.
A new system Lacunas (Gaps) was launched (http://lacunas.inct.florabrasil.net), another product of INCT Virtual Herbarium of Flora and Fungi, which aims to facilitate the identification of taxonomic and geographic distribution information and knowledge gaps by experts.
Another system has been launched for testing purposes - INCT Biogeography Flora of Brazil – that is being funded by the Ministry of Science and Technology as part of its SisBiota Project . This system aims to expand the knowledge on the biogeography of each species of Brazil´s Flora using occurrence data available in the Virtual Herbarium of Brazil, the active participation of specialists, and the techniques of ecological niche modeling. The public interface is available at http://biogeo.inct.florabrasil.net.
This is the summary of the results of 2012 in terms of online data and applications.
Pathogenic Fungi Collection (Fiocruz-CFP) is on-line
The collection is constituted by approximately 300 fungal strains which are agents of systemic mycosis (genera Cryptococcus, Histoplasma and Coccidioides), opportunistic mycoses (genera Candida, Aspergillus and Penicillium), and cutaneous and sub-cutaneous mycoses (genera Sporothrix, Trichophyton, Trichosporon, Epidermophyton, Microsporum, Fusarium, Fonsecaea, Cladosporium, Exophiala and Malassezia) representing recognized species (human and animal pathogens).
Arthropod collection integrated to the speciesLink network
The Collection of Apterous Vectors Arthropods of Importance in Health of the Instituto Oswaldo Cruz Communities (CAVAISC) owns approximately 20 thousand ticks, mites, fleas and lice specimens. The Henrique Aragãos Collection has a great historical and scientific relevance collection and also integrates CAVAISC.
A new fish collection integrates its data to the speciesLink network
The NUPEM Fish Collection (NPM) currently holds approximately 25,000 specimens in over 1,800 lots, representing about 450 fish species. A significant part of continental fish fauna from Norte Fluminense and deep-sea Campos Basin is represented in the collection. The NPM also includes specimens collected in other Brazilian regions as well as other countries in the Americas, Africa, Asia and Oceania, acquired through exchanges with foreign institutions. The collection represents adequately the fish diversity from Norte Fluminense and the Campos Basin, regions heavily threatened by several environmental impacts. The NPM is recognized in the most recent compilation of ichthyological collections of the "American Society of Ichthyologists and Herpetologists" as well as "Catalog of Fishes".
HERBAM collection integrated to the speciesLink network
Flora collection of Meridional Amazonia which includes the arc of deforestation or corridor of conservation units. The herbarium HEBAM of the State University of Mato Grosso includes 10 thousands curator units. Today it is the biggest collection of the Amazonian portion of Mato Grosso State.
New collection integrated to the speciesLink network
The Orchidarium of the Laboratório de Biologia Molecular e Biossistemática de Plantas (LBMBP-USP), Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto (FFCLRP-USP), maintains an important collection of orchids from different regions of the world, but with emphasis on native species of the state of São Paulo, southeast Brazil. The collection is mainly focused on maintaining the species related to the projects developed in the laboratory LBMBP-USP, which are related to systematics, floral and reproductive biology, anatomy and histochemistry, evolution of pollination systems and floral resources of Orchidaceae, with emphasis on Oncidiinae, Stanhopeinae, Laeliinae and subfamily Vanilloideae. Vanilloideae is one of the most important subfamilies within Orchidaceae, because it includes the genus Vanilla, whose fruits are used in the production of flavor vanillin. Moreover, recently the lab has been dedicated to the reproduction of endangered orchid species, especially from the interior of state of São Paulo, with the purpose of reintroduction in areas considered as potentially protected. Thus, the Orchidarium has a very important role, acting as a potential DNA bank of native and exotic species, as well as being a precious source of specimens for studies on morphology, anatomy, histochemistry, and reproductive biology.
New Search Interface
Today we are launching a new search interface for Brazil’s Virtual Herbarium (http://inct.splink.org.br) and the speciesLink network (http://www.splink.org.br). Each user can now customize his/her preferences and also produce inventories, graphics, and maps with the results of the search. Instead of describing the interface, we ask you to please test the system and give us feedback. We thank CNPq for funding this development through one of its National Institutes of Science and Technology – The Virtual Herbarium of Flora and Fungi.
Change in the speciesLink's architecture
Seeking to improve the availability, reliability, performance, and load balancing of the speciesLink network, two new servers were purchased to work together as primary and secondary servers. In terms of software, we adopted the native replication system for PostgreSQL database, present since version 9.0, where changes are allowed only on the primary server and sent asynchronously to the secondary server that only accepts connections and queries that do not modify data.
Using this architecture, if the primary server fails, the secondary server becomes the primary server until the problem is resolved. The network also uses a load balancing technique to distribute workload, where all processing that is currently done on a single server will be bundled into two, and in the future, if necessary, even more servers.
The development of this new architecture was expected to be completed by the end of 2012 and went into production early November. This development was possible thanks to the support of CNPq through one of its National Institutes of Science and Technology - The Virtual Herbarium of Flora and Fungi.
New DataCleaning elements
The verification of municipality is being done differently. Before, if the collection point was very close to the limit of the municipality, the record was considered suspect. The tool now applies a 1 km buffer around each collection point making the verification of the coordinates less restricted. The application uses the geographical base of the municipal boundaries of the IBGE.
Other implementations of the data cleaning tools that were introduced include:
1. The application now separates blank catalogue numbers from repeated numbers.
2. The application shows a new inconsistency or incompleteness of taxonomic data. Whenever a hierarchical field is filled, the tool assumes that the fields hierarchically superior cannot be blank. For example, the DataCleaning report now shows records that have the species field populated and the genus field blank.
3. The same concept applies to the geographic data and the application now shows records with the municipality field populated and the state field blank.
These last two applications are available on the dataCleaning report with the title of 'other inconsistencies' within the existing taxonomic and geographic data inconsistencies.
The DataCleaning tools are applied whenever a collection updates its data. Therefore, examples can only be found for those holdings that were updated after November 05, 2012.
New data provider: CFEUnioeste - Coleção de Fungos Entomopatogênicos do Laboratório de Biotecnologia Agrícola, Universidade Estadual do Oeste do Paraná
This collection has 50 entomopathogen isolates from Beauveria bassiana, Metarhizium anisopliae, Isaria fumosorosea and Nomurae rileyi species. All of them were obtained from soil or insects from different regions of Brazil.
New data provider: OUPR - Herbário Professor José Badini, Universidade Federal de Ouro Preto
In the nineteenth century the herbaria of the School of Pharmacy of Ouro Preto OUPR (1891) and the of the School of Mines were structured in the state of Minas Gerais. The Herbarium Professor José Badini was founded in 1986, at the Institute of Mathematical and Biological Sciences (ICEB), at the Federal University of Ouro Preto, where the collections of the herbaria of the School of Pharmacy, School of Mines Herbarium and Herbarium Magalhães Gomes were incorporated, retaining the acronym OUPR. Among important historical collections of the OUPR Herbarium are Schwacke, Leonidas Damázio, Alvaro da Silveira, C. T. de Magalhaes Gomes and his brothers, Ducke, Costa Sena, Alfredo T. Baeta Neves, Mello Barreto, Campos Porto, Loefgren, Jacinto and Bruno Godoy, and Moacyr do Amaral Lisboa. The collection currently holds about 35,000 herbarium specimens of the Brazilian flora and exotic species. It also has several typus described mainly by the botanists Alvaro da Silveira, Leonidas Damázio, Schwacke, Moacyr do Amaral Lisboa, and José Badini. This heritage, which dates back more than a century, is always requested for consultation by various institutions and researchers from Brazil and abroad, for research in taxonomy, floristics, pharmacology, ecology and other sciences. Among the current collections of greatest importance in number of specimens are those collected by Prof. José Badini, who sampled mainly Ouro Preto and its region. The Herbarium Professor José Badini covers mainly the flora of the region known as Iron Quadrangle at Minas Gerais state, mainly of rocky fields (quartizite) and ferruginous fields (also called Canga), and forests (riparian and semideciduous forests). The Herbarium is registered at the Brazilian Network of Herbarium and Index Herbariorum, which contributes to the dissemination of this collection in the scientific community, in addition to being recognized as Custodian of the Genetic Heritage at the Ministry of Environment (Resolution No 61, DOU 07.08.2004, section 1, page 104).
New data provider: HJ - Herbario Jataiense Prof. Germano Guarim Neto, Universidade Federal de Goiás
With 8000 specimens collected primarily in the Cerrado of the Central Plateau, Sierra Caiapó Cuesta, and the micro region southwest of Goiás. Relevance: area is being systematically collected for the first time. Holdings are open for loans and exchanges.
New data provider: HUTO - Herbário da Universidade de Tocantins, Fundação Universidade de Tocantins
This herbarium was established in 2005 and is located at the University of Tocantins in the city of Palmas. It is part of the Brazilian Herbaria Network of the Botany Society of Brazil and in 2011 it joined the INCT Virtual Herbarium of Flora and Fungi of Brazil, coordinated by the Federal University of Pernambuco and financed by CNPq.
New data provider: HFSL - Herbarium Dr. Ary Tupinambá Pena Pinheiro, Faculdade São Lucas, Porto Velho, Rondônia
The Dr. Ary Tupinambá Pena Pinheiro Herbarium was founded on October 18, 2002. It is situated at the headquarters of St. Luke's College, and currently has 5664 specimens of Phanerogamic flora belonging to 127 botanical families of the Cronquist system and bryophytes, fungi and pteridophytes. Currently, the herbarium has an area of about 53.62 square meters. There is a room for the collection and one for the curator, and an ante room for material handling. The Herbarium also has a library with several books, Dictionary of Plants, as well as journals, books and various theses.
New data provider: SP-Bryophyta - Maria Eneyda P. Kauffman Fidalgo, Instituto de Botânica
The SP herbaria has the biggest collection of bryophyte samples in Brazil, with 90,000 exsiccatae. There are samples from all Brazilian states and ecosystems, and more than 99 countries. The number of specimens in the bryophyte group are always more than the number of exsiccatae, because there are several species in the same sample. This herbaria is the second in numbers of type bryophyte specimens housed in Brazil.
New data provider: Fiocruz-CHIOC - ColeÇÃO HelmintolÃ³a do Instituto Oswaldo Cruz, Fundação Oswaldo Cruz
To date, the Helminthological Collection of the Oswaldo Cruz Institute (CHIOC) preserves about 37,000 numerical lots that can vary from one to hundreds of specimens per lot, that have been deposited since 1913. They represent a great diversity being recovered from a wide range of hosts captured in different biomes that include the Amazon, Atlantic forest, Cerrado, Caatinga, Swamplands, Pampas, Urban and Continental and Marine Waters. Due to donations of foreign specimens, there are helminths from the five continents. It aims at maintaining a collection for the development of taxonomic studies, science education and dissemination of scientific research, to preserve the genetic heritage of helminths collected from hosts of the world's fauna deposited in CHIOC by researchers from Brazil and abroad, and also covering other groups of invertebrates. The collection consists of samples preserved in whole mounted and wet material. It was referred to as a collection, for the first time by Faria and Travassos (1913). In the early 80's CHIOC was reported in The Guide to the Parasite Collections of the World (Rego, 1982). In 1991 it was recognized as an institutional collection. It is the result of field work of Gomes de Faria and his disciple Lauro Pereira Travassos, and deposits made by researchers of the time as Adolpho Lutz, Oswaldo Cruz, Gaspar Viana, among others. The collection has increased with the incorporation of private and institutional collections of the late nineteenth and early twentieth century (Noronha, 2004a, b). It was reported in the Guide to Helminthological Collections of Latin America (Knoff et al., 2010). In addition to periodic maintenance and modernization in the basic organizational structure and the preservation of CHIOC, the collection routine involves computerization and staff training, there is also the disclosure and dissemination of its scientific information to the public, which has been carried out through printed and online catalogs, audio-visual material of its history, and direct services, "in loco" or by e-mail, to technical courses, undergraduate, postgraduate students and research scientists who need information.
