EMODnet 2015
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This document summarizes marine trait data available within the Encyclopedia of Life (EOL). It details that EOL contains over 500,000 trait records for around 290,000 marine taxa, inferred from 178 taxonomic nodes. Example datasets described include tissue mineralization records for 70,106 marine species, as well as data on distribution, habitat, and ecological associations. The structure of the trait data within EOL is also outlined.
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TraitBank is the structured data service of the Encyclopedia
of Life. Launched in 2014, it currently hosts 9 million
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administrative ones (eg: IUCN status, type specimen
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masses of phytoplankton and tissue mineralization types
of algae and invertebrates. Hosted records include all
available metadata, including detailed attribution, url of
data source if online; organism information including sex
and life stage; date, locality and method information for
field studies, and any other fields provided by the source.
TraitBank is not a repository. Most hosted records are
deposited with a scholarly publication, or an institutional
or aggregator database. Presence in TraitBank makes
individual records findable by EOL search (http://eol.org/
data_search) or web search engine. Search results on EOL
are available by CSV download and records are available
to semantic web applications via a JSON-LD web service,
including all metadata. Fresh Data is a data search service
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funded by NSF. Interested occurrence data providers
will register to be indexed. Their data will be deposited at
GBIF, using the IPT, if possible, and in TraitBank otherwise
(eg: presence/absence or abundance data, if GBIF
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group. Registered researchers will also be able to save and
publish their data queries, which will alert them if new
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Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2
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This document discusses using ancient DNA analysis to study archaeological remains. It notes that ancient DNA is typically fragmented into small pieces 100-500 base pairs long. Contamination from other sources is also a major issue. However, ancient DNA analysis can be used to study species phylogenies, hominin evolution, past diets and behaviors, origins of domestication, and population histories. As a case study, the document discusses analyzing ancient DNA from pygmy hippopotamus remains on Cyprus to learn about population dynamics and what caused their extinction 12,000 years ago alongside human arrival and climate change. Stable isotope analysis of bones and teeth can also provide clues about past diets.
Amlc
TraitBank is the structured data service of the Encyclopedia
of Life. Launched in 2014, it currently hosts 9 million
data records for 1.7 million taxa, including trait records
(eg: cell size, life history traits) and other attributes including
administrative ones (eg: IUCN status, type specimen
repository). Marine datasets include verbal localities
from WoRMS, habitat categories from AlgaeBase, water
temperature ranges based on known occurrence records
from OBIS, and literature derived datasets including cell
masses of phytoplankton and tissue mineralization types
of algae and invertebrates. Hosted records include all
available metadata, including detailed attribution, url of
data source if online; organism information including sex
and life stage; date, locality and method information for
field studies, and any other fields provided by the source.
TraitBank is not a repository. Most hosted records are
deposited with a scholarly publication, or an institutional
or aggregator database. Presence in TraitBank makes
individual records findable by EOL search (http://eol.org/
data_search) or web search engine. Search results on EOL
are available by CSV download and records are available
to semantic web applications via a JSON-LD web service,
including all metadata. Fresh Data is a data search service
in development primarily for the Citizen Science community,
funded by NSF. Interested occurrence data providers
will register to be indexed. Their data will be deposited at
GBIF, using the IPT, if possible, and in TraitBank otherwise
(eg: presence/absence or abundance data, if GBIF
cannot accommodate them). Searchers can query the
index for recent records by time, location and taxonomic
group. Registered researchers will also be able to save and
publish their data queries, which will alert them if new
data appears matching their criteria, and alert the data
provider that their data was delivered to a subscriber.
10 years of global biodiversity databases: are we there yet?
The document discusses the progress made over the past 10 years towards achieving a vision of having comprehensive biodiversity information accessible online. It examines several key components of this vision including developing a global taxon inventory, linking names to primary literature, assembling georeferenced species records, and creating machine-readable taxon trait data. For each component, it provides details on the scope of the task, current resources addressing it, and how complete the work is so far, noting many challenges that still remain.
Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2
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 CARCACE project deepwater platforms - modular designs for in situ experim...
