Virtual BiodiversityViBRANT-infrastructureSEVENTH FRAMEWORK

PROGRAMME

The ciliatespecies names list project

Dave Roberts

Genotype Phenotype Biotic Interactions Environment Human Effects

Niche & Pop. Ecology

Biodiversity Loss

Phylogenetic Trees

Taxonomy

Geographic Dsitributions

Range Maps Forecasts of Change

Conservation & management

Products

Data

GenBank MorphBank Interactions Geospatial Census

IUCN

TreeBase

IPNI, Zoobank

Pop. data

GBIF

Extent of Occurrence AquaMaps

AquaMaps

Systems

Biodiversity informatics landscape

Key problemsLandscape is complex, fragmented & hard to navigateMany audiences (policy makers, scientists, amateurs, citizen scientists)Many scales (global solutions to local problems) Figure adapted from Peterson et al (2010)

Systematics and Biodiversity, 8: 159-168

Identifiers

A key to find something in a database.

10.4467/16890027AP.14.016.1597

JUNG et al, 2014Characteristics mean M SD SE CV Min Max nBody, length 217 220 17.5 3.9 8.1 185 250 20Body, width 45.3 45 5.5 1.2 12.1 36.3 55 20Body, length:width ratio 4.8 4.8 0.6 0.1 11.8 3.5 5.6 20Anterior body end to end of adoral 65 65 4.4 1 6.7 55 72.5 20 zone, distanceBody length:distance from anterior 0.3 0.3 0.03 0.01 9.1 0.22 0.35 20 body end to end of adoral zone, ratioAdoral membranelles, number 56.4 56 2.7 0.6 4.7 52 62 19Anterior macronuclear nodule, length 24.6 24.4 3.8 0.8 15.3 16 32 20Anterior macronuclear nodule, width 8.2 8 0.9 0.2 11.3 6.4 9.6 20Macronuclear nodules, number 2 2 0 0 0 2 2 19Micronuclei, length 5.8 5.6 0.9 0.2 15.3 4.8 8 20Micronuclei, width 4 4 0.7 0.2 16.9 3.2 4.8 20Micronuclei, number 2.6 2 0.7 0.2 26.9 2 4 19Frontal cirri, number 3 3 0 0 0 3 3 19Buccal cirri, number 1 1 0 0 0 1 1 19Cirri behind right frontal cirrus, number 1 1 0 0 0 1 1 19Postperistomial cirri, number 1 1 0 0 0 1 1 19Left frontoventral row, number of cirri 62.5 63 4.2 1 6.8 55 72 19Right frontoventral row, number of cirri 52 52 3.7 0.9 7.1 46 58 19Left marginal cirri, number 59.2 60 3.3 0.8 5.6 53 66 19Right marginal cirri, number 59.1 59 3.1 0.7 5.3 53 66 19Dorsal kineties, numberb 5 5 0 0 0 5 5 19Dorsal kinety 1, number of bristles 37 38 4.1 1 11.2 29 44 19Dorsal kinety 2, number of bristles 35.3 35 3.1 0.7 8.9 29 40 19Dorsal kinety 3, number of bristles 31.1 30 4.4 1 14.2 25 40 19Dorsal kinety 4, number of bristles 6.1 6 1.6 0.4 26.1 4 9 19Dorsal kinety 5, number of bristles 27.8 28 3.1 0.7 11 24 37 19Caudal cirri, total number 5.4 5 0.9 0.2 16.6 4 7 19Caudal cirri in dorsal kinety 1, number 3.9 4 0.8 0.2 19.8 3 5 19Caudal cirri in dorsal kinety 2, number 1.5 1 0.5 0.1 34.8 1 2 19

