The document discusses IRMNG, the Interim Register of Marine and Nonmarine Genera. IRMNG aims to provide a single point of access to classify and retrieve information on genera and species names across all kingdoms. It currently contains over 450,000 genera compared to around 178,000 in the Catalogue of Life. IRMNG aggregates data from various sources and provides additional information on names like taxonomy, synonyms, and attributes. The document outlines IRMNG's content and capabilities and notes it is a work in progress with the goal of realizing a comprehensive taxonomic name resolution service.
David Remsen lecture on Tuesday, Sept 15, 2009, for the Biodiversity Informatics Course, a Swedish Taxonomy Initiative (Svenska Artprojektet) course at the Swedish Natural History Museum, Stockholm, supported by the Swedish Species Service (ArtDatabanken) and the Swedish GBIF node.
Botanists and annotations printer friendlyWilliam Ulate
Findings from I Annotate 2016 concluded that the uptake of web annotation could be sufficiently moved forward by tackling three key issues: 1) interoperability, 2) domain use cases, and 3) user centered design. The Center for Biodiversity Informatics at the Missouri Botanical Garden has identified valuable use cases for developing in-depth user assessments of annotation needs in the specific domain of botanists. This presentation will share those use cases and talk about next steps in serving the annotation needs of botanists and their relevance for the larger scientific domain.
A presentation given by Don Kirkup at the KikForum
Abstract:
A brief overview of some Kew “key” projects, potential areas of overlap and possible exchange mechanisms.
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.
iEvoBio Keynote: Frontiers of discovery with Encyclopedia of Life -- TRAITBANK Cyndy Parr
Talk presented at iEvoBio 2014 conference in Raleigh, North Carolina. Though there's a similar title and overlap with the talk I posted last week, there is new material here especially geared towards an informatics crowd savvy in the tools and technology.
Natural Language Provessing - Handling Narrarive Fields in Datasets for Class...Andrew Ferlitsch
Abstract: It is common for government and public datasets to include narrative fields, such as inspection reports, incident reporting, surveys, 911 calls, fire response, etc. In addition to categorical fields, such as datetime, location, demographics, these datasets tend to include a narrative description (e.g., what happened). It is typically in the narrative field that the most interesting data resides for the purpose of classifying. The problem, is that since the narrative is human interpreted and entered, each entry may be unique and if we use the whole entry as a single value, one will end up with an overfitted model that works only on the training data.
In this presentation, I will cover how natural language processing techniques are used to convert narrative fields into categorical data.
Level: Intermediate
Requirements: One should know basics of linear regression models. No prior programming knowledge is required.
pro-iBiosphere Towards Open Biodiversity Knowledge COOPEUS 2013millerjeremya
Invited presentation, meeting of COOPEUS - Connecting Research Infrastructures WP6, in conjunction with EGI (European Grid Infrastructure) Technical Forum, Madrid, Spain, September 2013
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
David Remsen lecture on Tuesday, Sept 15, 2009, for the Biodiversity Informatics Course, a Swedish Taxonomy Initiative (Svenska Artprojektet) course at the Swedish Natural History Museum, Stockholm, supported by the Swedish Species Service (ArtDatabanken) and the Swedish GBIF node.
Botanists and annotations printer friendlyWilliam Ulate
Findings from I Annotate 2016 concluded that the uptake of web annotation could be sufficiently moved forward by tackling three key issues: 1) interoperability, 2) domain use cases, and 3) user centered design. The Center for Biodiversity Informatics at the Missouri Botanical Garden has identified valuable use cases for developing in-depth user assessments of annotation needs in the specific domain of botanists. This presentation will share those use cases and talk about next steps in serving the annotation needs of botanists and their relevance for the larger scientific domain.
A presentation given by Don Kirkup at the KikForum
Abstract:
A brief overview of some Kew “key” projects, potential areas of overlap and possible exchange mechanisms.
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.
iEvoBio Keynote: Frontiers of discovery with Encyclopedia of Life -- TRAITBANK Cyndy Parr
Talk presented at iEvoBio 2014 conference in Raleigh, North Carolina. Though there's a similar title and overlap with the talk I posted last week, there is new material here especially geared towards an informatics crowd savvy in the tools and technology.