Lacunas (data/knowledge Gaps)
A tool was launched today that presents the status of the data available through the speciesLink network for each species listed in the List of Species of the Brazilian Flora. Reports are only available in Portuguese at http://lacunas.inct.florabrasil.net .
Data repatriation from the Field Museum of Natural History - a product of the Reflora project coordinated by Brazil´s Virtual Herbarium of Flora and Fungi
We communicate the integration of 35.181 records of Angiosperms, Bryophytes, Pteridophytes, Fungi and Lichens collected in Brazil. This is a collection of great historic importance. Of the approximately 16 000 records with the collection year, about 75% are before 1971. The main collectors (with over 500 records each) are: A. F. M. Glaziou (2671), F. Sellow (2408), C. F. P. Martius (2038), R. Spruce (1851), A. Ducke (1475), G. Gardner (1457) J. S. Blanchet (1309), E. H. G. Ule (1292), A. F. C. P. Saint-Hilaire (1270), J. B. E. Pohl (1201), L. Riedel (1065), B. A. Krukoff (662). The main families, also with more than 500 records are Erythroxylaceae (4302), Fabaceae (2892), Rubiaceae (2408), Myrtaceae (2001), Asteraceae (1754), Euphorbiaceae (1293), Melastomataceae (1251), Solanaceae (811 ), Apocynaceae (668), Lauraceae (598) Malpighiaceae (589), Asclepiadaceae (576), Bignoniaceae (546), Annonaceae (516).
Data from biological collections of the Federal University of Mato Grosso (UFMT)
The following biological collections of the Federal University of Mato Grosso have integrated data from their holdings to the speciesLink network
. The Entomology Sector of the Zoological Collection of UFMT includes the biggest dry insect collection in Mato Grosso state. It began its activities in the 70's as a regional collection. It still has a regional scope for most groups, with the exception of the Coleoptera belonging to super family Scarabaeoidea, a big collection (more than 200,000 prepared and identified specimens and more than 2.5 million specimens being currently prepared) with a worldwide scope.
. The collection of Aquatic Invertebrates from the Institute of Biosciences of UFMT is providing data from the Aquatic Ecoregion Project Paraguay-Pantanal. 128,312 individuals are deposited in 1735 lots. This collection comprises 762 lots of Mollusca with a total of 25,260 specimens identified to the species level; 245 lots of the Odonata with 292 specimens identified at genus/morphospecies, 203 lots of Trichoptera with 3526 samples identified at genus/morphospecies , 119 lots of Ephemeroptera with 16,637 individuals identified at family level, 17 lots of Plecoptera with 424 individuals identified at the family level; 135 lots of Coleoptera with 18,978 identified at the family level, 64 Hemiptera with 349 individuals identified at family level; 11 lots of Megaloptera with 27 individuals identified at family level; Lepdoptera 25 lots with 394 individuals at the level of the order Diptera and 154 lots of 62,425 individuals identified at family and subfamily. The identification of Mollusca, Odonata and Trichoptera were validated by experts. Information related to the locality, geographic coordinates, date of collection, sampling effort, abundance and density, shape file and other observations related to each record can be obtained upon request and authorization.
. The collection houses about 4,000 specimens of mammals, mainly marsupials, small rodents, and bats from the state of Mato Grosso, Brazil.
. The Ornithological Collection of the Department of Ornithology of the Zoological Collection of UFMT (SOCUFMT) began in 1983 as a regional collection. Today it remains as a reference collection of regional biodiversity, but has also collected in neighboring states such as Rondonia and Para.
. The fish collection holds freshwater fish mainly from the Upper Paraguay (Pantanal Wetland) and Amazonian headwaters of Northern Mato Grosso. The collection encompasses more than 45 of the total of 71 Neotropical fish families and increases exponentially each year.
UMFT-A and UFMT-R
. The Herpetological Sector of the UFMT Zoological Collection (Herpetological-Reptilia Collection) is a regional collection. UMFT-A holds more than 13.000 specimens of over 186 species and includes an important amphibian holding from Mato Grosso. UFMT-R also is a regional collection and holds more than 10.000 specimens of over 248 species and represents an important reptile holding from Mato Grosso Both UFMT-A and UFMT-R are heterogeneous collections and contain specimens from different regions of the state with representative sample of the Cerrado, Pantanal e Amazon biomes.
. The arthropod collection of the Bioscience Institute of the Federal University of Mato Grosso (PANTANALBIODAT/CAP/UFMT) comprises the most important organismic DATA BASE of the Pantanal region (Myriapoda: over 2000 specimens, Arachnida: over 3000 specimens, Insecta: over 18000 taxa of various taxonomic levels (genus and / or species). This collection is a result of 13 years of intensive field work by scientists of the Laboratory of Ecology and Taxonomy of Arthropods (LETA) in various Pantanal habitats.
Data from the Fundação Ezequiel Dias (Funed) biological collections
The following biological collections from the Fundação Ezequiel Dias are sharing their data with the speciesLink network:
, initially with 601 specimens, and the
, with 52 specimens, aim to contribute to the knowledge of the biodiversity of the Brazil, especially in State of Minas Gerais and to become reference collections.
The slides collection of pollen grains has 4600 slides belonging to approximately 1000 plant species, distributed in 650 genera and 164 botanical families. This collection receives many technical visits for pollen identification and contributes with numerous monographs, dissertations, theses and papers. The study of pollen grains, spores and other microscopic palinomorphs, fossils or not, is called palynology. Melissopalinology is the specific study of pollen grains identified on honey samples with the aim of determining plant species visited by bees to produce bee products. This is a valuable tool that can be used in ecological studies on pollination and on botanical origin of bee products. In Brazil, and even around the world, there are few slide collections of pollen grains available for scientific community specially representing Brazil.s Cerrado flora.
The snake collection from the Ezequiel Dias Foundation began in 1987 and today holds 2809 specimens, probably the largest collection of snakes in the state of Minas Gerais. The Scientific Collection of Snakes of Funed can contribute to studies of taxonomy, biogeography, ecology and natural history. Nine families and 133 species of snakes have been registered. About 90% of the collection consists of snakes collected in the state of Minas Gerais.
Dengue virus (DENV) shows a substantial genetic diversity, evident in the existence of four different serotypes. The collection of Dengue virus of FUNED, currently has 27 DENV isolates, representatives of four different serotypes and genotypes circulating or that have circulated in the state of Minas Gerais/Brazil. The DENV are isolated in C6/36 cells (line derived from Aedes albopictus) and stored in a freezer at -80 ° C, together with the sequence of 511 bp from C-prM junction inserted into plasmid and cloned in Escherichia coli.The database of the samples included in the Institutional Collection contains information from the town of origin, year of collection, nucleotide sequences, viral serotype and genotype. The molecular tools and strategies used to detect viral and / or developed to implement this collection using mainly the real-time PCR and molecular cloning, has contributed to the molecular and epidemiological study of DENV, conducted by Serviço de Biotecnologia e Saúde/Funed.
HUCS Herbarium of the University of Caxias do Sul
HUCS, founded in 1983, holds more than 40.000 voucher specimens among fungus ,lichens and plants grown in the northeast of the state of Rio Grande do Sul and also from national and international exchanges. The Herbarium maintains the historical collection of Jürgens and Stier, German geographers who collected ferns in the state in the beginning of the 20th century.
The Mollusc Collection of the Instituto Oswaldo Cruz is now part of the speciesLink network
The collection holds more than 6,000 lots of preserved shells and animals of the Americas . from Canada to Tierra del Fuego - as well as several countries from other continents. The collection includes lymnic molluscs of the families Planorbidae, Pomatiopsidae, Hydrobiidae, Lymnaeidae, Physidae, Ancylidae, Ampullariidae, and Thiaridae (Gastropods); Corbiculidae and Sphariidae (Bivalvia), most of them preserved in Railliet-Henry solution, but also in 70% alcohol. With approximately 150 000 specimens of molluscs, the CMIOC is source for more than 150 publications of the Laboratory and supports various activities such as identification, loan of specimens, and qualification of human resources in medical malacology and systematics. The collection is fully databased.
Data from Evandro Chaga.s Sandfly Collection
We would like to communicate the integration of data from the Sandflies. Collection of the Leishmaniasis Laboratory of the Evandro Chagas Institute in Ananindeua, Pará. This is a research collection with 126 species of fauna from the state of Pará, including 107 types (holotypes/alotypes and paratypes).
New collections added to the network
The Science and Technology Museum of the Catholic University of Rio Grande do Sul (MCT-PUCRS) is integrating its data in the speciesLink network. The bee collection has been participating since 2007, and now in March, data from the herbarium and from the collections of amphibians, birds, crustaceans, fossils, mammals, mollusks, fish, reptiles, arachnids, and insects have been added. Together these collections are sharing about 200 thousand records. The fish collection of the Federal University of Rio Grande do Sul (UFRGS) is contributing with more than 12 thousand records.
Therefore, thanks to the integration of data from these collections and continuous updating of the majority of participating collections, the speciesLink network has passed the 5 million barrier and is now serving 5.15 million records.
We would like to thank all collaborators for this achievement.
speciesLink balance 2011
The speciesLink network ends 2011 with a total of 4.890.005 records online, of which 1.934.074 are georeferenced by the collections and 1.698.482 are georeferenced using automatic georeferencing tools. About 543 thousand records (11%) are data repatriated from biological collections abroad. In terms of online records the network grew 22% and in number of collections 14,6% (from 205 collections in 2010 to 235 in 2011). Over 93% of the records refer to voucher specimens and the updating index is 58,33%, meaning that 137 collections updated their online data in 2011.
As to usage, the number of records actually downloaded by users (as html, Excel, xls, visualized in maps, etc.) was of approximately 257 million, which amounts to approximately 52 times the total amount of records available. It is as if all online records were downloaded 4 times every month. These are not answers to queries, but answers to queries that are actually visualized.
All holdings together have about 16 million records, but only 30% are available online. This means that Brazil must still invest in digitization efforts for the advancement in knowledge about biodiversity.
But Botany should be highlighted. CRIA is a partner of Brazil.s National Institute of Science and Technology - The Virtual Herbarium of Flora and Fungi that is being financed by CNPq (The National Council for Scientific and Technological Development), under the coordination of Prof. Leonor Costa Maia of the Federal University of Pernambuco. The Brazilian herbaria that are part of the network hold about 4.8 million specimens, 2.8 million of which have their data published online (58%) and the herbaria that participate in the repatriation program are serving 537 thousand data records. In three years the records made available by Brazilian herbaria more than duplicated, whereas those of herbaria abroad grew 40%. The Brazilian herbaria that are part of this network, present an updating index greater than 88%. As to data usage, about 208 million records were downloaded, which represents 61 times the amount of records online or that the equivalent to all data records were downloaded more than 5 times a month.
