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.
Iczn(The International Commission on Zoological Nomenclature )Al Nahian Avro
The International Commission on Zoological Nomenclature (ICZN) acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature - a set of rules for the naming of animals and the resolution of nomenclatural problems.
1.Definition and basic concepts of Biosystematics, , Historical perspectives of Biosystematics and Taxonomy, Stages of taxonomic procedures-alpha taxonomy, Beta taxonomy and Gamma taxonomy,
Neo taxonomy.
The power of names smithsonian talk-2013-iczn_nomenclature&bioinformatics-v2Ellinor 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
Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2Ellinor 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.
Iczn(The International Commission on Zoological Nomenclature )Al Nahian Avro
The International Commission on Zoological Nomenclature (ICZN) acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature - a set of rules for the naming of animals and the resolution of nomenclatural problems.
1.Definition and basic concepts of Biosystematics, , Historical perspectives of Biosystematics and Taxonomy, Stages of taxonomic procedures-alpha taxonomy, Beta taxonomy and Gamma taxonomy,
Neo taxonomy.
The power of names smithsonian talk-2013-iczn_nomenclature&bioinformatics-v2Ellinor 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
Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2Ellinor 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.
An International Cooperative Digital Library for Taxonomic Literature: The Bi...Martin Kalfatovic
An International Cooperative Digital Library for Taxonomic Literature: The Biodiversity Heritage Library. Martin R. Kalfatovic. American Library Association Annual Meeting. Collaborative Digital Initiatives: Show and Tell and Lessons Learned. June 30, 2008. Anaheim, CA.
The iPlant Tree of Life Project and ToolkitNaim Matasci
The iPlant Tree of Life Project and Toolkit: Building aCyberinfrastructure for Plant Science Research
Given at the National Museum of National History in 2011
An overview of iPlant and iPToL
Biodiversity Heritage Library : Development and PartnerhipsNancy Gwinn
Biodiversity Heritage Library. Development and Partnerships. Nancy E. Gwinn. Biodiversity and Ecosystems Informatics Group, National Science Foundation, March 24, 2008, Washington, D.C.
nternational Biodiversity Projects and Natural History Museums: Current stat...Klaus Riede
Background / Purpose: The 21st century started with an impressive number of international biodiversity initiatives, such as the International Year of Biodiversity (2010) and the recently launched United Nations Decade on Biodiversity ( http://www.cbd.int/2011-2020/ ). Main conclusion: Most nations are now members of the Convention on Biological Diversity and expressed a strong commitment for safeguarding Earth´s biodiversity through their National Biodiversity Action Plans and work programs supporting taxonomy, such as the Global Taxonomy Initiative. Internet projects such as the Global Biodiversity Information Facility provide unprecedented opportunities for taxonomists and Natural History Museums to make their efforts visible through the federation of separate museum databases: users can search for species, visualise localities on a map and recall pictures of museum specimens made available by “Virtual Museums”. However, availability of multimedia data is still limited, particularly for type specimens. Taking European museums as an example, I demonstrate the potential of successful virtual museum projects and analyse priorities and needs for further digitisation, which is a pre-requisite for repatriation of biodiversity data from tropical countries. Improved access to collections is also among the main tasks of the recently established CETAF secretariat in Brussels ( Consortium of European Taxonomic Facilities ). This new institution will function as a European voice for taxonomy and systematics, and hopefully helps to sustain orphaned EU activities from former projects supporting taxonomy, such as the European Distributed Institute of Taxonomy .
Chris Lyal - Taxonomy and the Web - integrating the piecesICZN
More and more calls for information about species
What is this?
What species live in my country / national park?
What species are eating my crops?
What happens to them if I manage the environment?
Nigel J. Robinson - ZooBank and Zoological Record - a partnership for successICZN
Since its origin in 1864, ZR has had a close association with the taxonomic community, particularly with the Zoological Society of London. ZR was founded in 1864 by a group of scientists associated with the British Museum. It continued, supported by Society until 1980 when a partner was sought and BIOSIS took over production activities. In 2004, BIOSIS realised that with limited resources we could not achieve our aims and put our ideas into practice without further partnerships, so in January 2004, BIOSIS (including ZR) was acquired by the Thomson Corporation, and the new ownership is now starting to pay dividends. Over that 150 years or so, there have been difficult times, but ZR is still here and still has the same purpose it had in 1864 - to serve the community and disseminate taxonomic, biodiversity and zoological information for the benefit of scientific research.