ORIGIN 1 gtttatttga taatcaaatt tacatggata accgtggtaa ttctagagct aatacatgct 61 gttaagcctg acttttagga agggctgtat ttattagata acaaaccaat attccccgtg 121 tctattgtga tgactcataa taactgatcg aatcgcatgg accttgtccg cgatacatca 181 ttcaagtttc tgccccatca gctttcgatg gtagtgtatt ggactaccat ggctttaacg 241 ggtaacggag gattagggtt cgattccgga gagggagcct gagaaacggc taccacatct 301 aaggaaggca gcaggcgcgt aaattaccca atcctgactc agggaggtag tgacaagaaa 361 taacggaccg aagcctatgt ttcgggattg caatgagtag aatttaaacc cctttacgag 421 gatcaattgg agggcaagtc tggtgccagc agccgcggta attccagctc caatagcata 481 tattaaagtt gttgcagtta aaaagctcgt agttggattt ctggaggggt gccgaagtcc 541 gctcgatagc gtgtgctgag gcgcccttcc atccttctgt taacgtttct tggtattcag 601 ttactggttt cgggctcaga tattttacct tgagaaaatt agagtgttcc aggcaggctt 661 gcgccggaat acattagcat ggaataatag aataggactt ttgtctcctt tgttggtttg 721 agggactgaa gtaatgatta atagggatag ttgggggcat tagtatttaa ttgtcagagg 781 tgaaattctc ggatttgtta aagactaact tatgcgaaag catttgccaa ggatgttttc 841 attaatcaag aacgaaagtt aggggatcaa agacgatcag ataccgtcct agtcttaacc 901 ataaactatg ccgactaggg atcggaggcg cgtactatcc gccttcggca ccttatgaga 961 aatcaaagtc tttgggttct ggggggagta tggtcgcaag gctgaaactt aaaggaattg 1021 acggaagggc accaccagga gtggagcttg cggctcaatt tgactcaaca cgggaaaact 1081 taccaggtcc agacatagtg aggattgaca gattgatagc tctttcttga ttctatgggt 1141 ggtggtgcat ggccgttctt agttggtgga gtgatttgtc tggttaattc cgttaacgaa 1201 cgagacctta gcctactaac tagtcgaacc aatcccgatt ggctacgact tcttagaggg 1261 actttgtggg ttaaacacaa ggaagtttga ggcaataaca ggtctgtgat gcccttagat 1321 gtcctgggcc gcacgcgtgc tacactgata catacagcga gtacttccca gctccgcgag 1381 gcagctggta atcagcaata tgtatcgtga tggggataga tctttggaat tatagatctt 1441 gaacgaggaa ttcctagtaa gcgcaagtca ttaccttgcg ctgattaagt ccctgccctt 1501 tgtacacacc gcccgtcgct cctaccgatt tcgagtgatc cggtgaacct tttggactgc 1561 g

KF471024

Identifiers

10.4467/16890027AP.14.016.1597

JUNG et al, 2014Characteristics mean M SD SE CV Min Max nBody, length 217 220 17.5 3.9 8.1 185 250 20Body, width 45.3 45 5.5 1.2 12.1 36.3 55 20Body, length:width ratio 4.8 4.8 0.6 0.1 11.8 3.5 5.6 20Anterior body end to end of adoral 65 65 4.4 1 6.7 55 72.5 20 zone, distanceBody length:distance from anterior 0.3 0.3 0.03 0.01 9.1 0.22 0.35 20 body end to end of adoral zone, ratioAdoral membranelles, number 56.4 56 2.7 0.6 4.7 52 62 19Anterior macronuclear nodule, length 24.6 24.4 3.8 0.8 15.3 16 32 20Anterior macronuclear nodule, width 8.2 8 0.9 0.2 11.3 6.4 9.6 20Macronuclear nodules, number 2 2 0 0 0 2 2 19Micronuclei, length 5.8 5.6 0.9 0.2 15.3 4.8 8 20Micronuclei, width 4 4 0.7 0.2 16.9 3.2 4.8 20Micronuclei, number 2.6 2 0.7 0.2 26.9 2 4 19Frontal cirri, number 3 3 0 0 0 3 3 19Buccal cirri, number 1 1 0 0 0 1 1 19Cirri behind right frontal cirrus, number 1 1 0 0 0 1 1 19Postperistomial cirri, number 1 1 0 0 0 1 1 19Left frontoventral row, number of cirri 62.5 63 4.2 1 6.8 55 72 19Right frontoventral row, number of cirri 52 52 3.7 0.9 7.1 46 58 19Left marginal cirri, number 59.2 60 3.3 0.8 5.6 53 66 19Right marginal cirri, number 59.1 59 3.1 0.7 5.3 53 66 19Dorsal kineties, numberb 5 5 0 0 0 5 5 19Dorsal kinety 1, number of bristles 37 38 4.1 1 11.2 29 44 19Dorsal kinety 2, number of bristles 35.3 35 3.1 0.7 8.9 29 40 19Dorsal kinety 3, number of bristles 31.1 30 4.4 1 14.2 25 40 19Dorsal kinety 4, number of bristles 6.1 6 1.6 0.4 26.1 4 9 19Dorsal kinety 5, number of bristles 27.8 28 3.1 0.7 11 24 37 19Caudal cirri, total number 5.4 5 0.9 0.2 16.6 4 7 19Caudal cirri in dorsal kinety 1, number 3.9 4 0.8 0.2 19.8 3 5 19Caudal cirri in dorsal kinety 2, number 1.5 1 0.5 0.1 34.8 1 2 19