Thanks to the Reflora Program also part of the Virtual Herbarium, and with the support from CNPq, a new image service was developed. We close the year of 2011 with 9 herbaria of Brazil and 2 abroad sharing 72 thousand images online, including 13,500 high resolution images of types. New York Botanical Garden (NYBG) is serving 58,290 images while the National Museum of Natural History of Paris (P) is serving 6,197 images of its Saint-Hilaire collection. Brazilian Herbaria that are sharing images include Unicamp (UEC/4.098 imagens), Museu Botânico Municipal de Curitiba (MBM/1.360), Instituto de Botânica de São Paulo (SP/1.015), Universidade Federal de Minas Gerais (BHCB/688), Museu Nacional (R/638), Reserva Natural Vale (CVRD/5), Herbário Prisco Bezerra da Universidade Federal do Ceará (EAC/30), herbário da Universidade Federal de Goiás (UFG/30) and Universidade Federal de Pernambuco (UFP/20).
Both textual data and images were integrated to the administrative interface of the List of Species of Brazil's Flora. This way specialists can visualize occurrence points of specimen data held in herbaria to validate geographic distribution information and can also associate the images to the vouchers cited. As accepted names, the List closes the year with 42,730 species for Brazil.s flora, with 4,409 Fungi , 4,057 Algae, 1,521 Bryophytes, 1,196 Pteridophytes, 26 Gymnosperms, and 31,521 Angiosperms. A total number of 2.243 imagens are associated to list names, 414 from Flora brasiliensis, 1.570 repatriated from New York (1.389) and Paris (181) and the rest from Brazilian herbaria: SP (94), BHCB (66), UEC (38), R (30), MBM (29) e EAC (2).
We would like to highlight the importance of cooperative work and of financial support, given to a public data infrastructure, principally by CNPq, The National Council for Scientific and Technological Development, an agency linked to the Ministry of Science and Technology and Innovation (MCTI).
New collections have joined the network in December, 2011
Herbário Alarich Rudolf Holger Schultz (HAS) do Museu de Ciências Naturais - Fundação Zoobotânica do Rio Grande do Sul
HAS was created in 1971 to conserve the flora of Rio Grande do Sul, becoming the major part of its collection of material from this State, but with material of other states in Brazil, especially of Santa Catarina and São Paulo. The HAS Collection is accredited by CGEN/MMA as depositary of samples of the genetic component (Resolution Nº 5, 29.08.2002). Nomenclatural types are 165, with digital photographic record. The most represented families are Asteraceae, Bromeliaceae, Fabaceae, Myrtaceae and Poaceae and also contains good collections of ferns and lichenized fungi. HAS maintains a reference collection of endangered species in RS. The collection of algae currently has more than 13,300 bottles of liquid containing primarily microalgae and cyanobacteria in fresh water, with representatives of six major divisions and nine classes: Cyanobacteria, Chrysophyceae, Xantophyceae, Bacillariophyceae, Cryptophyceae, Dinophyceae, Euglenophyceae, Chlorophyceae and Zygnematophyceae. This collection also has more than 6,200 permanent slides of Bacillariophyceae. It is the herbarium with the largest number of bottles/ lots in liquid in Brazil. It is a member of INCT The Virtual Herbarium of Flora and Fungi of Brazil.
Herbário Rosa Moche (SLUI), State University of Maranhão
The SLUI herbarium has a small structure of approximately 100 m2, with a collection of some 4500 specimens, a wood collection (with 174 specimens), a carpoteca (35 specimens), and a palinoteca. There are also collections of some particular regions: Amazon, Cerrado, riparian and coastal vegetation. The construction of a proper building proper and adequate installations have been approved, with funding from FINEP. It is a member of INCT The Virtual Herbarium of Flora and Fungi of Brazil.
Herbário do Jardim Botânico Plantarum (HPL)
The herbarium of the Botanical Garden Plantarum was founded by its director Harri Lorenzi in 2002, but its collection began in 1990. Since 2008 it is part of the Index Herbariorum and of the Brazilian Herbaria Network of the Brazilian Society of Botany. It holds more than 15 thousand exsiccates, 95% of which are Angiosperms of the following families: Acanthaceae, Araceae, Arecaceae, Begoniaceae, Gesneriaceae, Maranthaceae e Passifloraceae. The collection has 40 types, mostly Arecaceae of the genera Syagrus. HPL faz parte do INCT Herbário Virtual da Flora e dos Fungos. It is a member of INCT The Virtual Herbarium of Flora and Fungi of Brazil.
Herbário Centro Norte Mato Grossense (CNMT), Federal University of Maranhão
The CNMT Herbarium began its activities in 2010 and is located at UFMT . Campus of Sinop, in the city of Sinop, Mato Grosso State, Brazil. The collection of the CNMT Herbarium has approximately 5.000 herbarium specimens (exsiccatae) of various plant groups (algae, bryophytes, ferns, gymnosperms and angiosperms) from collects in the region, particularly in the Amazon and cerrado biome, since the city is located in the Amazon rainforest-cerrado transition.
Fish Collection of the Federal University of Mato Grosso (CPUFMT)
The fish collection of the UFMT comprises a rich depository of freshwater fishes mainly from the Upper Paraguay (Pantanal Wetland) and Amazonian headwaters of Northern Mato Grosso State. The collection encompasses more than 45 of the total 71 Neotropical fish families and increases exponentially each year.
Coleção Entomológica do Instituto Oswaldo Cruz (Fiocruz-CEIOC)
The Entomological Collection of Oswaldo Cruz Institute (CEIOC) has about 5 million specimens referring to almost all known insect orders, with emphasis on Coleoptera, Lepidoptera, Hymenoptera and Diptera. Collections of high historical and scientific importance also belong to the CEIOC, as those organized by Costa Lima and Joseph Zikán.
Ten years of the speciesLink project
This month, November 2011, we celebrate ten years of the start of the project financed by FAPESP (2001-2005) that resulted in the development of the speciesLink network. Its initial goal was to develop a system to integrate data from 12 biological collections of the State of São Paulo with SinBiota (Biota/Fapesp's information system) and the Species Analyst network, coordinated by the University of Kansas. SinBiota was designed to receive, store, search, retrieve and disseminate data collected by surveys conducted under the Biota program. The speciesLink network aimed at integrating these data with legacy data available at biological collections and to initiate a study on modeling species distribution in close collaboration with the University of Kansas.
Thanks to the work of the societies of botany, zoology, and microbiology, and the action of many collaborators from Brazil and abroad, the network now includes 220 biological collections (subcollections included), five from abroad, repatriating data from samples collected in Brazil. There are 4.5 million records freely and openly available online, only from the collections, with approximately four million from collections located in Brazil. If the estimate that our collections hold approximately 30 million units is correct, we have past the mark of 10% of the data from our holdings online. This is certainly a great achievement, but this number also shows the enormous challenge that is still ahead of us.
If we analyze only data on plants, Brazilian herbaria are providing about 2.9 million records online, which represent about 50% of the total number estimated for the country. If we compute the sum of all data (online and offline) of the herbaria that are part of speciesLink, potentially the network holds more than two thirds of the samples of the country.
The strong development on botanical data integration and dissemination certainly reflects the work of the Botanical Society of Brazil, which for years has been discussing the process of computerization and the strategy of the Brazilian Herbaria Network. One must also mention the support from CNPq to one of its National Science and Technology Institutes, the Virtual Herbarium of Flora and Fungi and the coordination and articulation of the project's steering committee. Another important support from CNPq to this Virtual Herbarium concerns the Reflora program that made it possible not only to work with data repatriation (more than 536 thousand records from abroad) but also in serving about 18 thousand images associated with the textual data through a dynamic image server.
We must also acknowledge the support given by the Ministry of Science and Technology and its agency Finep to the SICol network, which integrates data from microbial collections and is also part of speciesLink.
In addition to data collections, the network also integrates observation data, especially data from SinBiota, from the Ecological and Economic Zoning of Acre and from OBIS - Ocean Biogeographic Information System, an informative component of the Census of Marine Life, more specifically from the "Tropical and Subtropical Western South Atlantic OBIS" node, coordinated by the University of São Paulo. Altogether 333 thousand observation records are available on-line.
The whole network, with observation and voucher data, from the country and repatriated, is serving over 4.8 million records, 1.9 million of which are georeferenced.
I would like, on behalf of CRIA's team, to thank everyone for their support and commitment in making all this scientific information into a truly public good, available to all interested.
New collections have joined the network in November, 2011
Coleção de Leptospira da Fundação Oswaldo Cruz (Fiocruz-CLEP)
CLEP holds Leptospira spp. strains isolated from humans and several animal species. The collection comprises of Reference Strains obtained from international collections and strains of clinical origin, isolated in different brazilian states, representing the circulating serovars in the country. Method of preservation include: Cryopreservation in liquid nitrogen (-196ºC) and freezer at -80ºC, and passages in semi solid EMJH medium every six months.
Coleção de Bactérias da Mata Atlântica (Fiocruz-CBMA)
The Bacteria Collection of the Atlantic Forest, CBMA is hosted by the Laboratory of Molecular Genetics of Microorganisms, located in the Leonidas Deane Hall, Manguinhos/ FIOCRUZ. Campus, Rio de Janeiro, Brazil. Its purpose is: to sample, isolate, characterize and preserve the diversity of culturable bacteria from the soil of the Atlantic Forest. CBMA represents the primary resource of a fraction of this biome microbiota that can be used for basic studies and biotechnology. As a collection it is the witness to these studies, enabling their traceability. Since the strain taxonomy is defined by the information contained in the ribosomal 16S rRNA gene, and therefore can be freely accessed and applied to distinct studies. The CBMA is affiliated to the World Federation for Culture Collections, WFCC, under the registration number WDCM958. Currently, the Collection houses more than 800 strains corresponding to 100 morphotypes recovered from eight collecting sites from five soil types. So far, the identification of 100 of strains, by means of 16S ribosomal gene and comparison of ~1300bp sequence with the Ribosomal Database Project (RDP) defined the presence of the following bacteria genera: Acinetobacter, Amycolatopsis, Arthrobacter, Bacillus, Burkholderia, Collimonas, Cupriavidus, Dyella, Enterobacter, Klebsiella, Leifsonia, Mycobacterium, Paracoccus, Paenibacillus, Phyllobacterium, Pseudomonas, Ralstonia, Serratia, Silvimonas, Streptomyces e Variovorax
Herbário da Reserva Natural Vale (CVRD)
The herbarium of Vale.s Natural Reserve was registered in the Index Herbariorum in 1979 and published in The Herbaria of the World, in 1981, being internationally recognized as CVRD. Collecting activities in the reserve began in 1963 and became a systemized activity as of 1978 when research on the flora of the area were intensified. Since then, knowledge about the local flora is continuously increasing and includes the discovery of new species.
New collections have joined the network in September, 2011
Herbário Pe. Dr. Raulino Reitz (CRI)
The Collection of the Herbarium at the Universidade do Extremo Sul Catarinense comprises an important collection of plant biodiversity in the region. the collection currently has 9.000 specimens and is registered in the Index Herbariorum.
