The Sam Adams talk

10 years of global biodiversity databases: are we there yet?

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BHL, BioStor, and beyond

Tony Rees IRMNG 2015 presentation

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The human story s ts (solutions)

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Unknown knowns, long tails, and long data

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Sam adams report

Alexandra Barca

Samuel Adams analyzed its social media presence over a two week period. On Twitter, roughly 47% of tweets shared news or promoted events while 36% were about the company and 17% showed personality. On Facebook, 53% of posts were about the company, 20% shared news, and 27% showed personality. Samuel Adams had more followers and engagement across most social media platforms than competitor Yuengling. The report provided recommendations for Samuel Adams to improve engagement by responding directly to customers more, sharing exclusive news, and posting more frequently and varied content.

Sam adams apsotw hugo fournier

PHD

This document outlines a sponsorship activation plan for Samuel Adams during the Olympics in the UK. It proposes creating a character named "Sam Adams", an arrogant American tourist, who will fuel brand fame by criticizing British culture and cheering for US teams. A sampling idea ties free beer giveaways to US wins over UK teams. Vice UK is proposed as the media partner to create webisodes and articles bringing the character to life on social media. The goal is to make Sam initially annoying but eventually loveable as an outsider accepting of UK culture and high quality beer.

Boston Brewing Company Mini Presentation

Kelsey_Schmidt

This document provides an overview of the Boston Beer Company through a mini-presentation. It includes analyses of the company's financial performance and stock price, its competitive positioning among major beer players and craft beers, and its resources and capabilities. The company positions itself as an "American Craft Brewer" and competes based on its small, independent size and attention to quality rather than price. It holds a niche position between larger domestic brewers and smaller microbrews.

OBF Address at BOSC 2012

Hilmar Lapp

The Open Bioinformatics Foundation (O|B|F) was founded in 2001 as a not-for-profit organization to provide collaborative infrastructure for bioinformatics projects. It owns assets for projects like Bio* and EMBOSS and organizes events like BOSC. The volunteer-run organization is governed by a Board of Directors and provides advocacy, code development support, and mentoring. The presentation discusses growing O|B|F's membership and redefining what it means to be an O|B|F-affiliated project in order to better support the community.

Bio::Phylo - phyloinformatic analysis using perl

Rutger Vos

Bio::Phylo is a BioPerl-compatible phyloinformatics toolkit that implements EvoIO concepts and technologies. It can be used for phyloinformatics workflows and data transformation, PhyloWS servers and clients, visualization, and analysis and simulation of tree shapes. Future directions include tighter integration with BioPerl, extending PhyloWS functionality, and SWIG backends for other tools like HyPhy, NCL, and Beagle.

Jonathan Eisen: Phylogenetic approaches to the analysis of genomes and metage...

Jonathan Eisen talk for #SCS2012 at #ISMB "Networks in genomics and bioinfor...

Bio4j

Pablo Pareja Tobes

Bio4j is a graph database for integrating biological big data. It stores data from sources like Uniprot, Gene Ontology, NCBI Taxonomy, and Enzyme Database in a graph structure, with nodes for entities and edges for relationships. This allows for more flexible querying and analysis of interconnected biological data compared to traditional relational databases. Bio4j uses the Neo4j graph database and is open source.

J Goecks - The Galaxy Visual Analysis Framework

The document describes Galaxy, an open-source web-based platform for visual analysis of genomic data. Galaxy provides tools for obtaining, integrating, analyzing, visualizing, sharing and publishing complete genomic analyses through a graphical user interface. It allows users to easily chain tools and create complex analysis workflows. The document highlights several Galaxy visualization tools, including Trackster for interactive exploration of large genomic datasets, Paramamonster for parameter space exploration, and Circster for circular genome-wide views. Future directions include expanding visualization capabilities to other data types and integrating multiple coordinated views.

The role of cost in yeast gene expression

Michael Barton

Energetic costs are an important factor in genome evolution and selection. The biosynthesis of proteins, nucleic acids, and other cellular components requires energy in the form of ATP and NADPH. This energetic cost is reflected in trends of genome organization and gene expression across organisms. Systems biology approaches using genome-scale metabolic models can estimate the biosynthetic costs and predict how costs influence expression levels of transcripts, proteins, and amino acids to minimize energy expenditure while meeting cellular demands. Understanding the relationship between energetic costs and genome evolution provides insight into the pressures that shape life at the molecular level.