Natural Language Provessing - Handling Narrarive Fields in Datasets for Class...Andrew Ferlitsch
Abstract: It is common for government and public datasets to include narrative fields, such as inspection reports, incident reporting, surveys, 911 calls, fire response, etc. In addition to categorical fields, such as datetime, location, demographics, these datasets tend to include a narrative description (e.g., what happened). It is typically in the narrative field that the most interesting data resides for the purpose of classifying. The problem, is that since the narrative is human interpreted and entered, each entry may be unique and if we use the whole entry as a single value, one will end up with an overfitted model that works only on the training data.
In this presentation, I will cover how natural language processing techniques are used to convert narrative fields into categorical data.
Level: Intermediate
Requirements: One should know basics of linear regression models. No prior programming knowledge is required.
pro-iBiosphere Towards Open Biodiversity Knowledge COOPEUS 2013millerjeremya
Invited presentation, meeting of COOPEUS - Connecting Research Infrastructures WP6, in conjunction with EGI (European Grid Infrastructure) Technical Forum, Madrid, Spain, September 2013
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Transcript: Selling digital books in 2024: Insights from industry leaders - T...BookNet Canada
The publishing industry has been selling digital audiobooks and ebooks for over a decade and has found its groove. What’s changed? What has stayed the same? Where do we go from here? Join a group of leading sales peers from across the industry for a conversation about the lessons learned since the popularization of digital books, best practices, digital book supply chain management, and more.
Link to video recording: https://bnctechforum.ca/sessions/selling-digital-books-in-2024-insights-from-industry-leaders/
Presented by BookNet Canada on May 28, 2024, with support from the Department of Canadian Heritage.
Welcome to the first live UiPath Community Day Dubai! Join us for this unique occasion to meet our local and global UiPath Community and leaders. You will get a full view of the MEA region's automation landscape and the AI Powered automation technology capabilities of UiPath. Also, hosted by our local partners Marc Ellis, you will enjoy a half-day packed with industry insights and automation peers networking.
📕 Curious on our agenda? Wait no more!
10:00 Welcome note - UiPath Community in Dubai
Lovely Sinha, UiPath Community Chapter Leader, UiPath MVPx3, Hyper-automation Consultant, First Abu Dhabi Bank
10:20 A UiPath cross-region MEA overview
Ashraf El Zarka, VP and Managing Director MEA, UiPath
10:35: Customer Success Journey
Deepthi Deepak, Head of Intelligent Automation CoE, First Abu Dhabi Bank
11:15 The UiPath approach to GenAI with our three principles: improve accuracy, supercharge productivity, and automate more
Boris Krumrey, Global VP, Automation Innovation, UiPath
12:15 To discover how Marc Ellis leverages tech-driven solutions in recruitment and managed services.
Brendan Lingam, Director of Sales and Business Development, Marc Ellis
Climate Impact of Software Testing at Nordic Testing DaysKari Kakkonen
My slides at Nordic Testing Days 6.6.2024
Climate impact / sustainability of software testing discussed on the talk. ICT and testing must carry their part of global responsibility to help with the climat warming. We can minimize the carbon footprint but we can also have a carbon handprint, a positive impact on the climate. Quality characteristics can be added with sustainability, and then measured continuously. Test environments can be used less, and in smaller scale and on demand. Test techniques can be used in optimizing or minimizing number of tests. Test automation can be used to speed up testing.
Encryption in Microsoft 365 - ExpertsLive Netherlands 2024Albert Hoitingh
In this session I delve into the encryption technology used in Microsoft 365 and Microsoft Purview. Including the concepts of Customer Key and Double Key Encryption.
The Metaverse and AI: how can decision-makers harness the Metaverse for their...Jen Stirrup
The Metaverse is popularized in science fiction, and now it is becoming closer to being a part of our daily lives through the use of social media and shopping companies. How can businesses survive in a world where Artificial Intelligence is becoming the present as well as the future of technology, and how does the Metaverse fit into business strategy when futurist ideas are developing into reality at accelerated rates? How do we do this when our data isn't up to scratch? How can we move towards success with our data so we are set up for the Metaverse when it arrives?
How can you help your company evolve, adapt, and succeed using Artificial Intelligence and the Metaverse to stay ahead of the competition? What are the potential issues, complications, and benefits that these technologies could bring to us and our organizations? In this session, Jen Stirrup will explain how to start thinking about these technologies as an organisation.