This document describes the CARCACE project which aims to study ecosystems created by large organic falls in the deep Atlantic Ocean. The project involves deploying cow carcasses at 1000m depth in the Setubal Canyon and Azores to study community succession over time. New platform designs were developed to deploy and monitor the carcasses, including a floating platform and reinforced concrete platform anchored to the seafloor. The concrete platform was deployed in March 2011 to begin the first experiment of the CARCACE project.
C2.02: Informing Priorities for Biological and Ecosystem Observations, suppor...
C2.02: Informing Priorities for Biological and Ecosystem Observations, suppor...Blue Planet Symposium
There are increasing opportunities to expand observation of ocean biology from advances in individual sensors to development of national and global networks. To leverage these opportunities, the ocean community has defined essential variables, initially in physical oceanography. In 2013, a Biological Integration and Observation Task Team (BIO-TT) was formed under the IOOC to focus on biological essential variables for U.S. IOOS. The primary goals of the BIO-TT were a) to improve availability of observations on the existing IOOS core biological variables (defined by BIO-TT as phytoplankton species; zooplankton species and abundance; fish species and abundance), and b) to identify and prioritize additional cross-cutting federal agency biological and ecosystem observation needs.
To address these objectives the team (1) completed a survey of federal agencies for existing core variable datasets and identified needs for biological and ecosystem observations and (2) conducted an expert workshop to explore best available science of biological and ecosystem observing, and determine implementation strategies for biological and ecosystem observation needs identified from the survey. To build upon the actions and recommendations made previously by several other groups working towards the development of a global, coordinated ocean observation system, the BIO-TT Expert Working Group activities followed the guidelines developed by the Framework for Ocean Observation (2012) and the prioritization themes identified by the GOOS Biology and Ecosystems Panel (IOC 2014).
Workshop participants agreed that the highest priority is to include species and abundance of core functional groups (pelagic and benthic) not currently represented among the IOOS core variables. This presentation will summarize key results from the survey and then focus on analyses, outcomes and recommendations from the expert workshop for new and enhanced biological variables as part of IOOS.Fishing for the Right Content in a Sea of Free E-books
The document discusses how the Biodiversity Heritage Library identifies relevant content from the large number of free e-books available. It explains that BHL refines its search criteria by removing broad topics, identifying useful subject headings from previously ingested titles, and targeting specific bibliographic fields and call numbers. This allows BHL to cast a wide net initially but then evaluate results to select content most aligned with its focus on biodiversity and natural history.
Using Supercomputers and Supernetworks to Explore the Ocean of Life
The document summarizes Dr. Larry Smarr's presentation about the CAMERA project, which uses supercomputers and networks to explore microbial genomic data from ocean samples. The CAMERA infrastructure provides researchers worldwide with access to over 1 billion base pairs of metagenomic sequence data through an online portal. Analysis of this data has expanded knowledge of microbial biodiversity and gene families, providing insights into evolution and relationships between microbes and human health.
Sherborn: Thompson & Pape - Sherborn’s critical influence in getting informat...
The order Diptera (Insecta), flies, is a megadiverse group, representing some 15% or more of the known species of organisms. Scientific names are tags to concepts (hypotheses), called species, by which we organize our knowledge of biodiversity. Our Systema Dipterorum provides an index to all scientific names related to flies, so access to our knowledge about them is readily available. Sherborn more than a century ago attempted to provide such an index to all animal names. He did provide an index to all names published up until and including 1850. We compare our indexes, revealing how standards have changed and the number of names increased. Today, more and better resources are being made available to us, such as the Biodiversity Heritage Library, and our standards are higher (new International Code of Zoological Nomenclature), but regardless of all the change, Sherborn for his time provided an almost perfect (99.9%) index.
Bioinformatics A Biased Overview
The document provides an overview of bioinformatics and examples of how it is used at different biological scales and levels of complexity, from genomics to proteomics to biological networks and systems biology. It discusses how bioinformatics integrates biological data from different sources and scales to offer new biological insights. Examples are given of how bioinformatics is applied to analyze genomic, metagenomic, and proteomic data as well as protein structures and interactions.
Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
06.09.15
Invited Talk
2006 Synthetic Biology Symposium
Aliso Creek Inn
Title: Building a Community Cyberinfrastructure to Support Marine Microbial Ecology Metagenomics
Laguna Beach, CA
Tim Capps Masters Degree Publication
Exposure to perchlorate induced the formation of macrophage aggregates in the trunk kidney of zebrafish and mosquitofish. Zebrafish exposed to 18 mg/L perchlorate in water for 8 weeks had a greater percentage of kidney sections occupied by aggregates compared to controls. Male mosquitofish exposed to increasing concentrations of perchlorate up to 92 mg/L also showed more aggregates, significantly different from controls at 92 mg/L. The concentrations causing effects are within ranges found in some contaminated habitats.
, 20130104, published 27 March 20139 2013 Biol. Lett. Matt.docx
1) Cavefish species in the family Amblyopsidae have lost a significant portion of their hearing range compared to their surface-dwelling relatives. Cavefish can only hear up to 800Hz while surface fish can hear up to 2kHz.
2) Cavefish have lower hair cell densities in their ears compared to surface fish, which may contribute to their reduced hearing abilities.
3) Ambient noise measurements found high intensity noise peaks near 1kHz in cave streams, suggesting cavefish lost the ability to hear those frequencies as it provides no advantage underground.
52 Million Points and Counting: A New Stratification Approach for Mapping Glo...
The document summarizes a presentation about mapping global marine ecosystems using Ecological Marine Units (EMUs). EMUs divide the ocean into 3D units based on properties like temperature, salinity, oxygen, and nutrients from 52 million data points. 37 distinct EMU clusters were identified. EMUs support applications like predicting how warming may impact seagrass habitats and developing a framework for ocean monitoring networks. Future work includes developing Ecological Coastal and Freshwater Units using a similar approach.
Behavior ontology workshop princeton
Presented at 2014 Animal Behavior Ontology workshop at Princeton, NJ in association with the Animal Behavior Society annual meeting.
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iEvoBio Keynote: Frontiers of discovery with Encyclopedia of Life -- TRAITBANK
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10 years of global biodiversity databases: are we there yet?
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Michel digital nomenclature-gna-zoobank-2014-co-namesconfv2
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The CARCACE project deepwater platforms - modular designs for in situ experim...
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Fishing for the Right Content in a Sea of Free E-books
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Building a Community Cyberinfrastructure to Support Marine Microbial Ecology ...
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, 20130104, published 27 March 20139 2013 Biol. Lett. Matt.docx
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Encyclopedia of Life v3- constructing a linked data model
The document discusses constructing a linked data model for the Encyclopedia of Life by linking taxonomy, texts, and trees. It presents a simplified diagram of the core relationships between taxonomy entities like authors, publications, taxon names, and taxa. The goal is to build a biodiversity knowledge graph by connecting these entities.
Fellows and Rapid Response
Two EOL programs: the Rubenstein Fellows program, which supports outreach-minded researchers in content creation activity in their area of interest; and Rapid Response, which assembles content as needed for taxa expected to receive wide attention due to news events sor outreach efforts of our educational partners.
Serious games
This document discusses serious games, which are games designed for purposes other than pure entertainment. It notes that serious games aim to be both fun and provide a predictable outcome or utility. The document also mentions different types of serious games and who plays them, as well as factors that contribute to their success, including being fun, realistic, having clear rules and objectives, interactive storylines, and challenging gameplay that encourages high cognitive activity.
Ispot
Sir David Attenborough endorsed the iSpot project, which encourages people of all ages and backgrounds to identify plants and animals by taking photos and receiving identifications. iSpot has grown significantly since launching, with over 14,500 registered users who have made over 190,000 observations and uploaded over 125,000 images covering over 5,000 species, most identified to the species level. Developments include expanding iSpot locally, mobile apps, and launching in South Africa later this year.
