This document provides an overview of taxonomy and taxonomic assessments. It defines taxonomy as the science of naming, describing, and classifying organisms. Taxonomists identify and classify species based on morphological, genetic, and other observations. The document discusses taxonomic names, hierarchies, synonyms, homonyms, and how classifications can vary between taxonomists. It outlines sources of taxonomic data, requirements for assessments, and methods for conducting manual or automated assessments to clean data and reconcile taxonomies by checking names against controlled lists. Validation of assessment outputs is also discussed.
People First Specially Abled Achievers Award 2015Dharmendra Kumar
The Largest platform ever :-
* To recognize the talent of specially abled
* Campaign for Employment of specially abled
* Awareness and Exposure to the among common man about
disability
* Bring together the talent hub of specially abled to the main
stream
* Bringing out the exclusivity of the International Day of
Persons with Disability through awareness, recognition,
interaction and entertainment.
People First Specially Abled Achievers Award 2015Dharmendra Kumar
The Largest platform ever :-
* To recognize the talent of specially abled
* Campaign for Employment of specially abled
* Awareness and Exposure to the among common man about
disability
* Bring together the talent hub of specially abled to the main
stream
* Bringing out the exclusivity of the International Day of
Persons with Disability through awareness, recognition,
interaction and entertainment.
The presentation describes Assistive Tech for People With Disabilities.
There is no doubting the powerful role that technology has played and will continue to play in changing the world in which we live. People with disabilities meet barriers of all types in their day to day life.
However, technology is helping to lower many of these barriers. Overall, technology aims to allow people with disabilities to participate more fully in all aspects of life (home, school and community) and increases their opportunities for education, social interactions, and potential for meaningful employment. Therefore creating greater independence and control among disabled individuals.
TEDx Manchester: AI & The Future of WorkVolker Hirsch
TEDx Manchester talk on artificial intelligence (AI) and how the ascent of AI and robotics impacts our future work environments.
The video of the talk is now also available here: https://youtu.be/dRw4d2Si8LA
Franz 2017 uiuc cirss non unitary syntheses of systematic knowledgetaxonbytes
Invited Presentation given at the University of Illinois Urbana Champaign iSchool, Center for Informatics Research in Science and Scholarship, CIRSS Seminar, Friday, February 17, 2017.
A talk based on my chapter in _Species Problems and Beyond_ (CRC Press, 2022) in which I argue that some concepts are neither model-based as Nercessian argues, nor theory-derived, but come from the operative traditions as they develop out of folk concepts.
Polytraits: A database on biological traits of marine polychaetesSarah Faulwetter
Presentation of Polytraits at the EMODnet Traits Vocabulary workshop in Paris. The presentation gives a short overview of the polytraits database and discusses its problems.
The presentation describes Assistive Tech for People With Disabilities.
There is no doubting the powerful role that technology has played and will continue to play in changing the world in which we live. People with disabilities meet barriers of all types in their day to day life.
However, technology is helping to lower many of these barriers. Overall, technology aims to allow people with disabilities to participate more fully in all aspects of life (home, school and community) and increases their opportunities for education, social interactions, and potential for meaningful employment. Therefore creating greater independence and control among disabled individuals.
TEDx Manchester: AI & The Future of WorkVolker Hirsch
TEDx Manchester talk on artificial intelligence (AI) and how the ascent of AI and robotics impacts our future work environments.
The video of the talk is now also available here: https://youtu.be/dRw4d2Si8LA
Franz 2017 uiuc cirss non unitary syntheses of systematic knowledgetaxonbytes
Invited Presentation given at the University of Illinois Urbana Champaign iSchool, Center for Informatics Research in Science and Scholarship, CIRSS Seminar, Friday, February 17, 2017.
A talk based on my chapter in _Species Problems and Beyond_ (CRC Press, 2022) in which I argue that some concepts are neither model-based as Nercessian argues, nor theory-derived, but come from the operative traditions as they develop out of folk concepts.
Polytraits: A database on biological traits of marine polychaetesSarah Faulwetter
Presentation of Polytraits at the EMODnet Traits Vocabulary workshop in Paris. The presentation gives a short overview of the polytraits database and discusses its problems.
Franz. 2014. Explaining taxonomy's legacy to computers – how and why?taxonbytes
Slides presented on the Euler/X projected (http://taxonbytes.org/prior-work-on-concept-taxonomy-2013/ & https://bitbucket.org/eulerx/euler-project) - for the conference "The Meaning of Names: Naming Diversity in the 21st Century", CU Natural History Museum, September 30, 2014.
Species delimitation - species limits and character evolutionRutger Vos
Lecture slides for the program orientation Evolutionary Biology at the Institute of Biology Leiden, the Netherlands. Thursday, September 7th, 2017.