Coleção de Triatomíneos do Instituto Oswaldo Cruz (Fiocruz-CTIOC)
The collection of Triatomíneos from the Oswaldo Cruz Institute (CTIOC) is one of the oldest collections of the institution as it began to be formed in 1909 with the discovery of Chagas disease. It is currently formed by the Herman Lent Collection (CHL), with 9,000 copies , 3,374 registered in the open collection, and the Carcavallo Rodolpho Collection (CRC) with 15,000 copies with 5,674 registered. A collection has material preserved in alcohol 70 º GL (25 species) and a living collection maintained in the insectary of Triatominae, with 46 species currently kept in 150 glass plates. This collection provides live material for researchers who work with vectors of Chagas disease. The collection of Triatominae is linked to the National Laboratory and International Reference on Triatominae Taxonomy of the Oswaldo Cruz Institute and is the National Reference Center of the Ministry of Health.
Coleção de Ceratopogonidae (Fiocruz-CCER)
The Collection of Ceratopogonidae of the Instituto Oswaldo Cruz (CCER) presents types, reference and voucher specimens of medical, veterinary and agricultural importance. A thousand specimens are slide-mounted, dry on pins and samples of specimens preserved with naphthalene or in Kahle-Drietrich solution. Most specimens are from neotropical fauna with hematophagous, predators and pollinators habits. Until now, 703 samples are catalogued and computerized. In CCER the bigger Brazilian collection of Culicoides with 131 neotropical species, and Collection .Saulo Soria. with 1.343 specimens, belonging to 36 pollinators species of Theobroma cacau from different cocoa-producing countries are incorporated. The collection preserves 115 type species from 11 genera belonging to 13 countries of Latin America and U.S.A.
Coleção de Simulídeos do Instituto Oswaldo Cruz (Fiocruz-CSIOC)
The taxonomic groups that comprise the collection are mainly representatives of the family Simuliidae of the Neotropical region, but also of Holarctic and Australian Regions. The size of the collection is approximately 35,000 lots, of which about 10% are identified. Among the unidentified lots in the collection, approximately 8,500 are dry lots, totaling about 10,000 lots and in humid conservation, 25,000 lots (about 15 lots per location). All locations have logged coordinates and about 1,800 locations are computerized and 310 georeferenced. The collection also houses the historical collections of Lutz and Cesar Pinto (about 400 slides and 830 pinned specimens). The Simuliidae Collection of the Instituto Oswaldo Cruz (CSIOC) installed at the Laboratório de Simulídeos e Oncocercose is considered a reference in supra-specific and specific representativeness to the group besides owning information patrimony concerning the knowledge of 30 years of research in the areas identified as Brazilian focus of onchocerciasis and mansonelliasis, diseases vectored by some species of the family Simuliidae. The CSIOC collection was recognized as trustee by the National Council of Genetic Patrimony - CGEN / MMA on 05/01/2011, under accreditation number 039/2011/SECEX/CGEN.
The 2011 version of List of Species of the Brazilian Flora
The 2011 version of the List published in 2010 has just been launched with many new features. The list now associates images with textual information, including of types, thanks to the collaboration with the National Institute of Science and Technology-The Virtual Herbarium of Flora and Fungi. New types of data also include forms of life and substrates, differentiated for Algae, Briophytes and Angiosperms+Gymnosperms+Pterodophytes, and Fungi. New data also includes the occurrence of species in different types of vegetation and the distribution o algae in different hydrographic regions. Another novelty are statistics that synthesize species richness per state, region and phytogeographic areas.
This list now is dynamic. All information validated by specialists is automatically made available online. CRIA (Centro de Referência em Informação Ambiental) is responsible for the development and maintenance of the system.
The Project, coordinated by the Botanical Garden of Rio de Janeiro, has the support of the Ministry of the Environment, of CNC Flora, and CNPq and is available at
New herbaria integated in the INCT Virtual Herbarium Network
Data from 3 new herbaria are now available online: Herbário of the Instituto de Ciências Naturais from Porto Alegre, Rio Grande do Sul; Herbário of the Fundação Universidade Federal de Mato Grosso do Sul from Campo Grande; and the Herbário of the Universidade Federal de Santa Catarina de Florianópolis.
The Herbarium ICN holds a vast collection of preserved plant specimens (ca. 160.000) which are available for post graduate students and researchers. The botanical groups included are Angiosperms, Gymnosperms, Monilophytas, Bryophytes, Algae, Fungi and Lichens, in addition to special collections including DNA and carpoteca. Part of this collection is organized in a digital database. The Herbarium ICN maintains exchanges with around 76 national and 40 foreign institutions. One important aspect is that this collection keeps 319 type-specimens of plants, mainly from the flora of southernmost Brazil, including specimens from Pampa and Araucarian Forest Biomes.
The CGMS Herbarium (Universidade Federal de Mato Grosso do Sul, campus de Campo Grande, Brazil) holds a collection of about 35.000 specimens, and 10.000 in the process of incorporation due to donation of duplicates from the HMS Herbarium, distributed recently and extinct. The collection of the CGMS, the largest of Mato Grosso do Sul, is heterogeneous with specimens from different regions of the state. Thus the CGMS Herbarium, includes specimens from the Pantanal, Chaco, Cerrado, Seasonal ForestThe collection predominantly holds specimens of Angiosperms, and some specimens of Pteridophytes, Bryophytes and Lichens.
The Herbarium FLOR from the Federal University of Santa Catarina, founded in 1964, has a collection of approximately 37.000 exsiccates of vascular plants, 2.200 fungi and 1.000 algae. Its collection is the second largest in Santa Catarina and is especially focused on the State's flora.
Crustacea Collection . Museum of Zoology at Unicamp
The Crustacea collection of the Museum of Zoology "Prof. Adão José Cardoso" located at the State University of Campinas (UNICAMP) is being implemented and has nearly 100 lots with 500 recorded specimens. Most of the collection is destined to researchers interested in Crustacea.
The new image server of the INCT Virtual Herbarium of Brazil's Flora and Fungi (HVFF) is launched
Thanks to the support of the CNPq, as part of its Reflora program, during the 62nd National Congress of Botany, the image server and associated web services of the HVFF was launched. There are more then 16 thousand images freely and openly available, most in high resolution, of samples kept in herbaria in Brazil and abroad. The following herbaria provided images:
New York Botanical Garden - Brazilian records: 8.805 high resolution images of type specimens
Herbarium Musei Parisiensis - holdings of Saint-Hilaire: 4.534 high resolution images
Herbário do Instituto de Botânica de São Paulo: 1.015 imagens em alta resolução dos tipos
Herbário do Museu Nacional do Rio de Janeiro: 638 high resolution images of type specimens
Herbário da Universidade Estadual de Campinas: 292 images
Herbário da Universidade Federal de Minas Gerais: 47 images
Herbário da Universidade Federal de Goias: 30 images
All images are freely and openly available through HVFF's search interface (http://inct.splink.org.br) and through and administrative interface organized by herbarium available at http://reflora.cria.org.br/admin
All criticisms and suggestions are more then welcome.
New herbaria integrated to the National Institute of Science and Technology (INCT) Virtual Herbarium of Plants and Fungi (HVFF)
Two herbaria from Ilhéus now have their data integrated to HVFF: CEPEC . Herbário do Centro de Pesquisas do Cacau and HUESC of the State University of Santa Cruz
CEPEC has approximately 140 thousand exsiccates, being the 2nd largest holding of the northeast of Brazil with about 10 thousand data records on vascular plants from the state of Bahia. This herbaria has about 2 thousand types and holds samples from the main protected areas of Bahia, such as PARNAs Chapada Diamantina, Serra das Lontras, Descobrimento, Pau-Brasil and Monte Pascoal, REBIO Una, PAREs Serra do Conduru e Wenceslau Guimaraes and RPPNs Serra Bonita, Serra do Teimoso e Ecoparque de Una. CEPEC is making about 108 thousand records available online of which more the 61 thousand are georreferenced.
HUESC has approximately 14.500 records and is making 6.762 available online ( 60% georreferenced). About 90% of the records are from Bahia.
New herbarium integrated to the National Institute of Science and Technology (INCT) Virtual Herbarium of Plants and Fungi (HVFF
The Alexandre Leal Costa Herbarium of the Federal University of Bahia has approximately 100 thousand records, 71.400 of which are online, with about 60 mil georreferenced. More then 90% of the online records are from Bahia.
New herbarium integrated to the National Institute of Science and Technology (INCT) Virtual Herbarium of Plants and Fungi (HVFF)
The Herbário Rondoniensis of the Federal University of Rondônia (RON) integrated its data to the INCT HVFF network. RON has about 4400 samples and aims at becoming a representative collection of the state. Most of the collection is from and impacted area of the Usina de Santo Antônio e Jirau. Other collections include those of the Plano Agropecuário e Florestal de Rondônia (PLANAFLORO), carried out between 1996-1997. It includes an auxiliary collection RON-e.
New collectin of the Fundação Oswaldo Cruz integrated to the SICol network
The collection of Fungi from the Amazon of the biological collection of the Instituto Leônidas e Maria Deane (CBILMD) is now part of the SICol and speciesLink networks.
The Collection of Fungi from Amazon, CFAM, is part of the Biological Collections from Institute Leonidas and Maria Deane (CBILMD), and holds strains isolated from different microbiomes in the Brazilian Amazon, region with a poorly known microbial diversity. The most common genera in the collection are Penicillium, Aspergillus and Trichoderma, isolated from various sources such as, air, soil, water, plants, fruits, man and other animals. All cultures are identified to genus and other species level belonging to the phylum Zygomycota, Ascomycota and anamorphic fungi. The collection consists of 834 cultures of filamentous fungi, preserved under mineral oil, in distilled water, at -20 °C and lyophilized, and is kept in quadruplicate in each method of preservation. In addition to receiving deposits, the CFAM provides cultures under requests, besides services of isolation and identification of fungi, as well as training of students and professionals in fungal taxonomy. These requests are coming from national and international educational and/or research institutes. CFAM is characterizing stored cultures regarding bioactive molecules of interest health and biotechnology as well as on their morphological characteristics, through projects developed by undergraduate and postgraduate students (Master and Doctorate) in the country. The CFAM is affiliated to the World Federation for Culture Collection, WFCC, under registration number WDCM 957. morfológicas, através de projetos desenvolvidos por alunos de graduação e pós-graduação (mestrado e doutorado) do país. A CFAM é filiada a World Federation for Culture Collection, WFCC, sob o registro WDCM 957.
New collection from the Fundação Oswaldo Cruz integrated to the SICol network
The Bacterial Culture Collection of Health Importance consists of four sub collections: Collection of Enteropathogenic Bacteria (CENT), Culture Collection of Hospital Bacteria (CCBH), Collection of Listeria (CLIST) and the Collection of Campylobacter (CCAMP). It was formally acknowledged by the IOC in 2001. The collection contains expressive representation of native micro-biodiversity in relation to the main human and animal patogens. The direct connection with the lines of research of the Laboratories of Enterobacteria, Bacterial Zoonoses, Hospital Infection Research and the Reference Services/MS in national scope promotes the characterization of strains using the latest technological procedures (phenotypic methods and genotypic methods based on DNA analysis). It comprises a large number of pathogenic bacteria (200,000 isolated bacteria and 840 reference strains) of interest for medicine, veterinary and environment fields of research, thus becoming an essential tool for health technological development. Currently, the main request is from public institutions, and national and international scientific communities.
