The Biodiversity Informatics Landscape: Elements, Connections and Opportunities. Article metadata Introduction Methodology Results Discussion Next steps Annex 1.
Increasing Research Impact by Cross-Linking NCBI & EMu Records - The Plant Press. From Plant Press, Vol. 20, No. 2, April 2017.
By Tom Hollowell and Vicki Funk While modern systematics research usually involves genetic analyses, sequences such as those submitted by researchers to the National Center for Biotechnology Information’s (NCBI) public databases still rely on voucher specimens held in all biological collections (including herbaria) for identification and future reference. Genetic sequences are usually submitted to NCBI in association with a researcher’s scientific publications.
NCBI accession numbers are generated, but they are not automatically associated with data about voucher specimens, including National Museum of Natural History (NMNH) Botany records. Unique digital identifiers everywhere. A recent letter in Nature: Members of the Consortium of European Taxonomic Facilities have adopted a consistent citation system for an estimated 20 million biological and geological specimens from European collections.
We encourage researchers, publishers and other institutions to engage with this initiative by citing the full specimen identifier in their publications and data sets. These specimens provide reference material for research on evolution, genetics, mineralogy, ecology and taxonomy — hence the need for a reliable identification system for citation (see A. Güntsch et al.
Where exactly? Historical and modern geo-referencing challenges and solutions. Leaf mysteries revealed through the computer's eye. UNIVERSITY PARK, Pa. -- A computer program that learns and can categorize leaves into large evolutionary categories such as plant families will lead to greatly improved fossil identification and a better understanding of flowering plant evolution, according to an international team of researchers.
Mapping the Indian collection. Always happens this way.
No sooner do I find something interesting, that something similar turns up. Case in point my post last week on the Seedlot Selection Tool. It was just a few hours after I happened across the SST that I ran into NBPGR’s PGR-Clim. Ok, it’s not quite the same thing, but almost. PGR-Clim maps out the Indian genebank’s holdings of chickpea, pearl millet, pigeonpea, sorghum and wheat on a background of rainfall and temperature now, in the 2020s and in the 2040s. For example, here’s what the pigeonpea collection looks like relative to todays’s temperatures.
What Gets Stored in a Cookie? This site stores nothing other than an automatically generated session ID in the cookie; no other information is captured. DNA Banks and Genetic Resources Repositories in the United States. iDigBio is actively compiling a list of DNA banking facilities and genetic resources repositories in the United States that maintain collections of nucleic acid extracts (DNA or RNA) or preserved tissues suitable for genetic and genomic studies of biodiversity.
The following resources (listed alphabetically by institution) represent collections currently known by or reported to iDigBio. Each entry includes the name of the institution, a brief description, and institutional link. To report the availability of genetic resources at your institution, or to revise or update an existing entry, please contact Grant Godden. Ancient plant DNA in lake sediments - Parducci - 2017 - New Phytologist. Abstract Summary Recent advances in sequencing technologies now permit the analyses of plant DNA from fossil samples (ancient plant DNA, plant aDNA), and thus enable the molecular reconstruction of palaeofloras.
Hitherto, ancient frozen soils have proved excellent in preserving DNA molecules, and have thus been the most commonly used source of plant aDNA. However, DNA from soil mainly represents taxa growing a few metres from the sampling point. How well documented is Australia's flora? Understanding spatial bias in vouchered plant specimens - Haque - 2017 - Austral Ecology. Scientific user requirements for a herbarium data portal. ArticlesAbout.
A specialist’s audit of aggregated occurrence records. RAINBIO: mega database on distribution of vascular plants in tropical Africa. Using the “Natural History Large Hadron Collider” to tell us about plant diversity. Tropical forest, Liberia.
Pixnio The world’s herbaria hold millions of samples of plants, and until recently they have been largely the domain of taxonomists – those scientists who describe diversity. Herbarium taxonomists compare specimens collected in different parts of the world, assess variation and then come to conclusions about what to name as new, and what to call the same.
Our ability to talk about plant diversity depends upon this activity – without names, we would be unable to tell each other about distribution – and as so alarmingly today, decline – of the some half a million plant species with which we share the planet. Interview: Natasha de Vere. Ecologist and conservationist Dr Natasha de Vere talks to Tom Ireland about DNA barcoding every species of native flowering plant in the UK, and the crisis facing plant-pollinating insects around the world The Biologist 64(1) p22-25 In 2012, Wales became the first country in the world to DNA barcode every single one of its 1,143 native flowering plants. The project, led by Dr Natasha de Vere, has inspired countless countries to make similar databases of the genetic diversity within their borders. Enabling High-throughput Image-based Phenotyping.
By Shelley Littin, CyVerse A key aspect of CyVerse infrastructure, in the eyes of its designers, is its flexibility – the extent to which community members can mix and match various CyVerse resources to suit their development, research, or educational agenda. Nathan Miller, a scientist in the Spalding Lab at the University of Wisconsin–Madison’s Department of Botany and Center for High Throughput Computing, works closely with CyVerse as he writes computer code to develop software programs that analyze images and videos of plants to determine plant phenotype, the measurable physical characteristics of plants.
Unmet Needs for Analyzing Biological Big Data: A Survey of 704 NSF Principal Investigators. Biotechniques - The International Journal for Life Science Method. DNA extracted from herbarium specimens is highly fragmented; therefore, it is crucial to use extraction protocols that retrieve short DNA molecules. Improvements in extraction and DNA library preparation protocols for animal remains have allowed efficient retrieval of molecules shorter than 50 bp. Here, we applied these improvements to DNA extraction protocols for herbarium specimens and evaluated extraction performance by shotgun sequencing, which allows an accurate estimation of the distribution of DNA fragment lengths.