Epistemic Interaction - tuning interfaces to provide information for AI supportAlan Dix
Paper presented at SYNERGY workshop at AVI 2024, Genoa, Italy. 3rd June 2024
https://alandix.com/academic/papers/synergy2024-epistemic/
As machine learning integrates deeper into human-computer interactions, the concept of epistemic interaction emerges, aiming to refine these interactions to enhance system adaptability. This approach encourages minor, intentional adjustments in user behaviour to enrich the data available for system learning. This paper introduces epistemic interaction within the context of human-system communication, illustrating how deliberate interaction design can improve system understanding and adaptation. Through concrete examples, we demonstrate the potential of epistemic interaction to significantly advance human-computer interaction by leveraging intuitive human communication strategies to inform system design and functionality, offering a novel pathway for enriching user-system engagements.
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
SAP Sapphire 2024 - ASUG301 building better apps with SAP Fiori.pdfPeter Spielvogel
Building better applications for business users with SAP Fiori.
• What is SAP Fiori and why it matters to you
• How a better user experience drives measurable business benefits
• How to get started with SAP Fiori today
• How SAP Fiori elements accelerates application development
• How SAP Build Code includes SAP Fiori tools and other generative artificial intelligence capabilities
• How SAP Fiori paves the way for using AI in SAP apps
UiPath Test Automation using UiPath Test Suite series, part 4DianaGray10
Welcome to UiPath Test Automation using UiPath Test Suite series part 4. In this session, we will cover Test Manager overview along with SAP heatmap.
The UiPath Test Manager overview with SAP heatmap webinar offers a concise yet comprehensive exploration of the role of a Test Manager within SAP environments, coupled with the utilization of heatmaps for effective testing strategies.
Participants will gain insights into the responsibilities, challenges, and best practices associated with test management in SAP projects. Additionally, the webinar delves into the significance of heatmaps as a visual aid for identifying testing priorities, areas of risk, and resource allocation within SAP landscapes. Through this session, attendees can expect to enhance their understanding of test management principles while learning practical approaches to optimize testing processes in SAP environments using heatmap visualization techniques
What will you get from this session?
1. Insights into SAP testing best practices
2. Heatmap utilization for testing
3. Optimization of testing processes
4. Demo
Topics covered:
Execution from the test manager
Orchestrator execution result
Defect reporting
SAP heatmap example with demo
Speaker:
Deepak Rai, Automation Practice Lead, Boundaryless Group and UiPath MVP
GraphRAG is All You need? LLM & Knowledge GraphGuy Korland
Guy Korland, CEO and Co-founder of FalkorDB, will review two articles on the integration of language models with knowledge graphs.
1. Unifying Large Language Models and Knowledge Graphs: A Roadmap.
https://arxiv.org/abs/2306.08302
2. Microsoft Research's GraphRAG paper and a review paper on various uses of knowledge graphs:
https://www.microsoft.com/en-us/research/blog/graphrag-unlocking-llm-discovery-on-narrative-private-data/
Elizabeth Buie - Older adults: Are we really designing for our future selves?
IRMNG presentation March 2012
1. www.obis.org.au/irmng
IRMNG – the Interim Register of
Marine and Nonmarine Genera:
rationale and current status
Tony Rees – CSIRO Marine and Atmospheric Research, Australia
for: GN-CoL names and taxonomy sharing workshop, Hawaii, March 2012
2. The Dream…
Imagine a system that would…
• Automatically classify “any” genus & species name to kingdom /
phylum / class / order / family (as far down as possible) – “what is
this critter” – plus hierarchical relations e.g. parents / children /
siblings
• Return whether a current (valid) or non-current name e.g.
synonym
• Check spelling for correctness, also authority details, plus supply
original publication ref. as available
• Return associated attributes such as extant / fossil status, habitat
information, geographic / geologic range, more…
• Work seamlessly, with a single point of entry, across all groups
and geologic epochs including present day
• Be as up-to-date as possible (latest content), and authoritative
(maintained by relevant experts)
Tony Rees: IRMNG March 2012
3. Realising the Dream…
• For extant taxa: role of Cat. of Life, however ~30% of species still to
go; for fossil taxa: PaleoDB (unknown proportion missing, maybe
50%?)