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The document discusses the Encyclopedia of Life (EOL) project, which aims to create a digital page for every known species on Earth. EOL's goals are to facilitate unprecedented global collaboration between experts and novices to build scientifically credible species pages. These pages will provide value to multiple audiences like scientists, educators, and policymakers. Typical species pages include information like descriptions, distributions, ecology, and links to external resources. The EOL has over 2.8 million taxon pages contributed by 117 partners, and continues growing as new species are discovered. Examples of partner tools and resources that contribute content to EOL pages are provided.
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The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
Although Artemia has been known to man for centuries, its use as a food for the culture of larval organisms apparently began only in the 1930s, when several investigators found that it made an excellent food for newly hatched fish larvae (Litvinenko et al., 2023). As aquaculture developed in the 1960s and ‘70s, the use of Artemia also became more widespread, due both to its convenience and to its nutritional value for larval organisms (Arenas-Pardo et al., 2024). The fact that Artemia dormant cysts can be stored for long periods in cans, and then used as an off-the-shelf food requiring only 24 h of incubation makes them the most convenient, least labor-intensive, live food available for aquaculture (Sorgeloos & Roubach, 2021). The nutritional value of Artemia, especially for marine organisms, is not constant, but varies both geographically and temporally. During the last decade, however, both the causes of Artemia nutritional variability and methods to improve poorquality Artemia have been identified (Loufi et al., 2024).
Brine shrimp (Artemia spp.) are used in marine aquaculture worldwide. Annually, more than 2,000 metric tons of dry cysts are used for cultivation of fish, crustacean, and shellfish larva. Brine shrimp are important to aquaculture because newly hatched brine shrimp nauplii (larvae) provide a food source for many fish fry (Mozanzadeh et al., 2021). Culture and harvesting of brine shrimp eggs represents another aspect of the aquaculture industry. Nauplii and metanauplii of Artemia, commonly known as brine shrimp, play a crucial role in aquaculture due to their nutritional value and suitability as live feed for many aquatic species, particularly in larval stages (Sorgeloos & Roubach, 2021).
bordetella pertussis.................................ppt
Bordettela is a gram negative cocobacilli spread by air born drop let
Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
Bob Reedy - Nitrate in Texas Groundwater.pdf
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Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
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https://www.etran.rs/2024/en/home-english/Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
The pygmy halfbeak Dermogenys colletei, is known for its viviparous nature, this presents an intriguing case of relatively low fecundity, raising questions about potential compensatory reproductive strategies employed by this species. Our study delves into the examination of fecundity and the Gonadosomatic Index (GSI) in the Pygmy Halfbeak, D. colletei (Meisner, 2001), an intriguing viviparous fish indigenous to Sarawak, Borneo. We hypothesize that the Pygmy halfbeak, D. colletei, may exhibit unique reproductive adaptations to offset its low fecundity, thus enhancing its survival and fitness. To address this, we conducted a comprehensive study utilizing 28 mature female specimens of D. colletei, carefully measuring fecundity and GSI to shed light on the reproductive adaptations of this species. Our findings reveal that D. colletei indeed exhibits low fecundity, with a mean of 16.76 ± 2.01, and a mean GSI of 12.83 ± 1.27, providing crucial insights into the reproductive mechanisms at play in this species. These results underscore the existence of unique reproductive strategies in D. colletei, enabling its adaptation and persistence in Borneo's diverse aquatic ecosystems, and call for further ecological research to elucidate these mechanisms. This study lends to a better understanding of viviparous fish in Borneo and contributes to the broader field of aquatic ecology, enhancing our knowledge of species adaptations to unique ecological challenges.