Chamberlain PhD Thesis

schamber

1. A study examined how proximity to sunflower crops affects species interactions on wild sunflowers. 2. It found that proximity to crops altered the abundance and community structure of both mutualist pollinators and antagonist seed predators and folivores on wild sunflowers. 3. Specifically, mutualist pollinators were more abundant near crops while antagonist seed predators and folivores were more abundant farther from crops.

Procter Vamsas Bosc2009

bosc

This document summarizes an approach called VAMSAS that enables sharing of data like sequences, alignments, and annotations between different bioinformatics tools. It describes how VAMSAS uses a shared XML document and client library to allow tools to access and update shared data, view events in other tools, and better integrate workflows. Examples of tools like TOPALI and Jalview that could benefit from this approach are discussed.

20120622 fridayadelboden

Yannick Wurm

The document discusses organizing computational biology projects. It recommends using a logical directory structure with a common root directory for related projects. Within each project directory, it suggests top-level directories for data, results, source code, documents, and binaries. For results directories, it advises creating subdirectories for each experiment with names indicating the date and topic. Maintaining a lab notebook to document experiments and their progress and conclusions is also recommended.

VIZBI 2014 - Visualizing Genomic Variation

This document discusses visualizing genomic variation from DNA sequencing data. It begins by defining genomic variation such as single nucleotide polymorphisms and structural variations. It then discusses analyzing multiple samples, showing affected genes and clustering individuals. The document outlines challenges in visualizing high-dimensional genomic data from deep sequencing at scale, while maintaining computational performance for interactivity. It proposes representing rearranged chromosomes based on segment relationships to focus on functional impacts.

Intro to data visualization

This document provides an introduction to data visualization. It discusses what data visualization is, why it is used, and the stages involved in creating visualizations from data. Key points include: - Data visualization involves using visual representations of data to help people analyze and communicate information more effectively. - Visualizations are used for tasks like recording information, analyzing data to support reasoning, and communicating information. - The process of creating visualizations involves understanding the properties of the data, properties of images and perception, and rules for mapping data to visual encodings. - Important considerations include which visual variables to use to encode different data properties, principles of visual perception, and enabling interaction with the data. Validation of the effectiveness of

Tetrahymena genome project 2003 presentation by Jonathan Eisen

Surfacing the deep data of taxonomy

The document discusses how taxonomy data is increasingly available in digital formats, with names, publications, and sequences stored in databases. However, the majority of taxonomic names are still only found in the legacy scientific literature not available online. Creating a single comprehensive database of all scientific names linked to their original publications and other related data would help resolve issues around ambiguous names and dark taxa. However, this remains a significant challenge due to the vast amount of legacy literature not currently accessible or digitized.

The neurobiological nature of free will

Björn Brembs

Our own experience of our free will has been classified as either supernatural or an illusion because it is difficult to reconcile with macroscopic determinism as well as with microscopic quantum randomness. The former constituting a prison in which no freedom can exist, the latter signifying destructive chaos rather than creative action. Lost in this dichotomy is the demonstrated constructive combination of chance and necessity in complex systems, such as evolution. Recent converging evidence from neuroscience, ecology and genetics suggests that nervous systems, including human brains, have evolved neural circuits that harness (potentially quantum) chance events by embedding them in the controlling architecture of neuronal rules, in order to carefully inject them as creative components into ongoing goal-directed behavior. This presentation contains evidence that this form of behavioral variability may constitute a necessary neural mechanism for free will to evolve in humans.

Evolution of the RecA Protein: from Systematics to Structure 1995 talk for CA...

This document discusses the evolution of the RecA protein and its use for bacterial systematics. It finds that phylogenetic trees constructed from RecA sequence data are highly congruent with trees constructed from 16S rRNA sequence data. Both RecA and 16S rRNA trees resolve bacterial relationships with similar degrees of resolution. The analysis supports the use of RecA comparisons for molecular systematics studies of bacteria. It also finds that studying patterns of amino acid substitutions in RecA can provide insights into the protein's structure-function relationships.

ORCID Principles

Martin Fenner

1) ORCID is a non-profit organization that launched in 2010 to create a central registry of researcher identities and link them to contributions such as publications, datasets, and patents. 2) ORCID aims to support reliable attribution of authors and enable discovery and evaluation of researchers' scholarly works by transcending boundaries and making profile data freely available in standard and open formats. 3) ORCID will be sustained through a combination of free and fee-based services, with fees set to ensure its long-term viability as a not-for-profit focused on persistent identification.

Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2

Ellinor Michel

Global Digital Infrastructure for Biological Nomenclature and Taxonomy Ellinor Michel, Dep’t of Life Sciences, The Natural History Museum, London, UK, (e.michel@nhm.ac.uk) Richard L. Pyle, Natural Sciences Dep’t, Bishop Museum, Honolulu, HI, USA Robert P. Guralnick, Dep’t of Ecology & Evolutionary Biology, Univ Colorado, Boulder, CO, USA Jon Todd, Dep’t of Earth Sciences, The Natural History Museum, London, UK, The future for interoperable scientific information is digital, yet scientific names, the handles for all biodiversity information, remain without an integrated system tied to published descriptions and museum type specimens. Descriptions and type specimens provide standards for the otherwise fluid concepts of biological taxa. We are working to unify the infrastructures for biological nomenclature across nomenclatural codes (including zoological (ICZN - http://iczn.org/), botanical (ICNafp - http://www.iapt-taxon.org/nomen/main.php) and bacterial (ICNB) codes) through the Global Names Architecture (GNA). Our initial focus is on animal names, as these comprise the largest component of metazoan biodiversity and ZooBank (zoobank.org) is the first code-related online nomenclatural registration system. Users are applied scientists in agriculture, medicine, veterinary science and climate change research; biodiversity researchers such as ecologists, physiologists; archives such as museums; the scientific publishing community – in short, all users of scientific names of organisms based on the work of taxonomists.

The Biodiversity Heritage Library Mass Digitizing Project: A Grandeur in this...

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The document summarizes the upcoming lab activities for the week which includes a species interaction lab on Saturday July 18th and assignments due that day. A population ecology worksheet is due on Monday. The document provides links and instructions for editing a Wikipedia page as part of the lab assignment, as well as links on how to upload images and other editing tips. Background information on human and other population growth models are also presented.

Nomenclature for the Future: The power and challenges for stable and sensible...

ICZN

This document discusses the future of scientific naming for animals and the challenges involved. It notes that scientific names serve as links between past and current knowledge about a species. While millions of animal species are estimated to exist, only a small fraction have been named so far. The document advocates for registering all new and existing scientific names in ZooBank to create a global standardized nomenclature system and infrastructure. This would help link names to taxonomic and bibliographic data across different databases for improved information sharing and analysis of biodiversity.

Biodiversity Heritage Library : Development and Partnerhips

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drielinger

This document discusses the Biodiversity Heritage Library (BHL) project and its role in supporting other biodiversity initiatives like the Encyclopedia of Life (EOL). The BHL aims to digitize published literature on biodiversity and make it openly accessible online. It has already digitized over 4 million pages and works closely with groups like EOL to integrate taxonomic data. The document outlines the BHL's goals, partnerships, digitization process, and how it brings together distributed information on species through its use of taxonomic intelligence.

Biodiversity Heritage Library: A Conversation About A Collaborative Digitizin...

The document discusses the Biodiversity Heritage Library (BHL), a collaborative project to digitize literature related to biodiversity and make it openly accessible online. It describes the goals of the BHL, participating institutions like natural history museums and botanical gardens, the types of literature being digitized, and challenges around metadata and linking digitized content to taxonomic databases.

The power of names smithsonian talk-2013-iczn_nomenclature&bioinformatics-v2

Ellinor Michel

I gave this talk at the Smithsonian National Museum of Natural History in April 2013. It deals with ZooBank and the registration of scientific names of animals, the role of type specimens and archives for both specimens and literature. It should be of interest to taxonomists, and people working on biodiversity bioinformatics and scientific bibliography. The talk had significant input from several co-authors: Richard Pyle, David Patterson, Daphne Fautin and Jon Todd. The Smithsonian presentation was hosted by the AAZN (American Association of Zoological Nomenclature). I gave a similar talk in November 2012 at the invitation of the Field Museum, Chicago, which is available in full online here (54 minutes): http://vimeo.com/55796036 and linked with a short promo piece on scientific nomenclature here (2.8 minutes): http://vimeo.com/54956625

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Consortium for the Barcode of Life (CBOL)

This document discusses building a knowledge graph called Ozymandias to link biodiversity data for Australian fauna. It describes linking specimens, publications, researchers and more using identifiers. Demos are proposed to link the Australian Fauna Database to literature to add images and information about taxonomists. Knowledge graphs integrate diverse data sources and make more connections and information visible than traditional databases. They rely on unique identifiers for people, publications and other objects.

Stoeckle - All Birds Barcoding Initiative

The All Birds Barcoding Initiative has opened new research opportunities with its global atlas of avian mitochondrial DNA diversity. The initiative has published over 13,000 barcode records from museum collections, representing over 3,000 bird species. Private records include an additional 12,000 sequences and 1,000 species. The avian barcode library is a valuable research tool that can be used to analyze large-scale patterns in biodiversity and evolution, population biology, and biogeography.