Lecture notes are here: https://docs.google.com/document/d/e/2PACX-1vRIv5mKK1fjBby--u97emC7hrqXUbxFQZe63P1FpguuhHLG6xykbwXKeKXCUE5W-LSpakXYCI621xCK/pub
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My talk at TDWG 2013 showing our work on linking different biodiversity information systems to improve the quality of the data on both sides. We enabled an interoperability workflow between data aggregators, such as GBIF or VertNet, and other biodiversity information aggregators, like Map Of Life, with information such as IUCN expert range maps, regional checklists or gridded surveys. Although this was a work in progress at the time of the presentation (therefore the "warning" sign), we were able to show that intercommunication between both systems allowed us to detect spatio-taxonomic biases and issues in both sources. We also explored the possible causes for those errors and tried to model the error rates, finding that new data, published through new mechanisms showed better error rates. We concluded that even though we still lack more work to get a deeper understanding, we believe that we are getting into a new age of biodiversity information sharing, where quality, and not that much quantity, is becoming the key feature. We also believe that the Integrated Publishing Toolkit (IPT), developed by GBIF, might be the banner of this new movement towards a better quality data sharing and that it might be because it is an easier-to-use tool, because building auxiliary tools and mechanisms for improving the quality is easier, or simply because people are getting aware of the importance of having a good quality data set.
Biodibertsitatea... eta niri zer axola?Javier Otegui
Azken aldi honetan “biodibertsitate” hitza baino ez dugu entzuten, eta ia gehienetan berri txarrak dira: espezieen suntsipena, desertifikazioa... Eta niri zer? Ez naiz tropikoetan bizi ezta bale-arrantzaz. Zergatik biodibertsitatea zainduz kezkatu behar naiz, hirian bizi bainaiz? Ziur al gaude honetaz? Agian ez dugu pentsatzen genuen bezain ondo ezagutzen. Biodibertsitatea ez da hain urruna, eta hau ezagutzea eta mantentzea uste dugun baino garrantzitsuagoa da. Bere berezko balioaz gain, gizakiak biodibertsitatearen beharrean gaude alderdi ugarietan, bai zuzenean baita zeharka ere. Gainera, uste dugun baino gertuago dago: biodibertsitatea ez da oihan tropikala edo baso birjina soilik, hiriak badauka ere bere biodibertsitate berezia eta honen beharrean uste dugun baino gehiago gaude.
2. ¡ What is Taxonomy?
§ CBD – “Taxonomy is the science of naming, describing and
classifying organisms and includes all plants, animals and
microorganisms of the world”
§ Using morphological, behavioral, genetic and biochemical
observations, taxonomists identify, describe and arrange
species into classifications, including those that are new to
science.
¡ Taxonomy is related to:
§ the identification of an organism
§ Placing the organism in context with the rest of living
organisms
TAXONOMY – WHAT IS IT?
3. ¡ Taxonomy is based on names
¡ Humans have always given names
¡ Binomial nomenclature
¡ Define individuals and groups
¡ Each name defines a taxon
TAXONOMY – TAXONOMIC NAMES
4. ¡ Organization and
classification of
organisms
¡ According to common
features
¡ Taxonomic
classification
TAXONOMY - HIERARCHIES
http://wp.lps.org/jbenson2/blog/2012/01/18/january-18-taxonomy-chart-lab
5. ¡ Taxonomy has a strong subjective component
¡ Classifications depend on the expertise and point of
view of the specialist
¡ Lots of episodes of:
§ Name removals
§ Taxon splits
§ Taxon merges
§ Different organizations according to different features
¡ Some cases…
TAXONOMY – NAMES AND TAXONOMIES
6. ¡ Two different names are applied to the same organism
¡ Expert argues that two originally different taxa are the same
¡ Generally one name remains, the other is considered a
synonym and no longer valid
TAXONOMY - SYNONYMY
Photo: Arthur Chapman
Antilocapra americana
Ord, 1815
Antilocapra anteflexa
Gray, 1855
7. ¡ Two different names are applied to the same organism
¡ Expert argues that two originally different taxa are the same
¡ Generally one name remains, the other is considered a
synonym and no longer valid
TAXONOMY - SYNONYMY
Photo: Arthur Chapman
Antilocapra americana
Ord, 1815
Antilocapra anteflexa
Gray, 1855
8. ¡ The same name is applied to two different organisms
¡ New description using “already taken” name
¡ Generally, oldest name prevails and newest has to change
TAXONOMY - HOMONYMY
Echidna
Cuvier, 1797
Echidna
Forster, 1777
Photo: David R
Photo: Petr Baum
9. Photo: David R
Photo: Petr Baum
¡ The same name is applied to two different organisms
¡ New description using “already taken” name
¡ Generally, oldest name prevails and newest has to change
TAXONOMY - HOMONYMY
Echidna
Cuvier, 1797
Echidna
Forster, 1777
10. Photo: Petr Baum
¡ The same name is applied to two different organisms
¡ New description using “already taken” name
¡ Generally, oldest name prevails and newest has to change
TAXONOMY - HOMONYMY
Echidna
Cuvier, 1797
Tachyglossus
Illiger, 1811