New herbaria integrated to the speciesLink Network
The following herbaria, that are part of the National Institute of Science and Technology Virtual Herbarium of Flora and Fungi, are sharing their data with the network.
UFG - Herbário da Universidade Federal de Goiás
The Herbarium of the Federal University of Goias was formed through two projects: one about the Flora of Goiânia and the second one about the Flora of Goias State (now the states of Goias and Tocantins). These projects began in 1969 and ended in 1974 and resulted in 9.605 inventories. The herbarium today holds 43,226 samples of great interest to the Flora of Goias and Tocantins.
HUEG - Herbário da Universidade Estadual de Goiás
This herbarium has 7,000 samples of vascular plants, biophytes and macroscopic fungi of the Cerrado, predominantly of the state of Goias.
HFSL-Fungos - Herbário Dr. Ary Tupinambá Penna Pinheiro - Fungos
This herbarium has 5.664 specimens of flora and is making 180 records of fungi from the state of Rondônia available.
MIRR - Herbário do Museu Integrado de Roraima
This herbarium from the state of Roraima has 8,982 samples representing an important holding of the region.
Another herbarium that is now part of the network is that of the
Universidade Estadual do Sudoeste da Bahia (HUESB)
. It has about 7,000 samples from the transition area between the Atlantic Rain Forest and Caatinga.
New collections of Fiocruz integrated to the speciesLink Network
ColTryp - Coleção de Trypanosoma de Mamíferos Silvestres, Domésticos e Vetores
The ColTryp has isolates of Trypanosoma cruzi obtained from sylvatic, domestic and vectors host species included in eight orders of mammals and one of vector, collected in Brazilian biomes with different phytogeographic characteristics. The sample are maintain cryopreserved with low passages in LIT or/and NNN. Method of preservation: Cryopreservation in Nitrogen Liquid (-196ºC).
CMT - Coleção Micológica de Trichocomaceae
The collection consists of 446 fungal cultures. The main focus is the toxigenic species with importance to human and animal health that belong to the genera Aspergillus and Penicillium, besides Fusarium, genus that belongs to the family Nectriaceae. These molds are considered important because of their potential carcinogenic, teratogenic and mutagenic effects (OMS, International Agency for Research on Cancer) and also due to the severe negative impacts on the economy and industry (CAST). For fungal preservation the freeze-drying method is employed preferentially. It is also used the method of freezing at -40° C in glycerol, the method of Castellani, the agar fragment blocks in polypropylene tubes and the periodical sampling technique. Currently the L-drying method is been tested.
Integração dos dados da Coleção de Echinoidea do Museu de Zoologia da Unicamp
The Echinoidea collection of the Museu de Zoologia "Prof. Adão José Cardoso" of the State University of Campinas (UNICAMP) is in its initial phase and holds about 20 lots with about 60 catalogues samples.
Results of 2010
CRIA's mission is to disseminate data and information freely and openly on the Internet to all interested, without distinction. Its goal is to develop a common platform for data access in support of science and decision making at the local, regional and national level, integrated with global initiatives. It focuses on species and specimen data of Brazil.
CRIA's 2007-2010 strategic plan set a target for the end of 2010 to integrate data from 150 collections, reaching 3 million records. We ended 2010 with 4,012,333 records, from 205 biological and data collections, 1,438,092 (36%) georeferenced by providers and 1,267,698 georeferenced through tools. Depending on the accuracy required, georeferencing index is of up to 67%.
Comparing 2009 with 2010 the network grew from 179 to 205 holdings (14.5%) and from 3,551,913 records to more than four million in December 2010 which represents an increase of 13%. In four years (2006-2010) there was an increase of 244% in the number of records. The updating rate of collections in 2010 was 63%. It is interesting to compare that number with the updating rate of herbaria participating in the INCT - Virtual Herbarium of Fungi and Flora project which is 85%. This demonstrates the importance and need for resources for digitizing and articulation.
Finally another interesting feature is the proportion of data from biological collections (with associated samples) and observation data. 93% the data available comes from biological collections.
Again I would like to thank the collaboration of all who made this progress possible.
New holdings integrated to the speciesLink network
Data from two collections were recently integrated to the speciesLink network: Herbarium Uberlandense of the Federal University of Uberlândia (HUFU) and the Fonoteca Neotropical "Jacques Vielliard".
HUFU has about 60,000 and is an important reference collection for the flora of the Cerrado of Minas Gerais.
FNJV is the largest Brazilian animal sound collection, including invertebrates and all classes of vertebrates. It has more than 15,000 digital files and several others to be incorporated.
Answering a demand from a curator, each collection's page (manager module) now has links to the data cleaning report and to a query page specific for that collection.
Another new feature is that the result of a query (http://www.splink.org.br) besides HTML, MS-Excel, and XML files, can be displayed as KML files. KML is a file format used to display geographic data in an Earth browser such as Google Earth, Google Maps, and Google Maps for mobile.
New holdings integrated to the speciesLink network
Data from two herbaria were recently integrated to the speciesLink network: Herbarium of the Federal Technological University of Paraná, Campo Morão Campus (HCF) and the Virtual Herbarium of A. de Saint-Hilaire from the National Museum of Natural History of Paris.
HCT has 9,085 samples mostly from the region around Campo Mourão and the Virtual Herbarium of A. de Saint-Hilaire integrates data from samples collected by Saint-Hilaire during his travels in Brazil between 1816 and 1822.
New holding integrated to the speciesLink network
Data from the herbarium of the Federal University of Minas Gerais (BHCB) was integrated to the speciesLink network.
This collection holds 143,000 exsicates mainly from the state of Minas Gerais. Today this is the largest herbarium of Minas Gerais and holds more the 500 types.
New holding integrated to the speciesLink network
Data from the herbarium of the Catholic University of Pernambuco was integrated to the network. This collection holds 3.000 plant species with emphasis on trees from the Caatinga and Atlantic Forest of the Northeast of Brazil. It also has a wood collection with more than 5,000 samples.
New holdings integrated to the speciesLink network
Data from two herbaria were recently integrated to the speciesLink network: Herbário do Parque da Ciência Newton Freire Maia (IRAI) and Herbário da Universidade de Brasília (UB).
IRAI herbarium was established in 2007 and is located within the Newton Freire Maia Science Park in Pinhais, Parana. Its aim is to disseminate and popularize science. It has specimens collected in the Area of Environmental Protection Irai and in the area of the Afonso Pena International Airport in Curitiba. 2,344 records are online with 74 georeferenced at source and 2,236 georeferenced automatically.
The Herbarium of the University of Brasilia was founded in 1963 and has around 190,000 specimens of phanerogams and 40,000 cryptogams (1,600 types). Samples are mainly from the Cerrado (significant collections of the Federal District, Goiás, Maranhão, Minas Gerais, Mato Grosso and Tocantins), Amazon Region (exchanges under curatorship of Dr. John Murça Pires), Atlantic Forest (exchanges under the curatorship of Dr. Graziela Maciel Barroso and Myrtaceae of Paraná) and from abroad (exchanges under the curatorship of Dr. George Eiten). The herbarium is providing 107,349 records online, with 42,647 georeferenced at source and 13,502 georeferenced automatically. 75% of its collection online is from the Midwest (over 75,000 records) with about 39,000 records from the Federal District.
New Search Interface Available
Thanks to the support of the projects "National Science and Technology Institute - Virtual Herbarium" and "Pollinators of Brazil" a new
was developed for the speciesLink network.
The new system presents two options: simple and advanced search. Both options present three basic steps: (i) selection of the data provider(s); (ii) searching criteria; and (iii) results. In order to advance to the next step users must click on the option NEXT.
The first step, where the user selects the data provider was not modified. All providers appear as being selected and users may uncheck all and select one or more or can select the type of collection wanted based on metadata. Once data providers are selected, the user must move to the next step where the searching criteria are defined. In the case of a simple search, fixed fields are presented and at least one field must be filled out.
In the case of advanced search all DarwinCore fields are searchable. Fields may be associate through operators such as and/or. There are also a number of options such as exact word, phonetic, etc. An important aspect is that the order of the conditions may alter the result, so we strongly recommend that users read the help text in order to understand the logic of the system.
When searching for a State or Province of Brazil, if users type the correct name or official abbreviation the system will search for both options. By typing State equal to SP, the system searches for both "SP" and "São Paulo". Records with S.Paulo will not be found.
It is possible to search for blank fields. If a user, for example, wishes to find records of a specific genus that have not been identified to the species level they may search for that genus and for records that have no data in the species field by typing the word blank.
The third step is the presentation of the results. Besides being able to retrieve all records as html, xml or Excel files it is possible to visualize the results as an inventory. When searching for a specific species, for example, one can have as an output the number of specimens found per State. Another important feature is that the limit of 25 thousand records was removed.
New holdings from the Zoological Museum of Unicamp
The Asteroidea collection of the Museum of Zoology "Prof. Adão José Cardoso", UNICAMP (ZUEC-AST) is being implemented and currently has about 30 lots and about 40 specimens listed. These specimens are from southeastern Brazil and were sampled through the Biota / FAPESP Program - Bentos Marinho project, in the State of São Paulo. The process of cataloging the collection and computerization is underway.
Centro de Pesquisa René Rachou
The René Rachou research center is sharing their data on sandflys, triatomines e malacological collections through the speciesLink network.
Brazil's National Museum Herbarium (R and R types)
The collection holds about 550,000 specimens, 95% of vascular plants. The Herbarium has great historical importance as it has holdings of Glaziou, Freire Allemão, Brade, Hoehne, Lutz, Riedel, Schwacke, Sellow, and even the Emperor Dom Pedro II. There are collections coming from the Amazon, Marechal Rondon Expeditions, Alberto Sampaio, Polo Northwest, the Upper Xingu, Fernando de Noronha, Restinga National Park Jurubatiba, among others. The type collection has a total of 5,600 specimens and is part of the "Latin American Plants Initiative" (LAPI) of the Mellon Foundation. The Herbarium of the National Museum is part of the Virtual Herbarium INCT Flora and Fungi.
Ecological Economic Zoning Acre
Acre's Secretary of Environment (SEMA) is sharing data used in the state's Ecological Economic Zoning for the following groups Amphibia, Avifauna, Mammalia, Ichthyofauna, and Herpetofauna. The following maps were also integrated to the system: vegetation, soils, conservation units, indigenous lands, settlements, roads, main rivers, municipal boundary and headquarters of Acre.
BAH - Herbário Antônio Nonato Marques, Empresa Baiana de Desenvolvimento Agrícola is sharing its data on flowering plants with about 16,000 catalogued species. The Herbarium is specialized on toxic and medicinal plants, fodder, invasive species, honey, and hardwood.
Summary of 2009
2009 ended with 3,551,913 data records from 179 data and biological collections. Growth is due to updating of existing collections and the integration of 23 new collections in 2009.
