Global Genome Biodiversity Network-Global Genome Initiative Awards Program

From GGBN Wiki
Revision as of 21:15, 15 June 2020 by KatharineBarker (talk | contribs) (→‎Institution:National Biodiversity Cryobank of Canada, Canadian Museum of Nature)
Jump to: navigation, search

GGBN new logo small.pngGGI logoHorizontal RGB black.png

We are happy to announce the GGBN-GGI Awards Program. The program provides funding for projects that support the discoverability of new genetic collections through the Global Genome Biodiversity Network's Data Portal. The next submission deadline for proposals will be in spring 2021. The proposal review committee will consider requests for up to 30,000 USD with clearly articulated budget justifications. All data from funded projects must be made available online on the GGBN Portal before 1 September 2022.

Contents

GGBN/GGI Awards Program

Eligibility

Any institution with non-human genetic resources, to include both current and prospective members, who are pursuing or have achieved GGBN core membership are eligible to apply. Institutions with successful proposals who have not yet joined GGBN must − as a minimum − become an associate GGBN member by signing the GGBN MOU prior to the awarding of funds and become a core GGBN member upon project completion.

Technical Requirements

At the end of the project, for publishing data through GGBN, your collection should have: (i) a database to manage your specimens and samples according to GGBN requirements, (ii) a web server to publish your data, and (iii) BioCASe or IPT to map your database to the GGBN Data Standard. Both BioCASe and IPT are open source software, one of them must be installed in order to make collections discoverable through GGBN. Voucher specimen data should be provided to GBIF in parallel. If your collection does not have a database for the management of DNA and tissue collections, GGBN provides an open-source software that can be used (http://wiki.ggbn.org/ggbn/DNA_Module). Technical support is provided by GGBN. Please see GGBN’s IT requirements and mandatory and recommended fields for sharing data with GGBN for additional information.

Proposals

Budget requests will exclusively support the addition and publication of new genetic sample records on the GGBN Data Portal, e.g. contractual labor for short-term staff for processing and/or databasing genetic specimens, informatics support for preparing institutional databases for online discoverability, new servers required for online discoverability, and/or travel costs for visiting experts to facilitate sample processing and online discoverability. Proposed projects must support the discoverability of new collections through the GGBN Data Portal and support the goals of GGBN and GGI, including:

  • increasing the visibility and discoverability of genetic samples (e.g. tissues and DNAs) through public release on GGBN data portal (http://www.ggbn.org/ggbn_portal/)
  • Increasing the taxonomic (families, genera, species) representation of genetic samples through the GGBN Data Portal. Applicants should make use of the Gap Analysis Calculator when developing their proposals for funding in order to identify to what extent existing collections reflect familial or generic gaps in GGBN (see: http://www.globalgeno.me/)

Evaluation Criteria

  • Complementarity: how do your institution’s holdings complement those already uploaded by GGBN members?
  • Size, scope, and quality of your collection: geographic scope, age of samples, genomic quality (if known), the total number of samples, species, genera, and families to be made discoverable through the GGBN Data Portal.
  • Genomic Novelty: number of families, genera, and species to be made discoverable through the GGBN Data Portal not currently represented in GGBN.
  • Adherence to GGBN best practice: to what degree does your collection meet GGBN best practices for data and collection management? I.e. does or can your institution meet GGBN’s technical requirements and implement the GGBN data standard, or follow GGBN’s guidance on Access and Benefit Sharing, as required for GGBN membership? Please be aware that information on the status and legality of permits for samples is tracked as part of the GGBN data standard.
  • Efficiency: how much of this project can be accomplished per US dollar?
  • Community: to what extent does this project contribute to the GGBN community?
  • Timeline and milestones for completion.

Proposal Format

The body of the proposal should be no more than three single-spaced pages (with a 1,5 cm margin on all sides) and address complementarity to existing GGBN collections, size, scope and quality of the collection, taxonomic novelty, adherence to GGBN best practice, efficiency, community, and timeline. Applications that do not conform to the guidelines will be rejected.

Selection and Notification

All proposals will be evaluated by a committee composed of GGBN members. Please contact Katie Barker, GGBN and GGI Program Manager, (barkerk@si.edu) with any questions regarding the scope, ranking criteria, or clarifications for this proposal call.