This presentation discusses ZR, and the new free Index to Organism Names service which serves to demonstrate our commitment as Thomson to this initiative. I will also discuss how the partnership between ZR and ICZN might work from the ZR perspective.
Sherborn: Evenhuis - Charles Davies Sherborn and The Indexer’s ClubICZN
Charles Davies Sherborn was an indexer. And he followed a long line of indexers. And a longer line of indexers followed him. They/we are all members of “The Indexer’s Club”. A club of obsessed individuals who, for some weird reason, find it necessary to not only facilitate a semblance of order, but to make sometimes incredibly huge amounts of information available to others [sacrificing their social lives and labouring on what spouses and colleagues may consider esoteric projects in order to save others from the same work]. And in doing so, encumbering most of the day and the wee hours of the night with a passion and fervour few other human beings can even begin to understand. This presentation will explore the bits of Sherborn’s life that led to that passion for indexing; and touch upon the impact he has had on bibliographies and researching the dates of publication; upon nomenclature; and upon the indexing of names — and it will attempt to explain why he did this and where we all can go as a result.
Sherborn: Fautin & Alonso-Zarazaga - LANs: Lists of Available Names – a new g...ICZN
Article 79 of the ICZN Code, which appeared first in the Fourth Edition, outlines a procedure for adding large numbers of names to the List of Available Names simultaneously, as a Part of the List. This feature has gained importance with the development of Zoobank, because the LAN can be an important adjunct to or component of Zoobank. Article 79 describes a deliberative process, detailing steps for submission and for consideration by the public and Commission, and their chronology: submission must be by “an international body of zoologists,” and the proposed Part must be available for “comments by zoologists” for 12 months, followed by another 12-month period for comments on the proposed Part as revised in light of comments received. However, Article 79 it is mute about the contents of the submission. It is clear that adding a Part to the List will prevent long-forgotten names from displacing accepted ones – thus, for taxa on the List under the provisions of Article 79, nomenclatural archeology will not be worthwhile. Beyond that, Commissioners who participated in writing the Fourth Edition are divided about the intent of Article 79: some aver it is intended to document every available name within the scope of the Part, others it is to pare the inventory of names within the scope of the Part. The comprehensiveness of the names in the Part is critical because, according to Article 79.4.3, “No unlisted name within the scope (taxonomic field, ranks, and time period covered) of an adopted Part of the List of Available Names in Zoology has any status in zoological nomenclature despite any previous availability” (names may subsequently be added only “in exceptional circumstances,” according to Article 79.6). Under the first interpretation, the Part functions as a strictly nomenclatural archive. Under the second interpretation, the Part pares away nomina dubia, so Parts of the List resulting from actions under Article 79 are like the Approved Lists of Bacterial Names that took effect on 1 January 1980 – taxonomically recognizable as well as nomenclaturally available. It is critical that a consistent basis for implementing Article 79 be adopted; it is unrealistic to expect unanimity, given the diversity of opinion among those who helped craft Article 79.
Sherborn: Scholz - BHL-Europe: Tools and Services for Legacy Taxonomic Litera...ICZN
Literature research is the base for the scientific work of taxonomists. Therefore, large and well-curated natural history libraries are a very important prerequisite to carry out scientific projects efficiently. The library work, however, has several serious limitations that slow down the work significantly. The natural history library corpus is highly fragmented and scattered. In particular much of the early published literature is rare or is only available in a very few libraries. A lot of time and effort is involved to find and collect all scientific works that are necessary for a specific project.
Today, quick and easy access to digital literature is more and more important to facilitate scientific work. Over the last few years a large number of library resources for taxonomists have been made available online. Since 2007, the Biodiversity Heritage Library (BHL) project is digitising the biodiversity literature holdings of numerous libraries in the UK and USA and making them available on the internet.
Since 2009, the eContentplus project Biodiversity Heritage Library for Europe (BHL-Europe) is developing four different access routes to the biodiversity literature digitised by many European and global partners over the last years. With the Global References Index to Biodiversity (GRIB, http://grib.gbv.de/), BHL-Europe provides in collaboration with the EDIT project a union catalogue of library holdings of many European and US libraries. This will facilitate the search for literature, either digitised or not. This tool will also facilitate the management of digitisation projects all over the world and collect scan request from the scientific community. For an effective access to already digitised literature, BHL-Europe is building a multilingual portal for the scientific community. This portal will also have functionalities currently not available in the BHL portal. The BHL-Europe Portal will, for example, facilitate the search for common and scientific names of biological organisms as well as person names through the implementation of various webservices (e.g. Catalogue of Life, VIAF). The backbone of the portal is a preservation and archive system built on a customised storage infrastructure housed by the Natural History Museum in London. We are currently collecting digitised literature from 27 different content providers on our servers, including all the content that is currently available through the BHL portal (http://www.biodiversitylibrary.org). In order to serve also a broader audience, the digitised literature available by BHL-Europe is also accessible by Europeana, Europe's digital library, archive and museum (http://www.europeana.eu/).