ORIGIN 1 gtttatttga taatcaaatt tacatggata accgtggtaa ttctagagct aatacatgct 61 gttaagcctg acttttagga agggctgtat ttattagata acaaaccaat attccccgtg 121 tctattgtga tgactcataa taactgatcg aatcgcatgg accttgtccg cgatacatca 181 ttcaagtttc tgccccatca gctttcgatg gtagtgtatt ggactaccat ggctttaacg 241 ggtaacggag gattagggtt cgattccgga gagggagcct gagaaacggc taccacatct 301 aaggaaggca gcaggcgcgt aaattaccca atcctgactc agggaggtag tgacaagaaa 361 taacggaccg aagcctatgt ttcgggattg caatgagtag aatttaaacc cctttacgag 421 gatcaattgg agggcaagtc tggtgccagc agccgcggta attccagctc caatagcata 481 tattaaagtt gttgcagtta aaaagctcgt agttggattt ctggaggggt gccgaagtcc 541 gctcgatagc gtgtgctgag gcgcccttcc atccttctgt taacgtttct tggtattcag 601 ttactggttt cgggctcaga tattttacct tgagaaaatt agagtgttcc aggcaggctt 661 gcgccggaat acattagcat ggaataatag aataggactt ttgtctcctt tgttggtttg 721 agggactgaa gtaatgatta atagggatag ttgggggcat tagtatttaa ttgtcagagg 781 tgaaattctc ggatttgtta aagactaact tatgcgaaag catttgccaa ggatgttttc 841 attaatcaag aacgaaagtt aggggatcaa agacgatcag ataccgtcct agtcttaacc 901 ataaactatg ccgactaggg atcggaggcg cgtactatcc gccttcggca ccttatgaga 961 aatcaaagtc tttgggttct ggggggagta tggtcgcaag gctgaaactt aaaggaattg 1021 acggaagggc accaccagga gtggagcttg cggctcaatt tgactcaaca cgggaaaact 1081 taccaggtcc agacatagtg aggattgaca gattgatagc tctttcttga ttctatgggt 1141 ggtggtgcat ggccgttctt agttggtgga gtgatttgtc tggttaattc cgttaacgaa 1201 cgagacctta gcctactaac tagtcgaacc aatcccgatt ggctacgact tcttagaggg 1261 actttgtggg ttaaacacaa ggaagtttga ggcaataaca ggtctgtgat gcccttagat 1321 gtcctgggcc gcacgcgtgc tacactgata catacagcga gtacttccca gctccgcgag 1381 gcagctggta atcagcaata tgtatcgtga tggggataga tctttggaat tatagatctt 1441 gaacgaggaa ttcctagtaa gcgcaagtca ttaccttgcg ctgattaagt ccctgccctt 1501 tgtacacacc gcccgtcgct cctaccgatt tcgagtgatc cggtgaacct tttggactgc 1561 g

Pseudouroleptus jejuensis

KF471024

Current taxonomic data production

Figure from Costello M.J et al, 2013. doi: 10.1126/science.1230318

Typically generated by small communities for “local” research projects

Publications based on countless specimens, images, maps, keys and datasets

Scratchpads

Virtual Research Environments

Making taxonomy digital, open & linked

http://scratchpads.eu

Taxonomy & LiteratureLice, mosquitos, freeloader flies, ...

(rapid upload and management of names, synonyms & bibliographic data)

Freeloader Flies, fungus gnats, ...(publication of Scratchpad data in the ZooKeys journal and export to Encyclopedia of Life)

Taxon descriptions & Publications

European Mosquito Bulletin, Phasmid Studies, ...(submission, review & dissemination of articles)

eJournals

Termites, bryozoa, ... (character matrices exporting to SDD and Nexus format, phylogenies, specimen records & maps)

Characters, Phylogeny & Specimens

Image GalleriesDragon trees, nanno fossils, cockroaches, fungi, polychaetes, ...