Submission

Submit the proposal as a single PDF to GGI@si.edu with the required contents in the following order: Application Form, Proposal text, CVs of Principal Investigators (PI) and CO-PIs, or institutional contacts. The Summary Tables and Results Tables requested in the Application Form should be submitted in Excel format as a separate file from your proposal pdf. A short email (sent to GGI@si.edu) is also requested from your director indicating the PI’s or primary contact’s name, project title, and approval of the submission of the proposal.

Selection and Notification

Proposal requests will be peer-reviewed by a committee selected by the GGBN Executive Committee. After the proposal evaluation, institutions of selected proposals should expect to meet with committee members to discuss logistics and to answer questions. Please contact Katie Barker (barkerk@si.edu) for questions regarding project scope and evaluation criteria.

Note: Non-GGBN members applying for funding must sign GGBN’s MoU as associate or core members!

The Global Genome Biodiversity Network-Global Genome Initiative Awards program 2020 Awardees

Institution: Marine and Coastal Research Institute, INVEMAR

Country: Colombia

Title: Preserving and sharing the marine genetic diversity of Colombia through the tissue collection of the Marine Natural History Museum of Colombia - Makuriwa of INVEMAR

Number of samples added to GGBN: 2,180

Number of new families provided to GGBN: 7

Number of new genera provided to GGBN: 8

Abstract: The National Biodiversity Cryobank of Canada (NBCC) houses >36,000 tissue samples not yet discoverable through GGBN. This project will initiate the NBCC’s data publishing with a collection of 5,500 scarab beetle tissues. The project scope includes data digitization and tissue subsampling. The collection, primarily from the Neotropics, includes comprehensive coverage of Chilean Scarabaeoidea, 49 paratypes of recently-described species, and at least four families and 68 genera new to GGBN. This project will include the implementation of procedures and workflows consistent with GGBN best practices that will become fundamental to NBCC operations, thereby establishing a solid framework for continued data publishing.

Institution: National Biodiversity Cryobank of Canada, Canadian Museum of Nature

Country: Canada

Title: Making a taxonomically significant collection of scarab beetles at the National Biodiversity Cryobank of Canada discoverable through the GGBN Portal

Number of samples added to GGBN: 5,500

Number of new families provided to GGBN: 4

Number of new genera provided to GGBN: 68

Abstract: The National Biodiversity Cryobank of Canada (NBCC) houses >36,000 tissue samples not yet discoverable through GGBN. This project will initiate the NBCC’s data publishing with a collection of 5,500 scarab beetle tissues. The project scope includes data digitization and tissue subsampling. The collection, primarily from the Neotropics, includes comprehensive coverage of Chilean Scarabaeoidea, 49 paratypes of recently-described species, and at least four families and 68 genera new to GGBN. This project will include the implementation of procedures and workflows consistent with GGBN best practices that will become fundamental to NBCC operations, thereby establishing a solid framework for continued data publishing.

Institution:Ocean Genome Legacy Center

Country:United States of America

Title:Expansion of OGL Sample Sharing Through the GGBN Data Portal

Number of samples added to GGBN:66,151

Number of new families provided to GGBN: 189

Number of new genera provided to GGBN: 791

Abstract:The Ocean Genome Legacy Center (OGL) has been a data-contributing core member of GGBN since 2014. However, recent advancements adopted by GGBN have resulted in a divergence between OGL and GGBN data standards, preventing continued OGL resource sharing on the GGBN platform. To address this, OGL will modify its database to accommodate GGBN required fields and controlled vocabulary, curate its records, and administer an instance of the IPT. This will increase GGBN marine records by ~59,000, or ~40%, will add 189 families and 791 genera new to GGBN, and will create an efficient pipeline for future data sharing.

Institution: Pontificia Universidad Católica del Ecuador (BIOWEB, Escuela de Biología)

Country:Ecuador

Title:Preserving and sharing Ecuadorian genetic diversity

Number of samples added to GGBN:40,000

Number of new families provided to GGBN:32

Number of new genera provided to GGBN:454

Abstract:The biocollections of Pontificia Universidad Católica del Ecuador (PUCE) are the largest in Ecuador with over 2 million specimens. Its genome bank holds over 64,000 genomic samples and nearly 8,000 DNA extractions of which over 40,000 have not been uploaded to the GGBN database. The purpose of this project is to update and clean up our genome bank database and make our records discoverable through the GGBN portal. The GGBN portal currently holds data from over 30,000 tissue samples from the PUCE herpetological collections (QCAZ museum).