8.Isolation of pure cultures and preservation of cultures.pdf
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Current descriptions of immersive learning cases are often difficult or impossible to compare. This is due to a myriad of different options on what details to include, which aspects are relevant, and on the descriptive approaches employed. Also, these aspects often combine very specific details with more general guidelines or indicate intents and rationales without clarifying their implementation. In this paper we provide a method to describe immersive learning cases that is structured to enable comparisons, yet flexible enough to allow researchers and practitioners to decide which aspects to include. This method leverages a taxonomy that classifies educational aspects at three levels (uses, practices, and strategies) and then utilizes two frameworks, the Immersive Learning Brain and the Immersion Cube, to enable a structured description and interpretation of immersive learning cases. The method is then demonstrated on a published immersive learning case on training for wind turbine maintenance using virtual reality. Applying the method results in a structured artifact, the Immersive Learning Case Sheet, that tags the case with its proximal uses, practices, and strategies, and refines the free text case description to ensure that matching details are included. This contribution is thus a case description method in support of future comparative research of immersive learning cases. We then discuss how the resulting description and interpretation can be leveraged to change immersion learning cases, by enriching them (considering low-effort changes or additions) or innovating (exploring more challenging avenues of transformation). The method holds significant promise to support better-grounded research in immersive learning.
在线办理(salfor毕业证书)索尔福德大学毕业证毕业完成信一模一样
学校原件一模一样【微信：741003700 】《(salfor毕业证书)索尔福德大学毕业证》【微信：741003700 】学位证，留信认证（真实可查，永久存档）原件一模一样纸张工艺/offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
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2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
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Basics of crystallography, crystal systems, classes and different forms
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The use of Nauplii and metanauplii artemia in aquaculture (brine shrimp).pptx
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bordetella pertussis.................................ppt
bordetella pertussis.................................ppt
Authoring a personal GPT for your research and practice: How we created the Q...
Authoring a personal GPT for your research and practice: How we created the Q...
The binding of cosmological structures by massless topological defects
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waterlessdyeingtechnolgyusing carbon dioxide chemicalspdf
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Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
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Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
Unlocking the mysteries of reproduction: Exploring fecundity and gonadosomati...
8.Isolation of pure cultures and preservation of cultures.pdf
8.Isolation of pure cultures and preservation of cultures.pdf
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ESR spectroscopy in liquid food and beverages.pptx
ESR spectroscopy in liquid food and beverages.pptx
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
Describing and Interpreting an Immersive Learning Case with the Immersion Cub...
EMODnet 2015
- 1. Marine trait data within EOL: structure and statistics Jen Hammock1, Katja Schulz1, Jorrit Poelen2 1- Smithsonian’s National Museum of Natural History 2- Global Biotic Interactions
- 2. Global Access to Knowledge About Life on Earth http://eol.org/data_search
- 12. Resource file structure, modified Darwin Core Archive
- 13. Example
- 16. Example: tissue mineralization biogeography • 70,106 hits out of 130,160 OBIS records • 3659 out of 7943 taxa
- 17. Example: tissue mineralization biogeography • ~500,000 trait records total in EOL • for ~290,000 taxa • inferred from 178 taxonomic nodes according to WoRMS and AlgaeBase • Also available: crystal structure, derivative compounds…
- 18. Marine data estimates Large datasets OBIS environmental data ranges (155,000 taxa) WoRMS distribution keywords Habitat keywords textmined from EOL Ecological associations data, GloBI & GoMexSI (78,000 records) Tissue mineralization (290,000 taxa) Type specimen repository (~50,000 taxa) Small datasets Copepod life history and size Phytoplankton cell mass, volume, shape PolyTraits- polychaete life history, physical description Mollusk shell dimensions See all datasets
- 24. Thanks! This work was supported by: The Smithsonian’s National Museum of Natural History The Sloan Foundation David M. Rubenstein Jen: hammockj@si.edu
Editor's Notes
- Taxon selection currently checks Catalog of Life and NCBI. When available, it will use our new consensus classification, to be based closely on Open Tree of Life.
- Taxon selection currently checks Catalog of Life and NCBI. When available, it will use our new consensus classification, to be based closely on Open Tree of Life.
- Don’t need details, eg: WoRMS propagation
- Don’t need details, eg: WoRMS propagation
- Don’t need details, eg: WoRMS propagation
- Where did these come from? Andrew Barton, Nick Record, Sarah Faulwetter and colleagues, LifeWatch Greece, Craig McLean, Nescent, Femorale
- Call to action! Use data or contribute data. Contact Jen