This document discusses various topics related to monitoring and measuring biodiversity on a global scale. It mentions several key organizations and initiatives, including the Earth Summit, IPBES, NCBI, GBIF, TDWG, and Darwin Core, that are involved with assessing global biodiversity patterns and developing standards for exchanging biodiversity data. The document emphasizes that monitoring biodiversity as a comparative science requires access to data, use of identification aids, metadata standards, networks to share information, and applying data to understand changes over space and time.
The document provides information for participants attending the Asia Pacific Procurement Forum at the Asian Development Bank headquarters from August 24-25, 2009. It details the venue, airport transfers, hotel accommodations, access to ADB, meals, allowances, country information, and contacts for inquiries. The conference will be held at the ADB headquarters in Manila, Philippines and participants have been booked at the Crowne Plaza Hotel. ADB will cover accommodation costs and provide allowances to sponsored participants.
The document discusses the issue of uneven distribution of biodiversity data around the world, with much of the data held by small publishers and citizen scientists. It notes that these "small data publishers" face challenges in discovering, accessing, managing and publishing their data according to standards. The document calls for developing standards and tools that make it easier for small data publishers to capture, organize and share their biodiversity data in order to help mobilize this important but hard to access data.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
This presents the need and possibility of creating CEFE courses over the internet using Web 2.0 technologies. This was presented in the Balkan CEFE Trainer's Conference in Belgrade last April 10, 2010.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
The document provides information for participants attending the Asia Pacific Procurement Forum at the Asian Development Bank headquarters from August 24-25, 2009. It details the venue, airport transfers, hotel accommodations, access to ADB, meals, allowances, country information, and contacts for inquiries. The conference will be held at the ADB headquarters in Manila, Philippines and participants have been booked at the Crowne Plaza Hotel. ADB will cover accommodation costs and provide allowances to sponsored participants.
The document discusses the issue of uneven distribution of biodiversity data around the world, with much of the data held by small publishers and citizen scientists. It notes that these "small data publishers" face challenges in discovering, accessing, managing and publishing their data according to standards. The document calls for developing standards and tools that make it easier for small data publishers to capture, organize and share their biodiversity data in order to help mobilize this important but hard to access data.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
This presents the need and possibility of creating CEFE courses over the internet using Web 2.0 technologies. This was presented in the Balkan CEFE Trainer's Conference in Belgrade last April 10, 2010.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive function. Exercise causes chemical changes in the brain that may help protect against mental illness and improve symptoms.
Setting the Scene for ViBRANT – Strategy, Philosophy and Communicationvbrant
The document discusses the future of scientific publishing and open access. It envisions a future where publications are semantically marked up and linked to external data sources to enable advanced text mining and knowledge extraction. Treatments of species would be structured using XML to define content and be linked to identifiers, bibliographic metadata, and other sources. This would allow publications to be queried and analyzed by both humans and machines. Prospective publications could be semantically enhanced from the start, while tools are needed to mark up legacy literature. The goal is open access to scientific knowledge beyond traditional PDFs.
The document discusses the future of scientific publishing and open access to scientific literature. It envisions a future where publications are semantically marked up and linked to external data sources to enable advanced text mining and knowledge extraction. Treatments of species would be structured using XML to define content and be linked to identifiers, bibliographic metadata, and other sources. This would allow publications to be queried and analyzed by both humans and machines. Prospective publications could be semantically enhanced from the start, while tools are needed to mark up legacy literature. The goal is open access and dissemination of scientific findings funded by public resources.
The document discusses several "sins" or bad practices that are commonly seen in bioinformatics, including reinvention, lack of reuse, inconsistent naming schemes, and lack of collaboration and data sharing. It provides examples of these issues and argues that greater emphasis should be placed on standards, collaboration, and leveraging existing tools and data. The document also acknowledges that some reinvention may be necessary due to evolving technologies and unmet needs in the field.
The Seven Deadly Sins of BioinformaticsDuncan Hull
Keynote talk at Bioinformatics Open Source Conference (BOSC) Special Interest Group at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) in Vienna, July 2007 by Carole Goble, University of Manchester.
This document discusses the challenges of analyzing large datasets from metagenomic shotgun sequencing experiments. It notes that while sequencing costs have decreased significantly, the computational analysis of the massive amounts of data generated still poses major challenges. It introduces the concept of "digital normalization" as an approach to reduce dataset sizes while retaining most of the biological information by removing redundant reads. The document advocates for making analysis tools and datasets openly accessible to help advance understanding of microbial communities from metagenomics studies.