To date, most digitisation of taxonomic literature has led to a more or less simple digital copy of a paper original – the output has effectively been an electronic copy of a traditional library. While this has increased accessibility of publications through internet access, for many scientific papers the means of indexing and locating them is much the same as with traditional libraries. OCR and born-digital papers allow use of web search engines to locate instances of taxon names and other terms, but OCR efficiency in recognising names is still relatively poor, people’s ability to use search engines effectively is mixed, and many papers cannot be directly searched. Instead of building digital analogues of traditional publications, we should consider what properties we require of future taxonomic information access. Ideally the content of each new digital publication should be accessible in the context of all previous published data, and the user able to retrieve nomenclatural, taxonomic and other data / information in the form required without having to scan all of the original paper and extract target content manually. This opens the door to dynamic linking of new content with extant systems – automatic population and updating of taxonomic catalogues, ZooBank and faunal lists, all descriptions of a taxon and its children instantly accessible with a single search, comparison of classifications used in different publications, and so on. The means to do this is currently marking up content into XML, the more atomised the mark-up the greater the possibilities for data retrieval and integration. Mark-up requires XML that accommodates the required content elements and is interoperable with other XML schemas, and there are now several written to do this, particularly TaxPub, taxonX and taXMLit, the last of these being the most atomised. Building on earlier systems for mark-up of legacy literature ViBRANT is developing a new workflow and seeking to increase the automated component of the process. Manual and automatic data and information retrieval is demonstrated by projects such as INOTAXA and Plazi. As we move to creating and using taxonomic products through the power of the internet, we need to ensure the output, while satisfying the requirements of the Code, is fit for purpose in the future.
Sherborn: Pilsk, Joel Richard & Kalfatovic - Unlocking the Index Animalium: F...ICZN
Smithsonian Institution Libraries received funding in 2004 to digitize Sherborn’s Index Animalium. The initial project was to digitize the pages images and re-key the data into a simple data structure. As the project evolved, a more complex database was developed to enable quality searching to retrieve species names and to search the bibliography. The OCRed, scanned Index Animalium was re-keyed to the specifications of 99.995% accuracy rate. Working off the lessons learned by MBL WHOI Library’s project for Neave’s Nomenclator Zoologicus, simple expressions were used to break apart the re-keyed text. Coinciding with the development of the Biodiversity Heritage Library (2005), it became obvious there was a need to integrate the scanned Index Animalium, BHL’s scanned taxonomic literature, and taxonomic intelligence. The challenges of working with legacy taxonomic citation, computer matching algorithms, and making connections have brought us to today’s goal of making Sherborn available as open linked data. The goal is to allow repurposing of data, partnering with others to allow machine-to-machine communications and sharing information for broad discovery and access.
GDG Cloud Southlake #33: Boule & Rebala: Effective AppSec in SDLC using Deplo...James Anderson
Effective Application Security in Software Delivery lifecycle using Deployment Firewall and DBOM
The modern software delivery process (or the CI/CD process) includes many tools, distributed teams, open-source code, and cloud platforms. Constant focus on speed to release software to market, along with the traditional slow and manual security checks has caused gaps in continuous security as an important piece in the software supply chain. Today organizations feel more susceptible to external and internal cyber threats due to the vast attack surface in their applications supply chain and the lack of end-to-end governance and risk management.
The software team must secure its software delivery process to avoid vulnerability and security breaches. This needs to be achieved with existing tool chains and without extensive rework of the delivery processes. This talk will present strategies and techniques for providing visibility into the true risk of the existing vulnerabilities, preventing the introduction of security issues in the software, resolving vulnerabilities in production environments quickly, and capturing the deployment bill of materials (DBOM).