Institution: Steinhardt Museum of Natural History

Country:Israel

Title:Digitizing the major vertebrate tissue collection in the Middle East

Number of samples added to GGBN:10,418

Number of new families provided to GGBN:3

Number of new genera provided to GGBN:76

Abstract:The Steinhardt Museum of Natural History houses the largest, most important collection of East Mediterranean vertebrates (marine and fresh water, desert and Mediterranean vegetation) in the world. It contains thousands of tissue samples of taxa: from geographic variants to species and higher taxa not represented anywhere else. We propose to catalog these samples making our database compliant with GGBN data standards. This will add nearly 10500 samples to the GGBN portal, including at least 669 genera and 2 families – many of which are not currently represented (e.g., 76 new genera).

The Global Genome Biodiversity Network-Global Genome Initiative Awards program 2019 Awardees

Institution: Centro de Ornitología y Biodiversidad (CORBIDI)

Country:Peru

Title:Preserving treasures: saving the Peruvian herpetofauna genome

Number of samples added to GGBN: 3,800

Number of new families provided to GGBN: 2

Number of new genera provided to GGBN: 22

Abstract: Founded in 2007, CORBIDI’s herpetological collection now has more than 20,000 specimens. However, as the collection became larger, so the expenses related to its maintenance became larger too, awakening a need to get more funds continuously. During 2017 we got to be financed by the GGBN with 30,000.00 USD and our equipment and software for maintenance changed radically. Furthermore, the curation quality of our specimens and its data increased considerably. At the end of our first proposal, we reached to deliver the data of 9004 samples. Now we want to continue improving some details in our collection management (especially related to the taxonomy of our samples) and want to increase the number of endemic taxa in our renewed genome bank.

Institution: Missouri Botanical Garden

Country:USA

Title:Sharing Novel Genetic Plant Samples From The Missouri Botanical Garden DNA Bank Through the GGBN Portal

Number of samples added to GGBN: 25,000

Number of new families provided to GGBN: 120

Number of new genera provided to GGBN: 1,500

Abstract:The Missouri Botanical Garden DNA Bank houses >25,000 tissue samples, comprising 419 plant families, 3425 genera and almost 11000 different species, collected in ca. 65 countries, with an emphasis in locally rare and endemic species from Madagascar, New Caledonia, Gabon, Cameroon, Nicaragua, Bolivia, and Ecuador. About 30-40% of these taxa are currently not represented in GGBN. The goal of this project is to make the collection fully accessible to researchers worldwide by integrating these tissue samples, their associated voucher information and specimen images with the GGBN portal and GBIF using the IPT, following GGBN sample and data standards.

Institution: University of California, Los Angeles, UC Conversation Genomics Consortium

Country:USA

Title:Integration of CALeDNA, a growing collection of California soils, sediments, and water, and their environmental DNA data, into GGBN, GBIF, and Global Biotic Interactions

Number of samples added to GGBN: 1,000

Number of new families provided to GGBN: 954

Number of new genera provided to GGBN: 4,154

Abstract:CALeDNA is a growing initiative where thousands of community scientists collect environmental samples from California's diverse ecologies to be a permanent research resource, and where researchers sequence environmental DNA from a sizeable subset (currently ~1000) using emerging techniques spanning sampling, sequencing, and analysis. This proposal is to develop and onboard all CALeDNAassociated eDNA samples and data to the GGBN database and its partner databases, to align collection methods and metadata with GGBN standards, to ease the deposition of data to GGBN for future years, and to form an relationship with GGBN to inform standards development as the eDNA field diversifies.

Institution:University of Karachi, Centre for Plant Conservation

Country:Pakistan

Title:Data expansion and advanced record maintenance in Centre for Plant Conservation, University of Karachi, Pakistan

Number of samples added to GGBN:1,000

Number of new families provided to GGBN: equal to or less than 28

Number of new genera provided to GGBN: equal to or less than 428

Abstract:Centre for Plant Conservation at the University of Karachi is the hub of academic and research activities, provides opportunities for collaborative research in Pakistan. More than 150,000 plant species are found in the Herbarium and more than two thousand plant species are growing in the Botanic Garden. Most of the specimens are several decades old and there should be new collections. There is also a need for an advanced system for record maintenance. If we compete for our problems we will be able to add maximum and significant data to GGBN portal.