The document discusses how to interpret a person's genome sequence. It explains that while we can identify genetic variations and inherited conditions, a genome sequence alone does not reveal much because DNA is complex code that is difficult to decipher. Environmental factors and how genes interact also influence traits. The document outlines the process of genome sequencing, mapping reads to a reference, variant calling, and challenges in interpretation due to incomplete knowledge and versioning issues.
CONFidence 2014: Davi Ottenheimer Protecting big data at scalePROIDEA
We are meant to measure and manage data with more precision than ever before using Big Data. But companies are getting Hadoopy often with little or no consideration of security. Are we taking on too much risk too fast? This session explains how best to handle the looming Big Data risk in any environment. Better predictions and more intelligent decisions are expected from our biggest data sets, yet do we really trust systems we secure the least? And do we really know why "learning" machines continue to make amusing and sometimes tragic mistakes? Infosec is in this game but with Big Data we appear to be waiting on the sidelines. What have we done about emerging vulnerabilities and threats to Hadoop as it leaves many of our traditional data paradigms behind? This presentation, based on the new book "Realities of Big Data Security" takes the audience through an overview of the hardest big data protection problem areas ahead and into our best solutions for the elephantine challenges here today.
MongoDB World 2016: Building the internet of Living Things with MongoDBMongoDB
This document discusses building an "Internet of Living Things" using nanopore sequencing and MongoDB. It describes Oxford Nanopore Technologies' goal of enabling analysis of any living thing by any user in any environment. It outlines various applications like human and animal genome sequencing, as well as bacterial, viral, plant, and food sequencing. It introduces Oxford's MinION and PromethION nanopore sequencing devices. It then discusses using MongoDB to store and enable complex analyses of nanopore sequencing data by users worldwide. Examples are given of current applications like sepsis diagnosis, environmental monitoring, and Zika virus research.
The document discusses Plazi's work on converting biodiversity literature into structured data through text mining and markup. Key points include:
- Plazi extracts scientific names, tables, references and geographic data from literature and converts it into semantically enriched text and RDF.
- Their pipelines currently have over 50,000 taxonomic treatments life and are providing data to databases like NCBI, GBIF and EOL.
- Future plans include collaborating with ContentMine for daily treatment extraction, releasing RDF and text mining versions 1.0, and expanding the biodiversity literature repository to 100,000 references.
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Nature 2.0 adds silicon & steel. AI, blockchain, IoT towards abundance.
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Related blog post:
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The document discusses making taxonomic literature openly accessible in digital format. It proposes marking up publications with XML tags to encode semantic information that allows machines to extract and link data. This would facilitate access to the estimated 100 million pages of existing literature as well as integration of new data. Key recommendations include adopting open access policies, understanding copyright, self-archiving publications, using structured formats like XML, and developing standards and infrastructure to support digitization and interoperability of biodiversity data.
This document discusses how information technology can help address sustainability challenges posed by the Anthropocene era and planetary boundaries. It describes how supernetworks, small world networks, and collective intelligence enabled by new communication technologies are building resilience through phenomena like early warning systems for disease outbreaks. However, these benefits are not guaranteed - positive outcomes require active work to develop the web for collaborative problem solving rather than just spreading junk. Collaboration between scientific and technological communities could help transform information flows into a global force for resilience.
This document summarizes Jack Gilbert's work mapping urban microbiomes. It discusses sequencing the microbiomes of Chicago to understand urban metabolism. Rapid urbanization is occurring globally as more people live in large cities, requiring massive infrastructure development. The document outlines efforts to map human activity patterns and microbiomes within homes, buildings, hospitals, waterways, and cities using sensors and genomic sequencing. The goal is to understand and predict microbiome changes across urban environments and facilitate areas like public health and pollution management.
Next generation genomics: Petascale data in the life sciencesGuy Coates
Keynote presentation at OGF 28.
The year 2000 saw the release of "The" human genome, the product of a the combined sequencing effort of the whole planet. In 2010, single institutions are sequencing thousands of genomes a year, producing petabytes of data. Furthermore, many of the large scale sequencing projects are based around international collaboration and consortia. The talk will explore how Grid and Cloud technologies are being used to share genomics data around the planet, revolutionizing life science research.
What is synthetic biology? How quickly is it developing? How does it work? What do we need to know about the synthetic biology industry? What impact does this all have on biodiversity and farmers? What are GMO 1.0, GMO 2.0, GMO+?