Speakers:
Bob Boule
Robert Boule is a technology enthusiast with PASSION for technology and making things work along with a knack for helping others understand how things work. He comes with around 20 years of solution engineering experience in application security, software continuous delivery, and SaaS platforms. He is known for his dynamic presentations in CI/CD and application security integrated in software delivery lifecycle.
Gopinath Rebala
Gopinath Rebala is the CTO of OpsMx, where he has overall responsibility for the machine learning and data processing architectures for Secure Software Delivery. Gopi also has a strong connection with our customers, leading design and architecture for strategic implementations. Gopi is a frequent speaker and well-known leader in continuous delivery and integrating security into software delivery.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
Generating a custom Ruby SDK for your web service or Rails API using Smithyg2nightmarescribd
Have you ever wanted a Ruby client API to communicate with your web service? Smithy is a protocol-agnostic language for defining services and SDKs. Smithy Ruby is an implementation of Smithy that generates a Ruby SDK using a Smithy model. In this talk, we will explore Smithy and Smithy Ruby to learn how to generate custom feature-rich SDKs that can communicate with any web service, such as a Rails JSON API.
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
Essentials of Automations: Optimizing FME Workflows with ParametersSafe Software
Are you looking to streamline your workflows and boost your projects’ efficiency? Do you find yourself searching for ways to add flexibility and control over your FME workflows? If so, you’re in the right place.
Join us for an insightful dive into the world of FME parameters, a critical element in optimizing workflow efficiency. This webinar marks the beginning of our three-part “Essentials of Automation” series. This first webinar is designed to equip you with the knowledge and skills to utilize parameters effectively: enhancing the flexibility, maintainability, and user control of your FME projects.
Here’s what you’ll gain:
- Essentials of FME Parameters: Understand the pivotal role of parameters, including Reader/Writer, Transformer, User, and FME Flow categories. Discover how they are the key to unlocking automation and optimization within your workflows.
- Practical Applications in FME Form: Delve into key user parameter types including choice, connections, and file URLs. Allow users to control how a workflow runs, making your workflows more reusable. Learn to import values and deliver the best user experience for your workflows while enhancing accuracy.
- Optimization Strategies in FME Flow: Explore the creation and strategic deployment of parameters in FME Flow, including the use of deployment and geometry parameters, to maximize workflow efficiency.
- Pro Tips for Success: Gain insights on parameterizing connections and leveraging new features like Conditional Visibility for clarity and simplicity.
We’ll wrap up with a glimpse into future webinars, followed by a Q&A session to address your specific questions surrounding this topic.
Don’t miss this opportunity to elevate your FME expertise and drive your projects to new heights of efficiency.
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Neuro-symbolic is not enough, we need neuro-*semantic*Frank van Harmelen
Neuro-symbolic (NeSy) AI is on the rise. However, simply machine learning on just any symbolic structure is not sufficient to really harvest the gains of NeSy. These will only be gained when the symbolic structures have an actual semantics. I give an operational definition of semantics as “predictable inference”.
All of this illustrated with link prediction over knowledge graphs, but the argument is general.
The Art of the Pitch: WordPress Relationships and SalesLaura Byrne
Clients don’t know what they don’t know. What web solutions are right for them? How does WordPress come into the picture? How do you make sure you understand scope and timeline? What do you do if sometime changes?
All these questions and more will be explored as we talk about matching clients’ needs with what your agency offers without pulling teeth or pulling your hair out. Practical tips, and strategies for successful relationship building that leads to closing the deal.
Nomenclature for the Future: The power and challenges for stable and sensible scientific names for animals-v2
1. Nomenclature for
the Future:
The power and
challenges for
stable and
sensible scientific
names for
animals
Ellinor Michel1,2,3
Richard Pyle1,3,4
Daphne Fautin1,3,5
David Patterson1,3,6
Jon Todd2,3
11
Int’l Commission on Zoological NomenclatureInt’l Commission on Zoological Nomenclature
22
The Natural History Museum, London UKThe Natural History Museum, London UK
33
Int’l Committee on BionomenclatureInt’l Committee on Bionomenclature
44
Bishop Museum, HI, USABishop Museum, HI, USA
55
University of Kansas, USAUniversity of Kansas, USA
66
Arizona State Univ, AZ, USAArizona State Univ, AZ, USA
2. All accumulated information of
a species is tied to a scientific
name, a name that serves as a
link between what has been
learned in the past and what we
today add to the body of
knowledge.