Institution:University of Torino, Dipartimento de Scienze della Terra

Country: Italy

Title:International collaboration in digitization leading to improved discoverability, and enhanced accessibility of genomic resources from several important Italian collections

Number of samples added to GGBN: 2234

Number of new families provided to GGBN: equal to or less than 9

Number of new genera provided to GGBN: equal to or less than 10

Abstract:Collaborate across institutions to facilitate rapid digitization of previously unavailable genomic resources associated with specimens at the Earth Science Department of the University of Torino in the MGPT-MPOC collection (bird skeleton collection) and Reptile collections held at the Civic Museum of Natural History of Carmagnola, Torino, Italy (MCCI). Enhance the accessibility of these resources to researchers in the United States by subsampling and depositing an aliquot with our partner institution, Texas A&M University.

The Global Genome Biodiversity Network-Global Genome Initiative Awards program 2018 Awardees

Institution: Denver Museum of Nature and Science

Country:USA

Title:Expansion of the Arctos/GGBN Data Pipeline

Number of samples added to GGBN: 820,000

Number of families provided to GGBN: 1,615

Number of genera provided to GGBN: 6,043

Abstract: In 2017, three Arctos institutions, the Museum of Vertebrate Zoology (MVZ), the University of Alaska Museum of the North (UAM), and the Museum of Southwestern Biology (MSB), received funding to develop the migration protocol to serve Arctos genomic data through GGBN. We now propose to add the Denver Museum of Nature & Science (DMNS). We request funds for 1) programming support to resolve integration issues to enable the VertNet IPT to publish new Arctos collections data through GGBN, including Arctos host/parasite and environmental sample use cases, and 2) collaboration on a standardized Arctos/GGBN submission pipeline to GenBank.

Institution: Hungarian Natural History Museum

Country:Hungary

Title:Preserving the past and the present for the future in the Hungarian Natural History Museum

Number of samples added to GGBN: 8,044

Number of families provided to GGBN: 283

Number of genera provided to GGBN: 970

Abstract: The Hungarian Natural History Museum hosts the most important DNA and tissue collection in Hungary. Our project would facilitate the integration of the collections into the GGBN system, focusing on the endemic taxa from the Pannonian Biogeographical Region, and rare taxa collected in the Balkan Peninsula, Anatolia, South-East Asia, Africa, and Central-America. Altogether 8044 specimens of 1859 species representing a wide range of taxonomical coverage (fungi, plants, invertebrates and vertebrates) are planned to be published through the GGBN Data Portal coupled with voucher specimen data to GBIF, including taxa from 352 genera that would provide new data to GGBN.

Institution: Natural History Museum of Los Angeles County

Country:USA

Title:Opening a Door to the Marine World: Invertebrate Diversity of the North American West Coast

Number of samples added to GGBN: 5,000-10,000

Number of families provided to GGBN: 371

Number of genera provided to GGBN: 515

Abstract: Marine macroinvertebrates represent a large fraction of phylogenetic diversity. The Diversity Initiative for the Southern California Ocean program of the Natural History Museum of Los Angeles County is amassing a regionally comprehensive collection of marine macroinvertebrates, specifically for genetic research. This important collection (3,558 specimen lots by May 2018, about 5,000 expected by September 2019) will greatly enrich GGBN holdings. A preliminary gap analysis indicates that 82 (of 371) collected families and 256 (of 515) collected genera are new to GGBN, with more novel taxa anticipated. Support will facilitate the publication of this ongoing collection’s specimen and DNA extract data.

Institution: Manaaki Whenua-Landcare Research

Country:New Zealand

Title:Digitizing New Zealand's only dedicated tissue collection for terrestrial arthropods

Number of samples added to GGBN: 5,165

Number of families provided to GGBN: 57

Number of genera provided to GGBN: 350

Abstract: New Zealand is a biodiversity hotspot of international significance and it is estimated that 80% of its arthropod species are endemic. The New Zealand Arthropod Collection holds the largest collection of NZ terrestrial arthropod in the world. While we currently share records from our morphological collection via GBIF, our ancillary holdings of tissue samples have never been cataloged. We propose to catalog these samples and modify our database management system to be compliant with GGBN standards. This will add at least 5165 samples of NZ beetles to the GGBN portal, including at least 350 genera and 15 families not currently represented.

