This document outlines a proposed model for a clearinghouse to integrate taxonomic and nomenclatural data from various sources. The clearinghouse would:
1) Separate taxonomic information from nomenclatural names to allow integration of data from different sources and expert working groups.
2) Contain both reviewed, authoritative data as well as provisional data imported from external sources.
3) Provide APIs and workspaces for experts to review, edit, and publish changes to taxonomic data and classifications.
Earth Sciences 4490: Getting Started on your Literature Review by Dan Sich, Earth Sciences Librarian, University of Western Ontario, Sept 24 & Oct 1, 2008
Rafael C Jimenez presents the Omics Discovery Index | OSFair2017 Workshop
Workshop title: How FAIR friendly is your data catalogue?
Workshop overview:
This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users?
DAY 3 - PARALLEL SESSION 6 & 7
Geology/Geophysics 9580/9680 Library Workshop, October 8 2008, by Dan Sich, Earth Sciences, Planetary Science and Physics & Astronomy Librarian, University of Western Ontario
PhyloTastic: names-based phyloinformatic data integrationRutger Vos
Lightning talk to the 2013 TDWG conference symposium on phyloinformatics, brief report on PhyloTastic with special attention to the taxonomic name reconciliation service TaxoSaurus.
Earth Sciences 4490: Getting Started on your Literature Review by Dan Sich, Earth Sciences Librarian, University of Western Ontario, Sept 24 & Oct 1, 2008
Rafael C Jimenez presents the Omics Discovery Index | OSFair2017 Workshop
Workshop title: How FAIR friendly is your data catalogue?
Workshop overview:
This workshop will build upon the work planned by the EOSCpilot data interoperability task and the BlueBridge workshop held on April 3 at the RDA meeting. We will investigate common mechanisms for interoperation of data catalogues that preserve established community standards, norms and resources, while simplifying the process of being/becoming FAIR. Can we have a simple interoperability architecture based on a common set of metadata types? What are the minimum metadata requirements to expose FAIR data to EOSC services and EOSC users?
DAY 3 - PARALLEL SESSION 6 & 7
Geology/Geophysics 9580/9680 Library Workshop, October 8 2008, by Dan Sich, Earth Sciences, Planetary Science and Physics & Astronomy Librarian, University of Western Ontario
PhyloTastic: names-based phyloinformatic data integrationRutger Vos
Lightning talk to the 2013 TDWG conference symposium on phyloinformatics, brief report on PhyloTastic with special attention to the taxonomic name reconciliation service TaxoSaurus.
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.
An introduction to assigning subject descriptors to an information object, including subject headings (LCSH, Sears) and other controlled vocabularies like thesauri (Getty AAT).
Basic overview of the Global Names Architecture and Darwin Core data standards presented to the Asian Regional Biodiversity Workshop in Bangkok, Thailand (Nov 2009).
Global Library of Life: The Biodiversity Heritage LibraryMartin Kalfatovic
Global Library of Life: The Biodiversity Heritage Library. Martin R. Kalfatovic. Boston Library Consortium Meeting. Boston Public Library. 18 March 2008. Boston, MA.
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.
An introduction to assigning subject descriptors to an information object, including subject headings (LCSH, Sears) and other controlled vocabularies like thesauri (Getty AAT).
Basic overview of the Global Names Architecture and Darwin Core data standards presented to the Asian Regional Biodiversity Workshop in Bangkok, Thailand (Nov 2009).