- Grimaldi & Engel, 2005
Names and the information revolution
Note: they don’t say THE scientific name (i.e., singular)
3. Equivalent of 318 volumes of Systema Naturae
Estimated 2-6 names for every valid (=currently
considered definable and ‘real’) species
4,398 Species
8. Scientific concept of biodiversity
Name
(Scientific, common,
provisional or open)
Type specimen
(objective standard)
Data &
Bibliography
9. Stability, transparency and testability
Name
(Scientific, common,
provisional or open)
Type specimen
(objective standard)
Data &
Bibliography
10. Archives for
Scientific concepts of biodiversity
Name
(Scientific, common,
provisional or open)
Type specimen
(objective standard)
Data &
Bibliography
Stable archives
needed
Natural History
Collections
Libraries
Publications
Data sources
14. E-only publication amendment
to ICZN Code published 4 Sept
ZooBank improved version
released, meeting
requirements of the
Amendment
From zoobank.org/statistics
15. • Now required for e-only publications
• Has general community support
• Registration of all names and nomenclatural
acts is strongly encouraged and being rapidly
implemented
• Next Step: ALL names (historical and future)
registered and cross-linked!
Registration in ZooBank
16. A name = ‘computer’ readable
code that links information
23. Zoological Names in the Future
• Global mandatory registration for all new
names – next edition of the Code?
• Ultimate Goal: Registered = Available
(Pyle & Michel, 2008; Minelli, 2013)
24. Logistics of populating ZooBank
• 16,000-20,000 new animal species described16,000-20,000 new animal species described
each yeareach year
• 1.9 million described extant species1.9 million described extant species
• 5-50 million estimated total extant species (R.5-50 million estimated total extant species (R.
May, E.O. Wilson, T. Erwin)May, E.O. Wilson, T. Erwin)
• Fossil species multiply this by some factorFossil species multiply this by some factor
Strategic approaches requiredStrategic approaches required
Publishers highly supportive and beginningPublishers highly supportive and beginning
to require ZooBank registrationto require ZooBank registration
Authors & databases contributing nowAuthors & databases contributing now
25. Logistics of populating ZooBank
Building tools to streamline the capture of prospective
content
•Publishers pipelines with XML tools
•Requested and required ZooBank registration by authors of
new papers
•(all e-only publications must be registered to be available)
Populating with retrospective content
•Major sources – Sherborn, Hymenoptera Names Server,
Hexacorallians of the World, etc.
•Committed individuals – Rod Bray, Takafumi Nakano
•Lists of Available Names (LANs)
30. LANs – Lists of Available Names
• Critical assembly of large
numbers of names
• Community debate
• Commission authoritative
ruling
Article 79 - An international body of
zoologists… in consultation with the
Commission may propose that the Commission
adopt for a major taxonomic field (or related
fields) a Part of the List of Available Names in
Zoology. The Commission will consider the
proposal and may adopt the Part subject to the
proposing body and the Commission meeting
the requirements of this Article.
31. 1)Ensures a candidate Part of the LAN is
thoroughly vetted
2)Pares away dubious names
• like the Approved Lists of Bacterial Names that took effect on
1 January 1980 – taxonomically recognizable as well as
nomenclaturally available
3) Prevents “nomenclatural archeology”
• long-forgotten names displacing accepted names
Creates a definitive nomenclatural inventory (a
new zero point) for a portion of the taxonomic
spectrum
Source of names for ZooBank
LANs – Lists of Available Names
32. Two Possibilities
to document every
available name
within the scope
of the Part
to pare the inventory
of names within the
scope of the Part
STRICTLY NOMENCLATURAL
TAXONOMIC COMPONENT
34. • Names are the anchor and link for biodiversity information
exchange
• Types provide stability and meaning for taxon names
• An stable archive of names is a critical taxonomic
infrastructure
• ZooBank aims to be the authoritative source for scientific
names of animals and is growing rapidly
• The future of nomenclature includes a harmonization of
biological codes, especially through technical tools such as
ZooBank and the Global Names Architecture
Conclusions
35. Natural History Museum, London
Bishop Museum, Hawaii
ITCN/ITZN supporting institutions
(MNHN (France), Senckenberg
(Germany), Naturalis, RBINS
(Belgium), AAZN (USA))
The Commissioners & Trustees of
ICZN / ITZN
ICB – International Committee on
Bionomenclature
Everyone pitching in on building
ZooBank content
THANKS
In 1758 it was feasible to create a catalog of life using ink on paper. <click> Today, it would require the equivalent of nearly 264 volumes of Systema Naturae to achieve the same thing. Or, you could fit the whole thing on a tiny memory card.