Biodiversity Knowledge Graphs

This document discusses building knowledge graphs to connect biodiversity data from various sources like publications, specimens, sequences, and locations. It notes some challenges like an increasing amount of sequencing data not connected to formal taxonomic names, disconnects between taxonomy and genomics, and much of the historical taxonomic literature being difficult to access. It also discusses imbalances in available data across regions, taxa, and between well-studied and under-studied species. Integrating these diverse data sources into knowledge graphs could help address these issues but also comes with its own challenges.

Writing The Encyclopedia Of Life (not EoL.org)

Vince Smith

The document discusses the goal of comprehensively inventorying and documenting Earth's biodiversity through the Encyclopedia of Life project. It notes that while about 1.8 million species have been described, the total number is estimated to be between 10-30 million. The challenges discussed include integrating fragmented data from different sources and communities, addressing issues around incentives, politics, and licensing to encourage global collaboration on the project. Technical challenges involve developing standards, platforms, and web services to aggregate and semantically link biodiversity data at large scale.

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ALEC (A List of Everything Cool)

This document describes ALEC (A List of Everything Cool), a project that aims to create a "Bibliography of Life" containing information on every taxonomic paper, taxonomist, and species in Wikidata. It provides an overview of the current status and capabilities of ALEC, including live queries to Wikidata and examples of information that can be viewed. It also discusses the major tools used, challenges faced populating Wikidata with bibliographic data, and plans for future improvements to the interface and expanding the data in Wikidata.

Wikidata and the Biodiversity Knowledge Graph

Wikidata could serve several roles in building a biodiversity knowledge graph: 1) Wikidata could provide identifiers, labels, and a way to query relationships (nodes and edges) between biodiversity items to form the basis of a knowledge graph. 2) Individual biodiversity databases could link their data to relevant Wikidata items while maintaining their own specialized knowledge graphs. 3) Wikidata could serve as a centralized source of both core biodiversity information and related contextual information like people, organizations, and locations, essentially becoming the biodiversity knowledge graph itself due to its large community and scope.

BioStor Next

This document discusses challenges with accessing and processing biodiversity literature and describes efforts to make literature from Biodiversity Heritage Library (BHL) more accessible and machine-readable. BioStor extracts text and figures from over 200,000 BHL articles and makes them searchable online. Efforts are underway to link BHL content to databases and Wikidata to connect literature to species and other entities. The goal is to extract more articles from BHL, enable geographic searches of content, break articles into smaller pieces, and embed literature within a biodiversity knowledge graph.

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This document discusses building knowledge graphs by connecting various data sources using identifiers and vocabularies. It identifies technical and social obstacles to doing so, including the need for globally unique identifiers, agreed-upon vocabularies, and standards for transmitting the graph. It notes that some of these obstacles are being overcome with solutions like DOIs, JSON-LD, and Wikidata, but that measuring progress on connectivity is more difficult than linear growth. It concludes that knowledge graphs already exist but are not evenly distributed, and that any combined graph should be free, open, and used for good.

Wild idea for TDWG17 Bitcoins, biodiversity and micropayments

Open data is freely available with attribution as currency, while funding work and demonstrating value can be difficult. Closed data requires monetary access through subscriptions, where development is funded and value is obvious financially. The document proposes using micropayments of bitcoins for accessing raw or cleaned biodiversity data, with the community mining bitcoins to fund processing raw data into cleaned datasets.

Towards a biodiversity knowledge graph

The document discusses obstacles to and progress in building knowledge graphs. It outlines technical obstacles like needing globally unique identifiers and agreed-upon vocabularies. Social obstacles include economic issues. Identifiers are key to connecting knowledge graphs. Metrics are needed to measure graph connectivity rather than just growth. Network effects are important to make graphs truly useful. Wikidata and Google's knowledge graph are examples of existing large knowledge graphs.

Cisco Digital Catapult

Digitisation involves making physical specimens, literature, and metadata available in digital form, including DNA barcodes. This allows joining up different types of biological data that were previously separate, such as specimens, published literature, and genetic sequences. Digitising collections allows broader access and use of biodiversity data through databases like GBIF, which has over 500 million occurrence records available online. However, different intellectual property policies can apply to literature, specimens, and genetic data. Efforts are underway to better link related biological records and publications through identifiers like ORCID for people, DOIs for publications, and LSIDs for plant names. The goal is to build a comprehensive knowledge graph that integrates all these different types of digital biological data.