• In mean time, could make progress by assembling global genera list,
and infilling with species names as available
genera
species
• IRMNG is an attempt along these lines… a work in progress, with
modest resourcing, but available for use now.
Tony Rees: IRMNG March 2012
4. IRMNG data sources
• Animal genera + auth’s from Nomenclator Zoologicus and
elsewhere, tax. placements and synonymies from multiple sources
including CoL, individual taxon treatments and printed works
• Botanical genera and auth’s from Index Nominum Genericorum
(ING) supplemented with other sources, tax. placements and
synonymies from multiple sources including GRIN (APGIII in the
main), Index Fungorum, AlgaeBase, CyanoDB, more
• Prokaryote genera, auth’s and tax. placements from LSPN
(Euzéby list), previous/non-valid names from multiple sources
• Virus genera and tax. placements from ICTV db (multiple versions
– very different through time)
• Species lists (all groups) from CoL 2006, Aphia/WoRMS 2006,
AFD, NZ Organisms Register + more.
Tony Rees: IRMNG March 2012
5. IRMNG content as at March 2012 (cf. e.g. Cat. of Life):
Cat. of Life (2011 version): IRMNG:
• 8k families • 19k families
• 178k genera • 454k genera
• 2.25m species names • 1.46m species names
(including synonyms) (including synonyms)
• Not all IRMNG genera yet linked to relevant families, but ~370k are
(remainder linked to higher taxon i.e. phylum, class or order)
• Extant/fossil, marine/nonmarine flags held for majority of names
• Nomenclatural status known for most names, tax. status i.e. valid
name/synonym for only a subset at this time (varies by group)
• Authority known for >97% of genera, publication details for “animal”
subset (from Nomenclator Zoologicus in the main)
• Fuzzy matching (TAXAMATCH) deployed over all web-based queries for
correction of potential errors in input names to be matched.
Tony Rees: IRMNG March 2012
6. IRMNG in practice – example genus = “Lawsonia”
• Same name is currently a valid genus in 3 Codes i.e. plants,
animals and bacteria (no barriers to this)
Tony Rees: IRMNG March 2012
7. Required base information is scattered in multiple
systems / printed works at this time
plant animal
bacterium
(etc.)
Tony Rees: IRMNG March 2012
8. Required base information is scattered in multiple
systems / printed works at this time
plant animal
bacterium
(etc.)
Tony Rees: IRMNG March 2012
10. IRMNG query as at March 2012
synonym
extant, habitat
of (as
flags
known)
children parents
Tony Rees: IRMNG March 2012
11. Note: IRMNG fields displayed on the web are only a
subset of full information held for any name, e.g.:
Tony Rees: IRMNG March 2012
12. IRMNG core fields
• IRMNG ID, Rank
• Extant/fossil, marine/nonmarine
• Scientific name (for species: epithet + flags + “according to” (could be “as
parent ID) per parent”)
• Authority • Date entered, last modified,
• Publication (as “microcitation” – subset deprecated (where required)
with link to refs. module)
• Source(s) for above
• Orthography verified against (under consideration…)
(authoritative source) • Intermediate ranks e.g. subfamily,
• Parent ID (+ “according to…”) – subgenus, also infraspecies (not
currently held)
Linnaean ranks only at this time
• Type genus / species indicator
• Nomenclatural status (+ relation with
other names as needed) + “according • Freshwater / terrestrial flags vs.
to…” present “nonmarine”
• Taxonomic status (same) • Geo flags (country codes etc.)
• Nomenclatural Code • Palaeo range (periods/epochs)
• Taxonomic or nomenclatural remarks • Vernacular names as available
Tony Rees: IRMNG March 2012
13. IRMNG is not just a “passive” aggregator…
Editorial / curatorial decisions / actions required to:
• Correct obvious data errors
• Assemble “complete” records from multiple sources (where one source
data deficient)
• Normalise authority data (in particular) to a “house style”
• Digitise or transcribe print material into electronic form where not
otherwise available
• Decide between conflicting content in data sources e.g. for authority
orthography/year, taxonomic placement, valid/synonym status and
more
• Cross-link names e.g. synonyms -> current names, basionyms ->
replacement names, misspelled names to their correctly spelled
counterparts, etc. etc.