It’s no surprise that the biodiversity community is going digital. <click> Many Natural History Museums are databasing their collections. <click> Historical literature is being digitized by the Biodiversity Heritage Library and others… <click> … and many modern scientific journals are embracing the digital age directly. <click> Authoritative Nomenclators have been built, <click> and a variety of groups are working to distill the taxonomic concepts from the sea of names. <click> Databases of observation records are growing at a fast rate, <click> as are genomic databases. <click> The internet has made feasible the cheap and easy dissemination of multimedia files related to biodiversity. <click> And, of course there is biodiversity content spread across the billions of web pages indexed by Google. <click> To make sense of it all, several organizations serve as aggregators of all this diverse content. And this is just a small sample of icons that could fit on a slide. This massive effort to digitize biodiversity information is a great step in the right direction. But it is only one step. We must now focus our energies on integrating all of this information in a coordinated, cohesive way. <click> The critical informatic piece to this puzzle is Taxonomy, because almost all of these data providers link their content to taxon names one way or another.
It’s no surprise that the biodiversity community is going digital. <click> Many Natural History Museums are databasing their collections. <click> Historical literature is being digitized by the Biodiversity Heritage Library and others… <click> … and many modern scientific journals are embracing the digital age directly. <click> Authoritative Nomenclators have been built, <click> and a variety of groups are working to distill the taxonomic concepts from the sea of names. <click> Databases of observation records are growing at a fast rate, <click> as are genomic databases. <click> The internet has made feasible the cheap and easy dissemination of multimedia files related to biodiversity. <click> And, of course there is biodiversity content spread across the billions of web pages indexed by Google. <click> To make sense of it all, several organizations serve as aggregators of all this diverse content. And this is just a small sample of icons that could fit on a slide. This massive effort to digitize biodiversity information is a great step in the right direction. But it is only one step. We must now focus our energies on integrating all of this information in a coordinated, cohesive way. <click> The critical informatic piece to this puzzle is Taxonomy, because almost all of these data providers link their content to taxon names one way or another.
To overcome these and other problems, we need to build a Global Names Architecture. The first and perhaps most critical component to integrating all of this biodiversity information is the broader adoption of Globally Unique Identifiers, or GUIDs. <click> If you already know about GUIDs, then the question of whether we should use LSIDs or DOIs or Handles, or PURLs or UUIDs is of secondary importance to their more general implementation. If you don’t already know about GUIDs, then learn about them, or trust your IT staff when they say then need support to implement them. Also, always keep in mind that they are intended for use by computers, not humans, so don’t worry about how ugly they may appear. But while GUIDs make things a lot easier, they do not, by themselves, solve the problem of linking the world’s biodiversity information.
GUIDs are globally unidque identifiers, readable only to computers The two major components of the Global Names Architecture currently under development are the Global Names Index, or “GNI”… <click> And the Global Names Usage Bank, or “GNUB”. <click> The GNI is optimized to manage information from content providers that treat names as text-string attributes of other data objects. For example, it provides a species-level index of content within data bases and facilitates linking of disparate data sources through species names. <click> The GNUB is designed to manage taxon names and their usages as curated data objects in and of themselves. These components will not only help build links among their own contributing data providers, but also to bridge the gap between them. <click> Services will allow the GNI to serve as a “gateway” into the GNUB. And, of course, the GNUB will serve as a source of validated taxon name strings back to GNI. The Global Names Architecture is currently in development with support from GBIF, the Encyclopedia of Life, and National Biological Information Infrastructure. A prototype of GNI is already available at globalnames.org, and the GNUB is currently being populated with content from Index Fungorum and ZooBank, the latter of which will include content from many of these taxon-specific nomenclators. <click> Ultimately, all of these content providers will be plugged into the Global Names Architecture, and the biodiversity data content will start to flow.
The good news is that Taxonomic names represent one of the greatest and long-lasting examples of true international cooperation in all of science, if not all of human history. <click> This is a result of the various Codes of Scientific Nomenclature; two of which have been in place for more than a century, and apply to all names going back to Linnaeus. In a sense, the Codes of Nomenclature represent our saving grace for organizing biodiversity information. Without their existence, longevity, and near-universal adoption, the prospects for integrating biodiversity information would be orders of magnitude more difficult today. Unfortunately, as important as these Codes of nomenclature have been and continue to be, there are still some issues to overcome.