Institution: Kunming Institute of Zoology, Chinese Academy of Sciences

Country:China

Title:Sharing genetic data at the Southern China DNA Barcoding Center with the global community

Number of samples added to GGBN: 25,000

Number of families provided to GGBN: 300

Number of genera provided to GGBN: 800

Abstract:The Southern China DNA Barcoding Center (SCDBC) is the only Central Node of the International Barcode of Life (iBOL) in Asia and provides sequencing, bioinformatics, and biorepository training to researchers across the region. Since 2011, SCDBC has assembled ~500,000 genetic samples from countries across Asia and processed ~25,000 samples for DNA barcoding (i.e., cytochrome c oxidase I sequencing). We aim to publish 25,000 DNA barcodes (from approximately 300 families and 800 genera) through the GGI-GGBN Awards Program. Almost all of the species represent putative new records for the GGBN Data Portal with the status of high priority for collection.

Institution: Rio de Janeiro Botanical Garden

Country:Brazil

Title:Publication and integration of the DNA Bank of the Rio de Janeiro Botanical Garden

Number of samples added to GGBN: 5,739

Number of families provided to GGBN: 126

Number of genera provided to GGBN: 431

Abstract: The Brazilian flora is considered one of the most diverse in the world and about 25% of the world plant species occur in the country. Facing the effects of global climate change and the continuous Brazilian forest loss, it is becoming urgent to have reliable and reusable genetic data to promote efficient species conservation strategies. In this project, we aim to increase data quality of the DNA samples deposited in Rio de Janeiro Botanical Garden DNA Bank (RBdna) and make it discoverable on the GGBN portal through an IPT installation, following GGBN criteria for data mapping and publication.

Institution: Biodiversity Education and Resource Centre, Abuja

Country:Nigeria

Title:Implementation of the National Biodiversity Information and Data System for Nigeria

Number of samples added to GGBN: 6,000

Number of families provided to GGBN: TBD

Number of genera provided to GGBN: TBD

Abstract: These collaborative partnerships (National Biodiversity Information Consortium, NBIC) will foster data-mobilization (about 100,000 Plant Herbarium specimens and 30,000 Animal and insect data, as well as 6,000 biodiversity data, inform of genetic materials stored as biodiversity DNAs) relationships and responsibilities for effective assessment of biodiversity across Nigeria. Specimens will be fully digitized and enhanced with geo-referencing and data cleaning according to international data standards. Data will be mobilized and published via a Central Biodiversity portal which will be linked to the GGBN portal.

Institution: Vietnam National Museum of Nature (pending)

Country:Vietnam

Title:Digitizing of Insect Tissue Collections at the Vietnam National Museum of Nature

Number of samples added to GGBN: 1,000

Number of families provided to GGBN: TBD

Number of genera provided to GGBN: TBD

Abstract:In 2016, the Vietnam National Museum of Nature (VNMN) joined GGBN as its 54th member. The VNMN collection currently includes DNA samples representing approximately 500 species. This project will significantly increase the number of endemic and rare species preserved for future genetic research by developing the VNMN tissue collection, with a focus on sampling insect species. Aside from their scientific value, many target taxa are also economically important. This project will contribute to the sharing of information and genetic research materials through the GGBN data portal.

The Global Genome Biodiversity Network-Global Genome Initiative Awards program 2017 Awardees

Institution: Biodiversity Research and Teaching Collections, Texas A&M

Country: USA

Title: Digitization of Vertebrate Tissue Collections at the Biodiversity Research and Teaching Collections

Number of samples added to GGBN: 35,000

Number of families provided to GGBN: 267

Number of genera provided to GGBN: 854

Abstract: Through time, each vertebrate division of Texas A&M University’s Biodiversity Research and Teaching Collections has grown to include genomic materials (i.e., tissues) associated with cataloged specimens. While we currently share our data via aggregators such as VertNET, and iDigBio, our databases often do not reflect if the specimen has an accompanying tissue. We estimate that we have 30,000 tissues associated with vouchers in our collection that need to be matched to voucher data and digitized, and an additional 5,000 tissues not associated with a voucher but with appropriate locality data that could be added to the GGBN portal.