The integration of new collections reflects the partnerships established with thematic networks. There are 4 new herbaria articulated through INCT - Virtual Herbarium of Flora and Fungi, 11 collections of the Biodiversity Research Program coordinated by INPA - Instituto Nacional de Pesquisas da Amazônia, 2 collections of the Capixaba network, 4 from Biota São Paulo (all of the Museum of Zoology, Unicamp) and one from Sicol, the Leishmania Collection of Instituto Oswaldo Cruz. As to updating, 60% of the collections that were participating before 2009 updated their data. Filtering the data to zoological, botanical and microbial collections, the percentage of collections that have updated their data in 2009 are respectively 64%, 68% and 10% within these networks.
The low rate of updating of SICol, is because its architecture has not yet migrated to that of the speciesLink network. The numbers indicate that the architecture where each data provider has full autonomy and ease to update their data and to determine what data is public or has restricted access, stimulates continuous updating. It also indicates the need for closer contact to the collections, since we can observe that as the older networks which no longer have project support, have lower updating rates.
We believe that organizing the collections into regional or thematic networks has also proved to be efficient. 2009 was the beginning of the activities of the National Institute of Science and Technology Virtual Herbarium of Plants and Fungi coordinated by Prof. Leonor Maia, from the Federal University of Pernambuco. 21 herbaria are participating in this project as collaborators and associate members. CRIA aims to make data and information freely and openly available on the Internet in a useful and usable format. The existence of a coordinating group responsible for organizing data providers strengthens CRIA's position as we can devote our time entirely in developing systems, tools and applications, leaving the articulation and political persuasion to be discussed among peers.
Collections from Rondônia
Reference collections of herpetofauna, mammals and birds of Rondônia from the Federal University of Rondônia are sharing their data through the speciesLink network. The collections are repositories of material collected at the upper Rio Madeira dams - Santo Antônio and Jirau. The collection CRHRO (herpetofauna) contains 22 families, 54 genera, 79 species and 228 specimens. The collection CRMRO (mammals) contains 9 orders, 29 families, 51 genera, 57 species and 133 specimens. The collection CRAR (bird) covers 4 orders, 4 families, 5 genera, 5 species and 8 specimens.
New holdings integrated to the speciesLink network
UFES-CTA - Coleção de Tecidos Animais do Departamento de Ciências Biológicas da Universidade Federal do Espírito Santo
This collection consists mostly of animal tissue of rodents, marsupials and neotropical bats, although samples from other taxonomic groups of mammals, amphibians and reptiles are also represented.
UFACPZ - Herbário da Universidade Federal do Acre
This herbarium was created in 1979 and currently has 18,378 specimens, all from the Brazilian Amazonian flora. The New York Botanical Garden is its main collaborator but the herbarium also has partnerships with Peru and Bolivia.
HUEFS - Herbário da Universidade Estadual de Feira de Santana
This herbarium has 151.500 specimens of algae, plants and fungi, but mainly of angiosperms from the semi-arid region. The Herbarium at the University of Feira de Santana is part of the INCT Virtual Herbarium of Flora and Fungi.
The speciesLink network brings great news about participating herbaria. Both botanical gardens of New York and Missouri have updated their data and the Smithsonian Department of Botany has joined the network with its data from Brazil. American herbaria that are sharing their data with the speciesLink network are providing 450 thousand records, of which about 145 thousand are georreferenced.
Some caracteristics of the repatriated data are:
, with 241.281 records of which 98.849 are georeferenced. Based on online data, families with more data are Asteraceae and Rubiaceae and the states with more records are Bahia, Minas Gerais, Goias, Rio de Janeiro and Paraná, which together represent more than 50% of the data. For more details see http://splink.cria.org.br/manager/detail?resource=NYBG_BR
, with 177.874 records of which 44.465 are georeferenced. Based on online data, families with more data are Bignoniaceae, Poaceae and Fabaceae and the states with more records are Amazonas, Minas Gerais, Bahia, Pará and Paraná which together represent about 50% of the data. For more details see http://splink.cria.org.br/manager/detail?resource=MOBOT_BR
(Smithsonian): with 37.662 records of which 2.289 are georeferenced. Based on online data, families with more data are Fabaceae and Poaceae and the states with more records are Minas Gerais, Amazonas, Bahia and Santa Catarina, representing about 50% of the total. For more details see http://splink.cria.org.br/manager/detail?resource=NMNH-Botany_BR
We would also like to announce the integration of the following Brazilian herbaria to the speciesLink network: HTSA - Herbário do Trópico Semi-Árido da Embrapa Semi-Árido and HVASF - Herbário Vale do São Francisco da Universidade Federal do Vale do São Francisco.
is providing 2.292 records to the network (total = 2.500) of which 1.385 are georeferenced. Arecaceae with about 60 espécies is the more represented family. Pernambuco and Bahia are the states with most records, 819 (36%) and 633 (28%) respectively. For more details see http://splink.cria.org.br/manager/detail?resource=HTSA .
is providing 5.884 records, but the geographic coordinates are blocked. This herbarium focuses on the flora of the Vale do São Francisco, but also has holdings from other ecosystems of the northeast of Brazil. Most representative families include Fabaceae, Euphorbiaceae and Malvaceae. Brazilian states with most records are Pernambuco with 3.667 records (63%), Bahia, with 1.312 records (23%), Ceará with 451 records (8%) and Paraíba with 250 records (4%). For more details see http://splink.cria.org.br/manager/detail?resource=HVASF
With the inclusion of these new collections and regular updating of the participating herbaria (47% of the participating herbaria have updated their database in the last 6 months), the network is now serving over 2.2 million records, of which 824 thousand are georeferenced.
New developments: Manager and Indicators
The speciesLink network has two new developments in the applications:
. Manager now only presents collections that are active. To visualize collections that are in process of joining the network, it is necessary to click on the option to see the collections that are off-line. Another column was also included to inform the amount of records that have been georeferenced through an application. It is important to know that any record that has blocked lat/long data is not automatically georeferenced. The last feature that has been added to Manager is the total number of collections at the bottom line.
The new indicator is the
. Collections are classified in three categories: those that have updated their on-line data more then 1 year ago; between 6 and 12 months ago; and less then 6 months ago.
As always, all suggestions are welcome.
New developments: Manager and Centralized Search
now presents a new column, the number of records with automatic georeferencing. All records from Brazil that do not have geographic coordinates but have data on the State and Municipality are automatically georeferenced by the system, based on data from IBGE. Three new fields are added: municipality lat, long, and maximum error. We hope to increase the usage of data for those applications where this precision is sufficient. Through
users can now access the number of total records, records on-line, georeferenced at origin (by the collection), and georeferenced by the system per collection or group of collections.
Another new development is the inclusion of the field
page. This implementation was requested by Murilo de Carvalho from the Ichthyology Lab from USP, Ribeirão Preto.
New Collection Integrated to the speciesLink Network
We are pleased to announce the integration of data from the herbaria of the Regional University of Blumenau (FURB) to the network. The herbarium aims at holding collections and stimulating research on the diversity of the flora of Santa Catarina, especially that of the Parque Nacional da Serra do Itajaí. It currently holds 10,000 exsiccates, with a teaching collections if wood, mosses, and ferns. The collection is digitized and can be easily searched for species and locality data. It is open for exchange, consultation, and loans. Donations of identified exsiccates are accepted.
We are launching a new tool that we hope will be of use to help improve the quality of georeferenced data. An existing application checks whether information on state and municipality for records from Brazil are coherent with the geographic coordinates expressed based on Brazil's official municipality database (IBGE). When they are not coherent they are presented as suspect records in the data cleaning report within the locality data box, item municipality name (Brazil).
These inconsistencies may be a result of errors in digitization, changes in municipality names and areas, or errors in geographic coordinate units.
The tool we are launching today tests this last possibility - an error in the interpretation of the coordinate unit. For all these suspect records with geographic inconsistency, the system:
(1) checks whether the values expressed can actually be degrees:minutes:seconds - DMS as opposed to decimal degrees - DD (DarwinCore standard).
(2) If so, the application assumes that the values are DMS and transforms them to DD and checks for geographic consistency.
(3) If the new values for geographic coordinates imply that the municipality expressed by the collection is the same as that of the IBGE database, a table is produced with these records, including the original values for the coordinates and the new values proposed.
(4) both points original and calculated are also shown on a map.
Both table and maps are accessible by clicking on the new feature within each collections data cleaning report (see
) that is presented immediately under municipality name (Brazil) and is named coordinate unit analysis (Brazil).
As is always the case with these tools, they are being developed to help curators with data cleaning and validation. They do not necessarily express the truth. All decisions must be made by those responsible for each collection.
New release of the infoXY tool
We are launching a new release (2.0) of the tool
that aims at helping biological collections in validating their georeferenced data. By entering data on geographic coordinates the tool returns information about the point, such as the name of the country, state or administrative region, and the name of the municipality or district. If the point is in the sea, the tool will calculate the distance to the closest coast, indicating the name of the country.
Information is obtained from
GADM (Global Administrative Areas)
, a database of the location of the administrative areas (boundaries) of the world. The current version of GADM maps 116,996 administrative boundaries.
New developments at the speciesLink network
Last month we launched an automatic georeferencing tool for records from Brazil that do not have geographic coordinates, but have information on municipality. The system adopts the coordinates determined for the municipality by IBGE (Brazilian Institute of Geography and Statistics).
We are now flagging "suspect" records when exhibiting search results within the
centralized search system
. "Suspect" records are those that the geographic coordinate is not consistent with country, state, and/or municipality data according to the IBGE database. They are points that don't fall within the geographic space registered by the collection. The system does not evaluate whether the species is aquatic or terrestrial. Therefore if a record has "Brazil" as the country data and the coordinate falls within Brazil's maritime boundaries, this record is not suspect even if one is considering a terrestrial specie, as there is no geographic inconsistency. At the same time, records that have not updated the municipality data, may have correct coordinates but will be shown as suspect records as, in this case, there is a geographic inconsistency.
By selecting options to filter data, if selecting:
a. "Georeferenced at source", you will be selecting all records with geographic coordinates registered by the data provider;
b. "Automatic georeferencing (municipality level)", you will be selecting all records from Brazil that have been automatically georeferenced at the municipality level;
c. "select suspect records", you will be selecting records where locality data and geographic coordinates have inconsistencies;
d. "select not suspect records", you will be selecting records where locality data and geographic coordinates are consistent.
When visualizing the data as a table (html or excel) the system now presents two sets of data for geographic coordinates: "Longitude/Latitude/Coordinate precision" and "Long county/Lat county/Error max (mt)", where the first set refers to data registered by the data provider and the second set are coordinates determined by the tool based on IBGE municipality database.
Also, when visualizing the data as an html table, there is a flag (icon) beside each suspect record. As an Excel spread sheet there is an extra column "Geo suspect" with values "0" (zero) or "1" (one), where "1" represents a suspect record.
These developments are a result of a project funded by
JRS Biodiversity Foundation
All suggestions and criticisms are more then welcome.
New tools available at the speciesLink network
We have the pleasure of announcing the availability of new tools at the speciesLink network.
1. automatic georeferencing at the municipality level
For all records from Brazil, that do not have geographic coordinates but have information on the municipality, we now run a tool that automatically georeferences these records based on the municipality data. The values are obtained from a
database from IBGE - Brazilian Institute of Geography and Statistics
.The system also calculates the distance between the point and the farthest border of the municipality and shows this as maximum error in meters.
We have not altered the data coming from the collections. We added 3 new columns to the centralized database: Long munic, Lat munic, and Max error (mt).