11. ¡ Taxonomic classifications are subjective
¡ Based on common features
¡ Different experts select different features
¡ Scientific names might remain the same
¡ Higher level taxa or groups might differ
¡ See example…
TAXONOMY – ALTERNATE
CLASSIFICATIONS
13. ¡ Issues with names hamper the use of
taxonomic names alone to be
effective
¡ New term: Taxon concept
¡ Name – Concatenation of characters
¡ Concept – Name + context
¡ Even if the name is the same, the
concept is different since it applies
to different organisms
TAXONOMY – NAME VS CONCEPT
14. TAXONOMY - STANDARDS
¡ Taxonomic names: Scientific name and all higher taxa
¡ Taxon concept: taxonConceptID, nameAccordingTo,
namePublishedIn…
15. TAXONOMY - STANDARDS
¡ Taxonomic names: Scientific name and all higher taxa
¡ Taxon concept: taxonConceptID, nameAccordingTo,
namePublishedIn…
Source in which the specific taxon concept
circumscription is defined or implied
16. TAXONOMY - STANDARDS
¡ Taxonomic names: Scientific name and all higher taxa
¡ Taxon concept: taxonConceptID, nameAccordingTo,
namePublishedIn…
For taxa that result from identifications, a reference
to the keys, monographs, experts and other sources
should be given
17. ¡ One of the most common issues
¡ Random alteration of one or more characters in a
name
¡ Possibilities:
§ Purely accidental
§ Due to low knowledge
¡ Tend to appear at the time of digitization
NOISE - MISSPELLINGS
19. ¡ Misidentification
§ A more obscure type of error
§ Wrongly identify a taxon
§ The only way of solving is through close examination by
expert taxonomist
§ Might not be resolvable at all
¡ Emptiness
§ Seriousness depends on missing level/s
§ Importance decreases as taxonomic rank increases
§ Scientific name missing?
§ Special cases: homonymies, synonymies…
NOISE – MISIDENTIFICATIONS &
EMPTINESS
20. ¡ Not defining used taxonomy
§ Can have the same effect as having only scientific name
§ We might complete hierarchy, but reliability?
§ Providing employed taxonomy (taxonomic concept)
§ Use identification qualifiers: “Sensu Otegui, 2013”, or “Sensu
Biologia Centrali Americana”
¡ Synonymies and homonymies
§ Again, background information (metadata, taxonomic concept)
needed
§ Use of identification qualifiers
NOISE – NATURE OF TAXONOMY
21. ¡ Instability of taxonomic identifications
¡ Background information greatly help
¡ Also having source of change records
NOISE – NATURE OF TAXONOMY
22. ¡ Aims of taxonomic assessments
§ Correct issues
§ Reconcile taxonomies
§ Complete hierarchies
¡ Basic general process – controlled name list
§ Take a name
§ Check if exists in a reliable list of names
§ Extract related information
§ Apply to our dataset
ASSESSMENTS
23. ¡ General Databases
§ Ideally, global high-quality information
§ Not complete
§ Rely on taxon-specific sources and their completeness
ASSESSMENTS – SOURCES OF DATA
24. ¡ General Databases
§ Ideally, global high-quality information
§ Not complete
§ Rely on taxon-specific sources and their completeness
¡ Thematic databases and regional checklists
§ If our collection is taxon-specific or location-specific
§ Gather all available knowledge on their topic
§ Reliable authoritative sources
ASSESSMENTS – SOURCES OF DATA
25. ¡ General Databases
§ Ideally, global high-quality information
§ Not complete
§ Rely on taxon-specific sources and their completeness
¡ Thematic databases and regional checklists
§ If our collection is taxon-specific or location-specific
§ Gather all available knowledge on their topic
§ Reliable authoritative sources
¡ Taxonomic Literature
§ Most specific source
§ Very high reliability
§ Hard to retrieve relevant literature
§ Some processing needed
ASSESSMENTS – SOURCES OF DATA
26. ¡ Free of misspellings
§ Ab initio, or manage to reduce to the minimum
§ Some of the tools (Refine, Excel processing…) to accomplish
this
§ Taxonomic reconciliation depends on this requirement
¡ Completeness
§ At least to certain point
§ This minimum is scientific name
§ But only scientific name might not be enough
¡ Helpful metadata
§ Not related to the organism, but to the process of identification
§ The person who identified, taxonomic classification
ASSESSMENTS - REQUIREMENTS
27. ¡ Manual
§ Removing inconsistencies, updating the wrong information
§ Taxonomy is an interpretation of explicit and implicit knowledge
§ Explicit knowledge – records
§ Implicit knowledge – human deduction
§ Machines are not good at interpreting implicit knowledge
§ Prone to errors. Automated approach recommended
¡ Automatic
§ Big amounts of data
§ Repetitive tasks
§ Removal of misspellings, checking against source, update
§ Only explicit knowledge. Explicit metadata mandatory
ASSESSMENTS - METHODS
29. ¡ After cleaning, validate output
¡ Check:
§ The data that has been corrected
§ The data that could not be corrected
§ The data that might have gone worse
¡ Taxonomic validation:
§ Expertise
§ Mixture of explicit and implicit knowledge
§ Not completely automatable
¡ If assessments fail:
§ Our data – Document and report reliability
§ Distributed data – Flag and report
VALIDATION