(rapid upload, annotation & display of images)

ICZN, GBIF, Sampled Red List Index for Plants, Global Plants Initiative ...(space for data collection, services, discussion & organisation)

Societies, Organisations & Projects

600

SitesUsers

2007 2008 2009 2010 2011 2012 2013

Active UsersSites

Users

ViBRANT Sp 2

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Scratchpad Overview

What are Scratchpads?

facilitate

through

that allow

and

development of online research communities

standardized environment of entering and curating data

sharing and interlinking

dissemination of research products

Are Scratchpads sustainable?

512 Scratchpads Communities

by 6,500 active registered users

covering 73,444 taxa

in 515,189 pages.

In total more than

1,300,000 visitors

65,000 unique visitors/month

Per month unique visitors to Scratchpads sites

Estimated running cost is in 100s of Euros/year.That buys and maintains hardware.It does not buy development.

The main features

Classification-term oriented system

Biological classifications

Non-biological classifications

Taxonomies Hierarchical controlled vocabularies

The main features

Dynamic Biological Classifications

This classification was created from Denis Lynn’s 2008 book, prepared as a text file and imported.

http://ciliateguide.myspecies.info/taxonomy/term/45711

Alternative taxonomies can be created.

The taxonomy can be edited directly or off-line by preparing batch files for import (in ITIS format).

Taxon Pages

An overview of the data related to a taxon

Created dynamically from content tagged with the taxon name

Credits the taxonomist(s) asserting that the data are correct for the taxon shown

Bibliography management

An inbuilt Bibliography managerFaceted browsingTaxon tagging and free keywordsImport from and export to all major formats - BibTex RTF XML RIS

Specimen/Observation data

Annotated full specimen/observation records

Linked to images and geo-referenced

Linked to GenBank accession numbers

Create phylogenetic trees

Based on Newick/NeXML

Different views

Character matrices – Key construction

Quantitative or qualitative characters

Auto generation of keys

Taxon based matrices [Specimens based character matrices]

Media handling

Bulk upload Metadata (EXIF & Aubudon core) Media galleries

Generation of custom pages

Tagged or not

External RSS

Twitter feeds

Media files

Enhanced communication tools

Working groups

Forums

Blog entries

Webforms

Newsletters

RSS syndication

Inbuilt comments

External services Integration

data mobilisation

more on the way…

Help & Support

In-site Support

Wiki

Training Courses (12 in 2012)

Ambassadors Programme

Embedded Issues Queue

Sandbox Site

http://help.scratchpads.eu

19.06.2014 - Birmingham, UK Scratchpads training course06.06.2014 - Online training course 4th online Scratchpads basic training course17.10.2013 - Kristineberg, Sweden Scratchpads training course in Kristineberg, Sweden11.10.2013 - Online training course 3rd online Scratchpads basic training course03.10.2013 - Thessaloniki, Greece Basic Training Course during the 13th Hellenic Botanical Society Conference17.09.2013 - Yaoundé, Cameroon 2 Scratchpads training course in Yaoundé, Cameroon on 17/09/201316.09.2013 - Yaoundé, Cameroon 1 Scratchpads training course in Yaoundé, Cameroon on 16/09/201303.09.2013 - Rome, Italy Training course during the Biodiversity Informatics Horizons 2013 Conference06.08.2013 - Natural History Museum, London Scratchpads basic training course26.07.2013 - Online training course Online Scratchpads basic training course

Recent Training Courses

User Rôles

Authenticated (unblocked) user: Able to access non-public content, create and edit own forum posts.

Contributor: Able to create content and edit own content.

Editor: Able to create and edit own content, and also edit other people's content.

Maintainer: Like editor, but also has administration privileges, including control of access of the other rôles to various functions on the site.

Summary

Denis Lynn’s 2008 revision contains 1,603 genera of ciliates.

12,073 species names were extracted from the Global Names project to populate that list.

With higher taxonomic ranks that gives 14,080 taxonomic names.

Many of those names are invalid (synonyms etc.) and many are missing, including many well-known taxa.

It is intended to be a starting point for revision of taxa and will feed back to Global Names and GBIF, i.e. after the application of taxonomic judgement.

The community can decide how to control access and updating of the content. For example, students (authenticated users) could submit their work to a supervisor (contributors) who, when approved, can batch upload the material.

Next Steps

It should be easy for people to contribute.

People should get credit for curating pages (their names should appear) and they lend their authority to the treatment shown. [NB use of an author identifier here would facilitate generating statistical evidence of impact]

There needs to be some organisation to manage data quality, possibly by using tiered rôles (c.f. Wikipedia).

The International Research Coordination Network for Biodiversity of Ciliates is well placed to move this forward.