Collections that have blocked their geographic coordinates, do not have their records georeferenced. We are respecting the decision of not showing coordinates for these species.
When carrying out a search the system now presents the total amount of records, total amount of originally georeferenced records, and number of records with automatic georeferencing per collection and totals. Please access
the centralized search page
and send us your comments and suggestions.
2. new map available through mapCria
A layer of Brazilian biomes was added as an option of mapCria (you will see this option when clicking on the globe). Description:
Biomas do Brasil
; copyright: IBGE; scale: 1:5.000.000
3. Google Interface
Another new feature is an interface with Google maps, maintaining the web service we developed (mapCria). So there are now 2 map options for users. The interesting feature of Google, besides the associated map and satellite image is the possibility to click on tags of occurrence data. By clicking on the tag one sees minimum data such as the source collection, scientific name, collector and collection date, and a link to the full record at the speciesLink network.
These developments are a result of a project funded by
JRS Biodiversity Foundation
All suggestions and criticisms are more then welcome.
New data integrated to the speciesLink network
The herbarium QCA from the Pontifícia Universidad Católica del Ecuador is now integrating its Amazonian data to the speciesLink network. 35,460 records are available on-line of which 34,257 (~ 97%) are georeferenced. We consider this integration important for a better knowledge of the flora from the Amazon region.
The network today is providing 2,866,828 records on-line, 1,262,478 (44%) of which are geo-referenced. This is the result of 157 collections and subcollections openly and freely sharing their non sensitive data on the Internet. Another interesting data is the frequency of updating. 47% of the participating collections have updated their data in the last 3 months and 18% in the last 3 to 6 months. Only 18% of the participating collections have not updated their on-line systems in the last year. This is important as it may reflect the fact that digitization is a routine, or that the architecture that gives total independence to data providers to update their systems whenever they choose is correct, or even that more and more people are perceiving the benefit of data sharing. I would also like to communicate the fact that The New York Botanical Garden has updated their database with records from Brazil that now has 225 thousand records, 90 thousand of which are georeferenced. It is interesting to have a look at the data cleaning reports and compare existing duplicates at NYBG that have different names when compared to data of other participating herbaria.
We are launching a new indicator that we believe will help evalute the level of regionalization of the speciesLink network. This indicator shows the number of collections and subcollections per Brazilian state. As the number of collections participating in the network increases, we believe that this indicator will show where investments in biological collections are most needed. Please check out the indicators at
Moure's Bee Catalogue
On July 23, 2008, Moure's Bee Catalogue was launched during an official cerimony at the "VIII Encontro sobre Abelhas", in Ribeirão Preto, SP, coordinated by Prof. Gabriel Melo, the project's coordinator. This is the result of Pa. Moure's lifetime work together with a large number of collaborators. Support was given by Finep (Financiadora de Estudos e Projetos).
This partnership between the Federal University of Paraná (UFPR) and CRIA made it possible to all interested have free and open access to the contents of this catalogue which is available at
With this, and again, thanks to the close collaboration with the scientific community we hope to continue aiming at knowing our biodiversity to promote better conservation and sustainable use practices in the country.
New collections integrated to the network
It is with great pleasure that we announce the integration of the following collections to the network:
HUEM | Herbário UEM
NUP | Coleção Ictiológica do Nupélia
MHNCI-Arachnida | Coleção de Arachnida do Museu de História Natural Capão da Imbuia
MHNCI-Aves | Coleção Ornitológica
MHNCI-Crustacea | Coleção de Crustacea do Museu de História Natural Capão da Imbuia
MHNCI-Entomologia | Coleção Entomológica do Museu de História Natural Capão da Imbuia
MHNCI-Herpeto | Coleção Herpetológica
MHNCI-Mamiferos | Coleção de Mamíferos
MHNCI-Miriapoda | Coleção de Miriapoda do Museu de História Natural Capão da Imbuia
MHNCI-Mollusca | Coleção de Mollusca do Museu de História Natural Capão da Imbuia
Aranhas-Solobioma | Coleção de Aranhas
DZUP-Cnidaria | Coleção de Cnidaria
HUEPG | Herbário UEPG
CECG | Coleção Entomológica dos Campos Gerais do Paraná
These collections belong the Taxonline network in Paraná that now has 32 collections.
The speciesLink network is now openly serving 2.770.759 records, 1.221.500 (44%) of which are georeferenced. Our aim of 2.5 million records for the first semester has been reached thanks to the work of all collections. We now work with the aim of 3 million records by the end of 2008.
We are launching 2 new indicators that we hope may be useful to analyze data that is available through the speciesLink network (see http://splink.cria.org.br/indicators). They are:
- taxonomic groups; and,
- Brazilian regions
The "taxonomic groups" indicator shows the number of records per group. If the user chooses to see all data, the result will be a pie with the number and percentage of records of animals, plants (here we include fungi in herbaria), microbial strains, and what we called "broad scope collections", meaning "collections" that hold all groups. When selecting animals, the pie will include vertebrates, terrestrial and aquatic invertebrates. And so on... The number of records presented is the number of records available on-line and the classification in specific groups is obtained through each collection's metadata.
The indicator "Brazilian regions" shows the number of on-line records per geographic region in Brazil for all records of all networks or for a specific taxonomic group or network. This indicator also shows the number of records per square km of the region. The idea is to compare the level of knowledge or the collecting effort of each region. We hope that this indicator may help identify information gaps and define priority areas for new inventories or priority digitization efforts to be carried out.
Other indicators available include:
- collectors: 20 collectors with the largest number of on-line records
- collection date: number of records per year
- States (Brazil): Pizza with the percentage of records on-line per Brazilian state
- families: 20 families with the largest amount of records on-line.
- digitization: Pie with the percentage of records, on-line, georeferenced, and off-line
- map: occurrence points of georeferenced records, plotted on a map
- types: number of type material available. As the system selects data based on whether the field is blank or not, numbers may include fields that have been filled out with things such as "non-type" or "?"
- Countries: pie with the number and percentage of records per country
- records: monthly average of data input and output
As usual, all comments and suggestions are welcome.
Herbaria from the Northeast of Brazil
It is with satisfaction that we announce the integration of data of herbaria from the Northeast of Brazil to the speciesLink network. This project is coordinated by Maria Regina Vasconcellos Barbosa. Data from the following herbaria are now openly and freely available:
1. ASE (Herbário da Universidade Federal de Sergipe), with an important holding of plants from the northeast, mainly from Sergipe.
2. EAC (Herbário Prisco Bezerra, Universidade Federal do Ceará), predominantly Angiosperms.
3. EAN (Herbário Jaime Coelho de Moraes, Universidade Federal da Paraíba)
4. HST (Herbário Sérgio Tavares, Universidade Federal Rural de Pernambuco), besides the forest inventory of the northeast, holdings from the flora of Fernando de Noronha are also available.
5. IPA (Herbário - IPA Dárdano de Andrade Lima, Empresa Pernambucana de Pesquisa Agropecuária), the oldest source of information about the Flora of the northeastern region of Brazil.
6. JPB (Herbário Lauro Pires Xavier, Universidade Federal da Paraíba), reference herbaria for the flora of Paraiba.
7. MAC (Herbário do Instituto do Meio Ambiente do Estado de Alagoas), main depository of the state of Alagoas
8. MOSS (Herbário Dárdano de Andrade Lima, Universidade Federal Rural do Semi-Árido, Mossoró, Rio Grande do Norte), more then 90% of its holdings (9800 records) are from the state of Rio Grande do Norte.
9. PEUFR (Herbário Professor Vasconcelos Sobrinho, Universidade Federal Rural de Pernambuco)
10. TEPB (Herbário Graziela Barroso, Universidade Federal do Piauí), with 23,130 records, the majority from the state of Piauí.
11. UFP (Herbário UFP - Geraldo Mariz, Universidade Federal de Pernambuco), with reference collections including typus, Bryophyta, Mixomycetes and Pteridophyta and Bromeliaceae and Cyperaceae.
12. UFP-Carpoteca (Carpoteca UFP, Universidade Federal de Pernambuco), teaching collection of fruits.
13. UFRN (Herbário UFRN, Universidade Federal do Rio Grande do Norte), with 7,700 records of 160 families: Fabaceae (1302), Poaceae (283), Rubiaceae (272), Asteraceae (232), Euphorbiaceae (329), Erythroxylaceae (230), Myrtaceae (203) and Convolvulaceae (202).
14. UFRN-Fungos (Herbário UFRN - Fungos, Universidade Federal do Rio Grande do Norte), with about 500 fungi from the northeast.
15. URM (Herbário Pe. Camille Torrand, Universidade Federal de Pernambuco), with about 79,000 records of fungi and 46,000 exsiccates, considered the largest collection of herborized fungi of Latin America.
It is important to acknowledge the work of Itamar Barbosa de Lima of the Lauro Pires Xavier Herbarium (Federal University of Paraíba) that worked in collaboration with CRIA's staff to integrate the collections.
Today, June 23, 2008, the network of herbaria from the northeast is serving 160,913 records to the network (40% of the total holdings) with approximately 20 thousand georeferenced records. About 90% of the records are from the Northeast of Brazil. This is an important step towards the consolidation of a data infrastructure on biodiversity that is made freely and openly available to all interested. Searching is available at
Museum of Zoology - Unicamp
We would like to highlight the work carried out by Unicamp's Museum of Zoology to make their records available to public access. The partnership with the speciesLink network dates from November of 2004, with the collections of amphibians, reptiles, fish, mammals and birds. At that time, none of the records were georeferenced. In March 2008 new collections were added to the network - Bivalvia, Gastropoda, and Ophiuroidea - and in May Polychaeta and Lepidoptera. The estimated amount of records of these groups is of about 170 thousand. 18% is on-line (30,483 records) of which 84% (25,569 records) are georeferenced. We would like to congratulate Unicamp's staff for this major achievement.
Herbaria of the Northeast Network
The process of integrating herbaria from the Northeast began this month. This work has the support of CNPq and is being coordinated by the Federal University of Paraiba. Eight collections have been linked to the speciesLink network from the states of Ceará, Paraíba, Pernambuco, and Piauí.
1. Herbário Prisco Bezerra (EAC), Universidade Federal do Ceará, Fortaleza, CE
2. Herbário Lauro Pires Xavier (JPB), Universidade Federal da Paraíba, João Pessoa, PB
3. Herbário Sérgio Tavares (HST), Universidade Federal Rural de Pernambuco, Recife, PE
4. Herbário Dárdano de Andrade Lima (IPA), Empresa Pernambucana de Pesquisa Agropecuária, Recife, PE
5. Herbário Professor Vasconcelos Sobrinho (PEUFR), Universidade Federal Rural de Pernambuco, Recife, PE
6. Herbário Geraldo Mariz (UFP), Universidade Federal de Pernambuco, Recife, PE
7. Herbário Pe. Camille Torrand (URM), Universidade Federal de Pernambuco, Recife, PE
8. Herbário Graziela Barroso (TEPB), Universidade Federal do Piauí, Teresina, PI
These collections hold about 330 thousand exsiccates, and a total of 113,379 records are on-line and 11,135 of these are georeferenced. The profile of each herbaria is available by clicking at the collection's acronym available at http://splink.cria.org.br/manager. Together, all herbaria that are integrated to the speciesLink network are providing 1.5 million records, all freely and openly available on-line.