Extraction with N-phenacylthiazolium bromide (PTB) buffer decreased median fragment length by 35% when compared with cetyl-trimethyl ammonium bromide (CTAB); modifying the binding conditions of DNA to silica allowed for an additional decrease of 10%. We did not observe a further decrease in length for single-stranded DNA (ssDNA) versus double-stranded DNA (dsDNA) library preparation methods. Figure 1. Figure 2. R.M.G, V.J.S., and H.A.B designed the experiments. DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples.
Research Spotlight: January 2017. TDWG 2016: Highlights for biodiversity research The Biodiversity Information Standards (TDWG) annual meeting in 2016 had the theme of "Standards Supporting Innovation in Biodiversity and Conservation". Understanding the use of biodiversity standards, and having clear and concise documentation, is essential for the creation, aggregation and downstream use of biodiversity data, and it is exciting to see the diverse TDWG community helping to clarify and expand on the already existing data standards.
Taxonomy, taxonomic resolution services and identifiers, and efforts to embrace concept reasoning were discussed widely in sessions (Go Nico Franz!) Throughout the meeting. iPhylo: Taxonomic name timelines for BHL. Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification. Global Plants, a collaborative between JSTOR and some 300 herbaria, is now the world’s largest database of digitized plant specimens ( accessed 20 April 2016). It currently contains images of 2,482,901 million herbarium sheets (Hannah Begley, Digital Librarian for Primary Sources, JSTOR, 4 May 2016). Articles. Articles. World data centre for microorganisms: an information infrastructure to explore and utilize preserved microbial strains worldwide. + Author Affiliations.
Mass Digitizing a Working Herbarium using a conveyor belt: Workflows, Strategies, Challenges. Please join us for Mass Digitizing a Working Herbarium using a conveyor belt: Workflows, Strategies, Challenges, a webinar presentation by Sylvia Orli, IT and Digitization Manager, US Herbarium (Smithsonian). Large-scale digitisation by Kew and Natural History Museum. As previously reported, Kew and the Natural History Museum, London (NHM) have combined forces to carry out a pilot project for the mass digitisation of their herbarium specimens. Kew and NHM staff recently travelled to Amsterdam to oversee the start of the pilot, which involves 70,000 specimens, and to see for themselves their herbarium sheets being imaged on the Digistreet conveyor belt system.
All of the herbarium specimen sheets arrived safely at the digitisation site in the Netherlands and were checked for damage to the paper, labels or plant material. All sheets were found to be in the same condition on arrival as when they left the herbaria in London, having been safely packed and secured for the trip. Before the process of imaging the material could begin, NHM and Kew staff gave on-site training to the team of three operators working on the DigiStreet conveyor belt system.
Upcoming game uses genetic science to create alien gardens - Kill Screen. Automated Plant Species Identification: Challenges and Opportunities. A tool for the analysis of chromosomes: KaryoType: Ingenta Connect. Abstract: The software KaryoType, an improved and completely renewed version of the previously existing NucType, was developed for plant chromosomes. The primary function of the software is to allow efficient chromosome measurements and karyotype analysis from microphotographs.
Karyotype characterization usually includes chromosome number, size, arm ratio, centromeric index, relative lengths and karyotype formula. Automated Plant Species Identification: Challenges and Opportunities. The number of species of macro organisms on the planet is estimated at about 10 million. Genome of 6,000-year-old barley grains sequenced for first time - Scienmag. An international team of researchers has succeeded for the first time in sequencing the genome of Chalcolithic barley grains.
This is the oldest plant genome to be reconstructed to date. The 6,000-year-old seeds were retrieved from Yoram Cave in the southern cliff of Masada fortress in the Judean Desert in Israel, close to the Dead Sea. UsingR. Arctos. BioNames. Compadre. Botanists at Trinity College Dublin have launched a database with information that documents significant ‘life events’ for nearly 600 plant species across the globe. Digitarium. Free, simple & effective.
Diversity:A Plant Dna Barcode Library. EDDMapS - Invasive Species Mapping Made Easy. Consortium of European Taxonomic Facilities. Global Genome Biodiversity Network. Global Plants Tour - June 2013. Herbaria@home project homepage. iDigBio Update for 2015. iDigBio & PhyloJIVE portal. TCN Resources - iDigBio. Rmarkdown + GitHub = Reproducible Research. iNaturalist.org · A Community for Naturalists. India: NBRI Online. Indian Botanists: Indian Institute of Science to Launch 'Online Digital Database' on Flora of Karnataka. Why are botanists locking away their data in JSTOR Plant Science? LandMark. Morphobank - Network Integrated Biocollections Alliance. Automated pipeline for nomenclatural acts. Nsca digitization. Phylogenetic Toolbox. PhyloJive – Integrating biodiversity data with phylogenies. NCSU Herbarium Creates Plant ID Mobile Apps (for Android)
Protected Planet. Resource and Reference Links. Seed Information Database: Royal Botanic Gardens, Kew. Small Collections Network. North American Network of Small Herbaria Home. Mapping a Social Network. SYNTHESYS - an integrated European infrastructure for researchers in the natural sciences. Connecting Content at the US National Herbarium - The Plant Press. The World Flora Online Project.
Big Data and the Science of the Christmas Tree. Beyond the Box Competition. Museum Specimens Find New Life Online. Bringing 'dark data' into the light: Best practices for digitizing herbarium collections. Digitization: A pilot for discovering plant diversity at Kew. Digitising Kew's microscope slide collection. Seeing the invisible history of leaves.