• Reconcile variant higher taxonomies as supplied to a single hierarchy
• Add nomenclatural or taxonomic remarks as required.
Tony Rees: IRMNG March 2012
14. Relevance to present meeting?
• Demonstrates utility of a single entry point to a system permitting
query on “any name” – i.e., a [comprehensive] Taxonomic Name
Resolution Service (TNRS) covering all life
• Envisage something like OBIS or GBIF, but for taxonomy – the
aggregator / central query point is not a content author, but
provides integration and value-added services
• IRMNG – based on static snapshot/s of multiple data sources; cf. a
“super catalogue” should be based on live feeds from relevant
authoritative sources, continuously updated as available (?+ some
static data not available as feeds)
• Maybe the static data lives outside the “data aggregation/query”
point, becomes a separately managed source
• How does / should GNA facilitate this?
• Will the need for an IRMNG (or IRMNG equivalent) disappear or grow
in the above scenario? (for example could this role be taken by
another player or group of players…)
Tony Rees: IRMNG March 2012
17. Size of the task: IRMNG 2011 content cf. Cat. of Life 2011
IRMNG –
Cat. of Life - % with IRMNG – % with
Oct 2011 -
2011 edition auth's Oct 2011 - auth's
fossil only
extant + fossil
Kingdoms 8 7 (0)
Phyla 111 153 (12)
Classes 288 509 (64)
Orders 1,233 2,645 (715)
Families 8,071 0% 19,639 22.1% (6,542)
Subfamilies - - - - -
Genera 178,515 0% 452,848 97.1% (90,278)
Subgenera - - - - -
Species (valid) 1,347,224 ~100% 1,020,519 ~100% (16,792)
Species (synonyms) 895,441 ~100% 440,738 ~100% (100)
• CoL has 70% of valid extant species names (of est. 1.9m total), thus maybe
also 70% of valid extant genera (with subset of genus-level synonyms)
• IRMNG has further ~180k extant genus names and ~90k fossil names at this
time (including syns) – est. ~25k still missing
Tony Rees: IRMNG March 2012
18. Taxonomic names:
what the customer is currently offered (+ more…)
publication discovery official taxon-specific integrated DB’s “all names”
registers DB’s
ICTV Viruses
ICTV Viruses ITIS
ITIS
CyanoDB
CyanoDB
DB
DB NCBI
NCBI
Taxonomy
Taxonomy
Index
Index WoRMS
LPSN
LPSN WoRMS
Fungorum
Fungorum etc.
(Prokaryote
(Prokaryote etc.
MycoBank
MycoBank
names)
names)
AlgaeBase
AlgaeBase
Plant GSD’s
Plant GSD’s
ICBN Decisions
ICBN Decisions
New Catalogue ChecklistBank
ChecklistBank
New Catalogue
names of Life
of Life
names The Plant
The Plant GNI
GNI
publishe
publishe List, IPNI,
List, IPNI,
d (in Journal
Journal TROPICOS,
TROPICOS,
d (in TOC’s, RSS
GNUB
GNUB
TOC’s, RSS ING
ING
primary
primary feeds,
Botany
feeds,
literature)
literature) text mining
text mining
Zoology PaleoDB
PaleoDB
Animal GSD’s
Animal GSD’s
Abstracting
Abstracting Nomenclator
Nomenclator
services
services Zoologicus
Zoologicus
Subject
Subject ION (Index of Organism
ION (Index of Organism
bibliographies
bibliographies Names)
Names)
Zoological
Zoological
Record
Record
Reviews,
Reviews,
secondary
secondary
literature
literature ICZN Decisions
ICZN Decisions other compilations e.g. regional lists,
other compilations e.g. regional lists,
Wikispecies, Wikipedia, more…
Wikispecies, Wikipedia, more…
Tony Rees: IRMNG March 2012
19. Two approaches - GNI and Cat. of Life
NameBank / GNI
• 20m+ names – all ranks, no hierarchy
• mix of “clean” and “dirty” names
• many duplicates
• extant + fossil, most sectors with at
least some names
Tony Rees: IRMNG March 2012
20. GNI search result
– “Lawsonia” (all
ranks returned)
(Mar 2012)
…candidate genus
names highlighted in
red (although could
be other ranks too)
… need access to
original taxonomic /
nomenclatural
resources to sort out
/ see if anything
missed
Tony Rees: IRMNG March 2012
21. Two approaches - GNI and Cat. of Life
NameBank / GNI Cat. of Life
• 20m+ names – all ranks, no hierarchy • <2m names – Linnaean ranks, in
• mix of “clean” and “dirty” names hierarchy
• many duplicates • all “clean”/ vetted names / relationships
• extant + fossil, most sectors with at • extant only, sectors either complete or
least some names absent
Tony Rees: IRMNG March 2012
22. Cat. of Life search result – “Lawsonia” (Mar 2012)
Tony Rees: IRMNG March 2012
Editor's Notes
Talk prepared for GN-CoL names and taxonomy sharing workshop, Hawaii, March 2012
