Revolutionizing the Research on Ants through new Methods and Technologies: the last 20 Years

Donat Agosti Plazi

[email protected] / #smir2015

XXII Simpósio de Mirmecologia, Ilhéus, BA, BrazilOctober 22, 2015

Revolutionizing the Research on Ants through new Methods and Technologies: the last 20 Years

Revolution: the Begin 1996

1996

Compare biodiversity over space, time, collector, habitat

What organism is it?

What do I know about it?

Where does it live?

1995/2000

Revolution: the Begin 1996

Citations:Better than most scientific papers

The origin

Revolution: the begin 1996 and its outcome

The Role of Revolution: Citations of the ALL-Book (Google Scholar)Book 458

Chapter 1: Alonso, L.E., and D. Agosti. Biodiversity Studies, Monitoring, and Ants: An Overview 162Chapter 2: Kaspari, M. A Primer in Ant Ecology (pdf) 85

Chapter 3: Andersen, A.N. A Global Ecology of Rainforest Ants: Functional Groups in Relation to Environmental Stress and Disturbance (pdf) 172

Chapter 4: Schultz, T.R., and T.P. McGlynn. The Interaction of Ants with Other Organisms (pdf) 94Chapter 5: Brown, W.L.Jr. Diversity of Ants (pdf) 220Chapter 6: Alonso, L.E. Ants as Indicators of Diversity (pdf) 164

Chapter 7: Kaspari, M., J.D. Majer. Using Ants to Monitor Environmental Change (pdf) 116

Chapter 8: Ward, P.S. Broad-scale Patterns of Diversity in Leaf litter Ant Communities (pdf) 112

Chapter 9: Bestelmeyer, B.T., D. Agosti, L.E. Alonso, C.R.F. Brandão, W.L. Brown Jr., J.H.C. Delabie, and R. Silvestre. Field Techniques for the Study of Ground-Dwelling Ants: An Overview, Description and Evaluation (pdf) 388Chapter 10: Delabie, J.H.C., B.L. Fisher, J.D. Majer, and I.W. Wright. Sampling Effort and Choise of Methods (pdf) 117

Chapter 11: Lattke, J.E. Specimen Processing: Building and Curating an Ant Collection (pdf) 36

Chapter 12: Brandão, C.R.F. Major Regional and Type Collections of Ants (Formicidae) of the World and Sources for the Identification of Ant Species (pdf) 41Chapter 13: Longino, J.R. What to Do with the Data (pdf) 89

Chapter 14: Agosti, D., and L.E. Alonso. The ALL Protocol: A Standard Protocol for the Collection of Ground-Dwelling Ants (pdf); versión en español (pdf) 179

Chapter 15: Fisher, B.L., A.K.F. Malsch, R. Gadagkar, J.H.C. Delabie, H.L. Vasconcelos, and J.D. Majer. Applying the ALL Protocol: Selected Case Studies (pdf); extended version (pdf) 21Total 2454

A revolution

Open Access to the papers that cite the Antbook: ca 80%

Questions

We don’t know about the usage of the standards protocol

We don’t have a repository of all the samples – though we begun

We don’t cover all the starta

We don’t cover regions outside the tropics

New version of the ALL book?

Revolution: the outcome

Revolution?

Marizete Santos

Revolution: the outcome

The Role of Revolution: The origin

RIO Earth Summit, 1992(Biodiversity Crisis)

The years before the Revolution: make the case for the bodiversity crisis

The Role of Published Biodiversity Literature Environmenta Policy

Published observation records

EU BON Policy Brief

The Role of Revolution: The origin

Science Citation Reproducibility

Global Infrastructure Stable archives Standards

revolution

Revolutions: Satellite Images and geographic data

antnet

Revolutions: Digital Imaging / Specimen digitization

The source

Antbaseantweb

Revolutions: DNA / Genomics

Online catalogue

Revolution: Names: Catalogue of the Ants of the World

Online catalogue2002

Antbase

Maintained since 2002, currently including 13,269 valid extant species, 682 fossil ant species, out of total of 173,257 valid speciesBasis for ITIS, Antweb, ZoobankAll TNUs linked to the pdf pf the cited pageBasis for Plazi treatmentsLinked with Biodiversity Literature Repository (as of Jan. 2016 all publications)

Alternative catalogue:currently 13,165 valid species, 726 fossils, including collaboration with antbase/HOL


Antbase/HOL Antcat

Coverage Taxonomy Taxonomy, faunistics, morphology etc

Completness Yes YesCombinations Yes ?Community editing Open Open

Linking Taxon Article

Repository BLR Amazon Cloud

Citation DOI n/aSource Zoobank, ITIS, COL n/a


HOL / antbase: few Statistics

Generic Specific

Average valid lifespan of a synonym 43.4 years 53.2 years

Median valid lifespan of a synonym 45 years 52 years

Number of synonymous taxa 504 4098

Maximum valid lifespan of a synonym 154 years 165 years

Minimum valid lifespan of a synonym 2 years 2 years

1758 1773 1788 1803 1818 1833 1848 1863 1878 1893 1908 1923 1938 1953 1968 1983 1998 20130

10

20

30

40

50

60

70

80

90

100

Number of pubs10-yr moving avg


1758177317881803181818331848186318781893190819231938195319681983199820130

2000

4000

6000

8000

10000

12000

14000

16000

Number of annos10-yr moving avg


1 5 9 13 17 21 25 29 34 38 43 48 54 58 65 72 87 95106

119135

180219

386843

0

20

40

60

80

100

120

140

Species per genus

Species per genus


Access to Literature

Digital Library: 2004

A Revolution

Before antbase.org, Harvard‘s Museum of Comparative Zoology could claim to be the only location with a complete set of ant systematics publications from 1758 - present.