Institution: Centre for Biodiversity Genomics (CBG), University of Guelph

Country: Canada

Proposal Title: Increasing the visibility of genetic samples at the Centre for Biodiversity Genomics

Number of samples added to GGBN: 1,590,340

Number of families provided to GGBN: 1,238

Number of genera provided to GGBN: 6,332

Abstract: The Centre for Biodiversity Genomics (CBG) at the University of Guelph maintains a globally unique natural history collection and is spearheading a novel approach to biodiversity research within Canada and internationally. To maintain continued accessibility of this digitized collection, the CBG aims to liberate more data and derivatives of the specimens it holds. Through the GGI-GGBN Awards Program, it proposes to publish nearly 1.6 million specimen and DNA extract records on GGBN by May 2018.

Institution: Centro de Ornitología y Biodiversidad (CORBIDI)

Country: Peru

Title: Preserving treasures: road to save the Peruvian herpetofauna genome

Number of samples added to GGBN: 6,200

Number of families provided to GGBN: 36

Number of genera provided to GGBN: 140

Abstract: With only nine years of creation and more than 17000 specimens, between amphibians and reptiles, the herpetological collection of CORBIDI is one of the most important collections in Peru. However, as the collection became larger, the expenses related to its maintenance, which we have not been able to cover. Consequently, our genome collection still lacks proper equipment and software for its maintenance and managing (e.g. high-quality equipment, databasing, online storage, and curatorship). We are confident that with the current importance of molecular systematics and genomic research for biodiversity conservation, our institution will be able to get the necessary funds to improve our genome and specimen collections.

Institution: The Czech Academy of Sciences, Institute of Vertebrate Biology

Country: Czech Republic

Title: African and Central European Vertebrates: Discoverability of Genomic Samples Located at the Institute of Vertebrate Biology, Czech Republic

Number of samples added to GGBN: 8,000

Number of families provided to GGBN: 30

Number of genera provided to GGBN: 110

Abstract: The recently established Genetic Bank of the Institute of Vertebrate Biology currently presents 500 vertebrate genomic samples from Central Europe at GGBN Data Portal. However, further >9000 tissue samples collected mostly in East Africa (small mammals), Central Europe (fish, mammals), Russia and some Asian, Balkan and Middle East countries (small mammals) are to be processed and databased. We aim, therefore, to use an already established data presentation pipeline to process and publish at GGBN Data Portal further at least 8000 samples from available collections. These collections include at least 133 species, 34 genera and three families not currently represented in GGBN.

Institution: Museum of Southwestern Biology

Country: United States

Title: Aligning Arctos with GGBN data standards

Number of samples added to GGBN: 750,000

Number of families provided to GGBN: 668

Number of genera provided to GGBN: 3,226

Abstract: Arctos (https://arctosdb.org/) is an online collection management information system that now serves data on over 3 million cataloged specimens from over 120 collections throughout North America. Arctos also is a community of museum professionals that collaborate on museum best practices and work together to continually improve Arctos data richness and functionality. Arctos has become a leader among museum data management systems supporting on-line museum data streaming. Modifications to Arctos are necessary for compliance with GGBN data standards, including ABS permitting information, and to export data in a GGBN-compatible format. We propose to program this functionality.

Institution: University of Johannesburg

Country: South Africa

Title: Data discovery from 10 years at the African Centre for DNA Barcoding (ACDB)

Number of samples added to GGBN: 7,452

Number of families provided to GGBN: 239

Number of genera provided to GGBN: 1,924

Abstract: The African Centre for DNA Barcoding (ACDB) was established in 2005 as part of the International Barcode of life project. The mitochondrial cytochrome c oxidase 1 gene (CO1) was adopted as the barcode for animals. Two plastid genes, rbcLa, and matK were recommended to barcode terrestrial plants. The past decade, we at the ACDB have used these core DNA barcodes to generate a barcode library for southern Africa. To date, the ACDB has contributed more than 21 000 plant barcodes and to the Barcode of Life Database (BOLD).

Retrieved from "http://wiki.ggbn.org/ggbnwiki/index.php?title=Global_Genome_Biodiversity_Network-Global_Genome_Initiative_Awards_Program&oldid=3294"