Hierarchical approach is in contrast to e.g. NameBank, GNI -- Names are not accepted without a parent (even if this is “Animalia (awaiting allocation)” in a few cases) -- Placeholder groups e.g. “Mollusca (awaiting allocation)” are erected at Order and Family level to allow addition of genus names not yet placed to family (for homonymy in particular, also because other details e.g. publication info, extant/fossil status may already be available)
Homonomy is a big problem – up to 15% of all genus names are homonyms/isonyms either within or across Codes (including some misspellings which collide with other “good” names) (*Isonyms: multiple publication instances of same name as new, based on same type or concept) Many genus names are valid across more than 1 Code (e.g. used in botany and zoology for different taxa), a handful of genus names are concurrently valid across three Codes as per this example: Lawsonia Worst example currently “ Wagneria ” – 14 instances in IRMNG, 2 valid, the rest are synonyms Cannot disentangle without a master list of genus names
IRMNG is a central aggregation point for all such information as readily available from multiple sources, both electronic and print, although the compilation of names / associated nomenclatural info. outstrips the full taxonomic information at this time. Incorporation of “TAXAMATCH” fuzzy matching also permits return of other names differering only slightly from the entered name, in case one of these is in fact the intended target (also permits a degree of data cleaning and reconciliation/dediplication).
The IRMNG web query interface also includes information on extant & habitat flags, synonymy (as held), sources of the data, information about parent and child taxa, and so on.
Currently IRMNG is structured around Linnaean ranks only i.e. kingdom / phylum / class / order / family / genus / species (no infraspecies are held at this time), may be extended in future. Deprecated records (e.g. duplicates detected during subsequent QA) are left on system with their IRMNG ID intact, in case referred to elsewhere, or require re-activation. Records are flagged as either current (valid) or non-current at the indicated Rank; not yet clear how to handle taxa considered non-current at designated rank, but current at another.
- Cat. of Life misses many genus-level synonyms / misspellings recognised elsewhere (including its source DB’s) - Genera not treated as distinct data objects in CoL (unless changed recently) i.e. no authorities, publication info, nomenclatural or taxonomic remarks - Coverage of fossils is considered valuable feature of IRMNG (though no systematic attempt at species ingestion as yet)
Many single sources of taxon names - often not integrated - newly published names discoverable only with some effort (although “official” registries/lists for prokaryotes, viruses) - considerable latency as names flow from published (at left) to aggregators (at right)
GNI / NameBank approach: collect as many namestrings as possible, any rank - User needs to explore source/s to determine taxonomic hierarchy and other information (if held) - Or: maybe one day, will be offered in a coherent hierarchy/list (but not any time soon)
GNI produces a (partial?) list of known orthographies (mix of all ranks) Species and below can generally be eliminated by pattern matching, leaving uninomial names i.e. genera and above (plus authorities), in multiple potential variants Note this suggests that there may be 3 genuinely distinct “Lawsonia” instances known to GNI at this time – although sometimes the situation is more opaque / potentially misleading (similar auth’s but different taxa, different auth’s but the same taxon, or no auth held).
Cat. of Life approach: stitch together authoritative lists for global sectors complete to species - Some sectors (30% of all extant taxa) not yet sourced, may have no lists - Information above species level is sketchy (e.g. no genus, family auth’s or other information) - Fossil taxa are omitted at this time
Catalogue of Life largely indexes species and infraspecies, genera are presented last with no authorities (although position in hierarchy can be accessed from this page) Note, only 2 “Lawsonia”s held, [at least] another one more somewhere not known to CoL (either missing, or out of scope i.e. fossil)