Through antbase.org‘s digital library, access to this body of literature is worldwide, and it is actively used (>10,000 visits in one month only).

2004

Users of antbase pdfs

Many other research projects

Alternative literature repositories

Revolution: Citations

Create a collection of all the articles citing the all book?Make it accessible for TDM?Create collections around each forthcoming publication

Revolution: Citations

Revolutions: citation

2015

Zookeys doi

DOI

Revolutions: citation and archive

Biodiversity Literature Repository

Large stable archive: CERNArchive part of a larger consortiumProvider of DataCite DOI, a standard for citing literature and dataEstablished copyright policy

http://biolitrepo.org


Biodiversity Literature Repository

Large stable archive: CERNArchive part of a larger consortiumProvider of DataCite DOI, a standard for citing literature and dataEstablished copyright policy

http://biolitrepo.org

January 1, 2016: All ant taxonomy literature will be availableAll ant publications in Zookeys, Journal of Hymenoptera Research and

Biodiversity Data Journal will make use of BLR DOI

You can contribute


You can contribute

Read the upload policy

For batch upload, contact [email protected]

Build your thematic corpus, e.g. ants of the Cerrado; articles citing the ALL book

New interface from January 1, 2016


You can search

http://refindit.org

Treatment: a well defined part of an article that defines the particular usage of a scientific name by an authority at a given time (a page(s) in a publication).

Revolution: Treatment

The special case taxonomic literature: The citated elements are treatments, not articles

(Catapano, 2012)

Revolutions: Treatment

Treatment citation Treatment

From article to treatmentOnline catalogueOpen accessOnline library«Linked data»2004


Treatment Graph for the Malagasy Ants Aphaenogaster

Fisher et al., in prep.

Treatment Graph for the Malagasy Ants Aphaenogaster

Original description

Re-description cites

cite

s /sy

nony

mize

s

Re-description

Re-de.Re-description

cites

Revolution: Treatment and TreatmentBank


Revolution: Treatment; Text and Datamining

Treatment Graph for the Ant Azteca alfari

https://github.com/plazi/TreatmentOntologies

https://github.com/plazi/TreatmentOntologies

Pseudomyrmex ants and Vachellia ant-acaciasare a classic example of mutualism in biology.

allenii

melanoceras

ruddiae

chiapensis

collinsii

cookii

cornigera

globulifera

hindsii

janzenii

mayana

sphaerocephala

boopis

flavicornis

hesperius

ita

janzenikuenckeli

mixtecus

nigrocinctus

nigropilosus

opaciceps

particeps

peperi

reconditus

satanicus

simulansspinicola

subtilissimus

veneficus

ferrugineus

gentlei

gracilis

Transbiotic link networkAssociated species linked throughreferences in taxonomic treatments

Acacia-ant species: Pseudomyrmex gracili

Treatment: redescription

Associated ant-acacia: Acacia gentlei

Ants Plants

Photocredits: Alex Wild

Treatment

Treatments linked through citations

Treatments: traits and interactions

Treatment Linking to external Resources

NCBI


article

treatment

Countries (Region)Australia (Queensland)

Export species materials citations (DwC)

Treatment Content Visualization

10.3897/BDJ.3.e5063

http://dx.doi.org/10.3897/BDJ.3.e5063

http://www.gbif.org/species/2154094

http://www.gbif.org/species/2154094

http://eol.org/pages/1217513/overview

http://species-id.net/wiki/Coremiocnemis_tropix

Revolution: semantically enhanced Publications

Zookeys doi

See e.g. Zookeys, Biodiversity Journal, Journa of Hymenoptera Research, RIO

https://commons.wikimedia.org/wiki/File:Iceberg.jpg

The Plazi Vision: The Giant Global Biodiversity Graph

LegalSocialTechnicalOntologiesInfrastructure

500 M pages 5*

What does this mean?

The Linking Open Data cloud diagram

Linked Open Data Cloud

Text

<tax:treatment> <tax:nomenclature> <tax:name> <tax:xid source="HNS" identifier="193329"/> <tax:xmldata> <dc:Genus>Mystrium</dc:Genus> <dc:Species>leonie</dc:Species> </tax:xmldata> Mystrium leonie </tax:name> <tax:status>n. sp.</tax:status> Fig 1 D - F </tax:nomenclature> <tax:div type="description"> <tax:p>HOLOTYPE WORKER: TL 3.95, HL 1.02, HW 0.95, CI 93, SL 1.30, SI 137, PW 0.73, ML 0.38. Mandible outer margin strongly curving to a sharp apical tooth, the apex parallel to the anterior clypeal margin. (Holotype with material in mandibles, so mandibles and anterior clypeus $ described below from paratypes.) Median clypeus....</treatment>

Semantic enchanced Text(TaxonX/Taxpub)

… alternatives: From human to machine readable text

RDF

LODPDF

HNS

HNS

The Scientific Challenge

The Scientific Challenge

article

treatment

CiteshttpURI

cites (DOI)

Scientific name

https://www.wikidata.org/wiki/Property:P1992

Feed Wikipedia with taxonomic data

The Role of Published Biodiversity Literature in EU-BON


EU BON Policy Brief



EU BON Policy Brief

Plazi SRS GBIF

Land Cover

Pheno logy Moisture

Topography

Morphology

Rainfall

Temperature

Biodiversity SpatialAnalyzer

Decision RuleOpt imizat ion Box

SpeciesDistribution

Map

BiologicalDataset

syntheses


Plazi SRS

find scan «OCR» markup store +access

CotentMine collaboration to implement Plazi workflow

Collaboration with ContentMine to extract treatments on a daily basis

http://www.slideshare.net/petermurrayrust/?

BioDiv

Thank you!

Donat [email protected]