Built in the 19th century, rebuilt for the 21st

The document discusses several topics related to digitization of biological data collections: 1) It describes how databases like GenBank rely on both experimentalist and natural history traditions by collecting and comparing natural facts from experiments. 2) Debates around creating GenBank in 1982 illuminated different moral economies regarding collecting/sharing data and attributing credit. 3) Both experimentalism and natural history traditions have shaped new ways of producing knowledge in life sciences through articulating these approaches in databases.

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This document discusses three problems related to linking specimens to evidence in biological databases: 1) linking specimens to DNA barcodes, sequences, and literature citations in databases like GBIF, 2) the relationship between physical biological collections and institutions and their digital representations in databases like GBIF, and 3) making Wikipedia pages on species more structured and machine-readable similar to Bouchout declarations. Suggestions are made to map specimen identifiers to other databases, provide live updates of digitization efforts, and allow for user-editable structured data.

Visualing phylogenies: a personal view

This document discusses challenges and opportunities in visualizing phylogenetic trees. It notes that while maps have predictable navigation, trees can be drawn in many different ways. The document explores using additional dimensions like time, latitude and longitude to represent evolutionary relationships. It highlights projects like GenGIS, OneZoom and Dendroscope that attempt to make large trees more intuitive to navigate. Finally, it questions why more phylogenetic trees are not archived in databases and how software could generate publication-quality visualizations directly from analyses.

Biodiversity informatics: digitising the living world

The document discusses biodiversity informatics and efforts to digitize information about the living world. It notes that GBIF has over 500 million specimen records but that none of the Kenya data actually comes from Kenya. It also discusses challenges with the Biodiversity Heritage Library in emphasizing older publications over recent scientific articles and representing information by scanned book pages rather than articles. The document raises issues about ensuring all scientific names are published and unique, and about making publications containing names accessible online.

Ebbe Nielsen Challenge GBIF #gb21

The document discusses the Ebbe Nielsen GBIF Challenge, which is a competition that offers cash prizes. The challenge is open to individuals, teams, and companies and asks participants to submit innovative uses of data mobilized by the Global Biodiversity Information Facility (GBIF). Winning submissions could include new visualizations of biodiversity data or utilizing new types of data. Prizes will be awarded to semifinalists and top finishers, with the top prize being €20,000.

GBIF Science Committee Report GB21, Delhi, India

The GBIF Science Committee met in Glasgow where they awarded prizes and developed the Ebbe Nielsen Challenge. CSIRO's Tony Rees was named the 2014 Ebbe Nielsen Prize winner. Young Researcher Awards were given to Vijay Barve and Caoimhe Marshall. The GBIF Ebbe Nielsen Challenge will foster innovation using GBIF data and have cash prizes. The committee discussed challenges around data types from sources like DNA sequences and literature, as well as data quality and coverage issues.

Building the Biodiversity Knowledge Graph

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The document discusses ways to improve the Global Biodiversity Information Facility (GBIF) data by addressing issues of coverage, quality, annotation, and incorporating new types of data. It suggests adding other literature sources to increase coverage, developing methods to measure reliability and allow editing to ensure quality, using stable identifiers and annotations on a platform like GitHub to enable corrections, and incorporating additional data types like names from nomenclators, phylogenies, and sequences from GenBank.

Biodiversity informatics: why aren't we there yet?

This document discusses challenges in biodiversity informatics based on various data visualizations. It finds that while sequencing data is growing exponentially, the description of new taxa is relatively constant. Much taxonomic literature from the 20th century is "dark" or inaccessible. Data is unevenly distributed across taxa, with more known about few species and little known about most. Integrating legacy literature and connecting it to modern genomic data remains a challenge. Crowd-sourcing of data is concentrated in areas with more smartphone users. GenBank contains valuable location and ecological interaction data beyond gene sequences.

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Why I blog instead of writing papers

This document discusses why the author blogs instead of writing papers. Some key reasons include: getting immediate feedback, having conversations in the comments, not being limited by journal space constraints, and establishing an "attention filter" through citations and social media engagement of blog posts. While blogging is a form of "vanity publishing," the author argues it can still be valid if the blog gets cited in peer-reviewed literature. Blogging also allows for a more open and transparent discussion of scientific findings compared to traditional peer-reviewed papers.

Social media

This document discusses various social media platforms and how they can be used for professional purposes. It outlines popular platforms like LinkedIn, Facebook, blogging and Twitter. It provides tips on using hashtags, retweets and follow Fridays on Twitter. It also discusses how these tools can be used for conference broadcasting, attracting attention to projects, asking for help and creating a consistent online identity or "brand".

Making data sticky