Presentation by Jim Thomas of ETC Group, during Redesigning the Tree of Life: Synthetic Biology and the Future of Food, 2-4 November 2017 in Toronto.
The Global Biodiversity Information Facility (GBIF) is an international initiative that aims to provide open access to biodiversity data. It currently has 50 participating countries and 40 international organizations contributing data. GBIF develops standards and tools to help aggregate and publish biodiversity data from various sources. This includes species occurrences, names, taxonomic information, and more. GBIF's data portal allows users to search, browse, and access over 181 million georeferenced records. GBIF is working to integrate biodiversity data on a global scale and support areas like conservation and monitoring of biodiversity trends.
Global Collection Dashboard – Using data we have to uncover data we don’tAxiell ALM
This document discusses the development of a global collections dashboard to provide summaries of digitized collection data from multiple institutions. It describes the types of data that can be analyzed, such as collection records with geographic, taxonomic, and object data. Methods for analyzing and visualizing the data like completeness rankings, searches, and comparisons between institutions are presented. The goal is to make more collection data accessible and help prioritize digitization efforts.
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Data Sharing Principles and Legal Interoperability for Essential Biodiversity...agosti
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This document summarizes a presentation about the Plazi Treatment Repository project. It discusses how Plazi aims to make over 1 million taxonomic treatments openly accessible by semantically enhancing and linking content from biodiversity literature. A major challenge is copyright restrictions on publications, which Plazi addresses by only including non-copyrighted content and material for internal use. The presentation argues for legal changes like mandatory research licenses to further remove barriers to information exchange.
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This document discusses a schema for describing and exchanging the content of taxonomic publications in a way that allows both human and machine access. It proposes using semantic markup like XML to tag elements in publications like names, descriptions, and references in a way that links related data across sources. This would allow content to be more accessible for tasks like data mining while maintaining context. The schema is part of ongoing work by Plazi to apply semantic markup to digitize existing publications and structure new ones for improved dissemination and reuse of taxonomic knowledge.
18. An example from the Neurocommons text mining
pilot:
• PubMed abstracts: > 16,000,000
• CNS classified abstracts: 874,727
• text mining recognized: 368,688
• text mining processed: 94,381
• extracted graph of 30,000+ relationships and 5,500
genes and proteins
“protein-protein
interaction networks”
John Wilbanks,
Neurocommons
31. Monitoring as a comparative
science
Change over time
Change over land use
32. What kind of and
how many ants?
Δt ?
Δt ? What is the impact of
Δt ? land use change?
Δ? Δt ?
What happens over
time?
Δt ?
What happens over
Forest Urban areas space and time?
Pasture Campus
Cacao / Cabruca
43. Before antbase.org, Harvard„s Museum of
Comparative Zoology could claim to be the only
location with a complete set of ant systematics
publications from 1758 - present.
Through antbase.org„s
digital library, access
to this body of
literature is worldwide,
and it is actively used
(>10,000 visits in one
month only).
44. What do we need for monitoring?
Access
Identification aids
45. Who are you?
What do you do?
Who is this? Where are you
from?
What do I know about her?
Where does she live?
46. What do we need for monitoring?
Access
Identification aids
What species is it?
65. This can also be applied to entire sections of text, such as
the treatment of a species and its parts.
<tax:treatment>
<tax:nomenclature>
<tax:name>
<tax:xid source="HNS" identifier="19
<tax:xmldata>
<dc:Genus>Mystrium</dc:Genus>
<dc:Species>leonie</dc:Species>
</tax:xmldata>
Mystrium leonie
</tax:name>
<tax:status>n. sp.</tax:status>
Fig 1 D - F
</tax:nomenclature>
<tax:div type="description">
<tax:p>HOLOTYPE WORKER: TL 3.95, H
1.30, SI 137, PW 0.73, ML 0.38. Mand
66. What do we need for monitoring?
Networks
get info – provide info
use standards
use open access / open source
67. What do we need monitoring?
Social networks
Information is not free in the
sense of „it doesn‘t cost anything“
68. What do we need?
Social networks
Information is not free in the
sense of „it doesn‘t cost anything“
Information depends on you!
70. Monitoring biodiversity depends
foremost on science (and good
scientists)...
... technology makes it just more
relevant and powerful.
71. Biodiversity data at work:
The use of our monitoring data by
IPBES is an indication that we
deliver data and information that
can be used beyond our own work
to save planet earth.
72. With my best thanks!
Donat Agosti
agosti@amnh.org
http://plazi.org
http://antbase.org