New Collections join speciesLink
The following collections joined the speciesLink network in March: the Bivalvia, Gastropoda, and Ophiuroidea collections of the Museu de Zoologia do Instituto de Biologia of the State University of Campinas (Unicamp) and the Herbarium Mogiense of the University of Mogi das Cruzes.
Network indicators are launched
With the number of records available (close to 2.3 million) it is now possible to visualize some interesting outputs by grouping data from different collections. One can now evaluate aspects such as the "movement" of data - input and output - of the whole network or of a particular group of collections. One can also see the number of records of each Brazilian state, and other aspects such as the "top 20" families or collectors. With time, as most of the Brazilian collections have digitized their data, theses indicators can be used to identify information gaps, both geographic and taxonomic. Indicators are available at
. All suggestions are welcome.
Balance of 2007
The speciesLink network ends the year of 2007 integrating biological collections' data belonging to 31 Brazilian institutions and 2 institutions from abroad. There are 38 plant collections and subcollections that together hold 2.6 million records and are serving about 1.5 million on-line, 625 thousand of which are georeferenced. These results are also thanks to the Botanical Gardens of New York and Missouri that today contribute with about 350 thousand records from Brazil, with about 30% georeferenced.
There are 84 zoological collections and subcollections participating in the network. Together they hold 4.8 million records and are serving 600 thousand on-line with about 50% georeferenced.
The speciesLink network also integrates data of a microbial collections network called SICol (see
). SICol is serving 9 thousand records. None are georeferenced.
Another 2 information systems are integrated to the speciesLink network: SinBiota and Obis Brazil). SinBiota is a database with observation data of inventories carried out in the State of São Paulo within the Biota/Fapesp program. OBIS Brazil is part of the Ocean Biodiversity Information System and in Brazil is coordinated by the University of São Paulo.
Today, December 19, 11:17 AM the network is serving, thanks to the work of all these collections, 2,274,330 records on-line, with 1,110,758 (49%) georeferenced.
Another important observation is that 28 collections have updated their information in December and only 23 have not updated their information for more then 6 months. 9 collections haven't updated their database since the support provided by Fapesp ended in november 2005.
We hope that 2008 with bring new opportunities of cooperation and resources to carry out the work that still has to be done. In our view, the network has been so successful thanks to the work and enthusiasm of all that believe in a cooperative action for the common good.
News in the network
Thanks to the partnership established with INPA (Instituto Nacional de Pesquisas da Amazônia) and those with biological collections from the State of São Paulo, Taxonline network from Paraná, Botanical Garden of Rio de Janeiro, the Capixaba network from Espírito Santo, the Pollinators' Network, and our partners from the botanical gardens of New York and Missouri, we have reached the number of 1,959,764 records that are being openly served to all interested.
The 2007 IUCN Red List of Threatened Species, the Revised List of Endangered Plants of Brazil, coordinated by the Fundação Biodiversitas, and the National List of Brazilian Endangered Fauna of the Ministry of the Environment of Brazil have been added to our names search system that can be accessed at
Also, when one searches the speciesLink network (see
) the result brings a link to the icon "sp" which is a search in our names search system. When this icon is red, this means that the species is in one of the red lists.
Another new development concerns sensitive data. Some collections filter geographic coordinates when serving data on endangered species. The speciesLink network now identifies data that has been filtered and presents it to users as "bloqueado" or "blocked". This way users can tell the difference between no data and data that has been filtered. If users have a legitimate need for the data they can then contact the respective curators to obtain it.
Another new feature concerns the data cleaning tool. Records that have data on the municipality of Brazil can now add geographic coordinates with associated error. The data cleaning report presents a table with these records and suggested coordinates (decimals and degrees) with maximum error based on the calculation of the municipality's official coordinates and the longest distance from its boundary.
The speciesLink Network has the pleasure of announcing the inclusion of collections from the State of Espírito Santo - rede Capixaba - to the network. This action is a result of the Research and Technological Development Program in Biodiversity of the Secretary of Science and Technology of Espírito Santo, that will implement an information system for managing biodiversity in the State.
This project is investing R$ 1.3 million on the collections and information system.
Pollinators and Herbaria
Thanks to the support of GBIF (Global Biodiversity Information Facility), the following collections were integrated to the network: CEMeC, Coleção Entomológica Moure & Costa, EBDA - Empresa Baiana de Desenvolvimento Agrícola, BA, Salvador; DSEC, Coleção Entomológica do Depto. de Sistemática e Ecologia da UFPB - Universidade Federal da Paraíba; LEBIC, Laboratório de Ecologia e Biogeografia de Insetos da Caatinga, UFCG - Universidade Federal de Campina Grande, PB, Patos; Plebeia UFPE, Plebeia - Coleção Entomológica de Polinizadores, UFPE - Universidade Federal de Pernambuco, PE, Recife; MCP, Coleção de Abelhas do Museu de Ciências e Tecnologia da PUCRS, PUCRS - Pontifícia Universidade Católica do Rio Grande do Sul, RS, Porto Alegre. These new collections are serving 38 thousand records (about 12 thousand georeferenced) and hold 140 thousand records. The pollinators network is also integrating data from collections that were already part of speciesLink: CEPANN, Coleção Entomológica Paulo Nogueira-Neto - IB/USP, with 38,613 records, all on-line with about 90% georeferenced; RPSP, Coleção de Abelhas do Departamento de Biologia - FFCLRP/USP with about 171 thousand specimens, 70 thousand on-line and about 80% georeferenced; DZUP Hymenoptera, Coleção Entomológica Pe. Jesus Santiago Moure (Hymenoptera), com 500 thousand specimens, with 14 thousand on-line and about 92% georeferenciados (Taxonline network).
The pollinators network is serving about 160 thousand records of which 115 thousand are georeferenced.
As to herbaria, speciesLink has a new herbaria on-line, the Herbaria Lauro Pires Xavier (JPB) from the Federal University of Paraiba. This herbaria holds 35 thousand exsicates and is serving data on 33,892 of them, 3,619 georeferenced.
Also about herbaria, records from collections held in Brazil that are deposited at Missouri Botanical Garden have been indexed and are available through the speciesLink Network. There is a total of 157 thousand records, with 45 thousand georeferenced. The herbaria network is now serving 968 thousand records (350 thousand georeferenced) openly and freely to all interested.
Some new tools were developed during the first semester thanks to the support of the JRS Biodiversity Foundation. We would like to highlight the following:
centralized search system
was developed. The basic architecture of a distributed network remains the same, with each collection having complete control over its own data and deciding what data can be made openly available. The difference is that all data sent to regional cache nodes is harvested and deposited in a centralized database to improve the performance of database searching. Every night the system checks to see if data has been added or modified.
(2) Collection classification system. To facilitate the selection of collections for searching purposes, a classification system was added to each collections' metadata. In the centralized system users can now quite easily select the collections of their choice.
(3) Maps. The Brazilian Ministry of the Environment has recently made available for public downloading, maps with protected areas and with priority areas for protection. These maps have been added to mapCRIA, our map service. Users when searching for a species and looking at its distribution on a map through the speciesLink network can now add these layers. They can also recuperate information about the layer by "clicking" on the option "i" and on a point on the map.
. This tool, originally developed to follow the evolution of collections and the network, is a picture of the number of collections and their holdings, indicating how much data is on-line, georeferenced, when it was last updated, and what software is being used.
Another element considered for data cleaning
The year collected is also now being analyzed to help collections identify possible typing errors. The data cleaning report now lists all records that are older then 75 years and those that the date collected is prior to the date the collection has been updated. For more information see the data cleaning reports for each collection available at
Balance of the Network
Besides the collections with the State of São Paulo, the speciesLink network is also integrating data from the
Botanical Garden of Rio de Janeiro
and from the
Taxonline Network of Parana
As to developments, highlights are spLinker, speciesBase, and openModeller.
is an application developed by CRIA in Java to enable biological collections that don't satisfy all prerequisites to serve data directly to the speciesLink network, to mirror their data at regional servers.
is a generic Microsoft® Access database developed in Visual Basic for Applications (VBA) to record generic taxonomic data. Its development was motivated by the increasing number of collections that wish to computerize their holdings and share data through the speciesLink network. speciesBase is a system to record taxonomic data associated to inventories, supported by foreign data tables.
is a fundamental niche modelling library, providing a uniform method for modelling distribution patterns using a variety of modelling algorithms. This developed is being supported by Fapesp and is the result of the collaboration between CRIA, INPE and Poli.
Technical report on-line
CRIA has submitted to Fapesp the
of the speciesLink project, referring to the period between October 2003 and 2004. This report (in Portuguese) is being made available on-line to disseminate the work that is being carried out and to receive suggestions and recommendations from the scientific community.
Launching of the speciesLink Network
Fapesp has the pleasure of inviting the community to the ceremony that will officially launch the speciesLink Network, a distributed information system to integrate data from biological collections. The ceremony will take place at the Foundation on October 05, 2004 at 10:30 AM. The speciesLink network permits dynamic, open, and free access and spatial visualization of biological data, potentially enabling the use of scientific information for decision making and in the formulation of policies and strategies for conservation and sustainable use of our biodiversity.
Meeting of the speciesLink Network
The first meeting of biological collections participating in the speciesLink Network was held in August 25 and 26. 62 researchers and students representing 26 collections were present. The meeting aimed at presenting all the tools and work developed and to discuss future actions of the network.
The Herbarium from Rio Claro (HRCB) IB/UNESP has just joined the speciesLink network
This herbarium has about 40 thousand exsiccates, with emphasis in plants of the cerrado and semi-deciduous forests in the State of São Paulo. There are also some specific collections from Picinguaba (Ubatuba) and Saibadela (Sete Barras), also within the state of São Paulo. At the moment there are 2593 records available.
Monitoring the speciesLink Network
It is CRIA's intention to launch a page with indicators that can help monitor the evolution of the network and help evaluate the developments of the project. The idea is to create automatic processes to gather data and make them available on-line to allow all users and providers to follow the progress made. The first parameter that is being made available is
access to the on-line system
. Different parameters such as "hits", "visits", "pages", and "sites" are shown. It is important to bear in mind that the speciesLink network hasn't been officially launched and is still in a developing and testing phase.
Analysis of the speciesLink network
CRIA prepared a brief
on the evolution of the speciesLink network in terms of the number of participating collections, the number of records on-line, and the number of georeferenced records. We believe that it is important to share this information to enable collections and users to evaluate and criticize the work that is being carried out. The report is in portuguese.
New collections joined the speciesLink network
Thanks to the support of FAPESP, four new collections joined the speciesLink network. They are the amphibian collection "Célio F. B. Haddad", of the Zoology department of UNESP Rio Claro, SP; the amphibian (Amphibia DZSJRP) and the bat collections of IBILCE/Unesp São José do Rio Preto; and the Herbaria "Dom Bento Pickel" of the Instituto Florestal of São Paulo.
Space for News
We are launching a space for news of interest to the
Link network. The intention is to publicize new datasets, developments, events, publications, and any other news of interest to the dissemination and sharing of primary data of biological collections of the country. All suggestions are more then welcome.
Centro de Referência em Informação Ambiental
Fundação de Amparo à Pesquisa do Estado de São Paulo