Global Library of Life: The Biodiversity Heritage LibraryMartin Kalfatovic
Global Library of Life: The Biodiversity Heritage Library. Martin R. Kalfatovic. Boston Library Consortium Meeting. Boston Public Library. 18 March 2008. Boston, MA.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
Comparing Evolved Extractive Text Summary Scores of Bidirectional Encoder Rep...University of Maribor
Slides from:
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Track: Artificial Intelligence
https://www.etran.rs/2024/en/home-english/
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
1. Champaign, 27th July 2017
A Clearinghouse
for Taxonomy & Nomenclature
Markus Döring, GBIF
2. CLEARINGHOUSE MODEL
For reviewFor review
For review For review
IPNI
Index
Fungorum
ZooBank
Global
Species
Database 1
GSD 2
GSD 3 …
Provisional
Datasets
Clearing House
Catalogue
of Life
(Reviewed)
“Index of
Names”
(Reviewed)
ExtendedCatalogueSeparates names & taxa
Different authorities: nomenclator & GSD
Integrate sources on distinct name
single consensus taxonomy
Provisional & authoritative sources
Offers a review queue to every source
3. NAMES
A unique name is based on:
Genus, species-, infraspecific epithet
Rank
Authorship regardless of spelling
Name types
Included: Linnean names, Named hybrids, Virus names
Exclude: hybrid formulas, cultivars, OTUs
NameID from nomenclator
Otherwise preliminary clearinghouse nameID
Major information (draft)
Code (ICN, ICZN, …)
Homotypic synonyms (basionym & replacement names )
Original publication
isFossil
Available
Conserved, rejected
Nomenclatural notes
Acacia (Juliflorae) aneura F. Muell. ex Benth. var. latifolia J.M. Black
Acacia (Juliflorae) aneura var. latifolia J.M. Black
Acacia aneura Benth. var. latifolia J. Black
Acacia aneura var. latifolia J. Black
Acacia aneura var. latifolia J.M. Black
4. TAXA
Single consensus view
Track historic concepts
Manage CoL classification in clearinghouse
Heterotypic synonymy
Assign taxon IDs
Computable rules based on synonymy & siblings
Reviewed and provisional taxon ids might differ
Supplementary CoL information
Distribution
Vernacular names
Lifezone & fossil flags
5. CLEARINGHOUSE API
All services expose both
Reviewed data only
Extended data including provisional information
Nomenclatural services
Name matching
List homotypic synonymy
Correct spelling
Name history (nomenclatural events around a basionym)
Taxonomic services
Search
Browse children
List entire synonymy
6. STAGING WORKSPACE
Initial import of sources, cleaning & interpretation
Reader for ACEF, DwC-A, TCS
Clean whitespace, html entities, encoding issues
Interpret values (e.g. dates, rank, country, language)
Parse names (if not parsed yet, DwC only)
Match to clearinghouse names (assign nameID)
Integrity checks for review
Check name structure, accepted name for synonyms, …
Check for duplicate name within source or outer CoL
More existing workbench checks, add over time
Change metrics (# of new, updated & deleted names)
Editorial decisions
Map taxa to CoL classification
Block name
Change name status
Publish to clearinghouse
Staging API for review, preview & editorial decisions
Staging
Workspace
Source
editorial
control
7. CLEARINGHOUSE WORKSPACE
Represents current best knowledge
Includes both reviewed & provisional placement
Maintains the CoL classification
Mints taxon identifier
Community contributions
Fully versioned
Comments everywhere
Edits in areas without authority
Content bots adding provisional information
Basionym relations
BHL literature links
Review queues for sources
Editorial decisions
Manage authorization for taxonomic groups
Move taxa to other group (to change source authority)
Release CoL
Clearinghouse
Workspace review
queue
Public
Staging
Workspace
Source
editorial
control
8. COL RELEASE SPACE
Contains latest interim (monthly) release
Not archived
Archive of all annual releases
API & portal expose them
GSD decides name fidelity
Name exactly as provided
Name spelling from nomenclator
Homotypic synonymy added
CoL
Release
Public
Clearinghouse
Workspace review
queue
Public
Staging
Workspace
Source
editorial
control
9. OPTIONS FOR EVOLUTION
Extended nomenclatural model
Nomenclatural acts
Type specimen
Name Author entities
Reference entities
More name relations
Concurrent taxon concepts
Multiple classifications
Multiple concepts per name
Allows precise identifications, national lists, etc.
Species images
Reference image selected by community
Editor's Notes
T1-23-06
The Global Biodiversity Information Facility: A Review of Progress and Challenges in Plant Data Mobilization and Integration
Siro Masinde1
Hobern Donald1
1. Global Biodiversity Information Facility (GBIF)
GBIF - the Global Biodiversity Information Facility (http://www.gbif.org/) is the leading aggregator of species occurrence data, including botanical and fungal data. As of January 2017, GBIF had more than 700 million records harvested from over 32,000 data resources published by more than 800 data providers. Since its establishment in 2002, GBIF has provided leadership in delivering tools, standards and best practices for mobilizing biodiversity data for free and open use by the research community and to support policy applications. Established tools and processes now support the aggregation and integration of species distribution data from natural history collections, field research, environmental genomics, citizen science and literature into a single, unified resource. Modern approaches to linked-open data management point the way to this data resource becoming the focal point for connecting the full spectrum of recorded information about species and communities. GBIF strives to provide well integrated data of high quality and in large quantity to enable users to query and summarize data, with answers that are as complete and accurate as possible. This can only be achieved if data providers worldwide mobilize large, high quality data across a wide spatial, temporal and taxonomic spectrum and publish them openly using interoperable standard data formats. We review GBIF progress in plant data mobilization and integration, and provide insights on future directions. We also highlight the challenges encountered and invite a discussion on future expectations of the botanical community and the role the community can play in developing and curating the GBIF database to meet the needs and expectations of users.
Keywords: data mobilization data integration data management GBIF linked-open data
No subgenus or infraspecific hierarchy for quadrinomials
Also valid / correct name?
Orthographic variants ???